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BenchCel X-Series User Guide

1. About the liquid library editor on page 244 Creating a liquid class on page 248 248 Chapter 11 Setting liquid handling definitions BenchCel User Guide Creating a liquid class About this topic Types of liquid classes to create Liquid compatibility Procedure This topic describes how to create a liquid class using the liquid library editor You must be logged on with an administrator or technician user account to perform this procedure You may want to create different classes for different Q Types of liquids For example water versus DMSO Q Volumes of liquids For example 1 uL versus 200 uL Q Liquid operations For example washing versus mixing INJURY HAZARD Velocity11 products are intended to be used with non hazardous aqueous liquids Please contact Velocity11 before using any non aqueous solvents or solvents generally considered to be hazardous To create a liquid class 1 Open the liquid library editor 2 Click New liquid entry 3 Inthe New Liquid Entry dialog box enter a name for the liquid class and click OK 4 Inthe list box at the top left replace the text New Liquid Type with a name for the new liquid This is the name of the liquid class 5 Inthe Note text box at the top right type a note describing the liquid library entry for your records 6 Enter values for the aspirate properties The following table describes these propertie
2. Click a tab to show a different series of data To close the window click the close box 199 200 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Updating a bar code input file Related information If you change a bar code input file while a protocol is running you must reload the file for the change to be registered To reload a bar code input file 1 Select Tools gt Reload Bar Code File The bar code input file is reloaded For information about See Selecting bar code files Setting general options on page 41 Using the FileReader About the FileReader plug in on page 164 Using bar code data files About this topic Bar code data files This topic describes how to create and use bar code data files in collaboration with bar code input files Read this topic if you are a technician or an administrator who writes protocols with Apply Label VCode tasks File format and location Bar code data files are tab delimited text files with the name filename dat They are stored in a location specified in the general BenchWorks options How they work A bar code data file acts as a lookup table that specifies what bar code fields to print on other sides of a plate The typical sequence of events is as follows 1 A plate with a south side bar code is downstacked into the system 2 The robot picks up the plate reads the bar code and verifies it against a bar code i
3. PREP1 Error Could not establish communications with Prep on j COM 1 Ignore amp Continue leaving device in current state Make sure that the device is turned on and that the communications cable is connected properly Click Diagnostics and try to resolve the problem in the device profile If that does not solve the problem contact the Velocity11 Service Center Chapter 13 Maintenance and troubleshooting 303 BenchCel User Guide Compilation warnings and errors About this topic This topic briefly describes compilation warnings and errors Compilation Warnings alert you to situations that seem to have incorrect intent but warnings that will not cause a collision or a device to fail Compilation warnings are displayed in the BenchCel log toolbar listing the task that caused the warning Warnings are generated for example when U Pipette tips are on the VPrep head at the start of the protocol so a tips off task is run before a tips on task Q No label is printed during a VCode task Compilation errors Errors alert you to situations where a protocol or device will fail Compilation errors are listed in the Log toolbar and a dialog box opens telling you how many errors were found If you are logged in with technician operator or guest privileges you are unable to continue with the protocol If you are logged in with administrator privileges the dialog box allows you to run the protocol despite the errors
4. South West North East Printing option Use this label Data type Task parameter s An array of Field 1 Field 2 Field 3 six strings Field 4 Field 5 Field 6 Integer Format to use Increment chars Starting increment Integer Numeric 0 9 Alphanumeric 0 Z Verify bar codes Reapply up to __ times Use existing bar code from side Printing option BenchCel User Guide Comments For example task side WEST field 2 matches the Field 2 text box in the West tab of the Protocol Task Parameters toolbar A number that corresponds to the bar code format that you want For information about formats see the VCode User Guide The number of alphanumeric characters that you want to be appended to the root data The number that you want to be printed on the first label 0 for numeric increments 1 for alphanumeric increments 0 for no bar code verification 1 for bar code verification The number of attempts made to verify a bar code Copies the bar code from this side of the plate 0 South 1 West 2 North 3 East 0 No label 1 Use this label 2 South 3 West 4 North 5 East 180 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Aspirate task The JavaScript Aspirate task properties are listed below along with the data type of the property the names of the corresponding aspirate properties in the Protocol Task Parameters toolbar and a
5. Chapter 4 Performing a run 71 BenchCel User Guide Open 1 1x Look in 6 FileReaderPluginD ata OQ fir My Recent Documents Desktop E FileReaderData txt My Documents PE My Computer KE a My Network File name Testo ata txt Places Files of type Text Documents txt J Cancel b In the new dialog box that opens inspect the list of names of the columns of the text file and the total number of rows in the file In the following screenshot the first six columns of the plug in file are repeated for each side of the plate FileReaderDil i Field 1 South Field 2 South2 Field 3 South3 Field 4 South Field 5 Souths Field 6 South There are 19 lines c Click OK If the file is not the one you intend to use you can cancel the run at the next step if needed In the Number of Cycles dialog box type in the number of times that you want to execute the protocol during the run If you want to run an indefinite number of plates see Running the protocol until you are done on page 72 below Number of Cycles x Number of times to run protocol Click OK The run starts 72 Chapter 4 Performing a run BenchCel User Guide Running the protocol until you are done What happens after a run starts Related information If User Message tasks are included in the protocol you are prompted to respond to them as they execute If there are no User Messag
6. Errors are generated for example when Q Operating parameters are out of range denoted by red text in fields of the Task Parameters toolbar Q A task asks a VPrep to pipette from a plate that does not exist in the system Q Volumes in pipette steps do not match such as when a dispense volume is greater than a previous aspirate volume Q Aspecific stacker has not been assigned to a stacker task Q A Signal task has no associated Waitfor task 304 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Resolving common problems and error messages About this topic The most common problems that can occur with the BenchCel relate to the following areas L Labware Q Stacker Robot Q Arm alignment This topic describes the possible causes and recommended actions for these types of problems Labware and stacker Problem Error Possible Cause Recommended Actions Message Wrong plate type The plate you are using is not the Check the plate you are using with the same as the plate type selected in labware parameters of the plate type the software selected in the software Use the correct plate or select the appropriate plate type in the software Incorrect value in the labware Open the Labware Editor dialog box and definitions for the plate type check the value in the Number of wells entry field Make sure that the displayed value matches the number of wells in the plate you are using
7. If the check box is selected plates that give a bar code misread are processed as normal but are then moved to quarantine instead of moving to the final destination specified in the protocol For information about See Using plug ins About the FileReader plug in on page 164 Definition of a plate instance About tasks processes and protocols on page 37 Setting the number of Setting the number of simultaneous simultaneous plates plates on page 91 Using bar codes About bar code reading and tracking on page 197 The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Chapter 5 Creating a protocol basics 91 BenchCel User Guide Setting the number of simultaneous plates About this topic Selecting the number This topic describes the concept of simultaneous plates and how to set the simultaneous plate number The number of simultaneous plates is the maximum number of plates belonging to a single process that are in the system at one time Plates that are in the system could be in the robot gripper on platepads VPrep module shelves plate hotels and so on Simultaneous plates do not include counterweight plates Setting the number of simultaneous plates is part of the process of setting up a plate instance In general the number of simultaneous plates to select for a plate instance depends on how many Q Tasks there are in the protoco
8. on page 155 Setting Pump Reagent pipette task parameters on page 157 Setting Wash Tips pipette task parameters on page 159 192 Chapter 8 Creating a protocol advanced topics BenchCel User Guide For information about See The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Understanding the configuration settings in a pipette task About this topic Information flow diagram Dozens of separate pieces of data are required by BenchWorks to complete a single pipetting task These range from the velocity at which to aspirate a liquid to the height at which the gripper should approach a plate that is sitting on a platepad These data are the configuration settings With the right privileges you can modify and add configuration settings to fine tune and extend the capabilities of your BenchCel How you can modify configuration settings is discussed in other topics This topic uses the example of an Aspirate pipette task to provide the conceptual background you need to understand U The relationships between the device manager labware editor liquid library editor task parameters and protocol file Q What information is stored in a protocol Q Why you perform certain steps when creating protocols Q How to resolve protocol errors Before reading this topic it may help to read Configuring a pipette process example on page 2 This topic presents t
9. x mm Theta Left On Right 2 cow _ Mon ow pay 5mm 323 96 5mm 5 009 5 Stacker Sensors Stacker 1 EHI Notches EH Rack present Plate presence Al Top right Move to sensor 32 Ei g position Air PST Bottom left Bottom right Current Teachpoint File Program Fist 1 Setup BTeachPoint xml pLabware foster 96 pp black O Show parameters The BenchCel animated display Robot control procedures Chapter 12 Using BenchCel Diagnostics 255 BenchCel User Guide The BenchCel animated display provides a visual way to represent teachpoints control the BenchCel and monitor the robots movement The graphical representation of the robot moves in real time mirroring the movement of the actual robot Typically the display is used for defining and managing teachpoints See About teachpoints on page 269 for more information il R Load all racks Release all racks Release Stack 3 Release Stack 4 Extend Clamps Release Stack 1 Release Stack 2 Retract Clamps Retract Clamps Extend Clamps Move to Stacker 1 Pick from Stacker 1 Transfer to Stacker 4 The following are procedures you can perform from the Controls page Procedure Home the robot Send the robot home Reset all robot servos Disable all robot servos Add a new teachpoint Check the stacker sensors Change labware parameters
10. VARIANT_BOOL The stack number is 0 based This method should be called after a pPresent successful connection Parameters Argument Argument Range Description Type Name SHORT sStack 0 to n l Which stack to check where n is the number of stacks LONG ReleaseStack SHOR T sStack LONG LoadStack SHORT sStack Chapter 14 BenchCel ActiveX controls 333 BenchCel User Guide Argument Argument Range Description Type Name VARIANT_ pLoaded Valid On a successful call the value BOOL pointer to pointed to by pPresent should receive indicate whether the stack is whether a loaded and has a plate available plate is for downstacking present Returns S_OK if successful other value otherwise Example Visual C Visual Basic 1Result 1Result m_Benchcel IsPlatePresent 1 amp bP BenchCell IsPlatePresent 1 bPlatePres latePresent ent Description Method to release a stack A released stack can be freely taken from the device for the loading or unloading of plates However the BenchCel cannot downstack from or upstack to a released stack The stack number is 0 based Note This method can also be used to perform the close clamp function Parameters Argument Argument Range Description Type Name SHORT sStack 0 to n l The stack to be released where n is the number of stacks Returns S_OK if successful other value otherwise Example Visual C Visual Basic 1Result 1Result BenchCel1 ReleaseStack 0 m_Benc
11. 6 Use the VPrep diagnostics software to prime the fluid lines between the pump and VPrep reservoirs by filling the lines with the appropriate fluid 7 Calibrate the Weigh Shelf if You are changing the liquid type used in the reservoir on the Weigh Shelf The pump module connected to the Weigh Shelf has been turned off Ifyou haven t calibrated it for a while 8 Ifyou are using disposable tips you may need to attach them before starting the run If so a Place a tipbox on the tipbox shelf b Use the VPrep diagnostics software to install the tips c Remove the tipbox Attaching tips is an important step Please refer to the VPrep User Guide for more information Chapter 3 Preparing for a run 63 BenchCel User Guide Related information For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 Next step if you are using a Setting up a VSpin counterweight VSpin plate on page 63 Next step if you are not using Installing a rack on page 64 VSpin User message tasks Specifying task order across processes on page 132 Setting up a VSpin counterweight plate About this topic The general process of preparing a Vspin with Access2 is described here For more detailed procedures see the Access2 User Guide About counterweight If you are using a VSpin in a protocol you need a counterweight plate to plates balance asample plat
12. Change the speed of the robot Jog the robot Control Gohome New teachpoint Disable all Stacker Sensors peie Speed Medium a X See Homing the robot on page 257 Sending the robot home on page 257 About stacker controls on page 264 About teachpoints on page 269 About teachpoints on page 269 Checking the stacker sensors on page 314 About the Labware Parameters group box on page 236 Changing the robot speed on page 261 About the Controls page on page 254 256 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Robot axes You can control the robot s movement in three directions Axis Description X The horizontal distance in millimeters along the rail from the home position Theta The angle in degrees that the grippers rotate from their home position Z The vertical distance in millimeters from the home position to a height 20 millimeters above the base of the column Related information For information about See Diagnostics About diagnostics on page 252 Opening diagnostics Opening BenchCel Diagnostics on page 253 General Settings page About general settings on page 277 Profiles page About profiles on page 282 Chapter 12 Using BenchCel Diagnostics 257 BenchCel User Guide Homing the robot About this topic Homing the robot Sending the robot home Related in
13. DAMAGE HAZARD Releasing the clamps when the robot is not supporting a stack of plates will drop the plates To extend clamps 1 Verify that the button displays Extend Clamps 2 Click Extend Clamps once to extend the stack clamps The name of the button changes to Retract Clamps The clamps extend If a stack is present at the stacker you commanded the stack is released by the clamps If the robot is holding a plate within the stacker the clamps grab the plate To retract clamps 1 Verify that the button displays Retract Clamps 2 Click Retract Clamps once to retract the stack clamps A confirmation dialog box opens Doing this might cause plates to drop Are you sure you want to open the clamps Plates might drop because the clamp actuators grab the stack but release any plates that might be present in the stack 3 If there are plates in the stack make sure the robot is holding the plate on the bottom of the stack 4 Click OK The clamps retract For information about See The animated display About the Controls page on page 254 Loading and releasing stacks Loading and releasing stacks on page 265 Chapter 12 Using BenchCel Diagnostics 269 BenchCel User Guide About teachpoints Teachpoints defined Related information A teachpoint is a point in space that the robot can move its grippers to and is defined by a set of axial coordinates A teachpoint is where the robot moves plates t
14. Example In the example shown below the protocol has four user messages that remind the operator to perform final run preparation tasks The user messages appear before the plates are downstacked The intended sequencing of the User Messages tasks can be ensured by the addition of Signal tasks to the other processes in the protocol gt gt gt J W LD j Costar 96 pp black 385 tips Manually Make sure Al Make sure Downstack from called unnamed 4 attach tips to the wells in left stacker is fully BenchCel Stack 1 384 pipettor on position loaded with fresh 384 plates 126 Chapter 6 Setting task parameters BenchCel User Guide Procedure To set User Message task parameters l 2 Add the User Message task to a protocol process In the Protocol Task Parameters toolbar select a Message will appear option using the following table as a guide Option First plate of the series only Every x plates Last plate of the series only User data entry into variable named Description Displays the message the first time it is encountered for that process during the run Displays the message the first time it is encountered for that process and then every x number of times it is encountered for that process during the run For example if the value of x is 3 the first plate and the fourth plates in the protocol will trigger the message Displays the message the last time it is encountered
15. 1 ee 142 Setting Aspirate pipette task parameters 0 00 cee ee eee 144 Setting Change Instance pipette task parameters 2 00 0c eee eee 146 Setting Change Tips pipette task parameters 0000 eee eee eee 148 Setting Dispense pipette task parameters 0 000 cee eee 150 Setting Dry Tips pipette task parameters cara es 153 Setting Loop pipette task parameters 1 0 0 0 00 ee ee 153 Setting Mix pipette task parameters 0 0 0 00 es 155 Setting Pump Reagent pipette task parameters 2 000 eee ee eee 157 Setting Wash Tips pipette task parameters 0 00 eee eee eee 159 Chapter 8 Creating a protocol advanced topics 163 Setting up the LabwareSelector plug in 2 0 es 164 About the FileReader plug in 2 0 eee 164 About the FileReader file format nananana naaa es 166 Using the FileReader plug in in a protocol 0 00 cee ee eee 168 Using JavaScript in BenchWorks 0 0 00 ee es 171 The JavaScript task object and properties nanoa es 178 Understanding the configuration settings in a pipette task 192 Working with device fileS 2 ad a e a A ee 195 About bar code reading and tracking 2 0 cc ee es 197 Using bar code input files dadkan duen a e E Oa a e E ee ee 198 Using barcode data TeS kearsen eee cee eae clas wae Sate ea ot ae OEA 200 iii Table of Contents BenchCel User Guide Chapter 9 Administr
16. 1 Click Log Out S Log Out Related information For information about See Managing users Adding and deleting a user account on page 205 User privileges About user accounts and privileges on page 204 Shutting down the BenchCel About this topic This topic describes when and how to shut down the BenchCel When to shutdown Shut down the BenchCel if you intend to Q Move it Q Leave it unused overnight Procedure To shut down the BenchCel 1 Make sure that the post run clean up procedure was followed after the last run Select File gt Exit to shut down the BenchWorks application If you use instruments that require a vacuum pump turn off power at the pump if the pump module has an on off switch Turn off the air supply to the BenchCel and other instruments On the connection panel turn the main power switch to the off position 6 Turn the power off on any instrument integrated with the BenchCel 82 Chapter 4 Performing a run BenchCel User Guide Related information For information about Clean up after a run Power connections See Cleaning up after a run on page 80 Connection panel description on page 22 Chapter 5 Creating a protocol basics 83 BenchCel User Guide Creating a protocol basics This chapter is for people with technician and administrator privileges It describes the process of creating a protocol and explains the parameters used to define
17. 4 Pre protocol defined A pre protocol is a collection of processes that are executed once before the protocol The processes are created in the pre protocol editor which is accessed by clicking the Pre Protocol Editor tab in the main BenchWorks window Priming reservoir pumps is an example of a pre protocol task When you click Start if there is a pre protocol it is executed first followed by the protocol Post protocol defined Pipette process task defined Run defined Pipette process link icon Pipette task defined Chapter 3 Preparing for a run 39 BenchCel User Guide A post protocol is a collection of processes which are executed once after the protocol The processes are created in the Post Protocol editor which is accessed by clicking the Post Protocol Editor tab in the main BenchWorks window A post protocol is typically used to clean the system after a protocol run When you click Start a pre protocol may run first followed by the protocol and then any post protocol processes A Pipette Process task is the parent of a sequence of pipette tasks that perform liquid handling procedures using a VPrep or Multimek A pipette process is sufficiently complex that it has to be defined by a group of separate sub tasks each with its own parameters An icon for a pipette process task is shown below s PI Pipette process 1 A run is a single protocol which includes any pre protocol and post protocol pr
18. 650 846 6600 Fax 650 846 6620 Service 1 800 979 4811 Sales 1 866 428 9811 Email info velocity11 com http www velocity11 com Table of Contents BenchCel User Guide Contents Chapter 1 Introduction 00 0 1 Who Should read this giden arena ae e aad s aap ce tate ware as area ee Seek 2 About Velocity11 user guideS 2 es 3 What this guide CoverS 1 0 eee 5 Whats new in this version seereis deara ee eee T Finding your software VerSiONS 1 0 0 es 8 Reporting BenchCel problemS 0 000 ce ees 9 Safety informations s 5 bo sre ed et Sire nha hh ORE ah Gas Be he ta Go thee aA 10 BenchCel hazard warningS 0 0 ccc ee eee 11 Chapter 2 BenchCel overview 13 BenchCel description 2 0 eee eee 14 BenchCel configurationS ossu sawka nr net pa EEk e eee 15 Pencae erTeatUE Seisein Gertie tea ha i ae Se a ee ba A 16 BenchCel accessories and integration options 0000 c eee eee 17 Laboratory setup requirements 0 0000 cee ee es 19 Utility and environmental requirementS 2 000 cee ee ee 20 The computer and networking 0 0 E ee ee 21 Connection panel description 2 ee e es 22 Stacker gripper control description 1 es 24 Connecting the controlling PC and BenchCel 0 00 0 eee ees 24 Connecting the BenchCel to compressed air 0 2 ce ee 26 About BenchWorkS 00 cee ee eee 27 Relationship
19. Aspirate pipette task adding 138 defined 144 JavaScript properties 780 setting parameters 144 aspirate velocity 155 159 aSpirate liquid class 144 aspiration quadrant 145 automatically release stacker racks after protocol finishes protocol rule 50 axes BenchCel robot 256 bar code auxiliary reader 17 error no read 317 errors 318 errors mismatch 318 field modifiers 106 fields example 198 format files 101 input file 165 198 labelling requirements 101 log file 53 107 misread errors 44 317 printer 197 readers about 197 updating input file 200 using data files 200 using input files 198 viewing input file 199 barcodelog txt 53 BenchCel about connecting 21 about error handling 301 accessories 14 17 animated display description 255 256 available configurations 15 changing the robot speed 262 compatible Velocity114 modules 18 compatible with other companies ments 18 compressed air requirement 20 26 connecting by Ethernet 25 connecting by serial 25 connecting compressed air 26 connection panel 16 creating a protocol 85 creating pre and post protocol processes 87 defining plate properties 229 definition 14 description 14 editing teachpoints 272 emergency stop accessory 18 front features 16 hazard warnings 11 integration plate 18 jogging the robot 255 instru Index BenchCel User Guide jogging the robot gripper posit
20. Aspirate velocity The rate at which to draw up liquid If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Dispense velocity The rate at which to dispense the liquid If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Dispense acceleration The rate of increase in velocity before the Dispense Velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here 156 Chapter 7 Setting pipette task parameters BenchCel User Guide 4 5 Property Description Distance from well The distance between the bottom of the bottom pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel Retract distance The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated This value allows the tips to move upwards or downwards during dispensing or aspirating to maintain a certain height below or above the surf
21. Click Save Changes to save your changes Or if you are in the Labware Classes page you can click Save Changes As to save as a new labware class For information about Defining labware General properties Plate properties BenchCel properties See L Labware editor overview on page 216 Q About the defining labware process on page 218 Defining general properties on page 225 Defining plate properties on page 226 Defining BenchCel properties on page 229 236 Chapter 10 Defining labware BenchCel User Guide About the Labware Parameters group box About this topic Labware parameters defined When to use Related information This topic briefly describes the Labware Parameters group box You may want to make quick changes to the labware parameters without opening the labware editor You can access the labware parameters directly from the Labware Parameters group box on the BenchCel Diagnostics Controls page The Labware Parameters group box contains the plate and BenchCel labware parameters found in the labware editor It does not contain the parameters relevant to the any of the instruments that are integrated with the BenchCel For editing labware classes and labware associated with the VPrep we recommend that you use the labware editor Typically the Labware Parameters group box is used when you are testing a new plate type or troubleshooting plate sensor error
22. Configuring a VPrep shelf as a device on page 142 Configuring a pipette process Q Configuring a pipette process example on page 136 Q Adding and configuring a Pipette Process task on page 140 Defining liquid handling About the liquid library editor on parameters page 244 Chapter 7 Setting pipette task parameters 159 BenchCel User Guide Setting Wash Tips pipette task parameters About this topic Wash Tips pipette task defined Before you start Procedure This topic describes how to set the Wash Tips pipette task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Wash Tips task A Wash Tips pipette task is used with a VPrep to wash pipette tips Before you start you need to have a VPrep shelf associated with the labware type with which you want to wash To wash pipette tips 1 Add the Wash Tips task to the pipette process 2 If you have defined a liquid class for the liquid you intend to use for washing select it from the Liquid class list box at the bottom of the Task Parameters toolbar 3 Complete the following properties Property Description Wash volume The volume of liquid to be aspirated and dispensed to each plate well Dispense only Select this if you want to dispense the wash liquid
23. Editing labware parameters Changing labware parameters on page 238 About the defining labware process About this topic This topic U Describes how to see what labware is already defined L Gives an overview of how to define labware Labware standards IMPORTANT All labware used with Velocity11 products must conform to the SBS microplate standards This includes deepwell and PCR plates Visit www sbsonline org for current SBS standards or contact your labware s manufacturer Finding out if a piece Before defining a piece of labware yourself you should make sure that it of labware is defined has not already been defined To find out if a type of plate is already defined 1 In BenchWorks click the Protocol Editor tab and select the plate icon in a process 2 Inthe Protocol Task Parameters toolbar see if the labware is among the available plate types Protocol Task Parameters Task Settings Advanced Settings Plate name Unnamed 1 Plate type 1536 Greiner Low Yolume Black lt From Plugin gt 1 Packard Lid 1536 Greiner Low Volume Black 7 Plugin 1536 Greiner Low Volume Black mc reiner Liq 1536 Nunc Black 253601 Simultaneous 24 Matrix Glass Tube Rack plates 384 BD Biocote Plate Black 354663 x i D J Overall process Related information Chapter 10 Defining labware 219 BenchCel User Guide If there is no entry for the plate it is not defined The overall pro
24. Labware editor overview on page 216 Q About the defining labware process on page 218 Editing labware parameters Changing labware parameters on page 238 Adding a labware entry Adding a labware entry on page 221 Chapter 10 Defining labware 223 BenchCel User Guide Renaming a labware entry About this topic Before you start Procedure Related information You can change the name of a labware entry In general this is something you might do if you just named a labware type and decided to give it a different name You must be logged on with an administrator or technician user account to perform this procedure Make sure that either Q The entry you are renaming is not already referenced in protocols or U Ifthe entry is referenced in protocols you update those protocols IMPORTANT If you rename a labware entry that is already referenced in protocols the link between the protocol and the labware data is broken and the protocol will not run until the protocols are updated To rename a labware entry 1 Open the labware editor 2 Inthe labware selection box on the left of the window select the labware entry to be renamed Click Rename labware entry In the V11Labware dialog box click OK to confirm that you want to rename this entry 5 Inthe Rename Labware Entry dialog box enter the new name for the plate and click OK For information about See Opening the labwar
25. Related information Chapter 8 Creating a protocol advanced topics 191 Data type Task parameters Tip touch horiz dist BenchCel User Guide Comments When the value for this parameter is zero the tips will move horizontally one well radius The well radius is defined in the labware database for the type of plate you are using If you want the tips to touch harder increase this value If you want the tips to touch more lightly enter a negative value Float Tip touch rise height The height that the tips should move upwards before touching the side of the wells Float Wash volume The volume of liquid to For information about Using JavaScript in BenchCel The JavaScript plate object and properties Apply Label task parameters Change Tips task parameters Dispense task parameters Dry Tips task parameters Loop pipette task parameters Mix task parameters Pump Reagent task parameters Wash Tips task parameters be drawn up into each pipette tip See Using JavaScript in BenchWorks on page 171 Using JavaScript in BenchWorks on page 171 About setting Apply Label task parameters on page 101 Setting Change Tips pipette task parameters on page 148 Setting Dispense pipette task parameters on page 150 Setting Dry Tips pipette task parameters on page 153 Setting Loop pipette task parameters on page 153 Setting Mix pipette task parameters
26. Setting pipette task parameters BenchCel User Guide Procedure Related information To fill a VPrep reservoir 1 2 Add the Pump Reagent task to the pipette process In the Pipette Task Parameters toolbar select Fill reservoir The Fill reservoir and Empty reservoir values determine whether the pumps will fill or empty the reservoir To empty the reservoir you must complete the Autofill Configuration information on the Shelves tab of the VPrep Diagnostics In the list box select the shelf on which the reservoir is located In the for text box type the pumping duration This is the time in seconds that the pumps pump In the at text box type the percentage of maximum pumping rate This combined with the pumping duration determines the volume of fluid moved In the every text box type a number that controls how frequently the liquid is pumped For example if you type 3 the pump will run every third time the task runs If you are using a Weigh Shelf in the If liquid is below this level text box enter the minimum percentage of liquid that you want the reservoir to contain A typical value is 45 If you are using a Weigh Shelf in the then fill reservoir to this level text box enter the maximum percentage of liquid that you want the reservoir to contain A typical value is 60 For information about See Defining labware About the labware editor on page 215 Configuring VPrep shelves
27. Wash tips pipette task to the pipette process Remove the task and add it again for the choice to appear 162 Chapter 7 Setting pipette task parameters BenchCel User Guide Washing the To wash the MicroWash tray manifold MicroWash tray 1 manifold Create a protocol process that contains only a pipette process 2 Adda Wash Tips task to the pipette process 3 Enter the following values for the task Property Wash volume Number of wash cycles Inflow pump Outflow pump 4 Run the process Related information For information about Defining labware Configuring VPrep shelves Configuring a pipette process Defining liquid handling parameters Value 0 0 Typically set below 100 The actual rate of inflow depends on the viscosity of the liquid and the height of the reservoir above the Microwash tray It is best to observe the height of the fluid in the tray and set the inflow pump value so that there is an even flow of liquid and the height does not rise to cause an overflow Typically set to 100 See About the labware editor on page 215 Configuring a VPrep shelf as a device on page 142 Q Configuring a pipette process example on page 136 Q Adding and configuring a Pipette Process task on page 140 About the liquid library editor on page 244 Chapter 8 Creating a protocol advanced topics 163 BenchCel User Guide Creating a protocol advanced t
28. a Click the list box down arrow for either the Up or Down movement controls b Select one of the increment options These are listed in millimeters 3 Click a blue Up or Down arrow to move the robot head in the z axis vertically 4 Monitor the current position of the robot by checking the number listed between the blue Up or Down arrows This shows the number of millimeters the robot is from the home position INJURY HAZARD Keep away from the robot when it is moving especially in the z axis direction The robot s z axis motor is particularly powerful It might not stop immediately in a collision and a gripper could pierce your hand 260 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Jogging the robotin To jog the robot in the x axis the xaxis 1 Select the increment that you want the robot to move by On 109 06 a Click the list box down arrow for either the Left or Right movement controls b Select one of the increment options These are listed in millimeters 2 Click a blue Left or Right arrow to move the robot head in the x axis horizontally 3 Monitor the current position of the robot by checking the number listed between the blue Left or Right arrows This shows the number of millimeters the robot is from the home position INJURY HAZARD Keep away from the robot when it is moving The robot is designed to stop if it contacts an object but movement along the x axis can
29. encountered during the run Scheduler error behavior Direct the BenchWorks scheduler on how to handle errors encountered during the run Error notification options Set up email notification in BenchCel to email or page you when a run error occurs Protocol error handling options Specify how the BenchCel should behave if it encounters an error while executing your protocol For information about The workflow this procedure belongs to The next step Protocol errorhandling options Error notification See Workflow for preparing for a run on page 32 Setting general errorhandling options on page 44 Setting protocol errorhandling options on page 47 Setting up email error notification on page 45 s Chapter 3 Preparing for a run BenchCel User Guide Setting general error handling options About this topic This topic describes the handling of general error options See Related information on page 45 for information about protocol error options and email error notification Procedure To set general error handling options 1 2 Select Tools gt Options Click the Error Handling tab of the BenchWorks Options dialog box In the Error Reporting group box select the devices for which you want to report errors Typically all of the devices are selected for a run If you want to perform a test run without plates clear the options for devices used in the protoc
30. erase all variables before protocol executes Q Automatically load stacker racks Pre protocol Rules Reset script context erase all variables before protocol executes Automatically load stacker racks Select this option if you want all variables to be cleared before the next protocol is executed Select this option if you want all racks on stacks to automatically load before the next protocol is executed For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Setting protocol rules on page 49 Using and resetting scripts Using JavaScript in BenchWorks on page 171 General options Setting general options on page 41 Chapter 3 Preparing for a run 49 BenchCel User Guide Setting protocol rules About this topic Protocol rules include Pipette plates in instance order This topic describes the protocol rules in the Protocol Options dialog box There are three rules in the Protocol Rules group box U Pipette plates in instance order Q Handle plates in instance order Q Automatically release stacker racks after protocol finishes Protocol Rules Pipette plates in instance order O Handle plates in instance order C Automatically release stacker racks after protocol finishes Default setting The default setting for the Pipette plates in instance order rule is for it to be checked and it should be left chec
31. identified To make sure that the QFill2 is identified 1 Check that the QFill Number is correct for the device that you want to communicate with This number identifies a specific QFill2 when there is more than one on the BenchCel You can determine the number of a QFill2 by referring to the label on the device by trial and error or by looking at the Device Number in the device manager QFill Diagnostics 1 OFill Number Comm Port a gt 2 Check that the COM Port number matches the serial port number for the device that you want to communicate with You can determine the COM Port number from the label on the serial port cable near where it plugs into the QFill2 The number is also the same as the Input number in the device manager After the QFill2 has been defined the COM Port number is added automatically when you select the QFill2 You should not need to change it About creating and You should not need to use the Create New QFill or Delete QFill deleting devices buttons These are for Velocity11 use only 292 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Procedure About the Filtration Port Related information Refer to the QFill2 user documentation for information about preparing to fill a plate To dispense into a plate l 2 Make sure that there is a plate on the QFill2 stage Make sure that the reagent bottle has sufficient liquid in it for the dispense Set the
32. or metal brushes to clean any BenchCel components or accessories Do not use any concentration of bleach sodium hypoclorite Do not allow cleaning agents to contact any electrical or sensitive mechanical components Chapter 2 BenchCel overview BenchCel User Guide BenchCel overview This chapter provides an overview of the BenchCel platform its operating requirements available accessories and integration options 13 14 Chapter 2 BenchCel overview BenchCel User Guide BenchCel description About the BenchCel Basic BenchCel components Standard BenchCel parts BenchCel defined The BenchCel is a microplate processing automation platform that is used to store microplates and move them to and from separate instruments Instruments defined Instruments are individual pieces of equipment that sit on either side of the BenchCel and process microplates For example a VCode instrument can apply a barcode to a microplate which can then be sealed by a PlateLoc instrument In this example the BenchCel transports the microplate from one of its stacker racks to the VCode then to the PlateLoc and then to another stacker rack Every BenchCel has the following Q Two to six stacker racks A plate handling robot A connection panel BenchWorks software DODO Computer Included with every standard BenchCel purchase are the following D Plate handling robot Stacker racks BenchWorks software Comput
33. the following table as a guide Each offset is measured from the bottom of the plate in millimeters Parameter Robot gripper Stacker gripper Sensor Error correction Comment Determines where the robot grips the plate Determines where the stacker grips the plate Determines where the plate sensors read the plates for orientation checking Leave this value at 0 zero 240 Chapter 10 Defining labware BenchCel User Guide 5 Enter new values or edit existing values for the Gripper position parameters using the following table as a guide DAMAGE HAZARD Set the Holding plate and Holding stack parameters so the grippers securely grasp plates without damaging them For each of these offsets Increasing the value narrows the distance between the robot grippers Decreasing the value widens the distance between the robot grippers The value should never be less than zero This value adjusts the position of a single gripper and is nota point to point adjustment between grippers Parameter Comment Open Adjusts the distance between the robot grippers when open Set this parameter so that the grippers release the plate when opened Holding plate Adjusts the distance between the robot grippers when holding a plate Holding stack Adjusts the distance between the robot grippers when holding a stack of plates This value is usually larger than the holding plate value because the grippers need to grip a stac
34. 1 Enter a value in the Prime volume text box and click Prime To shake the plate 1 Enter a value in the Shake time text box and click Shake 288 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Related information For information about See Diagnostics About diagnostics on page 252 Using the Multidrop Multidrop 384 User Manual For detailed information about the Multidrop refer to Thermo Electron Corporation s Multidrop 384 User Manual Using Nanodrop Diagnostics About this topic About Nanodrop profiles The Innovadyne Nanodrop dispenser is an 8 channel pipettor that dispenses 0 1 40 uL of liquid into each well It can be used either in stand alone mode or as a device within a protocol using the BenchCel This topic describes how to Q Manage Nanodrop profiles which are used to communicate with the computer Q Perform an individual operation such as a dispense or wash using the parameters set in a Quick Run Method QRM and referencing a calibration file for increased accuracy For detailed information about the Nanodrop see Innovadyne s Nanodrop User Manual A profile is one or more settings that are remembered after you exit BenchWorks In the case of the Nanodrop the only setting stored ina profile is the COM port which identifies the serial port to be used for communication between the device and the computer You need to have one profile for every Nanodrop on your
35. 117 setting parameters 117 pipette log file 52 Pipette plates in instance order protocol rule 49 pipette process configuration settings 192 creating for changing pipette tips 149 defined 40 link icon 39 linking a pipette task to 147 setting parameters 140 pipette process task adding 136 140 adding example 736 defined 39 pipette task defined 39 pipette tips 748 changing 148 149 touching 161 washing 159 pipetting operation example 736 piplog txt 52 Place Labware task setting parameters 178 Place Plate task defined 120 setting parameters 120 plate icon definition 37 setting parameters 88 versus task 38 plate object JavaScript 773 plate properties defining 226 PlateLoc see also Seal task setting up 67 PlatePierce see also Pierce task plate present indicator 264 plates BenchCel User Guide see also simultaneous plates plug in 85 FileReader format 766 FileReader about 764 setting up LabwareSelector 164 post aspirate delay property 249 post dispense delay property 249 post dispense volume 152 post protocol process defined 39 setting up 87 power supply main 22 powering up BenchCel 33 pre aspirate volume 160 preparing for a run instruments 67 preparing for run workflow 32 pre protocol process defined 38 setting up 87 pre protocol rules about 48 setting 48 pre run checks performing 69 presentation offset property 237 priming 285 287 printing a protocol
36. 190 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Property task quadrants task retract task tipOffset task tipTouch Data type An array of pairs of integers Float Float Boolean Task parameters Quadrants diagram Retract distance Distance from well bottom Enable tip touch Comments A quadrant is an evenly spaced array of locations that is addressable by the tips on a pipette head A 96 well head can dispense into a 96 well plate four quadrants of a 384 well plate and 16 quadrants of a 1536 well plate A 384 well head can dispense into a 384 well plate or the four quadrants of a 1536 well plate The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated This value allows the tips to move upwards or downwards during dispensing or aspirating to maintain a certain height below or above the surface of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel Whether you want the tips to touch the sides of the plate wells or not Property task tipTouchHorizontalDistance Float task tiptouchRiseHeight task volume
37. 39 39 17 PM Q5pHTS 1 No bar code No bar code pHTSO5001 No bar code 5 6 03 2 39 55 23 PM O6pHTS 1 No bar code No bar code pHTSO6001 No bar code 5 6 03 2 40 15 60 PM O7pHTS 1 No bar code No bar code pHTSO7OOL No bar code 5 6 03 2 40 34 62 PM O8pHTS 1 No bar code No bar code pHTS08001 No bar code 57 6 03 2 40 53 51 PM OSpHTS 1 No bar code No bar code pPHTS09001 No bar code 5 6 03 2 41 11 92 pm LOpHTS 1 No bar code No bar code pHT510001 No bar code 107 108 Chapter 6 Setting task parameters BenchCel User Guide Related information For information about See Creating a bar code input file Using bar code input files on page 198 Using bar code data files Using bar code data files on page 200 General options Setting general options on page 41 Creating a plate instance Setting up a plate instance on page 88 Using plug ins About the FileReader plug in on page 164 Log files About log and data files on page 51 Setting Delid Relid task parameters About this topic Delid Relid task defined Example This topic describes how to set the Delid Relid task parameters These tasks are used by the BenchCel to remove and replace labware lids Read this topic if you are Q An administrator or technician who writes protocols that uses this task Q An operator who needs to specify parameters for the Delid Relid tasks The Delid task removes a plate s lid using a device su
38. Bar_Code_File f gt north Bar_Code_File s gt east Bar_Code_File gt lt Bar_Code_File_Info Plate Has_Lid 0 Labwrare Costar 96 well plate Name Plate 1 Sealed 0 gt lt Bar_Code_Info gt south Bar_Code_File No bar code Has_Bar_Code 1 J gt west Bar_Code_File No bar code Has_Bar_Code 0 gt north Bar_Code_File No bar code Has_Bar_Code 0 gt east Bar_Code_File No bar code Has_Bar_Code 0 s gt lt Bar_Code_Into lt Plate gt Tasks lt Task0 Description Downstack from stacker2 Device Enable_Timed_Release 0 Icon 0 Object_Type DownstackPlate Release_Time_MS 10000 gt lt Stackers_To_Use Stacker Name stacker2 gt lt Stackers_To_Use gt lt TaskO gt lt Task1 Description Bar code plate Device vcode1 Icon 1 Object_Type BarcodePlate Type BarcodePlate gt south Bar_Code_Names 0 Base 10 File_Name Format 1 Increment_Characters 3 Lookup_Key 2 Max_erification_Attempts 0 Number _Of_Fields 2 Plugin_Name Preprinted_Side 0 Print_Label 1 Starting_Increment 1 Verify_Barcodes 0 gt Fields You can also open a protocol file in any browser that contains an XML parser such as Internet Explorer version 4 or later XML schema To create and edit protocols directly in XML you need to have the XML schema that defines the logical rules of a BenchWorks protocol If you want the schema please contact the Velocity11 Service Center Chapter 5 Creating a pro
39. BenchWorks version Chapter 1 Introduction BenchCel User Guide See Who should read this guide on page 2 What this guide covers on page 5 About general settings on page 277 Starting BenchWorks on page 34 This guide covers the hardware and software operations of the BenchCel This version of the guide is only for use with BenchWorks product version 3 x x file version 24 x and the following major software components Note Your BenchCel may not have all of the components shown in the following screen shot or may have components not shown here To find version information for your software l 2 Start BenchWorks Click Help and select About BenchWorks The About BenchWorks window lists the version number of the software and the version numbers of its major components About BenchWorks Eg BenchWorks product version 3 0 0 Benchworks file version 18 0 7 Copyright 2000 2005 Velocity11 All rights reserved StackerDevice 8 4 0 StorexDevice 1 8 0 TeleshakeDevice 2 3 0 TeleshakeHighSpeedDevice 2 3 0 UltramarkDevice 3 1 1 V11Labware dll 12 0 6 V11 Liquids dll 5 0 3 V11Security dll 3 0 2 VCode3KDevice 10 1 0 AliquotDevice 2 3 2 BenchCelDevice 7 0 2 BiolO ocx 4 0 1 BioTekWasherD evice 3 0 6 deviceenumerator dil 5 0 3 Echo550Device 2 4 0 EnvisionDevice 1 1 0 FlexispenseDevice 2 1 1 FlexispenseNewDevice 3 0 0 MultidropDevice 3 2 1 VersaScanDevice 2 4 1 MultiskanAscentDevice
40. Box called Stack1 Example process 2 Inthe pipette process editor create a pipette process to change tips such as in the following simple example Errr Pipette Process 1 Tips On Tips Off on VPREP1 Creating the process for the tip box Creating the pipette process for changing tips Chapter 7 Setting pipette task parameters 149 BenchCel User Guide Before you can add a Change Tips pipette task you must create a process for the tip box that will contain the tips Creating a process for the tip box 1 2 90 EN OG Click the Protocol Editor tab Click Add A plate definition icon appears in the Protocol Editor window In the Protocol Task Parameters toolbar a Type aname for the tip box in the Plate name text box b Inthe Plate type list box select the tip box that has already been configured for use on the shelf of the VPrep that you intend to use Note Make sure that you select and use a tip box without lids If the correct tip box is selected the Plates have lids check box is unavailable c Inthe Simultaneous Plates text box type the maximum number of tip boxes of this type that you want to be available to the system at one time d Ifthe tip boxes have a bar code on the south side or west side select the appropriate Incoming plates have a bar code check box and list box option Add the Downstack task to the Protocol Process window Set the Downstack task parameters Add the Pipette Proce
41. COoOocervucoeooe ec Status of the dispense Values are ERROR or OK These refer to the status of the bar code verification and not the dispense itself Note One log entry is created for every dispense task pair For example if 20 uL are aspirated and half is dispensed to one plate and half to another plate two piplog entries are created This example is treated as two dispense task pairs The bar code log file contains the date and time at which each bar code is applied and the text of each field Bar code fields are displayed in human readable form The reader output file defines the location of the data file lt file name gt dat for a plate reader The image root folder sets the folder in which images from a VersaScan are automatically stored For information about See The next step Setting log options on page 54 Adding a note Working with the Log toolbar on page 77 Bar code labeling Setting Apply Label task parameters on page 102 a Chapter 3 Preparing for a run BenchCel User Guide Setting log options About this topic Available options This topic explains how to configure the log options page of the BenchWorks Options dialog box You may not need to configure these options for every run The following types of log options are available in BenchWorks Q The type of log information to show in the Log toolbar of BenchWorks Screen settings Log task begin events on screen
42. For information about See Adding and deleting accounts Adding and deleting a user account on page 205 Setting up email Setting up email on page 206 Sending a registry file Moving or sending a registry file on page 208 Adding and deleting a user account About this topic About blank passwords Adding a user account We recommend that BenchCel administrators create an account for every user The privileges set for the account should be appropriate for the users job role This topic explains how to add and delete user accounts IMPORTANT If you do not assign a password to a user a blank password is automatically assigned This means that anybody can log in You must be logged in with an administrator user account to add a user account To add a user account 1 Select Tools gt Manage Users 2 Inthe User Editor dialog box click Add 3 Inthe User name text box type a name for the user 4 From the Access level list box select the privilege that you want to assign to the user 5 Assign a password a Click Change password b Enter a password in the New text box c Re type the password in the Confirm New text box d Click OK 6 Click OK 206 Chapter 9 Administrator procedures BenchCel User Guide Deleting a user account Related information You must be logged in with an administrator user account to delete a user account To delete a user account 1 Select
43. Parameters toolbar Either Type the volume that you want to move out of each pipette tip in the Dispense Volume text box Select the Empty tips check box You may need to drag the toolbar to widen it so you can see the check box Select this option if you want to empty the tips rather than deliver a specific volume of liquid Complete the remaining fields Field Description Dispense velocity The rate at which to dispense the liquid If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Dispense acceleration The rate of increase in velocity before the Dispense Velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Distance from well bottom The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel Retract distance The distance that the tips should move upwards per unit volume of liquid being dispensed This value allows the tips to move upwards during dispensing to maintain a certain height above the surface of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use You might want this value to be the same as the Tip Retract Dista
44. Plugin list box of the Protocol Task Parameters group box If the FileReaderdll is not available for selection it is because the FileReader dll file is missing from the plug ins folder Protocol Task Parameters Task Settings Advanced Settings Plate name Unnamed 1 Plate type Costar 96 pp black x Edit labware settings Plugin seene Simultaneous 1 plates C Plates have lids O Plates enter the system sealed 2 Populate the Apply label task fields a Click the Apply label icon in the Protocol Editor b Populate the Apply label task fields with the From user plugin button Chapter 8 Creating a protocol advanced topics 169 BenchCel User Guide Protocol Task Parameters Task Settings advanced Settings South West North East Printing Option Use this label ha Format to use 1 Number of Fields 2 Field 1 NAW INC Feld FLE Field 3 FILE Field 4 from Souh side Feld Field 6 use South Yf side Increment Chars 1 Starting Increment 1001 Numeric 0 9 Alphanumeric 0Z O O Verify bar codes and reapply upto 0 times Bar Code File Entry 4 Bar Codes NOT in file c Ifyou would like to use prefixes or suffixes enter them before or after PLUGIN in the relevant Field text box An example field with a prefix is shown in the following screenshot Field 2 Prefix PLUGI Running the protocol To run a protocol with a FileReader plug in file 1 Open the p
45. Release Stack 2 Retract Clamps Load Stack 1 Retract Clamps Click Release Stack once to command the robot to move to the stacker and hold the plate on the bottom of the stack The name of the button changes to Load Stack The stacker grippers retract and release the stack while the robot moves the stack up Then the stacker clamps extend and the robot releases the stack so that it is resting above the stacker grippers The rack is ready to remove from the stacker DAMAGE HAZARD Always remove stacks from the stackers before attempting to move the BenchCel 3 Lift the stacker rack up and off the base Loading and releasing all stacks Related information Chapter 12 Using BenchCel Diagnostics 267 BenchCel User Guide To speed up your workflow you may want to load or release all of your stacks simultaneously To load all stacks simultaneously 1 Load the stacks onto their stack base 2 Click Load all stacks in the upper right corner of the BenchCel animated display The stacker grippers will take hold of the plate clamps on the stack To release all stacks simultaneously 1 Click Release all stacks 2 Unload the stacks from the stacker heads For information about See Loading or releasing all stacker Loading and releasing stacks on racks simultaneously page 265 The animated display About the Controls page on page 254 Extending and retracting stacker clamps About this to
46. User permissions About user accounts and privileges on page 204 Job roles and responsibilities Who should read this guide on page 2 About tasks processes and protocols About this topic Plate icon defined Task defined This topic defines some terms that you need to know before you can understand or create protocols A plate icon represents the basic information about a plate or collection of plates and is the first icon in a process displayed in the protocol editor It has associated parameters that are defined in the Task Parameters toolbar The information it represents includes the type of labware used in the process how many plates are available for processing at one time whether the plates have lids and so on The following example icon represents a plate icon for a tipbox gt V11 Tip Box 96d60 called Test A task is an operation that is performed on one or more plates and is represented by an icon in the protocol editor It has associated parameters that are defined in the Task Parameters toolbar The following example icon represents a task for downstacking plates af Downstack from BenchCel Stack 2 38 Chapter 3 Preparing for a run BenchCel User Guide Process defined A process is a sequence of tasks that are performed on a plate icon The following diagram shows a process with one plate icon and four task icons 96 Costar Flat Bottom wLid gt y gt gt y 4 x p calle
47. WellMate query plate 296 WellMate about 293 disable all robot servos 255 dispense acceleration 151 155 160 dispense limits 750 Dispense pipette task adding 139 defined 750 JavaScript properties 782 setting parameters 157 dispense velocity 151 155 160 dispense volume 757 dispensing to waste 759 167 disposing of waste 70 distance from well bottom 151 Downstack task defined 109 setting parameters 109 Dry Tips pipette task 753 E Echo 550 supported instrument 78 email notification of errors by 46 206 setting up 45 206 when errors occur 44 emergency stop description 78 23 environment requirements 20 errors about 307 bar code reader 377 causes about 307 handling 307 hardware reporting 9 message display see Log toolbar notification of 46 206 reporting 9 Index 341 BenchCel User Guide setting handling options 44 setting handling options for protocols 47 setting options 43 setting scheduler behavior options 45 troubleshooting initialization 302 VCode 319 Ethernet connecting to 25 interface on connection panel 22 parts included 14 port 22 event messages see log toolbar F file device 322 format for protocol 84 protocol 322 protocol log 322 FileReader plug in 164 text file format 766 filtration station 292 Find button 4 finding the file 3 firmware version 6 FlexDrop supported instrument 78 fuse type 23 G general options setting 47 general
48. after the robot moves the bottom plate up so it rests on top of the clamp pads After a run has completed BenchWorks will query whether you want to release the stacks or not Two ways to load There are two ways to load and release stacks in the BenchCel animated and release display Q Load or release stacks individually with the Load stack or Release stack buttons above each stacker representation Q Load or release all stacks simultaneously with the Load all stacks or Release all stacks buttons 266 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Loading a stack using the display Releasing a stack using the display To load a stack l Verify that the button displays Load Stack in the BenchCel animated display Refer to the button at the top left of the following screenshot Release Stack 2 Retract Clamps Load Stack 1 Retract Clamps Click Load Stack once to command the robot to move to the stacker and grab the plate on the bottom of the stack The name of the button changes to Release Stack The stacker clamps retract and release the stack and the robot moves the stack down Then the stacker clamps extend and grab the plate stack by the stacker grippers The robot then releases the stack The rack is loaded To release a stack 1 Verify that the button displays Release Stack in the BenchCel animated display Refer to the button at the top right of this screenshot
49. be called at the beginning of a run The device is not expected to move Parameters None Returns S_OK on success other value on failure Example Visual C Visual Basic 1Result 1Result BenchCel1 ProtocolStartQ m_BenchCel ProtocolStartQ Description Method to be called at the end of a run The device might home during this call Parameters None Returns None LONG SetLabware BSTR bstrLabware LONG GetStackCount LON G pCount Chapter 14 BenchCel ActiveX controls 331 BenchCel User Guide Example Visual C Visual Basic 1Result 1Result BenchCel1 ProtocolFinishQ m_BenchCel ProtocolFinishQ Description Method to set the labware to use The selection will be in effect for all operations until a different labware is set If diagnostics are shown and the user selects a different labware the original labware will be restored when the diagnostics window is closed This method should not be called when any movement is in progress Parameters Argument Argument Range Description Type Name BSTR bstrLabware Valid Labware to be used for labware subsequent operations name Returns S_OK if successful other value if there was an error Example Visual C Visual Basic 1Result 1Result m_BenchCel SetLabware MyPlat BenchCell SetLabware MyPlateType eType Description Method to retrieve the number of stacks on the BenchCel device This method must be called after a successful connect
50. build up considerable momentum resulting in injury Jogging the robotin To jog the robot in the theta axis the theta axis 1 Select the increment that you want the robot to move by Theta EELE 5r 0 02 3 Click the list box down arrow for either the clockwise CW or counterclockwise CCW movement controls and select one of the increment options These are listed in millimeters 2 Click a blue CW or CCW arrow to rotate the robot head grippers around the thefa axis 3 Monitor the current position of the robot by checking the number listed between the blue CW or CCW arrows This shows the angle that the grippers are pointing by degrees Jogging the robot gripper position Related information Chapter 12 Using BenchCel Diagnostics 261 BenchCel User Guide To jog the robot gripper position 1 Select the increment that you want the robot to move by Grippers mm Click the list box down arrow for either the In or Out movement controls and select one of the increment options 2 Click a blue In or Out arrow to change the spacing between the gripper points 3 Monitor the current position of the robot by checking the number listed between the blue In or Out arrows This shows the number of millimeters the robot is from the home position For information See about Teachpoints About teachpoints on page 269 Opening diagnostics Opening BenchCel Diagnostics on page 253 Controls page Ab
51. creating a protocol on page 85 120 Chapter 6 Setting task parameters BenchCel User Guide Setting Place Plate task parameters About this topic This topic describes how to set the Place Plate task parameters for the BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the Place Plate task Q An operator who needs to specify parameters for the Place Plate task Place Plate task The Place Plate task moves a plate to any location This task has many defined uses The next task in the process after a Place Plate task moves the plate to another location Place Plate task and The Place Plate task can be used in combination with a platepad bar bar codes code reader to read a bar code The requirements for this are as follows U The platepad must be set up in the device manager as a bar code reader for the platepad U The plate icon for the plate must indicate that the plate has a bar code on the side that the bar code reader reads See Related information at the end of this topic for how to do this Whenever a plate is placed on this platepad the scheduler tells the bar code reader to read the plate s bar code Procedure To set the Place Plate task parameters 1 Add the Place Plate task to the protocol process 2 Inthe Task Settings page of the Protocol Task Parameter toolbar select the device to which you want to move the plate You may need to scroll down to mak
52. decrease the pressure You can see the sensor reading for the stacker gripper pressure in the Stacker Sensors group box of the BenchCel Diagnostics Controls page DAMAGE HAZARD Do not set the grip pressure lower than 15 psi 4 Open and close the stacker grippers two to three times to allow the pressure to adjust 5 Lock the locking ring by turning it clockwise until it is fingertight Chapter 13 Maintenance and troubleshooting 321 BenchCel User Guide Related information For information about See Stacker sensors group box Checking the stacker sensors on page 314 Stacker clamps Extending and retracting stacker clamps on page 267 Sending a bug report About this topic This topic describes how to send a bug report to Velocity11 Service Center from BenchWorks Requirements Before you can send a bug report Q The system s computer must be connected to a network with internet access Q The outgoing email server must be set up on the system s computer by a BenchCel or network administrator Sending a bug report A bug report is an email that you create and send from within BenchWorks The email automatically identifies your BenchCel and is sent directly to Velocity11 To send a bug report 1 Select Help gt Report a bug The Email Bug Report dialog box opens Email Bug Report xi Enter the text of the bug report here Email address Velocity11 should send a reply to Attach l
53. disp column For two quadrants the representation would be 1 1 1 2 When you run a script that dynamically changes the values of task properties there is a risk that a value will be set that causes a problem We therefore recommend that before using a script you run the simulator with each set of values that will be set by the script Running scripts cannot cause robot crashes because scripts cannot modify teachpoints However an incorrect task tipOffset property Distance from well bottom parameter on a VPrep could cause the pipette tips to crash into the bottom of the wells resulting in loss of sample and damage to plates In addition be aware that when a protocol is being compiled it uses the values displayed in the Protocol Task Parameters toolbar screen and not the values that will be set by any scripts This means that there may be errors in the protocol that are not detected during compilation The values that appear in the Task Parameter toolbar do not change to reflect the effect of any script Also scripts do not check pipetting volumes before the run begins so you must make sure that the pipetting steps make logical sense For example you will not be alerted beforehand if a script will attempt to aspirate 1 mL from a plate well that can only hold 0 5 mL Example scripts Script writing service Related information Chapter 8 Creating a protocol advanced topics 177 BenchCel User Guide Example 1 This sc
54. dispense volume a Inthe Volume Setup group box type the QFill2 volume into the text box b Click Update Volume Click OK The volume you last entered is saved until the next time a protocol is run which will override this value Volume Setup Enter volume in pL 2 Update Volume Filling Test Success Fail In the Filling Test group box click Start Monitor the success of the fill by looking at the Success and Fail indicators The Success and Fail indicators provide feedback from a sensor that measures pressure in the dispensing bottle The Fail indicator light is illuminated if the QFill2 is not turned on QFill2 has a disconnected communication cable Bottle fails to pressurize The Filtration Port defines the COM port used to provide vacuum sensor information for an optional filtration station on the QFill2 You should not need to change this number For information about See Diagnostics About diagnostics on page 252 Preparing a plate for filling QFill2 User Guide Chapter 12 Using BenchCel Diagnostics 293 BenchCel User Guide Using WellMate Diagnostics About this topic This topic describes how to use WellMate Diagnostics to Q Manage profiles Q Move the plate stage Q Execute dispense commands About profiles Profiles contain the initialization settings that enable BenchWorks to identify and communicate with the BenchCel Every device within the automation system must have i
55. each protocol task Before reading this chapter you should be familiar with the concepts presented in Performing a run on page 67 This chapter is not a tutorial on writing protocols it provides the basic reference information you need to create protocols 84 Chapter 5 Creating a protocol basics BenchCel User Guide About protocol files About this topic This topic provides an overview of the protocol file format File format Protocols are created in the drag and drop protocol editor When they are saved the information is written to a file in XML format In XML the elements indicate the protocol s properties and text within the markup tags gives the properties values Most users create and edit protocols in the protocol editor Advanced users have the option of creating and editing protocols directly in XML The XML files can also be useful for troubleshooting because you can for example see which device file is associated with the protocol XML example A protocol file viewed in an XML editor that colorcodes text is shown below lt xml version 1 0 encoding 4SCIl gt lt Velocity11 file Protocol_Data mdSsum 751 d03b4 66915854 7085chdasddl 706 version 1 0 gt Device File File_Name C Documents and Settings yme Desktop ma dev gt Description Description gt Process Muttiplier 1 Processes_To_Spaywn 1 Tip_Box_Process 0 gt lt Bar_Code_File_Info gt south Bar_Code_File gt yest
56. for a procedure Problem Error Message Plates are not held level by the robot at all times during a plate transfer Robot and scheduler error messages Error Message No plate in grippers Plate in grippers X position out of bounds Z position out of bounds Theta position out of bounds The gripper positions are too close Possible Cause Gripper points are out of alignment Possible Cause The robot did not detect a plate when it expected one The robot senses a plate in its grippers and is being asked to perform an action that requires it to not have a plate The robot has been commanded to move out of its range in the x direction The robot has been commanded to move out of its range in the z direction The robot has been commanded to move out of its range The values of the open and holding plate gripper positions of the labware are too close to each other Chapter 13 Maintenance and troubleshooting 307 BenchCel User Guide Recommended Actions Check the gripper alignment See Checking the arm alignment on page 309 for a procedure If grippers are out of alignment contact Velocity11 Service Center Recommended Actions If there is a plate in the grippers and it is incorrectly positioned use the Robot Diagnostics screen to move to a teachpoint and open the grippers which will release the plate After that use Robot Diagnostics to
57. gripper offset mm Lid resting height mm Lid departure height mm Property Description Robot gripper offset This refers to the offset for a Velocity11 robot The comparable parameter for the BenchCel robot is located on the BenchCel tab Thickness The distance in millimeters from the bottom surface of the plate to the top surface of the plate Measure using calipers Property Stacking thickness Can be sealed Sealed thickness Sealed stacking thickness Can have lid Lidded thickness Lidded stacking thickness Lid gripper offset Lid resting height Chapter 10 Defining labware 227 BenchCel User Guide Description The thickness in millimeters of two stacked plates minus the thickness of one plate Measure using calipers Example Thickness of two stacked plates x 23 14 mm Thickness of one plate 14 14 mm Stacking thickness 23 14 mm 14 14 mm 9 00 mm Plate Thickness i X Stacking Thickness t 00022 Select if the plate can be sealed Thickness of the plate with a seal in place Available only if Can be sealed is selected Stacking thickness of the plate with the a seal in place Available only if Can be sealed is selected Select if the plate can have a lid Thickness of the plate with a lid in place Available only if Can have lid is selected Stacking thickness of the plate with the lid in place Available only if Can ha
58. how to set the Change Instance task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Change Instance task The Change Instance pipette task is used in combination with a pipette loop to perform replicate dispense operations from a mother plate into a series of daughter plates Part of an example protocol which contains a mother plate and the first of 10 daughter plates is shown below 1536 Nunc Black _ 253601 called pi y oS y y Mother Plate 1536 Nunc Black Downstack from Pipette process 1 253601 called Stack Remove 1 Packard Lid Pair ne called Daughter y H Plate 1 18 1 Packard Lid Downstack from Pipette process 1 called Daughter Stack2 Plate 1 An example pipette process for the mother plate is shown below nen l O f _1 Pipette Process 1 Aspirate 100 00 pL Loop 10times Dispense 10 00 pL Change instance End of loop from Mother Plate into Daughter Plate 1 quadrants lin 1 quadrant s Note This example has been simplified for the purposes of explanation When the protocol runs 100 ul from each well of the mother plate are aspirated and 10 ul are dispensed into the first daughter plate Daughter Plate 1 When the Change Instance task is reached Daughter Plate 2 is moved into the syste
59. in instance order Automatically release stacker racks after protocol finishes Related information Default setting The default setting for the Handle plates in instance order rule is for it not to be selected When to select the rule Use this rule if you need the plates to be handled in the order in which they enter the system Explanation Consider a situation in which you are using BenchCel to seal plates using two PlateLocs and the first one runs out of seal stopping on plate 5 If this option is not selected the second sealer continues sealing and upstacking plates but plate 5 would be omitted and thus out of order If this option is selected the second sealer stops until you reload a new roll of seal and start the first sealer again and plate 5 is upstacked to its position in order Default setting The default setting for the Automatically release stacker racks after protocol finishes setting is for it not to be checked When to select the rule Use this rule if you have one or more stackers and you want all them to release their racks at the end of the protocol For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Setting log options on page 54 Chapter 3 Preparing for a run 51 BenchCel User Guide About log and data files About this topic Types of log and data files About opening log files This
60. information about See Opening diagnostics Opening BenchCel Diagnostics on page 253 258 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Moving the robot manually About this topic Procedure Related information This topic describes how to move the robot in manual mode You can move the robot manually in the x z and theta axes but first you must disable the robot s servo motors Move the robot manually when you want to position the robot by eye exactly where you want This is useful when you are creating a new teachpoint For example you could move the robot manually to a platepad and position its grippers to where they would grip a plate Then you could create a teachpoint there by pressing Use current position on the Teachpoint Details dialog box To move the robot manually 1 Open BenchCel Diagnostics dialog box to access the Controls page DAMAGE HAZARD Moving the robot in any of its axes without first disabling the servos could damage the robot s motors 2 Disable the robot servo motors for the x z and theta axes a Click Disable all on the Controls page of the BenchCel Diagnostics dialog box If the robot is above its lowest z axis height it will slowly sink until it reaches the lowest z axis height b Alternatively you can clear the On check boxes for the x z and theta axes in the Controls page of the BenchCel Diagnostics dialog box Note The robot head w
61. is identified by the name selected from the list box in the Pipette Task Parameters toolbar In this simple case there is only one name to select which is Process1 Task Parameters Use pipet process Selecting a VPrep Configuring the VPrep shelf Chapter 7 Setting pipette task parameters 137 BenchCel User Guide In this example there are two VPrep pipettors configured so you need to associate the one you want to use with the pipette process You do this in the Pipette Process Editor page In the following example the task will use VPrep1 VPrep2 remains available but is not used for this process Task Settings advanced Settings Available pipettors VPrep2 Pipettors that this task will use VPrep1 You want to aspirate 20 uL of 1X TE buffer from a reservoir This means that you have to configure a shelf of the VPrep to hold the reservoir that will contain the buffer You decide to use a 384 V11 Reservoir manual fill 21 5 deep plate type for the reservoir We know that the VPrep itself has already been configured in BenchWorks as a device because you were able to select it in the previous step We can also see it listed as a device in the device manager To open the device manager you click the Device Manager tab El Prep Precision Pipetting Station VPrep2 VPrep1 Each shelf that you want to use on the VPrep must also be configured as a device The shelves are already set up as device
62. is useful if you have devices where you want to use one type of labware on the device for some runs and another type for other runs of the same protocol This saves you from having to create a device file for each protocol that uses a different type of labware If you are always using the same labware you may not want to use this task The Place Labware task is only used in pre protocol processes The Place Labware task can only be used with labware that is stationary throughout the running of the protocol The Place Labware task allows you to associate a labware entry with a device just before starting a run instead of in the device file For example if in one protocol you restrict use of a device to labware only and in another protocol you restrict use of the same device to labware2 only there are two ways to handle this 1 Create two device files one called device for labware1 and another called device for labware2 where the labware type is specified in the Allowed prohibited labware device property 2 Create one device file where labware type is not specified then create a pre protocol for each protocol where the Place Labware task specifies the labware that must be used for the protocol Set labware Bi Y for protocol A ee Task Settings Advanced Settings Set labware for Place Plate type protocol A C321 at VPrep Which device would you like to use SONA SNET VPrep Standard Shelf v C
63. load the counterweight DAMAGE HAZARD To avoid a robot crash always place the counterweight into bucket 2 and leave the door open with bucket 1 at the front The sample plate will always be moved to bucket 1 by the robot For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Installing a rack on page 64 Setting Access2 task parameters Setting VSpin with Access2 task parameters on page 130 Using the VSpin with Access2 Access2 User Guide Using Access2 diagnostics Access2 User Guide Installing a rack About this topic Procedure This topic explains how to install a rack Before you can perform a run you load the BenchCel with racks containing plates specific to your application To install a rack l Verify that the clamps are extended in the stacker that you want to install the rack onto You can do this by visual inspection of the stacker If the rack does not easily fit onto the stacker head then you may need to extend the clamps Place a rack on the base unit lowering it so that the rectangular tabs drop into the slots in the gripper unit The rack can be placed with the open corner at the front or back Chapter 3 Preparing for a run Rack Stack of plates Stacker Gripper on inside of rack Clamp Stacker Head Riser BenchCel User Guide 65 66 Chapter 3 Prepa
64. millimeters from the bottom of the plate to the middle of the Stacker rack sensor window See Resetting the orientation sensors for a plate on page 313 for a procedure Open the BenchCel robot diagnostics and click the General Settings tab Adjust the value in the Plate presence threshold field Typically this value is 100 If you are getting a no plate present message when there is a plate decrease this value If you are getting a plate present message when there is none increase this value Open the Labware Editor dialog box and click the Stacker tab Adjust the Orientation sensor threshold max and or Sensor intensity values See Resetting the orientation sensors for a plate on page 313 for a procedure Check to ensure plates are located in the correct stack Install rack Open the BenchCel Diagnostics dialog box If there are no plates in the stack click the retract clamps command Shift the stacker s position a little without removing it and then click retry 305 306 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Robot and stacker grippers Problem Error Message Robot grippers are not grabbing plates correctly Plates are tilted or dropping from the stacker Possible Cause Gripper offset is incorrect Stacking thickness for the plate type is incorrect Plate thickness for the plate type is incorrect Gripper limits are incorrect Stacker gr
65. new values or edit existing values for the Sensors using the following table as a guide Parameter Sensor threshold Sensor intensity Check plate notches Comment Sets the sensor threshold value that determines the presence of a notch If the sensor value is below this threshold the device reports a notch in the comer corresponding to the orientation sensor If the sensor value is above this threshold no notch is reported Increase this value if the orientation notch sensor readings are too high with a notch present The default value is 100 To check the sensors see Checking the stacker sensors on page 314 This setting changes the intensity of the light emission that the sensors use to determine the presence of a notch or plate Some plates are more reflective than others Increase the sensor intensity if plate sensor readings are too low not significantly higher than the corresponding threshold value when either a plate is present or a notch is absent The default value is 50 Changing this setting affects the numeric value of the four notches sensors in the Stacker Sensors group box See Checking the stacker sensors on page 314 Turns on plate orientation checking Select the appropriate notches for the type of plate you are using These are called A1 for the top left notch Top right Bottom left and Bottom right 4 Enter new values or edit existing values for the Plate Offsets using
66. on page 125 96 Chapter 5 Creating a protocol basics BenchCel User Guide For information about Waitfor and Signal task parameters WellMate task parameters VSpin with Access2 task parameters Setting the order of tasks Checking for protocol errors Individual modules that perform tasks See Setting Waitfor task and Signal task parameters on page 127 Setting WellMate task parameters on page 128 Setting VSpin with Access2 task parameters on page 130 Specifying task order across processes on page 132 Simulating a run on page 97 About BenchWorks on page 27 About setting pipette task parameters About this topic This topic describes the differences between tasks and pipette tasks and provides cross references to topics about specific pipette tasks Pipette tasks versus Pipette tasks differ from tasks in the following ways tasks a protocol editor device manager Pipette tasks are added in the pipette process editor and not the U Pipette tasks refer to settings in the liquid library editor Q Pipette tasks may require you to configure a VPrep shelf in the Related information For information about the specific types of pipette tasks see the following topics For information See about Aspirate task parameters Setting Aspirate pipette task parameters on page 144 Change instance pipette Setting Change Instance pipette task task
67. page 36 36 Chapter 3 Preparing for a run BenchCel User Guide Logging in to BenchWorks About this topic Logging in Changing your password To log in to BenchWorks you need a user account created by an administrator This topic describes how to log in and change your password once you have a user account To log in to BenchWorks 1 Click Login Fou Log In 2 Select your account User Name from the list box User Authentication xi User Name Example User fa Password O 3 Enter your password and click OK You can change the password for your user account at any time To change your user account password 1 Click the Login button 2 Select your account User Name from the list box 3 Click the Change Password button 4 Inthe Change Password dialog box a Type your old password in the Old text box If the Old text box field is gray if there is no password currently selected for the account b Type your new password in the New text box c Type your new password again in the Confirm New text box d Click OK 5 Click OK Related information Chapter 3 Preparing for a run 37 BenchCel User Guide For information about See Workflow this procedure belongs Workflow for preparing for a run on to page 32 The next step About tasks processes and protocols on page 37 Creating user accounts Adding and deleting a user account on page 205
68. page 37 About user accounts and privileges on page 204 Chapter 5 Creating a protocol basics 87 BenchCel User Guide Setting up a pre protocol or post protocol process About this topic This topic describes how to set up a pre protocol and post protocol process Pre protocols and post protocols are processes that are carried out before and after the protocol is executed Use the pre protocol editor when you want a task performed before the protocol runs For example if you are dispensing reagents you may want to prime a pump with fluid Use the post protocol editor when you want to perform a task after the protocol runs For example you may want to flush lines with a buffer or cleaning agent Procedure To set up a pre protocol or post protocol process 1 Click the Pre Protocol or Post Protocol Editor tab If the tab is not available a Select Tools gt Options b Select the Show Pre Post Protocol Editor check box c Click OK 2 Click Add A pre protocol process icon appears in the Pre Protocol or Post Protocol Editor window 3 Ifthe Task Parameters toolbar is not showing select View gt Toolbars gt Protocol Parameters 4 Type in a name for the process in the Process name field 5 Create the pre protocol process as you would a protocol process by adding tasks and then setting the task parameters 6 When you are finished compile and check your pre protocol 88 Chapter 5 Creating a pro
69. pick up the plate and retry If there is a plate in the grippers and it is incorrectly positioned use the Robot Diagnostics dialog box to move to a teachpoint and open the grippers which will release the plate After that use the diagnostics to pick up the plate and retry If you encounter this error repeatedly contact Velocityl1 Service Center to upgrade your firmware or obtain workaround information for this problem Increase the difference between the two gripper positions 308 BenchCel User Guide Error Message Position error on the Theta axis Position error on X axis Position error on Z axis Position error on grippers Flash operation not successful Operation timed out Communication timed out Deadlock detected Thermal cutoff active for theta axis Chapter 13 Maintenance and troubleshooting Possible Cause The robot failed to move to the commanded position For example something is blocking the robot The robot encountered difficulty writing to its flash memory The robot encountered difficulty executing a command Communication to the robot or to a peripheral instrument was lost Every plate position is filled and there is nowhere to move any of the plates The theta motor is overheated INJURY HAZARD Be careful The robot head might be too hot to touch Recommended Actions Retry If that fails home t
70. plate instance on page 88 Setting the number of simultaneous plates on page 91 Adding and deleting tasks and pipette tasks on page 92 Q About setting task parameters on page 95 Setting task parameters on page 99 page 171 Q U Using JavaScript in BenchWorks on Q The JavaScript task object and properties on page 178 5 Creating a pipette process optional which includes Linking a Pipette Process task icon to a pipette processes Adding pipette tasks Setting pipette process task parameters 6 Creating additional processes and pipette processes 7 Creating a post protocol process optional 8 Adding user message tasks where needed 9 Compiling and saving the protocol 10 Testing the protocol with the simulator 11 Running the protocol Related information For information about About setting pipette task parameters on page 96 Adding and configuring a Pipette Process task on page 140 Setting pipette task parameters on page 135 This table step 4 and step 5 Setting up a pre protocol or post protocol process on page 87 Setting User Message task parameters on page 125 Compiling and saving protocols on page 93 Simulating a run on page 97 Performing a run on page 67 See Protocols including definitions of About tasks processes and protocols terms Privileges on
71. port on the BenchCel If you have another instrument connecting to the BenchCel that requires compressed air split the air supply tubing coming from the source Air input 3 ALE 00042 1 Own Related information For information about See Regulating stacker gripper Adjusting the stacker gripper pressure pressure on page 320 Chapter 2 BenchCel overview 27 BenchCel User Guide About BenchWorks About this topic What BenchWorks does BenchWorks prerequisites BenchWorks main window overview This topic gives an overview of BenchWorks the software that runs the BenchCel BenchWorks is the application that lets you control the BenchCel Through BenchWorks you can quickly automate a series of tasks BenchWorks lets you assemble a modular set of predefined tasks into processes To control the BenchCel with BenchWorks your computer must be connected to your BenchCel To connect your BenchCel to your computer see Connecting the controlling PC and BenchCel on page 24 When you open BenchWorks you are presented with the following window a ee Control toolbar BenchWorks pages Log toolbar Element Description Control toolbar Provides basic BenchWorks commands BenchWorks page Displays one of the six main BenchWorks pages Log toolbar Displa
72. properties for labware defining 225 general settings about 277 changing 278 global changes 287 Genetix aliQuot see AliQuot Genetix QFill2 Dispenser see QFill2 gripper stacker control 24 guest privilege 204 Handle plates in instance order protocol rule 50 hardware overview 76 hazard warnings 11 Home the robot 255 Homing Offsets 279 homing the robot 257 l image root folder 53 image inserting 232 Incubate task Index BenchCel User Guide defined 112 setting parameters 112 Innovadyne Nanodrop see Nanodrop instruments defined 14 preparing for a run 67 integration plate 78 J JavaScript about 171 cautions when using 176 examples 177 global functions 172 plate object 173 resources 171 scripts 85 script writing service 177 task object 174 178 variables 175 JavaScript scripts 86 job roles for readers of this guide 2 L Labcyte Echo 550 see Echo 550 labware adding 227 associating plate with a class 235 classes page 233 classes about 275 copying 224 customizing parameters 238 defining BenchCel properties 229 defining classes 233 defining general properties 225 defining plate properties 226 defining stacker properties 230 deleting 222 editor properties 275 editor about 275 inserting an image 232 looking for definition 278 methods for defining 274 opening parameters group box 237 plate icon 37 renaming 223 standards for 278 using parameters
73. properties of the robot Read this topic if you are an administrator or technician who is responsible for adding and editing labware entries Defining properties To define stacker properties 1 Click the Stacker tab of the labware editor 2 Enter the values for the available parameters according to the type of plate or labware you are defining The properties on the Stacker sub page are described in the following screenshot and table VStack Parameters Stacker gripper offset mm Presentation offset mm Orientation sensor offset mm Orientation sensor threshold max Orientation sensor threshold min Sensor intensity Use vacuum clamp O Property Stacker gripper offset Notch Locations 0 00000 0 00000 0 00000 CO ai Notch Notch O Notch Notch O C check orientation Description Adjusts the height at which the plate stage stops for the grippers to grip the plate with respect to the stacker s Grip teachpoint Change this value only if the stacker is not gripping the plates correctly Property Presentation offset Orientation sensor offset Orientation sensor threshold max Orientation sensor threshold min Sensor intensity Use vacuum clamp Notch locations Check orientation Chapter 10 Defining labware 231 BenchCel User Guide Description Adjusts the height of the stack This parameter does not apply to the BenchCel and therefore does not affect
74. resolving VCode errors see the VCode User Guide 320 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Adjusting the stacker gripper pressure About this topic Procedure The stacker gripper pressure determines how forcefully a stacker grips a plate It is set physically for each stacker and not in software This topic describes how to adjust the BenchCel gripper pressure When to adjust the grip pressure If the plates you are using are flimsy lower the grip pressure from the default pressure of 50 psi to avoid distorting them If your plate stack is heavily loaded with plates the plates are made ofa heavy material or are full of liquid the bottom plate may fall out of the stacker gripper In this case increase the stacker gripper pressure DAMAGE HAZARD Make sure the stacker gripper pressure does not exceed the maximum pressure specified in Performing pre run checks on page 69 To adjust the grip pressure 1 Locate the air pressure regulator Locking ring Air pressure regulator Open gripper flow Close gripper flow 00069 There are three knobs in the back of each stacker on the BenchCel The central knob controls the air pressure to both stacker grippers 2 Using your fingers or a pair of pliers unscrew the locking ring of the central knob by turning it counterclockwise 3 Turn the regulator clockwise to increase the pressure or counterclockwise to
75. s 2 12 04 6 32 52 89 PM Stackerl Source 1 Upstack Process time was 23 sec 2 12 04 6 32 52 69 PM Prep Completed pipette process 1 2 12 04 6 32 52 92 PM Robot Source 1 Fetching plate from Shelf 2 and placing at Stacker1 2 12 04 6 32 59 30 PM Stackerl Source 1 Upstack complete 2 12 04 6 32 59 33 PM Scheduler Protocol completed Ready 58 Chapter 3 Preparing for a run BenchCel User Guide Protocol log file The information given in a protocol log file is explained in the following information table Refer to the screenshot of the Excel file for the column letters Spreadsheet column A B Related information For information about Information Date and time that the entry was added Type of information Error Event Info Script DOODO User Origin of the information Either the Q Name of the plate Q Name of the device if it refers to a reagent Description of the log entry See The workflow for preparing todo Workflow for preparing for a run on a run The next step Log and data files Setting log options page 32 Understanding the protocol on page 59 Q Setting pre protocol rules on page 48 Q Working with the Log toolbar on page 77 Setting log options on page 54 Chapter 3 Preparing for a run 59 BenchCel User Guide Understanding the protocol About this topic This topic gives an overview of the informatio
76. same variable This is the reset script context feature To clear the reset variables default option 1 Select Tools gt Protocol Options The Protocol Options dialog box opens 2 Inthe Pre Protocol Rules group box clear the Reset script context erase all variables before protocol executes check box Pre protocol Rules Reset script context erase all variables before protocol executes O Automatically load stacker racks 176 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Quadrant representation Cautions In JavaScript an array is a built in object that stores a collection of like values called elements Each element is accessed by an index value that is enclosed in square brackets Index values can be non negative integers or strings The following example script declares an array with three elements var vehicle type new Array 3 vehicle type 0 car vehicle type 1 truck vehicle type 2 van Because a plate is already an array of wells locations on plates quadrants are represented in Velocity 1 JavaScript as an array of arrays for example the quadrant property of the task object for one task is represented as 1 1 In this representation the first number refers to the plate row and the second number refers to the plate column These numbers can be represented by variables in a script as shown in the following statement task quadrants disp row
77. the BenchCel that problems you cannot resolve let us know by Q Sending an email to service velocity11 com or euroservice velocity11 com Q Calling the Velocity11 Service Center at 1 800 979 4811 or 1 650 846 6611 Sending files When resolving software bugs or other problems we may ask you to send device and protocols files and the Velocity11 registry file from the Windows registry Reporting user guide If you find a problem with this user guide or have suggestions for problems improvement please take a minute or two to give us your feedback using the feedback button in the online help Your comments will be reviewed promptly and used to write the next version of the guide MX You can also send an email directly to documentation velocity11 com Related information For information about See Sending a bug report Sending a bug report on page 321 Sending a registry file Moving or sending a registry file on page 208 Pi Chapter 1 Introduction BenchCel User Guide Safety information About this topic Before using Safety labels Chemical hazards Waste disposal Product use This topic gives general information about BenchCel safety hazards Before using a BenchCel your organization should make sure that you are properly trained in Q General laboratory safety Q The correct and safe operation of the BenchCel Q The correct and safe operation of other lab automation systems or compo
78. the Controls page of the BenchCel Diagnostics dialog box 3 Select the correct Stacker from the list box 4 Click Move to sensor position 5 Adjust the orientation sensor intensity a Start with a intensity setting where the notch orientation readout values are near saturation about 200 b Gradually reduce the intensity until the readouts start to drop Note the values of the orientation sensor that is detecting the notched side or sides of the plate and the other sensors that are detecting the non notched sides of the plate 6 Set the orientation sensor threshold a Set the threshold to a number approximately halfway between the notch and no notch readouts noted from the previous step For example if the orientation sensors for the no notch sides ofa plate read 180 175 185 and the notched side read 100 set the threshold to 140 314 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Typical settings The following table lists some typical sensor values for plates Use it as a guide for the initial settings of the threshold and intensity values Plate Type Orientation Sensor Orientation Sensor Threshold Intensity Clear all types 100 50 Matte white 100 20 Shiny white 100 10 Matte black 60 80 Shiny black 60 50 Checking the stacker sensors About this topic Procedure Each stacker has the following sensors U Four plate notch sensors one for each plate corner Q A rack presence s
79. the order of the tabs in the Apply label task Protocol Task Parameters toolbar The six columns of a particular side correspond to the six fields in the protocol task parameters The column South3 is the column that contains the root data that will be printed on the south side of the plate in field 3 Each row of the table represents a different cycle in the run The first row contains the root data that will be printed during the first run cycle and so on The following screenshots show how the same plug in is used in a total of four fields on two sides of the plate Repeating columns Related information Chapter 8 Creating a protocol advanced topics 167 BenchCel User Guide South West North East South West North East Printing Option Printing Option Use this label Use this label Format to use 1 Format to use 1 Number of Fields 2 Number of Fields 2 Field 1 Field 1 PLUGIN Field 2 PLUGIN Field 2 Field 3 PLUGIN Field 3 PLUGIN Field 4 Field 4 Field 5 Field 5 Field 6 Field 6 Increment Chars 3 Increment Chars 3 Starting Increment 1 Starting Increment 1 Using these parameters data from the above plug in file would print the following labels Field Printed labels in run cycle 1 South Field 2 rlc2 South Field 3 rlc3 West Field 1 rlc7 West Field 3 rlc9 A text file with data for labels on only one side of the plate is sufficient to print the same labels on other sides of
80. to waste instead of dispensing it back into the reservoir of washing liquid Note The Dispense to waste at height of check box must be selected for this option to be available Enter the amount to dispense in the Wash Volume field Empty tips This option is only available if you select Dispense only Select this if you want to empty the tips regardless of the volume Number of wash cycles The number of aspirate dispense operations Aspirate velocity The rate at which to draw up the liquid If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here 160 Chapter 7 Setting pipette task parameters BenchCel User Guide 4 Property Aspirate acceleration Dispense velocity Dispense acceleration Distance from well bottom Retract Distance Pre aspirate volume Last cycle blowout volume Description The rate of increase in velocity before the aspirate velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here The rate at which to dispense the liquid If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here The rate of increase in velocity before the dispense velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor and can
81. topic describes the different types of logs that BenchWorks creates Log files record event and error information in text files that can be useful for troubleshooting Data files record data collected by devices such as plate readers The location of the three log files a data file and a folder are set in the Log Options page of the BenchWorks Options dialog box r File Settings aa Max number of each log file to maintain 0 Create new logs for every run Append timestamps to filenames Protocol log E protocol log txt Pipettor transfer log m piplog txt Bar code log Edl barcodelog txt Reader output file E Reader dat Image file root folder VersaScan only O Enable plate tracking in simulation mode These are listed in the following table and described in more detail later in this topic File Default file or folder name Protocol log file log txt Pipettor transfer log file piplog txt Bar code log file barcodelog txt Reader output file Reader dat Image file root folder A folder that you select Note You can change the default filenames to suit your own needs but they are referred to using their default names throughout this guide You can open a log file in any text editor but we recommend that you use the Windows application Notepad because with Notepad you can open the file during a run as the file is being written 52 Chapter 3 Preparing for a run BenchCel User Guide Protocol lo
82. up with it Defines the maximum speed at which this type of plate should be moved The general robot speed is set in BenchWorks If the plate specific robot speed set here is different from the general robot speed the slower of the two speeds is used Use calipers to measure the length in millimeters of the filter tip or pin tool in filter and pin tool plates For information about See Defining labware Q Labware editor overview on page 216 Q About the defining labware process on page 218 Editing labware parameters Changing labware parameters on page 238 Adding a piece of labware Adding a labware entry on page 221 Deleting a labware entry Deleting a labware entry on page 222 Defining BenchCel properties About this topic Properties Chapter 10 Defining labware BenchCel User Guide This topic describes the properties on the BenchCel sub page of the Labware Editor dialog box Note You must also define Stacker properties because they apply to the built in stackers of the BenchCel The properties on the BenchCel sub page are described in the following sceenshot and table All of the properties on this sub page only apply to the BenchCel Gripper Offset and Positions Robot gripper offset mm Gripper open position mm Gripper holding plate position ram Gripper holding lidded plate position mm 1 00000 Gripper holding lid position mm 4 50000 Gr
83. value will have no effect call will be ignored Visual C Visual Basic Set the speed to fast Set the speed to fast m_BenchCel speed 2 BenchCell Speed 2 Description Specifies whether the ActiveX should block during an execution of a command If true commands like PickAndPlace will not return until the action completes or an error occurs The result value return from the call will indicate success S_OK or 0 or failure If false the command will return immediately and fire an event to indicate successful completion of the command Errors will be indicated through one of two means 1 the return value might not be S_OK 0 in this case no event will be fired 2 an error event is fired When an error occurs the Chapter 14 BenchCel ActiveX controls 325 BenchCel User Guide ActiveX expects a call to Abort Retry or Ignore ShowDiagsDialog can be called to allow the user to exercise specific diagnostic corrective functions but when the main execution resumes a call to Abort Retry or Ignore is necessary to continue the operation Visual C Visual Basic Set the BenchCel to block until Set the BenchCel to block until the the command completes command completes m_BenchCel Blocking 1 m_BenchCel Blocking TRUE Setting up methods About this topic void AboutBox BSTR GetVersion Methods are functions that can be called by the container application Description Shows a small window that indicates some ve
84. want to change or check the appropriate check box using the following table as a guide Setting Comment Theta This offset changes the angle in degrees that the grippers home to It is measured from a line perpendicular to the x axis 280 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Related information Setting Comment X Changes the distance from the center of the robot s horizontal travel Find this distance by measuring the distance the robot travels from an arbitrary point to the far left and far right positions and averaging them Z Changes the distance between the bottom of the robot head and the column Ideally this should be 20 mm Gripper Changes the distance between the opposing gripper points This distance should be 87 5 mm Home unit after Checking this box tells the robot to home itself releasing stacks every time it releases a stack 5 Check the Robot Limits These values define the range of the theta x and z axes for the robot Robot Limits Theta xX mm Z mm Gripper mm IMPORTANT These offsets are set at Velocity11 and should not need to be changed Click OK for the settings to take effect IMPORTANT If you change the general settings and click OK the values are changed in BenchWorks which will affect protocols that you run afterwards For information about See Adjusting labware settings Maintenance and troubleshooting
85. you enter a time stamped note into the log See Working with the Log toolbar on page 77 30 Chapter 2 BenchCel overview BenchCel User Guide Relationships of BenchWorks components About this topic BenchWorks uses four file types to run the application What they are and how they work together to operate the BenchCel is described below What you should It is important to understand the way each of the main configuration know components in BenchWorks relate Loading some components automatically loads others For example loading a protocol file loads a device file Definitions Refer to the table below for information about these four BenchWorks configuration components Component Definition See Protocol file A file that contains instructions About protocol files for performing a run on page 84 Device file A file that contains Working with device configuration information for files on page 195 configured devices Profile A collection of settings stored About profiles on in the registry that manages page 282 how you connect to devices Teachpoint File A file that saves your teachpoint Managing teachpoint settings files on page 274 Configuration Refer to the table below to understand the relationships of these four component BenchWorks configuration components relationships ss Component Extension Opening this file loads Protocol bwl Q BenchWorks if it is not already runni
86. 157 BenchCel User Guide d Inthe Number of sides to touch text box type a value for the number of sides of the wells that you want the tips to touch 6 Inthe Plate to mix list box select the type of labware or device to mix in For information about See Defining labware About the labware editor on page 215 Configuring VPrep shelves Configuring a VPrep shelf as a device on page 142 Configuring a pipette process Q Configuring a pipette process example on page 136 Q Adding and configuring a Pipette Process task on page 140 Defining liquid handling About the liquid library editor on parameters page 244 Setting Pump Reagent pipette task parameters About this topic Pump Reagent task defined This topic describes how to set the Pump Reagent pipette task parameters This task is used when creating a BenchWorks protocol that uses a Velocity 1 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Pump Reagent task The Pump Reagent pipette task is used on a VPrep to pump liquid into an installed autofilling reservoir Reservoirs are typically filled with washing buffer or water and drained through the gravity drain IMPORTANT If you run an empty reservoir step and a fill reservoir step in the same protocol check the protocol to make sure that it will not lead to an overflow 158 Chapter 7
87. 2 0 0 VicValveDevice 4 0 0 NanodropDevice 1 1 1 VLidDevice 1 3 1 Original CodeDevice 3 2 1 YMixDevice 3 0 5 PipettorShakeShelfDevice 2 3 0 VPrepDevice 17 3 1 PlateLocDevice 6 2 1 VSpindccess2Device 1 1 3 PlatePierceDevice 4 1 0 VSpinDevice 4 2 2 QFillDevice 3 0 1 RempCSPDevice 2 1 0 RobotDevice 8 1 13 ShuttleRobotDevice 1 1 2 ST6StackerDevice 4 1 0 This product includes the JavaScript engine and Netscape Portable Runtime NSPR libraries distributed as part of the Mozilla project this software is copyright 1998 2001 by Netscape Communications Corporation and others NSPR code is used under the terms and conditions of the Mozilla Public License version 1 1 JavaScript code is used under the terms and conditions of the Netscape Public License version 1 1 WeighPadDevice 1 3 0 WellMateDevice 1 2 2 ZeissReaderDevice 2 1 0 Please contact Velocity11 to obtain a copy of the source code for the JavaScript engine and NSPA libraries 5 Chapter 1 Introduction BenchCel User Guide Supported firmware version What this guide does not cover BenchCel versions Related information This guide covers firmware version 2 2 8 The firmware version can be determined from the General Settings page of the BenchCel Diagnostics dialog box This guide does not cover the operation of the following Q Velocity11 instruments such as the PlateLoc VCode and VPrep when used in stand alone mode Q Other companies device
88. 2 0 65 PlateLoc 85 90 0 56 0 62 VCode 70 75 0 48 0 52 VSpin with Access2 80 90 0 55 0 59 For information about See Checking stacker sensors Checking the stacker sensors on page 314 Opening BenchCel Diagnostics Opening BenchCel Diagnostics on page 253 Chapter 4 Performing a run BenchCel User Guide Starting a run from BenchWorks About this topic This topic describes how to start a run using the Start button in BenchWorks Start a run after performing pre run checks and opening a protocol Procedure To start a run 1 Make sure that all instruments used in the protocol are in their home positions Refer to the instrument user guides for more information about homing 2 In BenchWorks click Start If this is the first run with this device file BenchWorks confirms communication with all devices and instructs the devices to home If there are no protocol compilation errors the Number of Cycles dialog box opens 3 Ifyou selected from plug in as the plate type the Labware dialog box opens asking you to select the labware type select the appropriate labware type from the list Please select the labware to use 96 Costar Flat Bottom w Lid 4 Ifyou are running a VCode and are using the FileReader plug in the Open dialog box opens asking you to select the text file that contains the bar code label data a Select the plug in text file that contains the data from the Open dialog box and click Open
89. 39 Field 2 Field 3 Dutch Roman 801 prop Field 3 Field 4 Dutch Roman 801 prop Field 4 Field 5 Dutch Roman 801 prop In the screenshot below you can see that three of the BenchWorks fields are used Field 2 Field 3 and Field 4 Format to use 2 Number of fields 3 Field 1 Field 2 DATE INC Field 3 DATE INC Field 4 My name Field 5 Field 6 Increment chars 3 Starting increment 1 Chapter 6 Setting task parameters BenchCel User Guide Field 2 prints a Code 39 symbology bar code that is incremented for each printing Field 3 prints the same bar code in the human readable Dutch Roman font The text entered into Field 3 is the same as that entered into Field 2 The information entered in Field 3 combined with the information entered into the Increment chars and Starting increment fields creates the following human readable bar code sequence Date001 Date002 Date003 Date004 Date005 Date006 Date007 The bar code log file Information about the bar codes that are applied during a run is saved in a bar code log file Because this is a tab delimited text file the data can easily be imported into a spreadsheet program File Edit Format View Help 2 37 29 O1pHTS 1 pHTS501001 2 38 07 PM O2pHTS 1 No No pHTSO2001 No 5 6 03 2 38 19 28 PM O3pHTS 1 No bar code No bar code pHTSO3001 No bar code 5 6 03 2 38 30 70 PM O4pHTS 1 No bar code No bar code pHTSO4001 No bar code 5 6 03 2
90. 60 privileges defined 204 effect of 204 types 204 process defined 38 profile creating 283 defined 30 282 editing 284 property acceleration 248 249 can be mounted 228 can be sealed 227 can have lid 227 240 can mount 228 check orientation 237 length of filter tip pin tool 228 lid departure height 228 247 lid gripper offset 227 241 lid resting height 227 241 lidded stacking thickness 227 lidded thickness 227 lower plate at VCode 228 maximum robot handling speed 228 notch locations 237 orientation sensor offset 237 orientation sensor threshold 237 post aspirate delay 249 post dispense delay 249 presentation offset 237 sealed stacking thickness 227 sealed thickness 227 sensor intensity 237 stacker gripper offset 230 stacking thickness 227 238 thickness 226 238 use vacuum clamps 237 velocity 248 249 zaxis acceleration into wells 249 zaxis acceleration out of wells 249 zaxis speed into wells 248 z axis velocity into wells 249 z axis velocity out of wells 249 protocol adding notes about 94 compiling 93 creating example 136 creating pre and post processes 87 defined 38 file finding 322 file format 84 filename extension 30 log file 52 322 log file example 58 optimizing 48 options setting rules 48 overall process of creating 85 printing 60 run until done 72 saving 94 setting rules 49 simulating 97 specifying order of tasks 132 understanding before a
91. AZARD The robot will move to a teachpoint using the most direct path If there is an object in the way the robot will collide with it If you have defined a teachpoint for an object that is in the path of the robot the robot will compensate for this and avoid a collision 276 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Selecting two teachpoints Procedure Related information In the BenchCel animated display you can select one or two teachpoints at a time It is useful to select a pair of teachpoints so that you can conveniently move the robot between them When you click a teachpoint marker controls appear permitting you to perform additional functions To select two teachpoints 1 Click one teachpoint marker A red border appears around the teachpoint marker indicating that the teachpoint is selected 2 Click asecond teachpoint marker A red border appears around the second teachpoint marker indicating that its teachpoint is selected These two markers will remain selected until you choose another teachpoint At that moment the first teachpoint marker you chose is deselected Note Occasionally command buttons on the animated display obscures a teachpoint you want to select Expose the obstructed teachpoint by deselecting the teachpoint whose command buttons are in the way For information about See Creating a teachpoint About teachpoints on page 269 The animated display A
92. BenchCel as illustrated in the following screenshot of a system that has two Nanodrop pipettors Nanodrop Diagnostics 1 0 2 0 Actions Profiles Nanodropl U EOMi Nanodrop2 COM3 All profiles should have been set at the factory so you should not need to create a new one unless you are adding another Nanodrop to your system If you have more than one Nanodrop on your BenchCel select the profile for the one with which you want to communicate To create a profile Managing profiles Running an individual operation Chapter 12 Using BenchCel Diagnostics 289 BenchCel User Guide To select a Nanodrop profile 1 Inthe Actions tab select the profile from the Profile list box 2 Click Connect You only need to create a new profile if you are adding a Nanodrop to your BenchCel To create a Nanodrop profile 1 Click the Profiles tab 2 Click Add 3 Inthe Profile Details dialog box type a name for the profile 4 Select an available communications port from the Serial port list box 5 Click OK To modify a Nanodrop profile 1 Open Nanodrop Diagnostics 2 Click the Profiles tab 3 Select the profile you want to modify and click Change 4 Enter your changes in the Profile Details dialog box 5 Click OK To delete a profile 1 Open Nanodrop Diagnostics 2 Click the Profiles tab 3 Select the profile you want to delete and click Delete Use Nanodrop Diagnostics to perform the following actio
93. BenchCel Microplate Handling Workstation X Series BenchWorks version24 x User Guide oie Agilent Technologies Notices Agilent Technologies Inc 2009 No part of this manual may be reproduced in any form or by any means including electronic storage and retrieval or translation into a foreign language without prior agreement and written consent from Agilent Technologies Inc as governed by United States and international copyright laws User Guide Part Number 65400 90002 January 2009 rebranded edition including June 2008 Labware Rack guide January 2006 BenchCel Workstation X series user guide Contact Information Agilent Technologies Inc Automation Solutions 5301 Stevens Creek Blvd Santa Clara CA 95051 USA Technical Support 1 800 979 4811 or 1 408 345 8011 service automation agilent com Customer Service 1 866 428 9811 or 1 408 345 8356 orders automation agilent com European Service 44 0 1763853638 euroservice automation agilent com Documentation feedback documentation automation agilent com Web www agilent com lifesciences automation Acknowledgements Microsoft and Windows are registered trademarks of the Microsoft Corporation in the United States and other countries Warranty The material contained in this docu ment is provided as is and is sub ject to being changed without notice in future editions Further to the max imum extent permitted by applicable la
94. Cel Diagnostics dialog box 2 Place a plate in one of the stackers 3 Command the robot to pick the plate and then to go home 4 Using the bar in front of the BenchCel visually check if the plate is parallel to the bar 5 Ifthe plate is not parallel the arms are out of alignment Example of gripper arms out of alignment Example of gripper arms in alignment Reference bar Reference bar Compare these planes at eye level Compare these planes at eye level Resolving labware problems About this topic Error messages When using a new labware type you may encounter some robot handling errors which will require adjustments to offsets and or sensor thresholds and intensities This topic identifies some of the typical problems you may encounter and provides some recommended solutions The following types of errors are generated when there are problems with the labware Q Wrong plate type Q Plate is rotated U No plate is present Plate is rotated or other conflicting messages Wrong plate type Plate is rotated Chapter 13 Maintenance and troubleshooting 311 BenchCel User Guide This error is generated when the notch sensors located in the stacker head detect a plate notch pattern inconsistent with the definition of that plate type in the labware database To resolve a wrong plate type error 1 2 Check to be sure you are using the correct plate type If you are u
95. Gai r 1 on VPrep 4 m i E AIt AJl E te Proce Fspirate 10 00 pL Dispense 10 00 pL Tips Off Pipette Process 1 Tips On on Prep from Plate 1 in column 1 into Plate 1 in column 4 Pipette task For information about The workflow this procedure belongs to The next step See Workflow for preparing for a run on page 32 Opening a protocol in BenchWorks on page 40 Opening a protocol in BenchWorks About this topic Procedure All runs on the BenchCel require a protocol This topic describes how to open a protocol that has already been created To open a protocol 1 Select File gt Protocol File gt Open 2 Navigate to the folder containing the protocol file 3 Select the protocol file and click OK You can also open a protocol by navigating to the bwl file in Windows and double clicking it This launches BenchWorks and opens the protocol Related information Chapter 3 Preparing for a run 41 BenchCel User Guide For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Setting general options on page 41 Setting general options About this topic When to use Procedure This topic describes how to configure the general options in the BenchWorks Options dialog box General options include the following Q Location of the bar code input or data file Q Maximum robot speed Q Visibil
96. However unless you explicitly save the protocol the changes are lost when you exit BenchWorks To save a protocol 1 Select File gt Save As 2 Inthe Save As dialog box navigate to the folder in which you want to save the protocol 3 Inthe File name text box replace the selected file name with a name of your choice You can add a description of your protocol to remind yourself of its features or for BenchCel operators to review before performing a run To add notes about your protocol 1 Click Tools and select Protocol Options 2 Type your notes into the Description Notes text box Description Notes This is a description of my latest protocol Note When you open a new protocol its associated description replaces the description of the previous protocol For information about See The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Setting up a plate instance Setting up a plate instance on page 88 Resolving protocol compilation Compilation warnings and errors on errors page 303 Setting the number of Setting the number of simultaneous simultaneous plates plates on page 91 Chapter 5 Creating a protocol basics 95 BenchCel User Guide About setting task parameters About this topic Task parameters defined Related information This topic describes what task parameters are and what they do After you have added a task you can set pa
97. Incorrect orientation offset See Resolving labware problems on page 310 for a procedure Orientation sensors need See Resetting the orientation sensors for adjusting a plate on page 313 for a procedure Problem Error Message Plate is rotated Conflicting messages regarding plate presence and orientation No plate in stack Stack not loaded Rack not present Possible Cause Plate was placed in the stacker rack in the wrong orientation Notch location is wrong in the labware definition for the plate Stacker orientation sensor offset is incorrect Orientation sensors need adjusting The plate presence threshold is not set to accommodate the range of plate types you are using Plate orientation sensors need adjusting Plates are not in the correct stack Stacker rack is absent Stacker clamps in the incorrect position to execute the command Stacker rack is out of position Chapter 13 Maintenance and troubleshooting BenchCel User Guide Recommended Actions Check the plate orientation in the stacker rack The notch should be in the back left corner as you face the BenchCel Open the Labware Editor dialog box and click the Stacker tab Check to ensure that the correct notch is selected in the Notch Locations group box Open the Labware Editor dialog box and click the Stacker tab Verify the Orientation sensor offset value This value is the distance in
98. MB RAM Windows 2000 or XP Professional operating system 50GB free hard disk space OQ Communication interface Dedicated 10BaseT Ethernet port two network cards if connecting to your company LAN RS 232 serial port 22 Chapter 2 BenchCel overview BenchCel User Guide Connection panel description About this topic This topic uses an illustration to point out the specific connections of the connection panel at the rear of the BenchCel Connection panelfor The diagram and the following table identify the inputs and outputs on utilities the connection panel Power indicator light Communication Ethernet port Air input On Off switch 00042 indicator light Safety interlock circuit Ethernet indicator light AC power entry Fuse holder Item Serial port Ethernet port Indicator lights Description A DB 9 RS 232 serial port that provides serial control of the BenchCel and firmware programming If you connect to the BenchCel using the serial port you do not need to connect through the Ethernet port An RJ 45 Ethernet port that provides ethernet control of the BenchCel Connect to the host computer with a shielded Cat 5 Ethernet cable If you connect to the BenchCel using the Ethernet interface you do not need to connect through the serial port Q Power indicator light is red
99. O Log pipettor debug messages Log task complete events on screen O Log robot motions on screen Q General settings that pertain to log and data file maintenance Max number of each log file to maintain 10 Llicrest gt new lese toeven Append timestamps to filenames Q The folders in which to store log and data files Protocol log protocol log txt Pipettor transfer log Ed piplog txt Bar code log El barcodelog txt Reader output file E Reader dat Image file root folder VersaScan only Q Checking the database connection and enabling plate tracking Database connection string Test amp Save O Enable plate tracking in simulation mode How messages displayed in the Log toolbar are controlled Setting log options procedure Chapter 3 Preparing for a run 55 BenchCel User Guide Event and error messages are displayed in the log toolbar With all message options turned on a large number of messages are displayed For simplicity you can hide types of messages that are not important to you The messages that are displayed during a run are controlled by U Selecting screen settings options in the Tools gt Options dialog box before a run Q Clicking tabs in the Log toolbar during a run Note Screen display settings do not affect the information saved in log files All error and event information is always saved To set log file options 1 Select Tools gt Options 2 Click
100. PM Intermediatea 1 IntaAlOl Intaool No bar code No bar code 1 1 93 12 54 12 78 PM vPrep 1 96 channels Qlsource 1 Masteragoo4 No bar code No bar code N 1 5 22 03 12 54 20 60 PM IntermediateB 1 IntB101 IntBOO1 No bar code No bar code 1 1 3 12 54 27 40 PM vPrep 1 96 channels Qisource 1 mastera0004 No bar code No bar code N 1 5 22 03 12 54 40 76 PM Qlsource 1 Master agod4 No bar code No bar code No bar co 0 0 OK 3 12 54 27 40 PM vPrep 1 96 channels Qlsource 1 mastera 004 No bar code No bar code N a 5 22 03 12 54 49 03 PM Intermediatec 1 Intcl01 IntcoOO1l No bar code No bar code a 1 The pipettor transfer log contains the following information separated by tabs U Aspiration timestamp Pipettor name Name of the plate aspirated from North bar code of plate aspirated from East bar code of plate aspirated from South bar code of plate aspirated from DODDO West bar code of plate aspirated from Bar code log file Reader output file VersaScan image file root folder Related information Chapter 3 Preparing for a run BenchCel User Guide Quadrant of the plate aspirated from number 1 16 Dispense timestamp Name of the plate dispensed to North bar code of plate dispensed to East bar code of plate dispensed to South bar code of plate dispensed to West bar code of plate dispensed to Quadrant of the plate dispensed to number 1 16 Volume of liquid dispensed in microliters
101. Protocol Task Pa rameters toolbar 166 tasks adding 92 defined 37 deleting 92 moving 93 specifying order in a protocol 132 types 95 teachpoint about 269 adding 270 deleting 273 editing 272 file definition 30 filename extension 30 moving between 275 selecting two 276 technician privilege 85 204 temperature operating range 20 Thermo Electron Multidrop see Multidrop Thermo Electron Multiskan Ascent see Multiskan Ascent thickness property 226 238 tip touch horizontal distance 152 156 tip touch rise height 752 156 tip touching 152 156 tipbox 749 tips see pipette tips toolbars closing 77 control 28 Log 29 77 transfer log 152 troubleshooting 299 bar code errors 317 files to send 322 initialization errors 302 U Upstack task defined 709 setting parameters 109 use vacuum clamp property 237 user account adding 205 creating 204 deleting 206 privileges 204 User Message task 72 defined 125 setting parameters 126 utility requirements 20 vV vacuum filtration see QFill2 VCode about 197 errors 319 setting up 61 velocity property 248 249 Velocity11 privilege 204 ViewLux supported instrument 18 volume blowout 152 156 160 dispense 151 mixing 155 post dispense 152 pre aspirate 160 wash 159 VPrep changing tips 149 configuring a shelf 137 142 reservoir 158 selecting 137 setting up 62 VSpin see also VSpin with Access2 task VSpin with Acce
102. Q Pre post protocol scripts Q The Advanced Settings tab Scripts can be written in two ways U Directly into the text box Q Asan external file that is located by clicking Browse Note You can also call an external file by embedding the open function in the text box The following screenshot shows a short script that prints the parameters of a task to the log toolbar just before the task runs In this case the script is written directly in the Advanced Settings text box Protocol Task Parameters Task Settings Advanced Settings Enter pre task script or click the browse button to load a script from an external file Browse ii in task print task x task x The BenchWorks interpreter supports the JavaScript 1 5 core functions and objects Velocity11 has also defined its own functions and objects that can be used in BenchWorks scripts The following BenchWorks defined functions are available globally meaning that they are not restricted to a particular object or programming context Function Description printQ Prints time stamped messages to the BenchWorks log Parameter Text string Example print plate name open Opens a file Parameter Text string Example open c benchworks workspace benchworks3 tex t txt BenchWorks defined objects Plate object Chapter 8 Creating a protocol advanced topics 173 BenchCel User Guide Function Description run Runs a progr
103. Resolving VCode bar code reader errors on page 319 302 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Resolving device initialization errors About this topic Device initialization process Resolving initialization errors This topic describes the device initialization process and suggests some things to try if you encounter problems with device initialization When you start BenchWorks the software loads the driver files for all the devices on your system A record of this process is displayed in the log toolbar When you open a protocol file the device file associated with that protocol opens The device file tells the software which devices are connected to the system Then for some kinds of devices an initialization step tests the communication between BenchWorks and the device During this process a message window opens displaying the name of the devices that the software expects to find Devices are removed from the list as the system computer determines that the devices are ready In the following example there are four devices that the software is trying to initialize Waiting for Devices xi Please wait while the Following devices initialize If there is a problem with initializing a device you receive an error message dialog box for that device The problem encountered is stated in the text field of the dialog box In this example BenchWorks could not initialize the VPrep device
104. Settings Available stackers Available stackers Stacker4 Stackers that this task will use Stackers that this task will use Use Stacker2 Use earlier earlier Use Use later later Add dynamically assigned stacker O Release a new plate every 1 seconds 3 To remove a stacker rack from your list of available stacker rack devices select it and click Remove 4 Ifyou have added more than one stacker rack you can change the order in which particular stackers racks are used a Select a stacker rack b Click Use earlier to increase the priority of the stacker rack or Use later to decrease the priority of it Related information Chapter 6 Setting task parameters BenchCel User Guide 5 To specify a time interval for when plates are made available to the system select the Release a new plate check box and type in an interval time You can use this feature to avoid a plate processing bottleneck that results in plates having different incubation times Consider a simplified example process in which plates are downstacked labels applied liquid dispensed into and then incubated for 10 minutes Applying the label only takes a few seconds while subsequent tasks take longer This creates a processing bottleneck If the dispense task takes 2 minutes plates that are ready for the pipetting step would have to wait In this example the first plate would incubate for approximately 5 minutes the second plate f
105. Shelf No Description y Labware Costar 96 pp black hs Liquid type None 2 The Liquid Library Editor dialog box opens Liquid Library Editor 5 0 3 Please select a liquid entry from the list below in order to view and edit its properties Use this box to enter a description of the liquid entry and any notes pertaining to its use 384 disposable tip 0 5ul 1 Qul a 384 disposable tip 11ul 50ul 384 disposable tip 1ul Zul 384 disposable tip 3ul 6ul 384 disposable tip 6ul 10ul z 384 disposable tip Wash 384 fixed tip 0 01ul 0 05ul 384 fixed tip prime 96 disposable tip 1 0ul 10ul 96 disposable tip 11 60ul 96 disposable tip 11ul 50ul Enter description of new liquid type here E Aspirate Parameters Z axis Aspirate Parameters 40 Velocity into wells 96 disposable tip 51ul 200ul 96 disposable tip wash Fixed Tip 0 005 0 010ul Fixed Tip 0 05ul 1ul Fixed Tip O2ul 10ul Fixed Tip 1 1ul 50ul Fixed Tip Prime a New liquid entry Save changes Aspirate Related information For information about The liquid library editor Creating a new liquid class Velocity 0 1 500 pl s Acceleration 1 1000 l s Post aspirate delay 0 300000 ms Copy values to dispense tab See 1 250 mm s Acceleration into wells 1 2000 mm s Velocity out of wells 1 250 mm s Acceleration out of wells 1 2000 mm s
106. Specifies acceleration during the dispensing stroke in microliters per second squared Specifies how fast the pipettor moves as the tips enter the wells in millimeters per second VPrep only Specifies the acceleration of the pipettor as the tips enter the wells in milliliters per second squared Specifies how fast the pipettor moves as the tips leave the wells in millimeters per second VPrep only Specifies the acceleration of the pipettor as the tips leave the wells in millimeters per second squared Specifies the time the pipettor waits after the dispense stroke before moving the tips out of the wells in milliseconds The changes are now stored in the liquid library database 250 Chapter 11 Setting liquid handling definitions BenchCel User Guide Related information For information about Opening the liquid library editor The liquid library editor See Opening the liquid library editor on page 246 About the liquid library editor on page 244 Chapter 12 Using BenchCel Diagnostics 251 BenchCel User Guide Using BenchCel Diagnostics This chapter explains how to use diagnostics software to control the robot and modules We recommend that only administrators and experienced personnel use the procedures in this chapter to diagnose errors with the BenchCel Velocity11 has also developed diagnostics software for other companies modules that can be used with the BenchCel Instr
107. Tools gt Manage Users 2 Inthe User name text box select the user you want to delete 3 Click Delete If you attempt to delete the account that is currently in use you receive an error message 4 Inthe Confirm Delete dialog box click Yes The password is deleted For information about See User accounts and privileges About user accounts and privileges on page 204 Setting up email Setting up email on page 206 Setting up email About this topic Requirements for email setup Setting up email This topic describes how to add an email address to BenchWorks so you can be notified by email or pager when there is a run error Email setup in BenchWorks enables you to do the following tasks Q Automatically be notified by email or pager when errors occur during a protocol run Q Send a bug report to Velocity11 Before you can send an email from BenchWorks Q The BenchCel computer must be connected to a network with internet access Q The outgoing email server must be set up on the system s computer To set up the outgoing email server 1 Select Tools gt Options 2 Inthe BenchWorks Options dialog box click the Email Setup tab 3 Inthe Mail Server Setup group box enter the name of your SMTP server name outgoing email server Chapter 9 Administrator procedures 207 BenchCel User Guide 4 If the server requires a user name and password a Select the Server requires authentication
108. aScript is made up of a core language plus Web browserspecific language It is processed by the JavaScript interpreter that is built into modern browsers The core JavaScript language can be used to write scripts that have nothing to do with web pages These scripts can be used for any application that includes a JavaScript interpreter BenchWorks is an example of such an application it uses a JavaScript 1 5 interpreter There are many JavaScript resources available online and in print If you want to learn more about JavaScript for use in BenchWorks look for resources that cover the core JavaScript language separately from the browser client side language and Document Object Model Web references You can find useful information at http www mozilla org js Print reference A good print reference is JavaScript The Definitive Guide Fourth Edition published by O Reilly You can use JavaScript to Q Print the parameters of a task to the BenchWorks log Q Run a command line that launches an external application such as a batch file or database updating program Q Simplify protocol writing for example by incrementing pipetting volumes each cycle of a protocol to perform a dilution series 172 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Where scripts are written About BenchWorks defined functions and objects BenchWorks defined global functions Scripts can be written in two places
109. aa es 238 Chapter 11 Setting liquid handling definitions 243 About the liquid library editor 2 0 0 ee 244 Opening the liquid library editor erare nra EP LELTE es 246 Creating a liquid class 1 es 248 Chapter 12 Using BenchCel Diagnostics 251 About diagnosticS 2 2 es 252 Opening BenchCel Diagnostics 0 000 ee eee 253 About the Controls Dage esed tot kw ted Gl eae WAR Mea ee AL ee heed bel ard 254 Homing the ODOt eiriiecece tiated kane a OS Se AS Sal Toe ae ek cee RE Oe ae 257 Moving the robot manually 0 0 ec ee eee 258 Jogging the robot 2 ees 259 Changing the robot Speed 1 ee 261 Using Move To Position commands 000 cee ee ees 263 About stacker controls aec naaa en naaa es 264 Loading and releasing stackS 0 ccc eee eee 265 Extending and retracting stacker ClampS 000 eee eee eee 267 Table of Contents BenchCel User Guide AbOUtteaChPOINtS aiaa enaa a Soe alae eee wa ee ee aia we oe eee we es 269 Addingza teachpoint 2 4 0 cols Se dds Ca Soe an ee ek had bee a ae 270 Editing a teaChpOint ec ooo ee ee eee eed ee See en eg ees eee be eo Rin Bae 272 Deleting a teachpoint 2 eee 273 Managing teachpoint files 0 00 cee ee eee 274 Moving between teachpointS aaaea ee eee 275 About gene ral Settingss si 2 S008 cae eae ie ie be ee bo et 277 Changing general settingS 0 cc ees 278 Making global g
110. abware editor overview on page 216 Q About the defining labware process on page 218 Editing labware parameters Changing labware parameters on page 238 226 Chapter 10 Defining labware BenchCel User Guide Defining plate properties About this topic This topic describes the parameters used to define a plate or other piece of labware in the Plate Properties sub page of the labware editor You must have a technician or administrator user account to perform this procedure Defining plate To define plate properties properties 1 Click the Plate Properties sub page tab of the labware editor 2 Enter the values for the available parameters according to the type of plate or labware you are defining The parameters on the Plate Properties sub page are described in the following screenshot and table Note Only the parameters associated with the Base Class you selected in the General Properties group box will be available Plate Dimensions and Gripper Offsets Plate Handling 3 00000 Robot gripper offset mm Lower plate at YCode 30 00000 Thickness mm O Can mount 28 40000 Stacking thickness mm O Can be mounted Can be sealed O Maximum Robot Handling Speed O Slow Medium Sealed thickness mm Sealed stacking thickness mm Can have lid Lidded thickness mm Miscellaneous Length of filter tip pin tool mm Lidded stacking thickness mm Lid
111. ace of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use Pre aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid and before mixing begins Last cycle blowout The volume of air to blow out when the tips volume are in the liquid once the mixing is complete This is typically the same as the pre aspirate volume If the VPrep head has fewer tips than the plate has wells select a quadrant configuration from the Quadrant s diagram to indicate in which well quadrant of the plate you want to mix To select a quadrant click a representative well Two possible examples are shown below Quadrant s Quadrant s 1ee0eo 5000 1 e0e 59000 0000 000o 0000 eceo If you want the tips to touch one or more sides of the plate wells a Select the Enable tip touch check box b Type a value for the Tip touch rise height This is the height that the tips should move upwards before touching the side of the wells c Typea value for the Tip touch horizontal distance When the value for this parameter is zero the tips will move horizontally one well radius The well radius is defined in the labware database for the type of plate you are using If you want the tips to touch harder increase this value If you want the tips to touch more lightly enter a negative value Related information Chapter 7 Setting pipette task parameters
112. achpoint About this topic Procedure Related information After you have created a teachpoint you can edit it Edits to your teachpoints are automatically saved to your current teachpoint file To edit a teachpoint 1 Double click the teachpoint marker that corresponds to the teachpoint you want to change Teachpoint markers are little square dots in the BenchCel animated display Load Stack 1 Load Stack 2 Release all stacks Retract Clamps Retract Clamps Stacker 2 teachpoint marker not selected LI hove to Stacker 1 Pick from Stacker 1 Transfer to Stacker 1 Pick from test1 Delid from test1 Transfer to Stacker 2 Test1 teachpoint marker selected The Teachpoint Details dialog box is displayed with values of the teachpoint in the text boxes 2 Do one of the following Modify the contents of the text boxes or check boxes using the information from About teachpoints on page 269 Follow the procedure in Moving the robot manually on page 258 then click Use current positions For information about See Teachpoints About teachpoints on page 269 Adding teachpoints Adding a teachpoint on page 270 Deleting teachpoints Deleting a teachpoint on page 273 Managing teachpoints Managing teachpoint files on page 274 Moving between teachpoints Moving between teachpoints on page 275 Selecting teachpoi
113. ack as the plate type and will ignore the plugin For information about See The plate icon About tasks processes and protocols on page 37 About the FileReader plug in About this topic Defining label field content Velocity11 has created a plug in for BenchWorks called FileReader dll This topic describes this plug in The FileReader plug in lets BenchWorks read from a tab delimited or a CSV comma separated values file to specify the content of label fields printed with a VCode Read this topic if you are a technician or an administrator who writes protocols with Apply Label VCode tasks and who wants the FileReader plug in to read and process the label text The Apply Label task provides several ways to define the contents of the label fields printed on a series of plates during a run However without plug ins and scripting for each label in a given run the Apply Label task cannot apply U Two different pieces of data from the same file L Two different increments for two fields Related information Chapter 8 Creating a protocol advanced topics 165 BenchCel User Guide Q Numeric increments for one field and alphanumeric increments for another different field In the following screenshot Field2 and Field3 use the same label input file for the data in the fields However this function is limited because there is no way to specify two different locations in the same file for the same label P
114. am as though it is being called from a command line Parameters Text string Required Allows you to initiate a command that you could otherwise enter into the Windows Run dialog box suchasnotepad text txt opens a file named text txt in Windows Notepad Q Boolean True False Optional Default is False If True BenchWorks waits for the function to complete before continuing blocking The BenchWorks JavaScript interpreter provides two objects that can be accessed by a script They are the plate object and task object The plate object provides access to properties of the plate that the current task is operating upon Properties The plate object has the following properties Property Data type Description plate name String Name of the plate plate instance Integer Plate instance number plate labware String Name of the labware type plate barcode Array Array of four strings corresponding to SOUTH 0 WEST 1 NORTH 2 EAST 3 Example plate barcode SOUTH mybarcode plate volume Array of An array of floating point numbers The arrays array size depends on the number of wells in the labware 96 384 or 1536 arranged in row column format This property is only enabled on BenchCel systems that have the volume tracking database option 174 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Task object Methods Methods are JavaScript functions invoked through an object The pla
115. ants Data type Float Integer Float Float String Float An array of pairs of integers Chapter 8 Creating a protocol advanced topics 185 Task parameters Last cycle blowout volume Number of mixing cycles Dispense acceleration Dispense velocity Liquid class list box Pre aspirate volume Quadrants diagram BenchCel User Guide Comments The volume of air to blow out when the tips are in the liquid This is typically the same as the pre aspirate volume The number of aspirate dispense operations The rate of increase in velocity before the Dispense Velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor The rate at which to dispense the liquid If you selected a liquid class this value is entered automatically from the liquid library editor The name of the liquid class The volume of air to be drawn up before the pipette tips enter the liquid A quadrant is an evenly spaced array of locations that is addressable by the tips ona pipette head A 96 well head can dispense into a 96 well plate four quadrants of a 384 well plate and 16 quadrants of a 1536 well plate A 384 well head can dispense into a 384 well plate or the four quadrants of a 1536 well plate 186 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Property task retract task tipOffset task tipTouch
116. arameters toolbar 3 Complete the following fields Field Description Aspirate volume The volume of liquid to be drawn up into each pipette tip Aspirate velocity The rate at which to draw up liquid If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor and cannot be edited here Distance from well bottom The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel Related information 4 Chapter 7 Setting pipette task parameters 145 BenchCel User Guide Field Description Tip retract distance The distance that the tips should move downwards per unit volume of liquid being aspirated This value allows the tips to move downwards during aspiration to maintain a certain height below the surface of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use You might want this value to be the same as the Tip Retract Distance for the Dispense pipette task Pre aspirate volume The volume of air to be drawn up before the pipette ti
117. art BenchWorks from a command line 1 2 In Windows select Start gt Run In the Run text box type cmd and click OK The command prompt opens At the command prompt change the current directory to BenchWorks workspace that contains the protocol file by typing cd Program Files Velocity11 BenchWorks Press ENTER Type the name of the BenchWorks protocol file followed by values for the switches that specify The protocol to run Your user name Your password The number of cycles for which to run the protocol An example is myprotocol bwl user your user name password your password runs number of run cycles Press ENTER to start the run The following screenshot shows a generic examples of the completed command prompt cx C WINDOWS system32 cmd exe Microsoft Windows XP Version 5 1 2666 lt C Copyright 1985 2661 Microsoft Corp C Documents and Settings jday gt cd Program Files Welocity11 BenchWorks C Program Files Welocity1i BenchWorks gt protocolfile bwl user myusername passwo rd imypsswd runs C Program Files Welocit yii BenchWorks gt For information about See Starting a run using the start Starting a run from BenchWorks on button page 70 Pausing a run Pausing or stopping a run on page 74 Monitoring a run Monitoring a run on page 76 74 Chapter 4 Performing a run BenchCel User Guide Pausing or stopping a run About this topic This topic des
118. ata file When setting Apply Label task parameters you need to select a bar code format which specifies the type number properties and location of fields that are printed on bar code labels Some formats are provided with the VCode but you can define others according to your needs Each format is identified by a number which you enter when setting up an Apply Label task For information about See Using bar code modifiers About combining bar code modifiers on page 106 Creating a bar code input file Using bar code input files on page 198 Using bar code data files Using bar code data files on page 200 General options Setting general options on page 41 Creating a plate instance Setting up a plate instance on page 88 Using plug ins About the FileReader plug in on page 164 Log files About log and data files on page 51 102 Chapter 6 Setting task parameters BenchCel User Guide Setting Apply Label task parameters About this topic Before you start Procedure This topic describes how to set the parameters for the Apply Label task Read this topic if you are Q Q An administrator or technician who writes protocols that uses a VCode An operator who needs to specify parameters for one or more of the apply label tasks Before working with Apply Label tasks read the VCode User Guide to learn about bar codes and label formats To set Apply Label task parameter
119. ate WellMate User Guide 298 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Chapter 13 Maintenance and troubleshooting 299 BenchCel User Guide Maintenance and troubleshooting This chapter tells you how to keep your BenchCel in good working order and what to do when you encounter a problem 300 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Routine maintenance About this topic Monthly maintenance After every run BenchCel instrument maintenance Related information This topic provides recommendations for maintenance including when and what to perform In general practice good housekeeping by cleaning up spills and routinely cleaning after using Every month check the following Q Robot head gripper arm points to ensure they are not too dull to grip the plates Q Stacker grippers to ensure they have not deteriorated U Visible moving parts to ensure they are not rubbing against each other Look for rub marks or noises that might indicate rubbing These are most evident on the white metal cover behind the robot head and anywhere the robot arms travel Main air pressure reads between 50 and 90 psi Check the x axis track to ensure it is free of debris such as pieces of chipped plates and microtubes For information about routine maintenance of the individual instruments integrated with your BenchCel see the relevant instrument s documentation For informati
120. ate in a full circle Related information For information about See Planning to add bar code labels to Using bar code input files on plates page 198 Adding the Apply bar code task to Setting Apply Label task parameters a protocol on page 102 Reading plates at a platepad Setting Place Plate task parameters on page 120 198 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Using bar code input files About this topic Bar code fields Bar code input files This topic describes how to create and use bar code input files Read this topic if you are a technician or an administrator who writes protocols with bar code reader or Apply Label VCode tasks When setting up a VCode you set task parameters that specify the content of bar code fields An example of a bar code field is NAW 1001 Bar code fields can be imported from bar code input files For detailed information about bar code fields and formats see the VCode User Guide Filename and location Bar code input files are text files with the naming convention filename bar They are stored in the location specified in the general BenchWorks options When to use You can use bar code input files to do the following Q Verify the bar codes on incoming plates which are plates that are downstacked into the system This function is set in the parameters for the plate icon of the incoming plates Incoming plates
121. ate volume pL aq The modified task is shown in the following diagram Pipette Process War 1 1 on VPrep1 m i It on VPrep1 from reservoirt quadrant 1 using To complete the pipetting operation we have to add a Dispense task and set the parameters Drag the Dispense task into the pipette process pane Pipette Process 1 on VPrep1 Pipette Process 1 Aspirate 20 0 pL Dispense 10 0 pL on VPrep1 from reservoir into Plate A quadrant 1 using quadrant 1 The task correctly defaults to dispense into Plate A but the dispense volume is incorrect and there is no associated liquid class After editing the task parameters the task is shown in the following diagram Pipette Process H H 1 on VPrep1 If lH i The protocol is now complete on VPrep1 from reservoirt into Plate A quadrant 1 using quadrant 1 using 1XTE 1XTE For information about See Setting up a plate instance Setting up a plate instance on page 88 Liquid library editor About the liquid library editor on page 244 Creating a pipette process task Adding and configuring a Pipette Process task on page 140 140 Chapter 7 Setting pipette task parameters BenchCel User Guide Adding and configuring a Pipette Process task About this topic Adding a Pipette Process task Setting Pipette Process parameters This topic describes how to configure a Pipette Process task This task is used when cre
122. ating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who may need to change Pipette Process parameters The first step in creating a pipette process is to add a Pipette Process task to the protocol editor Drag the Pipette process icon into the protocol process 384 Falcon TC f a a Plate Black gt 3 x y p 353962 called F unnamed 1 384 Falcon TC Downstack from Pipette process 1 Plate Black 353962 VStack4 called unnamed 1 Remove When you add the Pipette Process task a new pipette process is started in the pipette process editor The pipette process is identified by its Pipette Process link icon Pipette Process al 1 on VPrep1 y Because you can have more than one pipette process in a protocol you must link the Pipette Process task to the pipette process by setting the Pipette Process parameters Pipette Process 1 on VPrep1 To set the Pipette Process parameters 1 In the Protocol Editor window add a Pipette Process task to the protocol and then select it in the protocol sequence 2 Inthe Pipette Task Parameters toolbar select the pipette process that you want to use for this pipetting task Task Parameters Use pipet process Process 1 Process 1 Process 2 3 Ifthe pipette process is for a replicate pipetting series so that the same plate can be used over and o
123. ator procedures 203 About user accounts and privileges 0 0 2 aa ee es 204 Adding and deleting a user account 2 0 0 es 205 Setting up email rsr siase a ee es 206 Moving or sending a registry fille marcir erneta cee ee ee 208 Obtaining information about the BenchCel network cards 0000 210 Chapter 10 Defining labware 213 About defining labware in BenchWorksS 0000 ees 214 About the labware editors erer de ta Ee ee Shae eee aren tee cee eae a 215 Labware editor OVEMWIEW sac eck Seed a De Gila s Gia De Sale Gi we ee Oa oo 216 About the defining labware proceSS n aana aa aaa es 218 Opening the labware editor 2 ee 219 Adding a labware entry oeer roiya anae E ee ee 221 Deleting a labware entry 1 ee es 222 Renaming a labware entry 0 0 ce ees 223 Copying a labware entry erer ranea Ae DE ee 224 Defining general properes cred eae eae ee se nee ees es one eee ee ed 225 Defining plate properties 1 ee eee 226 Defining BenchCel properties rreri reden rae epa EERE es 229 Defining stacker Properties sicrie reer a Enw E EEDA E EEDE Fa EEUE 230 INSEMINE akma BE aia n Se a we hol a ET Bidar Bites ol E E E 232 Defining labware classes csn dedma yau eee ea e ked ea e ked ek a oa ee 233 About the Labware Parameters group DOX 1 aaraa 236 Opening the Labware Parameters group DOX 2 ce es 237 Changing labware parameters naana aa a
124. b 3 At the bottom of the toolbar enter a new value for the Estimated task execution time Estimated task execution time sec For information about See Compiling and saving a Compiling and saving protocols on protocol page 93 Resolving errors Compilation warnings and errors on page 303 The workflow that this Workflow for creating a protocol on procedure belongs to page 85 Chapter 6 Setting task parameters 99 BenchCel User Guide Setting task parameters This chapter gives the procedures for configuring the parameters for individual tasks in a protocol 100 Chapter 6 Setting task parameters BenchCel User Guide Setting AliQuot task parameters About this topic This topic describes how to set the AliQuot task parameters Aliquot task defined The AliQuot task moves a plate to an AliQuot where liquid is dispensed into the plate Procedure To set AliQuot task parameters 1 Add the AliQuot task to the protocol 2 Inthe Task Settings page of the Protocol Task Parameter toolbar type the volume of liquid that you want to dispense in the Enter dispense volume text box 3 Inthe Available devices list select the AliQuot device that you want to use for this task and click Add The name of the device moves to the Devices to use list 4 Ifyou intend to use a filter plate a Select the Use filtration check box b Complete the Begin filtration sentence to enter the remaining paramete
125. bout the Controls page on page 254 Chapter 12 Using BenchCel Diagnostics 277 BenchCel User Guide About general settings About this topic BenchCel information Related information The General Settings page of the BenchCel Diagnostics dialog box contains offsets and corrections that are set at Velocityl11 You should rarely if ever need to change them When adding new labware you may have to make some adjustments after initially defining the labware IMPORTANT Be very careful making changes to the general settings Incorrect settings can cause robot crashes resulting in gripper misalignment If you are unsure consult with a Velocity11 engineer before changing these settings to ensure that you input them correctly Velocity11 keeps records of the settings that were factory set for your machine When you make a service call to Velocity11 you may be asked to provide some information about your BenchCel This information is contained in the General Settings page The BenchCel group box at the top of the General Settings page contains the firmware version and the MAC address of the BenchCel You may be asked for this information when you make a service call BenchCel Firmware Version 2 0 7 0 MAC address 00 90 C2 C1 C2 04 For information about See Adjusting labware settings Maintenance and troubleshooting on page 299 278 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Changi
126. box In the Dispense volume text box enter the volume of liquid that you want to dispense into each well To shake the plate after the dispense enter a value into the Shake time text box Chapter 12 Using BenchCel Diagnostics 287 BenchCel User Guide 6 To purge the lines after the dispense select the Purge x times when complete check box and enter the number of times to purge If you want to return all liquid the value of x may need to be greater than one 7 To dispense into all wells make sure that the Entire plate option is selected 8 To only dispense into some of the wells a Select the Selected columns option b Click Clear All c Inthe number matrix click the numbers corresponding to the columns to dispense into In the following example liquid will be dispensed into columns 2 4 6 and 8 of a 384 well plate Entire plate Specific columns 1 Clear All 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 16 19 20 21 22 23 24 9 Click Dispense Performing non dispense operations You can perform basic non dispense operations using the buttons in the Multidrop Commands group box To purge the liquid lines 1 Enter a value in the Times to purge text box and click Purge If you want to return all liquid the value of x may need to be greater than one m Multidrop Commands Times to purge 1 10 Prime volume 5 1000pL 100 Shake time 1 60 s 5 To prime the liquid lines
127. box opens 8 Make sure that the labware you intend to use on this VPrep shelf is in the Labware classes allowed to use this device column and not in the prohibited column 9 Select File gt Device File gt Save to save the device file Related information For information about See Working with Device files Working with device files on page 195 Labware editor About the labware editor on page 215 144 Chapter 7 Setting pipette task parameters BenchCel User Guide Setting Aspirate pipette task parameters About this topic Aspirate pipette task defined Before you start Procedure This topic describes how to set the Aspirate pipette task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Aspirate task An Aspirate pipette task is used with a VPrep to draw up liquid from a plate or reservoir Before you start setting the Aspirate task parameters you need to associate a VPrep shelf with the labware type that will be used for the aspirating To set Aspirate pipette task parameters 1 Add an Aspirate pipette task icon to the pipette process editor window 2 If you have defined a liquid class for the liquid you intend to aspirate select it from the Liquid class list box at the bottom of the Pipette Task P
128. bware 275 command line BenchWorks launch 73 compiling a protocol 93 errors 303 warnings 303 compressed air requirement 20 26 computer connecting by Ethernet 25 connecting by serial 25 disk space option 44 networking see connecting by ethernet configuration components 30 configuration settings for pipette tasks 792 connection panel 22 indicator lights 22 serial interface 22 control toolbar buttons 28 controls page overview 254 copying a labware entry 224 creating a protocol workflow 85 creating process for a tipbox 149 D database copying 208 labware 152 156 161 183 186 191 208 liquid library 208 deadlock 97 97 308 deleting labware entries 222 deleting user accounts 206 Delid task defined 108 device configuring VPrep shelf 742 defined 195 initialization errors 302 device file 795 322 defined 195 definition 30 filename extension 30 loading 196 location 195 saving 195 device manager relationship with other configura tions 192 diagnostics about 252 finding the version number 8 identifying a QFill2 297 initializing Multidrop 286 Multidrop plate filling 286 Multidrop priming 285 287 Multidrop purging 285 287 Multidrop shaking 287 Multidrop using 285 Nanodrop using 288 opening 253 Qfill2 dispensing 292 Qfill2 filtration port 292 WellMate executing commands 296 WellMate plate stage 295 WellMate priming and purging 296 WellMate profiles 293
129. bware entry Deleting a labware entry on page 222 Chapter 10 Defining labware 225 BenchCel User Guide Defining general properties About this topic Before you start Procedure Related information After adding a labware entry define the general properties of the labware The general properties describe the type of labware that is being entered into the database and are visible on all of the sub pages of the labware editor This topic describes how to define the labware s general properties You must have a technician or administrator user account to perform this procedure You must have added a labware entry that you want to define To define the general properties of a piece of labware 1 2 Open the labware editor In the Description text box type in a description of the labware if desired For your reference in the Manufacturer part number text box enter the part number for the labware In the Number of wells list box select the number of wells in the plate In the Base Class group box select one of the options The option you select determines which labware editor properties are available For example when a base class of Microplate is selected the Length of filter tip pin tool mm property is unavailable Miscellaneous Length of filter 0 00000 tip pin tool mm For information about See Opening the labware editor Opening the labware editor on page 219 Defining labware Q L
130. ce from the bottom of the plate to the middle of the sensor window c Inthe Labware group box select the Show parameters check box 2 Check the plate sensor threshold and intensity a Open the BenchCel robot diagnostics and click the General Settings tab b Adjust the value in the Plate presence threshold field Typically this value is about 100 If you are getting a no plate present message when there is a plate decrease this value If you are getting a plate present message when there is none increase this value Chapter 13 Maintenance and troubleshooting 313 BenchCel User Guide Resetting the orientation sensors for a plate About this topic Before starting Procedure This topic describes how to reset the orientation sensors for a plate When to use Use this procedure when you are using a new plate type and you are getting wrong plate type or plate is rotated messages in error The typical situation for this procedure is when the new plate type has different optical properties than other plates with similar physical size Ensure that all the plate parameters have been properly defined in the labware editor Check and verify in the Labware Editor dialog box Q Plate properties parameters Q BenchCel parameters Q Stack parameters except orientation sensor threshold and intensity To set the orientation sensors fora new plate 1 Place a plate in one of the stacker racks on the BenchCel 2 Open
131. ceive no greater than Restricted Rights as defined in FAR 52 227 19 c 1 2 June 1987 U S Government users will receive no greater than Limited Rights as defined in FAR 52 227 14 June1987 or DFAR 252 227 7015 b 2 November 1995 as applicable in any technical data Safety Noticies A A WARNING notice denotes a hazard It calls attention to an operating procedure practice or the like that if not correctly performed or adhered to could result in personal injury or death Do not proceed beyond a WARNING notice until the indicated conditions are fully understood and met A CAUTION notice denotes a hazard It calls attention to an operating procedure practice or the like that if not correctly performed or adhered to could result in damage to the product or loss of important data Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met Letter to our Customers Dear Customer see sf Agilent Technologies The Agilent Technologies acquisition of Velocityl1 resulted in the following changes e Creation of Agilent Technologies Automation Solutions formerly Velocity11 e Renaming of some Velocityl1 products e New Customer Service and Technical Support contact information e New website address for product information Please make a note of the following changes as they impact this user guide Velocity11 product name changes Velocity11 product name Changes t
132. cess of defining a piece of labware is to l Add a labware entry 2 View each sub page of the Labware Entries page in turn entering values that are appropriate for the product you are using 3 Use the Labware Classes page to optionally associate the labware with one or more labware classes For information about See Moving the labware database to Moving or sending a registry file on another computer page 208 Defining labware About the defining labware process on page 218 Opening the labware editor Opening the labware editor on page 219 Editing labware parameters Changing labware parameters on page 238 Opening the labware editor About this topic Before you start This topic explains how to open the labware editor You open the labware editor when you want to Q DODO View existing labware entries or classes Edit labware entries or classes Add new labware entries or classes Delete labware entries or classes Rename labware entries or classes You must be logged on with an administrator or technician user account to open the labware editor 220 Chapter 10 Defining labware BenchCel User Guide Procedure To open the labware editor 1 In BenchWokks click Diagnostics 4 Diagnostics 2 Inthe Diagnostics pop up window expand the system icon if necessary Click Labware to select it Click Device Diagnostics Device diagnostics X Related information For info
133. ch as a plate hotel or vacuum delidding station The Relid task replaces the lid Neither the Delid nor Relid tasks have configurable parameters The Delid Relid tasks are used to remove and replace a plate lid A typical use for this task is shown below _ J _ i i Costar 96 pp black Downstack from Delid and retract Pipette process 1 Relid called unnamed 4 BenchCel Stack 1 arms to vertical In the example a plate is downstacked and the lid is removed The plate is pipetted at the VPrep and the lid is replaced If your system has a trash chute and you want to remove a plate s lid and put the lid in the trash use the Delid task and do not add a subsequent Relid task Procedure Related information Chapter 6 Setting task parameters 109 BenchCel User Guide Setting Delid Relid task parameters There are no task parameters for these processes For information about See Defining lidded plates Defining labware on page 213 Adding and deleting tasks Adding and deleting tasks and pipette tasks on page 92 Creating a protocol process Setting up a plate instance on page 88 Specifying task order Specifying task order across processes on page 132 Setting Downstack and Upstack task parameters About this topic Stacker task defined This topic describes how to set the Downstack and Upstack task parameters Read this topic if you are Q An administrator or technician who writ
134. check box b Enter the User name and Password that you use to access email on the network Error Notifications Recipient list for error notifications Mail Server Setup SMTP server name MainServer l abc wigit com Server requires authentication User name abc Password XXXXXXXX This information only needs to be set up once provided the email account remains active All email sent from BenchWorks is authenticated using this account Related information For information about See Sending a bug report Sending a bug report on page 321 Sending a registry file Moving or sending a registry file on page 208 208 Chapter 9 Administrator procedures BenchCel User Guide Moving or sending a registry file About this topic When to do this About moving data Important Exporting a registry key This topic provides instructions on how to export a Windows registry file for import to another computer or for emailing to Velocity11 Q To propagate a labware or liquid library database to other devices using a different controlling computer Q To email a labware or liquid library database when requested by personnel at Velocity11 The labware and liquid libraries are maintained in the Windows registry of the controlling computer When you use BenchWorks to make a change to the labware or liquid libraries the change is seen when accessing that information from the netwo
135. checked turns on plate orientation checking 232 Chapter 10 Defining labware BenchCel User Guide Related information For information about Defining labware General properties Plate properties BenchCel properties Inserting an image About this topic Procedure See Q Labware editor overview on page 216 Q About the defining labware process on page 218 Defining general properties on page 225 Defining plate properties on page 226 Defining BenchCel properties on page 229 To make it easier for operators to identify a plate type you can insert an image of each plate type in the labware editor This topic describes how to insert an image into the labware editor Image files must be in the JPG GIF or BMP format To insert an image 1 Click the Image sub page tab of the labware editor 2 Click the ellipsis button and browse to the folder location of the image file Image filename 3 Double click the image file The image appears below in the user interface Image filename E Wicroplato ipg L Related information Chapter 10 Defining labware 233 BenchCel User Guide For information about See Defining labware Q Labware editor overview on page 216 Q About the defining labware process on page 218 General properties Defining general properties on page 225 Plate properties Defining plate proper
136. chpoint markers on the BenchCel animated display Teachpoint files are written in XML and have an xml extension By default your teachpoint files are saved in the directory C Program Files Velocity11 Your default teachpoint file name is your BenchCel serial number followed by your company name In the Current Teachpoint File group box on the Controls page of the BenchCel Diagnostics dialog box you can create a new teachpoint file or load an existing one Current Teachpoint File Documents and Settings All Papena texte In most cases you will not need to create a new teachpoint file but will instead modify your existing one Create a new teachpoint file when you are adding or adjusting teachpoints and you do not want to corrupt your original teachpoint file To restore your original teachpoint file use the load procedure To create a new teachpoint file 1 Click New The Save As dialog box is displayed 2 Select a name and location for your teachpoint file 3 Click Save To load a teachpoint file 1 Click Load The Open dialog box is displayed 2 Select the location and name of your teachpoint file 3 Click Open For information about See Teachpoint details dialog box About teachpoints on page 269 Chapter 12 Using BenchCel Diagnostics 275 BenchCel User Guide Moving between teachpoints About this topic Procedure Each teachpoint is symbolized by a square dot called a teachpo
137. chpoints for objects that you want the robot to avoid colliding with Procedure To add a new teachpoint 1 Click New teachpoint on the Controls page of the BenchCel Diagnostics dialog box The Teachpoint Details dialog box is displayed Teachpoint Details x Name Theta 9 Use current x mm positions 0 Z mm 0 Approach height mm 0 Cavity depth mm 0 Respect clearance both ways O Something is above point o 2 Complete the dialog box using the following table as a guide Setting Comment Name A name for the teachpoint This name will appear in the BenchCel animated display Theta Sets the value of theta or the angle that the grippers will rotate from their home position in degrees X Sets the value of x or the horizontal distance from the home position in millimeters Z Sets the value of z or the vertical distance from the home position to a height 20 millimeters above the base of the column in millimeters Use current positions This will create a teachpoint from the robot s current axes values Related information Setting Approach height Cavity depth Respect clearance both ways Something is above point Chapter 12 Using BenchCel Diagnostics 271 BenchCel User Guide Comment As the robot approaches a teachpoint such as a platepad or module this is the height the robot maintains above that teachpoint to avoid colliding with it This setting o
138. cityl1 com europeansales velocity11 com midatlanticsales velocity11 com midwestsales velocity11 com northeastsales velocity11 com southeastsales velocityl1 com southwestsales velocity11 com westsales velocity11 com Description Available in 4 sizes Q Extra short 25 4 cm Q Short 45 7 cm Q Standard 66 0 cm Q Tall 86 4 cm Computer with a smaller footprint than the standard computer provided with the BenchCel Provides a temporary storage place for a plate Four platepads that are stacked vertically and configured as shelves in BenchWorks One or more bar code readers attached to a platepad Chapter 2 BenchCel overview BenchCel User Guide Accessory Description Integration Plate ESTOP interlock circuit Velocity 11 instruments Each instrument and platepad requires a different integration plate to attach to the BenchCel An emergency stop button connected to the safety The following Velocityl1 instruments can be integrated with the Bar code print and apply station BenchCel Instrument Description PlateLoc Thermal plate sealer PlatePierce Seal piercing station VCode VPrep Liquid dispenser VSpin with Access2 Other companies instruments Microplate centrifuge station The following instruments from other companies can be integrated with the BenchCel Before purchasing another company s instrument ask Velocity11 about integration requirements This list is updated frequently with
139. cks IMPORTANT See your BenchCel User Guide or VStack User Guide for the details on how to release a rack for removal or to prepare for loading a mounted rack To load labware into a standard or top load rack 1 If possible remove the rack from the device and place the rack on a flat level surface 2 Using both hands carefully slide a small stack of labware down through the top of the rack You can use one hand to support underneath the labware stack while the other hand holds the top of the labware to keep it level See the following figure WARNING Use care to avoid sliding your hand on the interior edges in the rack The edges can have sharp surfaces Figure Loading a standard rack Interior edges can be sharp 3 Standard racks only When you reach the bottom of the open slot transfer your hand positions so that you continue supporting the labware through the bottom slot Figure Supporting labware through the bottom slot ME Stacker grippers on tab interior hidden 4 Ensure that the bottom labware in the stack rests on the rack stacker grippers To unload labware from a standard or top load rack With your hands positioned as shown in the previous figures carefully slide the labware in small stacks up and out of the top of the rack Loading labware in a front load rack The doors on the front load rack provide easy access for loading labware into th
140. cks WARNING Do not hold a rack by the interior edges The interior edges can have sharp surfaces that can cause cuts if handled improperly CAUTION A rack that is fully loaded with labware can be heavy Grasp the rack handle firmly to prevent the rack from slipping or tilting To carry a rack Firmly grasp the rack by the handle Figure Carrying a front load rack Handle Interior edges can be sharp Lifting the racks Make sure to use the proper lifting technique when mounting a rack on a device or removing a rack from a device WARNING Avoid touching the interior edges of a rack when lifting the rack The interior edges can have sharp surfaces IMPORTANT See your BenchCel User Guide or VStack User Guide for the procedure to mount a rack on the device or to release a rack from the device To lift a rack Use both hands to grasp the rack securely around the four corners near the base as the following figure shows Figure Lifting a standard rack Interior edges can be sharp Loading labware into the racks Before loading the labware into a rack e Position the rack so that the opening is facing you e Determine how the microplates should be oriented in the rack For example if the BenchCel orientation sensing feature is enabled make sure the Al wells are oriented in the rack as specified Loading labware in standard and top load ra
141. cribes when and how to stop or pause a protocol that is running Use this procedure to Q Pause and continue a run for example when you want to Add or remove labware Clean up a spill Add buffer to a reservoir Diagnose a problem that you notice Perform an operation that is not part of the protocol Q Aborta run in a non emergency situation Procedure To pause or stop a run using Bench Works 1 In BenchWorks click Pause The Stop dialog box opens and the currently scheduled task continues to completion This may take a minute or more After that no more tasks are performed Continue Diagnostics Abort Process Scheduler paused Related information 2 You now have three choices If you want to Continue with the run Troubleshoot a problem or perform a manual operation Abort the protocol Chapter 4 Performing a run 75 BenchCel User Guide Then Click Continue Click Diagnostics and select the module that caused the error This opens the diagnostics software for that module allowing you to troubleshoot the problem For more information see Using BenchCel Diagnostics on page 251 Click Abort Process IMPORTANT Before continuing with a run make sure that the system is in a valid state for the protocol Make sure that you have not made changes that will cause an error such as moving a plate to a position that should not have a plate or ca
142. cronics tube rack ALSB Costar 384 black flatbottom Costar 384 polypro round bottom Costar 96 well plate Falcon 384 clear bottom Falcon 384 clear polystyrene Matrix 96 well Block Polypro MJ Research 384 well plate New plate Renamed Polyfiltronics 384 filter plate Test plate Tip Box Lid 11 Autofilling Reservoir 384 11 Autofilling Reservoir 96 11 Manual Reservoir 384 11 MicroWash 384 v11 MicroWash 96 V11 Tip Box 384d30 Vil a Box 384440 User Defined Labware Classes All labware classes Labware classes that this labware entry belongs to Intermediate Height TallPlates Uses Filter Platepad Uses Standard Platepad Uses Vacuum Platepad Velocity11 Labware TipBoxes Procedure Related information To add a labware class 1 Open the labware editor Chapter 10 Defining labware 235 BenchCel User Guide 2 Inthe Labware Classes page click New labware class 3 Inthe New Labware Class dialog box enter a name for the labware class and click OK The class appears in the list of labware classes To associate a type of plate with a labware class 1 Open the labware editor 2 Inthe Labware Classes page or Labware Classes sub page select an item from the middle column To select more than one item use SHIFT click or CTRL click If you want to move all entries click gt gt 3 Click gt to move the labware entries or labware classes to the right hand column 4
143. d Related information Chapter 6 Setting task parameters 105 BenchCel User Guide If you want to print Then A series of bar codes that a increment but which are not specified by a bar b code input file Type the root data that you want in the Field 1 text box Click Increment This adds the code INC to the root data In the Increment chars text box type the number of alphanumeric characters that you want to be appended to the root data For example if you want the series to increment from 01 enter 2 If you want it to increment from 001 enter 3 In the Starting increment text box type the number that you want to be printed on the first label for example 100 Select either Numeric or Alphanumeric depending on the increment style you prefer Alphanumeric increments use 0 9 A Z whereas numeric increments use 0 9 From a plug in that you Select From user plug in have developed 7 Return to step 6 and fill out another field until all required fields are completed Note If you enter information in a field that does not exist in the format you have chosen the information is ignored 8 Return to step 3 and define labels to put on other sides of the plate For information about Using bar code modifiers Creating a bar code input file Using bar code data files General options Creating a plate instance Using plug ins Log files See About combining bar c
144. d plate1 m 96 Costar Flat Downstack from Fpply label Seal for 1 8 Upstack to Bottom w Lid BenchCel Stack seconds at 170 C BenchCel stack called plate How a plateiconand Although the icon for a plate icon looks like a task icon its function is task differ different because it does not represent an action in a protocol This distinction becomes important when you are interpreting error messages Consider the following example protocol and error message The error refers to task 2 which is the Pipette Process task in the following diagram and not the Downstack task The first icon is the plate icon Costar 96 pp black Downstack from Pipette process 1 called unnamed 1 BenchCell Stack 3 Error in Test task 2 Pipette process 1 is required to process Test but does not Protocol defined A protocol is a collection of processes that run at the same time as defined in the process editor The following diagram shows one protocol with two processes Costar 96 pp m black called a yy B y TS yy gt unnamed 4 j v Costar 96 pp black Downstack from VSpin with Pipette process 1 Upstack to called unnamed 4 BenchCel Stack 2 Access spinning BenchCel Stack 3 for 5 seconds at 10 of maximum Costar 96 pp black called gt Ta gt gt unnamed 2 Costar 96 pp black Downstack from Incubate for 10 Seal for 1 8 called unnamed 2 BenchCel Stack 1 sec seconds at 170 C BenchCel Stack
145. d this topic if you are Q An administrator or technician who writes protocols using the Incubation task Q An operator who needs to specify parameters for this task Incubate task The Incubate task performs a timed incubation of a plate It is typically defined used for short incubations The number of plates that can be incubated simultaneously is limited by the number of platepads that are available for holding plates Process overview The overall process for a typical incubation is as follows 1 Incubation of the plate starts with the addition of an initiating reagent This would be performed by a liquid handling task such as a Pipette Process task 2 The plate is moved to a platepad When the plate arrives at the platepad the incubation time parameter that you specify starts timing 3 The plate is moved from the platepad to a reader The plate is moved when the incubation time parameter that you specify ends Incubation time The time parameter that you set for the incubation period is not the error actual time of incubation It represents the minimum time that the plate sits on the platepad where the incubation task is carried out The actual incubation period starts when the initiating reagent is added and continues until the plate is transferred to the next step in the process This means that the actual incubation is longer than the time parameter that you set by an amount that depends on the scheduling and o
146. d to the name of the log file This affects all log files c Click the ellipsis button for a log file or folder L d Navigate to the folder to which you want to save the log file e Click Save 5 In the BenchWorks Options dialog box click OK Note Checking the database connection and enabling plate tracking requires that you have an inventory management system Please contact Velocity11 for more information Related information For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Understanding the protocol on page 59 Log and data files Q Setting pre protocol rules on page 48 Q Working with the Log toolbar on page 77 Chapter 3 Preparing for a run 57 BenchCel User Guide Importing a log file to Excel About this topic This topic describes how to import a log file into Microsoft Excel Because comma delimited and tab delimited text files contain structured data you can quickly import them into Microsoft Excel automatically organizing their data into columns This feature is helpful for making it easier to analyze the data in log files Procedure To import a log file to Excel 1 Open Microsoft Excel 2 Drag the file onto the Excel window The data is imported fa Microsoft Excel ProcessLog Thursday February 12 2004 6_32_21 PM txt H Eile Edit View Insert Format Tools Data Window Help Adobe PDF Type a
147. e Task Perform pre run checks Start a run Monitor a run Pause a run Clean up See Starting a run from BenchWorks on page 70 Starting a run from a command line on page 73 See Performing pre run checks on page 69 Q Starting a run from BenchWorks on page 70 Q Starting a run from a command line on page 73 Q Monitoring a run on page 76 Q Working with the Log toolbar on page 77 Pausing or stopping a run on page 74 Cleaning up after a run on page 80 Chapter 4 Performing a run 69 BenchCel User Guide Performing pre run checks About this topic Procedure Related information This topic describes how to perform a preliminary check of the equipment To check that the BenchCel is ready fora run l Make sure that there are no stray plates in robot accessible places These include Platepads VCode plate stages VPrep plate stages PlateLoc plate stages Make sure that the instrument air pressures lie within the ranges in the table below To check the BenchCel air pressure you need to read the values from each stacker in the Stacker Sensors group box of the BenchCel Diagnostics Controls page You only need to do this occasionally depending on the application To check the air pressure for other modules refer to the relevant manuals Unit Air Pressure psi Air Pressure MPa BenchCel 50 90 0 34 0 62 VPrep 90 95 0 6
148. e BenchCel User Guide Labware editor overview About this topic This topic gives an overview of the organization of the labware editors user interface Labware Editor The labware editor has two tabbed pages pages Q Labware Entries where labware definitions are entered Q Labware Classes where defined labware is assigned to classes Labware Editor Labware Classes Labware Entries Sub pages page The Labware Entries page has the following sub pages Plate Properties BenchCel Stacker VPrep Well Definition Image Coo o ee oc Labware Classes The sub page tabs are located at the bottom of the page Some tabs may be hidden if they are not relevant Plate Properties Benchcel J Stacker VPrep Well Definition Image Labware Classes Labware selection box The labware selection box which is the left hand column is used to select a labware entry that you want to edit Labware Classes Please select a labware entry from the list below in order to view and edit its properties 1536 Greiner Low Yolume Black 783 1536 Greiner Low Volume Black w G 1536 Nunc Black 253601 4 Matriy Glace Tithe Rack Chapter 10 Defining labware 217 BenchCel User Guide Labware Entry General Properties group box The Labware Entry General Properties group box displays the labware entry general properties whose selections applies across all sub pages Labware Classes In the Labware Classes page y
149. e 6 ee 64 Chapter 4 Performing arun 67 ADO perrorming a Toae e eae ta cero cel Be ee eee ae ule eee a Ree bee 68 Performing pre run CheckS 2 ee 69 Starting a run from BenchWorkS sses a a aace aaa e aaa ees 70 Starting a run from a command line 2 saaa ae ees 73 Pausin OF StOp PIN ATUM ote eea EEL ie aL ech i area drew Beene sare es 74 MOnmitoringsa IUNIE 2 0 ence et heat ot Shee eb aoe Gey ecb ara ay echoes bela ee ete he 76 Working with the Log toolbar 2 cc es 77 CIE ANINE UP AEF a Toeni bee ee cee eS ee ee ee eee Be ay Bee oe ed 80 Logging out of BenchWorksS 2 0 ee ee ee eee 81 Shutting down the BenchCel cers r 20 0 ana e a ER e ees 81 Chapter 5 Creating a protocol basics 83 About protocol files rsss aua et os ha eee kee Sale 8 a A E anaes DSM es 84 Workflow for creating a protocol 1 ce eee 85 Setting up a pre protocol or post protocol process 000 c eee ees 87 Setting up a plate instance ees 88 Setting the number of simultaneous plates 0 0 00 eee 91 Adding and deleting tasks and pipette tasks snsna naaa aa 92 Compiling and saving protocolS saa ee 93 About setting task parameterS niesen sarta taaa inba ees 95 About setting pipette task parameters annaa n aaa ees 96 Simulating a TUN siia pa ae ke a a a de ee 97 Chapter 6 Setting task parameters 99 Setting AliQuot task parameters osci 0 0 e
150. e Dispense pair of tasks is looped four times Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Loop task The Loop pipette task allows you to repeat a set of tasks within a process 154 Chapter 7 Setting pipette task parameters BenchCel User Guide Procedure To set Loop pipette task parameters l Related information Open the Pipette Process Editor to display the process in which you want to add the Loop pipette task An example is shown below Pipette Process 1 Aspirate 10 00 pL Dispense 10 00 pL on VPrep1 from unnamed 1 into unnamed 1 in In the pipette process window click to select the Loop pipette task icon and drag it into the process in front of the first task that you want to be in the loop A Loop pipette task icon and End of loop pipette task icon are added to the process Pipette Process 1 Loop 4times End of loop Fspirate 10 00 pL Dispense 10 00 pL on VPrep1 from unnamed 1 into unnamed 1 in in 1 quadrant s 1 quadrant s Drag the End of loop pipette task icon to the other side of the last task you want to be in the loop Pipette Process 1 Loop 4times fepirate 10 00 pL Dispense 10 00 pL End of loop on VPrep1 from unnamed 1 into unnamed 1 in in 1 quadrant s 1 quadrant s Select the Loop task pipette icon and in the Pipette Task Parameters toolbar enter the number of times you want the tasks inside the loop to run For i
151. e a profile Parameters Argumen Argument Range Description t Type Name BOOL bModal TRUE FALSE Whether the diagnostics should be shown modally SHORT iSecurityLevel 0 3 The security level that the user has to operate the diagnostics 0 Administrator 1 Technician 2 Operator 3 Guest 1 No access Returns LONG no meaning Visual C Chapter 14 BenchCel ActiveX controls 327 BenchCel User Guide Example Visual Basic m_BenchCel ShowDiagsDialog TRUE 0 BenchCell ShowDiagsDialog 1 0 void Close BSTR GetLastError Visual C Description Method to disconnect from the BenchCel device Parameters None Returns None Example Visual C Visual Basic m_BenchCel CloseQ BenchCell Close Description Method to retrieve a text message explaining the last error This method can be called in blocking mode after a command returns with a failure code or in non blocking mode after the Error event has been fired Parameters None Returns None Example Visual Basic strError m_BenchCel GetLastError strError BenchCel1 GetLastErrorQ LONG Retry Description Method to retry an action after an error occurred For example if there is insufficient air pressure during a LoadStack operation the application can call Retry after the air pressure has been increased Parameters None Returns None 328 Chapter 14 BenchCel ActiveX controls BenchCel User Guide LONG Ab
152. e editor Opening the labware editor on page 219 Defining labware Q Labware editor overview on page 216 Q About the defining labware process on page 218 Editing labware parameters Changing labware parameters on page 238 Adding a piece of labware Adding a labware entry on page 221 Deleting a labware entry Deleting a labware entry on page 222 224 Chapter 10 Defining labware BenchCel User Guide Copying a labware entry About this topic Procedure Related information To save time when creating a new entry that is similar to an existing one you can copy an existing labware entry This topic describes how to copy an existing labware entry You must have an administrator or technician user account to perform this procedure To copy a labware entry 1 Open the labware editor 2 Inthe labware selection box on the left of the window select a labware entry Click Save changes as In the Save Labware Entry As dialog box type a name for the new entry that is different from the selected one and click OK The copied entry appears in the labware selection box For information about See Opening the labware editor Opening the labware editor on page 219 Renaming labware Renaming a labware entry on page 223 Editing labware parameters Changing labware parameters on page 238 Adding a piece of labware Adding a labware entry on page 221 Deleting a la
153. e front of a rack that is mounted on a device Figure Door mechanism on the front load rack Door Door Thumb tab Door release button Stacker gripper hidden To load labware in a front load rack IMPORTANT Before you attempt to load the labware in a mounted rack ensure the device is ready for loading For example the clamps in the BenchCel stacker head must be closed extended See your device user guide for details 1 On each side of the rack slide the Door release black buttons forward while pushing outward on the thumb tabs The rack doors open Figure Opening the front load rack 2 Place the labware directly through the open rack doors so that the bottom labware rests on the rack stacker grippers Ensure the labware is level and securely in the rack 3 To close the doors press the thumb tabs inward until the doors snap shut To unload labware from a front load rack IMPORTANT Before you attempt to unload the labware from a mounted rack ensure the device is ready for unloading For details see your device user guide 1 To open the rack doors slide the black Door release buttons forward on each side of the rack while pressing outward on the thumb tabs 2 Carefully lift the labware out through the front of the rack Accessing product user documentation Velocity11 product user documentation is available in the following formats e Online help available within the softwa
154. e manager i 6 E 5 o G gt 2 G Legend Data stored includes Device name y Device type such as Pipettor reagent shelf Parent device such as VPrep1 Robot approach height Labware classes allowed to be used on this device Plate type y To open click the Device Manager tab Data stored includes e Plate dimensions e Gripper offsets e Maximum robot speed e General description of labware e Assignment of labware class such as TipBoxes and TallPlates To open in the Device List toolbar double click Labware gt Flowof data Related information For information about Liquid library editor Labware editor Data stored includes e Aspirate Parameters e Dispense parameters e Equation editor liquid library editor To open in the Device List toolbar double click Liquids iz i 2 ge V 2 E Liquid class a y 2 Plate to 4 de To open click a pipette task Pipette Task wr 2 8 See About the liquid library editor on page 244 About the labware editor on page 215 Chapter 8 Creating a protocol advanced topics 195 BenchCel User Guide For information about See BenchWorks Relationships of BenchWorks components on page 30 Working with device files Device defined Device configuration Device file defined Device file location Sav
155. e tasks to remind you to empty liquid waste containers and refill liquid source containers set your own reminders using lab timers For convenience you can force the protocol to continue running by entering a sufficiently large value in the Number of times to run protocol field When the downstack becomes empty or the upstack becomes full you will be prompted with the option of adding or removing plates This feature saves you the time of having to restart the protocol when you are processing a large number of plates or when you are running plates intermittently After you start the run the following events occur Q Q E The Start button becomes unavailable and the Pause button becomes available Log messages on the Log toolbar indicate the start of the run Also log files record events as they are performed on all plates in the run according to the selected log file options The first instructions of the protocol are executed If User Message tasks are included in the protocol you are prompted to respond to them For information about See Pausing a run Pausing or stopping a run on page 74 Monitoring the log Working with the Log toolbar on page 77 Chapter 4 Performing a run 73 BenchCel User Guide Starting a run from a command line About this topic Procedure Related information This topic describes how to start BenchWorks and initiate a run directly from a command line To st
156. e tips should move downwards per unit volume of liquid being aspirated This value allows the tips to move downwards during aspiration to maintain a certain height below the surface of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use You might want this value to be the same as the Tip Retract Distance for the Dispense pipette task The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel The rate at which to draw up liquid If you selected a liquid class this value is entered automatically from the liquid library editor The volume of liquid to be drawn up into each pipette tip 182 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Comments The name of the plate A quadrant is an evenly spaced array of locations that is addressable by the tips on a pipette head A 96 well head can dispense into a 96 well plate four quadrants of a 384 well plate and 16 quadrants of a 1536 well plate Puts tips on to a VPrep head or removes tips from a VPrep head Comments The name of the plate The rate of increase in velocity before the Dispense Velocity is reached If you selected a liquid class this value is entered automatically from the liquid library edito
157. e when centrifuging in a VSpin This means that only one sample plate can be centrifuged at one time in a protocol Although if you are using the VSpin as a stand alone instrument then two sample plates can be centrifuged together Using a counterweight plate and centrifuging one sample plate at a time does not typically increase the length of a protocol run compared to spinning two sample plates at one time This is because the centrifuge task is not typically the time limiting step of a protocol Counterweight plate A counterweight plate is the same as a sample plate except that it is defined empty or contains water to provide a more accurate balance Ifa counterweight is not used a load imbalance error will result The load imbalance tolerance is 5 grams at 3000 rpm About loading A counterweight plate is required for each plate type that is used in a counterweight plates protocol For example if three different types of plates are centrifuged during a protocol then you need three different counterweight plates You must load the counterweight by hand using VSpin Diagnostics software to open and close the centrifuge door and move the robot 64 Chapter 3 Preparing for a run BenchCel User Guide Manually loading counterweight plates Related information To load a counterweight by hand Open VSpin Diagnostics The VSpin Control dialog box opens Follow the directions in the VSpin User Guide to open the VSpin door and
158. e your selection 3 Ifthe Place Plate task is the first task in the protocol and you want to require that the operator confirms the bar code on the plate that is placed check the Manually confirm bar code check box This can prevent the wrong plate from being used in the protocol To confirm the bar code when the plate is picked up the operator is prompted to enter the bar code of the plate that should be in the placed position If the two codes do not match an error is generated Related information Chapter 6 Setting task parameters 121 BenchCel User Guide For information about See Indicating bar codes on plate icon Setting up a plate instance on page 88 Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting QFill2 task parameters About this topic QFill2 task defined Procedure This topic describes how to set the QFill2 task parameters for the BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the QFill2 instrument Q An operator who needs to specify parameters for the QFill2 task Note In some versions of BenchWorks you will see QFill instead of QFill2 The QFill2 task dispenses liquids into plate wells and offers the options of vacuum filtration If you wa
159. eached If you selected a liquid class this value is entered automatically from the liquid library editor The tips will dispense outside the MicroWash tray chimneys Property task dispenseVelocity task heightAboveWaste task inFlowPercent task liquidClass task outFlowPercent task preAspirateAirGap Data type Float Float Integer String Integer Float Chapter 8 Creating a protocol advanced topics 189 Task parameters Dispense velocity Dispense to waste at height of text box Inflow pump Liquid class list box Outflow pump Pre aspirate volume BenchCel User Guide Comments The rate at which to dispense the liquid If you selected a liquid class this value is entered automatically from the liquid library editor The height in millimeters above the MicroWash chimneys at which the tips will dispense Used in combination with the dispense to waste property Enter a negative number to ensure that the tips are below the tops for the chimneys The relative rate of liquid flow into the MicroWash tray manifold This value should be high enough for the washing liquid to just bubble over the tops of the chimneys The name of the liquid class The relative rate of liquid flow out of the MicroWash tray manifold This value is typically zero because the fluid is drained by gravity The volume of air to be drawn up before the pipette tips enter the liquid
160. eating a protocol basics BenchCel User Guide Related information For information about See Recovering from deadlock Resolving common problems and error messages on page 304 Definition of a plate instance About tasks processes and protocols on page 37 Setting up a plate instance Setting up a plate instance on page 88 The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Adding and deleting tasks and pipette tasks About this topic Adding a task Deleting a task This topic describes how to add and delete tasks and pipette tasks After you have set up a plate instance for a process you can start adding tasks and pipette tasks You must always add a task to a process before you can define its task parameters To add a task 1 Ifthe Protocol Tasks toolbar is not showing select View gt Toolbars gt Protocol Tasks 2 There are various ways to add tasks to the protocol Click on a task icon and drag it from the task list to the protocol editor window until a vertical dashed line appears Double click the icon Copy or cut and paste task icons in the protocol To delete a task 1 Ina protocol editor select a task that is in a protocol process 2 Press the DELETE key on the keyboard 3 Click Yes in the Delete Task dialog box to delete the task Chapter 5 Creating a protocol basics 93 BenchCel User Guide Moving tasks Wh
161. ectly initialized 286 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Operating the To initialize a Multidrop Multidrop 1 In the Profile Settings group box select the desired Multidrop from the list box The value in the Com port changes to match the Multidrop you selected m Profile Settings Select multidrop profile to work with Multidrop Profile2 Initialize New Save Com port 3 C Prime 100 yL oninitialization S 1000yL If you want to prime the fluid lines when you initialize the Multidrop select the Prime check box and enter the volume of liquid you want to prime with 3 Click Initialize Creating and deleting devices Filling a plate You do not need to use the New Save or Delete buttons in the Profile Settings group box These are for Velocity11 use only To fill a plate 1 Refer to the Multidrop 384 User Manual for information about preparing to fill a plate In the Dispense Program group box select the number of wells in the plate m Dispense Program Select number of wells on plate 96 Note that all volumes will be rounded to the next lowest SuL value O 384 Prime Volume 0 1000pL 100 Dispense volume 5 1000pL 50 D is p e n S e Shake time 0 60 s 0 Purge 1 times when complete L Entire plate Specific columns If you want to prime the Multidrop enter the volume of liquid to prime with in the Prime volume text
162. ed through Innovadyne s Nanodrop software and the files can only be selected through the Velocityl 1 Nanodrop Diagnostics software QRM Quick Run Method files store collections of Nanodrop settings QRM files are created through Innovadyne s Nanodrop software and are selected through the Velocity 1 Nanodrop Diagnostics software Examples of settings stored in QRM files are U Dispense volume Syringe volume Tip clean enabled or disabled Aspirating air gap rate DODO Whether or not to wash For information about See Diagnostics About diagnostics on page 252 Using the Nanodrop Nanodrop User Manual Chapter 12 Using BenchCel Diagnostics 291 BenchCel User Guide Using QFill2 Diagnostics About this topic The Genetix QFill2 dispenser can be used either in stand alone mode or as a device within a protocol using the BenchCel In stand alone mode a QFill2 is operated using a built in keypad Velocity11 has developed QFill2 Diagnostics to allow users to operate a QFill2 using BenchWorks software This topic explains how to perform simple manipulations of a Genetix QFill2 in real time To use the QFill2 dispenser within a BenchWorks protocol set the parameters in the Protocol Task Parameter toolbar not in the diagnostics software Note In some versions of BenchWorks you will see QFill instead of QFill2 Identifying the QFill2 Before you can manipulate a QFill2 make sure that it is correctly
163. ee WellMate maximum robot handling speed property 228 MicroWash tray 161 162 Mix pipette task defined 755 JavaScript properties 184 setting parameters 155 mixing cycles 155 mixing volume 155 Molecular Devices instruments with SoftMax Pro see Softmax Pro monitoring a run 76 move to position commands 263 MSDS 10 Multidrop diagnostics using 285 filling a plate 286 initializing 286 priming 285 287 purging 285 287 shaking 287 supported instrument 79 Multidrop task defined 114 setting parameters 115 Multiskan Ascent supported instrument 79 N Nanodrop calibration file 290 diagnostics using 288 profiles 288 supported instrument 78 Nanodrop task defined 116 setting parameters 116 network connections obtaining IP addresses 211 viewing 210 notch locations property 237 Number of Cycles dialog box 77 O online help 3 opening the labware editor 220 operating system see Windows operating temperature range 20 operator privilege 204 options log and data file 54 protocol error 47 Index 343 BenchCel User Guide setting error 44 setting general 47 orientation sensor offset property 237 orientation sensor threshold max property 237 orientation sensor threshold min property 237 P pager notification of errors by 46 206 password changing 36 pausing a run 74 PDF guide 3 4 PerkinElmer FlexDrop see FlexDrop PerkinElmer ViewLux see ViewLux Pierce task defined
164. el User Guide Resolving non VCode bar code reader errors About this topic Types of bar code misread errors Bar code error option Bar code no read errors The information in this topic refers to errors generated by bar code readers that are not attached to a VCode These include L Robot bar code readers Q Optional VPrep shelf bar code readers Q Optional platepad bar code readers There are two types of bar code misread errors Error type Description Bar code no read A bar code reader is unable to read a bar code when it picks up a plate Bar code mismatch The bar code of the plate that is picked up does not match the bar code that BenchWorks expects for that plate Note BenchWorks does not attempt to read a bar code unless you have specified in the plate icon parameters that incoming plates have bar codes on that side The result of a bar code misread error depends on whether Halt on bar code misreads error option is selected If the option is selected Q The protocol pauses Q An error is generated in the log txt file and VPrep log file Q A dialog box opens allowing you to enter the correct bar code If the option is not selected Q An error is generated in the log txt file and VPrep log file Q The protocol continues without pausing so there are no recovery steps When a bar code cannot be read and the Halt on bar code misreads error option is selected an error message is ge
165. en editing a protocol drag and drop or use cut and paste commands to move tasks and groups of tasks To move tasks in a protocol 1 Ina protocol editor select a task or a group of tasks in a protocol process 2 Do one of the following Drag and drop the tasks to a new location in the protocol Use the Cut or Copy and Paste commands on the Edit menu to move the tasks Related information For information about See The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Setting up a plate instance Setting up a plate instance on page 88 Setting the number of Setting the number of simultaneous simultaneous plates plates on page 91 Compiling and saving protocols About this topic This topic describes how to compile and save a protocol When you compile a protocol BenchWorks checks to make sure that your protocol makes logical sense Compiling a protocol To compile a protocol 1 Click Compile Compile Oo Errors are reported in the Log toolbar Note Whenever you start a protocol BenchWorks automatically compiles it and checks for errors 94 Chapter 5 Creating a protocol basics BenchCel User Guide Saving a protocol Adding notes about the protocol Related information To save a protocol you must be logged on with an administrator or technician user account IMPORTANT When you edit a protocol the changes take effect immediately
166. eneral settings changes 2 0 0 0 eee ee eee eee 281 ADOUU PFOTIES osc egy TE eek EE Bega tees ERE eb Sere WT eels We Se 282 Creating a BenchCel profile 0 0 ec es 283 Managing DOMES a edea aie wid ae eae oe maw ee Se ee ele G ee A 284 Using Multidrop diagnosticS 2 e deea a e ee eee 285 Using Nanodrop Diagnostics teaa a EE EEE eee 288 Wsing OFII2 DieaSMOStleS sa sce et tues se eee ce ein Ow Soe E ce WER ee eee E ee 8 291 Using WellMate Diagnostics 0 00 ee ee 293 Chapter 13 Maintenance and troubleshooting 299 Routine MAINTENANCE se eta ete eed OP ne BEE ee Sa RS ode ee ed 300 ADOUT EMmOr AAMAS ssc du e258 eee She bei Eee Reel edie be ee a es 301 Resolving device initialization errorS es 302 Compilation warnings and errors 0 ees 303 Resolving common problems and error MeSSageS 000 cee ee es 304 Checking the arm alignment eaaa a a a eee eee 309 Resolving labware problemS 00 0 ee nes 310 Resetting the orientation sensors fora plate 0 ee es 313 Checking the stacker Sensors 2 0 ees 314 Resolving teachpoint problems 0 000 ee es 315 Resolving non VCode bar code reader errorS naaa uaaa 317 Resolving VCode bar code reader errorS 1 es 319 Adjusting the stacker gripper pressure 2 00 ce es 320 Sende A BUSS POM anene He weeks Sec ate e tarde we were eig ee hve EOR See ete A 321 Chapter 14 BenchCel ActiveX control
167. ensor Q A plate presence sensor Q An air pressure sensor for the stacker grippers When to use Before and after each run check the stacker sensors to make sure they are correctly sensing plate notches racks and plates and that the air pressure is within limits for your BenchCel application To check the stacker sensors 1 Open BenchCel Diagnostics See Opening BenchCel Diagnostics on page 253 From the Stacker list box select the stacker you want to monitor If the Notches read zero click Move to sensor position This commands the robot to move the plate to where the sensors detect it 4 Check the Stacker Sensors group box using the following table Stacker Sensors stacker 1 M otches BS Rack present Plate present Al Top right Ee Ef AA Position Air PSI Bottomeft Bottom right Chapter 13 Maintenance and troubleshooting 315 BenchCel User Guide Setting Comment Rack present This indicator light is green when a rack is present and red when a rack is not present To set the Rack sensor threshold see Changing general settings on page 278 Plate present Any number above the Plate in stack sensor threshold indicates a plate is present Numbers under the threshold are displayed red while numbers over the threshold are displayed white To set the Plate in stack sensor threshold see Changing general settings on page 278 Air PSD Displays the air pressure of the selected stac
168. er if ordered One power cord One 1 4 to 1 8 inch air hose reducer One 4 foot 1 8 inch air hose OoUoOLKOLOCUOD If you plan to use the serial connection Serial cables D If you plan to use the Ethernet connection Ethernet cables Ethernet hub or switch Related information For information about Available accessories Connecting the BenchCel to the computer Compatible devices BenchCel configurations Chapter 2 BenchCel overview 15 BenchCel User Guide See BenchCel accessories and integration options on page 17 Connecting the controlling PC and BenchCel on page 24 BenchCel accessories and integration options on page 17 Available stacker The BenchCel may be factory assembled with 2 4 or 6 plate stackers configurations Package Contents BenchCel 2X 2 Std Stacker racks BenchCel 4X BenchCel 6X BenchWorks includes OCX Dell desktop PC 4 Std Stacker racks BenchWorks includes OCX Dell desktop PC 6 Std Stacker racks BenchWorks includes OCX Dell desktop PC See BenchCel accessories and integration options on page 17 for additional accessories options and available integration packages 16 Chapter 2 BenchCel overview BenchCel User Guide BenchCel features About this topic This topic contains diagrams that display the main features of the BenchCel These diagrams show a BenchCel with two stacker racks connected to a PlateLoc and a VCode Fr
169. ers Chapter 2 BenchCel overview 21 BenchCel User Guide The computer and networking About this topic Computer functions Connecting to the BenchCel Minimum system requirements This topic describes the computer and network connection requirements for running a BenchCel You need a computer to control the BenchCel and run BenchWorks The computer you connect to the BenchCel is used to Q Control the BenchCel and its instruments Input bar code labelling instructions Store and export log files Store and export data collected by plate readers DODO Communicate with other computers on your company s network for exchange of files reporting of errors and accessing email The BenchCel can be controlled via Ethernet or serial cable If you connect the BenchCel to the host computer via Ethernet and the host computer is already connected to a company LAN or other local network you need a second separate network card for the BenchCel This lets the BenchCel and any of its ethernet controlled instruments operate on an isolated network Note If you purchased your computer from Velocity11 it will have two network cards If you connect the BenchCel to the host computer with a serial cable use the standard 9 pin RS 232 connector supplied with the BenchCel If you are using your own computer to run the BenchCel make sure that it has the following minimum requirements Q PC system Pentium 4 2GHz or better 256
170. es Vacuum Platepad Velocity11 Labware Labware Entry Membership Labware entries that are not a member of this labware class Labware entries that are a member of this labware class 384 ABGene short well plate 384 Matrix clear polystyrene 384 REMP micro tube rack 384 REMP square well 96 ABGene deepwell block 96 ABGene tube rack TRIPOS 96 Matrix clear polystyrene 96 Matrix tube rack 96 Micronics tube rack ALSB Costar 384 black flatbottom Costar 384 polypro round bottom Costar 96 well plate Falcon 384 clear bottom Falcon 384 clear polystyrene Matrix 96 well Block Polypro MJ Research 384 well plate New plate Renamed Polyfiltronics 384 filter plate Test plate Tip Box Lid 11 Autofilling Reservoir 384 11 Autofilling Reservoir 96 11 Manual Reservoir 384 11 MicroWash 384 11 MicroWash 96 11 Tip Box 384d30 11 Tip Box 384d40 11 Tip Box 96d200 384 ABGene deepwell In the Labware Classes sub page if you select a type of plate in the labware entry box on the left the far right hand column displays the classes that it is a member of Labware Entries Please select a labware entry from the list below in order to view and edit its properties 384 ABGene deepwell 384 ABGene short well plate 384 Matrix clear polystyrene 384 REMP micro tube rack 384 REMP square well 96 ABGene deepwell block 96 ABGene tube rack TRIPOS 96 Matrix clear polystyrene 96 Matrix tube rack 96 Mi
171. es protocols using the Downstack and Upstack tasks Q An operator who needs to specify parameters for these tasks The Downstack and Upstack tasks move plates into or out of BenchCel racks The process of moving a plate out of a stacker rack is called downstacking The process of moving a plate into a stacker rack is called upstacking Plates may be returned to the same or different stacker racks You can make a single task upstack to or downstack from more than one stacker rack For example in a downstacking task when all of the plates are removed from one stacker rack the robot will begin to pick plates from a second stacker rack The two stacker racks are referred to as pooled downstackers 110 Chapter 6 Setting task parameters BenchCel User Guide Procedure To set Downstack and Upstack task parameters 1 Add the Downstack or Upstack task to a protocol process g oy 1 Packard Lid Downstack from pply Tabel Upstack to called unnamed 1 Stackeri Stacker Stacker2 Stacker3 gt E 2 Inthe list of available stacker racks in the Protocol Task Parameters toolbar select a stacker rack to downstack from or upstack to and click Add To select more than one stacker rack SHIFFclick or CTRL click before clicking Add An asterisk next to a stacker in the list means that the stacker rack is currently assigned to a task that uses the same labware Task Settings advanced Settings Task Settings advanced
172. eters for individual pipette tasks in a protocol 136 Chapter 7 Setting pipette task parameters BenchCel User Guide Configuring a pipette process example About this topic The example Creating a protocol Downstacking a plate Adding a Pipette Process task This topic gives an example of how to construct a protocol sub process that performs a simple pipetting operation See Related information at the end of this topic for more information about creating a pipette process The goal of the pipetting operation in this example is to pipette 20 uL of 1X TE buffer from a reservoir on a particular VPrep into a Costar 96 well plate The first step is to create a new protocol by setting up a plate icon for the plate you want to pipette into Name the plate icon Plate A and select the Costar 96 well plate as the plate type Costar 96 pp black called Plate A Se Costar 96 pp black called Plate A The next step is to add a Downstack task that downstacks a plate from an appropriate stacker Costar 96 pp black called ay Plate A Costar 96 pp black Downstack from called Plate A BenchCel Stack 1 Next you add a Pipette Process task Costar 96 pp black called p y a y Plate A i f Costar 96 pp black Downstack from Pipette process 1 called Plate A BenchCel Stack 1 Because there can be a number of Pipette Process tasks in a protocol this particular pipetting operation
173. every operator to follow warnings and safety labels and keep out of the robot s workspace whenever it is likely to move 12 Chapter 1 Introduction BenchCel User Guide Removed safety guard injury hazard Safety interlock override hazard User account passwords damage hazard Improper cleaning hazard INJURY HAZARD Operating the BenchCel without safety guards or enclosure covers increases risk of injury We recommend that you enclose the BenchCel in a light curtain or safety guard This restricts access to the BenchCel while it is operating or shuts down the BenchCel if you breach the curtain or open the guard INJURY HAZARD Operating the BenchCel without the safety interlock circuit connected to an enclosure increases injury risk The BenchCel has a safety interlock circuit that must be closed for the system to operate A jumper can be used to close the safety interlock circuit but European directives regarding the safe operation of machinery require that you always connect the safety interlock to a safety guard or light curtain DAMAGE HAZARD Only fully trained BenchCel administrators should have access to and use of the user account passwords Improper use of the robot by untrained personnel can lead to damage to the machine For example the robot grippers could collide with a stacker if a teachpoint is not defined properly DAMAGE HAZARD Do not use harsh abrasives corrosive cleaning agents
174. evice file the new devices are registered with the Windows operating system 196 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Loading a device file Related information When you open a protocol file the device file associated with it is automatically loaded for you If you need to load a new device file for your current protocol use one of the following methods Method 1 Load a device file from Windows To load a device file from Windows 1 In Windows navigate to the device file 2 Double click the file BenchWorks is launched if it is not already running and the device file is loaded Method 2 Load a device file from within BenchWorks To load a device file from within BenchWorks 1 Select File gt Device File gt Open If you want to open a recently opened device file select it from the list of device files at bottom of the menu and the device file is loaded 2 Navigate to the folder that contains the file to load 3 Click Open Method 3 Load a device file from Protocol Options If you load a device file using the following method the device file will be saved with the protocol when you save the protocol To load a device file from protocol options 1 Click Tools and select Protocol Options 2 Inthe Protocol Options tab of the dialog box click the device file ellipsis button Device File C Documents and Settings me Desktop ma dev 3 Navigate to the folder that co
175. example Aspirate task description String Description of the task that is given under the icon in the protocol editor For example a downstack task that has the script print task description will send the following text to the protocol log Downstack from stacker2 Apply Label task The JavaScript Apply Label task properties are listed below along with the data type of the property and the names of the corresponding Apply Label task parameters The task side property is an array of four label_data objects Q task side SOUTH Q task side EAST Q task side NORTH Q task side WEST Each of these task side properties has nine properties representing the fields on the Protocol Task Parameters toolbar for the Apply Label task In the table below point can be replaced by SOUTH EAST NORTH or WEST For example the Printing option field for the south label see screenshot is represented as task side SOUTH printLabel Property task side point field task side point format task side point increment Integer Chars task side crement task side point base task side point verifyBarc Integer ode task side point maxVerify Integer Attempts task side point sourceBar Integer codeSide task side point printLabel Integer point startingIn Integer Chapter 8 Creating a protocol advanced topics 179 Protocol Task Parameters Task Settings Advanced Settings
176. file than you have with other profiles This topic describes how to create a new BenchCel profile To create a BenchCel profile 1 Make sure you have a teachpoint file that you want to associate with your new profile In the BenchWorks main window click the Device Manager tab Select the desired BenchCel from the Device List DS Click Device Diagnostics located at the bottom of the Device List toolbar In the Device Diagnostics window click the Profiles tab Click Create a new Profile Enter a name and click OK CN oo In the Profiles group box select the Connection type from the list Select Ethernet if your BenchCel is connected to your computer with an Ethernet connection If you have a serial connection select the COM port the connection is using If your BenchCel supports flow control select the Use flow control check box 9 If you selected an Ethernet connection select the device to associate with the profile Click Find available device 10 In the Discovered BioNet Devices dialog box select the appropriate BenchCel from the list and then click OK 11 Select a teachpoint file a Click the ellipsis button b Inthe Select a Teachpoint File dialog box navigate to the location of the file select it and click Open The file path appears in the Profiles group box 12 Click Initialize this profile to initiate communication to the BenchCel using the new profile 13 Click OK to save the c
177. flow out of the MicroWash tray manifold This value should be zero If you want to dispense the wash liquid to waste instead of dispensing it back into the reservoir of washing liquid a Select the Dispense to waste at height of check box b Type a value into the associated text box for the height above the chimney from which you want the liquid to be dispensed The value can be a positive or negative number The pipette tips move up and sideways to dispense the wash liquid between the chimneys into waste If you want the tips to touch the outside tops of the chimneys to remove drops from the tips select the Enable tip touching check box a Type a value for the Tip touch rise height This is the height that the tips should move upwards before touching the side of the wells b Type a value for the Tip touch horizontal distance When the value for this parameter is zero the tips will move horizontally one well radius The well radius is defined in the labware database for the type of plate you are using If you want the tips to touch harder increase this value If you want the tips to touch more lightly enter a negative value In the Plate to wash list box select the VPrep and shelf position of the MicroWash tray Plate to wash me Grade Water x MB Grade Water unnamed 2 If the name that you chose does not appear in this list you probably associated the VPrep shelf with the labware type after adding the
178. for a BenchCel with 2X 4X or 6X stack configuration Dimension 2X 4X 6X Height 43 cm 43 cm 143 cm w short stack 91 5 cm 91 5 cm 391 5 cm w standard stack 107 cm 107 cm 107 cm w tall stack 127 cm 127 cm 127 cm Width 43 cm 65 cm 130 cm Depth 20 cm 20 cm 20 cm Weight 21 8 kg 28 1 kg 32 7 kg 20 Chapter 2 BenchCel overview BenchCel User Guide Addition of instruments If you are integrating your BenchCel with a Velocity11 device or another company s device make sure to include adequate space to accommodate one or more instruments The following table provides space requirements for some of the more typical configurations Instrument Dimensions cm LxWxH VCode 28 4 x 28 4 x 61 PlateLoc 39 9 x 58 4 x 21 6 VPrep 25 9 x 78 7 x 38 1 PlatePierce 20 3 x 35 6 x 34 4 VSpin with Access2 71 4 x 32 7 x 24 8 Utility and environmental requirements Electrical requirements Compressed air requirements Environmental operating requirements The BenchCel requires access to the following source of power for the BenchCel operating computer and any integrated instruments Utility Requirement Electrical 100 206 VAC 50 60 Hz The BenchCel requires access to the following source of compressed air Utility Requirement Compressed air 28 Lpm at 6 bar 1 cfm at 80 psi The BenchCel requires the following environmental conditions Parameter Requirement Temperature 5 40 C Relative humidity 10 90 Elevation 1 2000 met
179. for that process during the run Displays a message that asks for input from the user The message is generated from a script that is added to one of the tasks 3 Type the message that you want to display 4 a Type the message title in the top text box This appears in the process line b Type the message body in the bottom text box If using a variable enter the name in the text box Protocol Task Parameters Task Settings Advanced Settings Enter a message to display to the user at this point in the protocol The protocol will be paused to display this message Message will appear First plate of the series only O Every 5 plates Last plate of the series only Message title Message body Related information Chapter 6 Setting task parameters 127 BenchCel User Guide For information about See The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Using JavaScript with BenchWorks Using JavaScript in BenchWorks on page 171 Signal tasks Setting Waitfor task and Signal task parameters on page 127 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting Waitfor task and Signal task parameters About this topic Waitfor and Signal tasks defined P
180. formation This topic describes when and how to home the BenchCel robot Homing Home the robot to make sure that all of its axes are calibrated correctly For example if you notice the robot is not accurately picking up or placing plates home the robot Sending home Send the robot to its home position when you want to quickly move it to a central location or out of the way When you command the robot to home it executes a sequence that resets the home position in the x y gripper and theta axes INJURY HAZARD Keep away from the robot when it is moving especially in the z axis direction The robot s z axis motor is particularly powerful It might not stop immediately in a collision and a gripper could pierce your hand To home the robot 1 Open BenchCel Diagnostics dialog box to access the Controls page 2 Click Home The robot homes The axis order of homing is gripper gt z gt x gt theta When you command the robot to go home it moves to the zero position of the x z and theta axes To send the robot to the home position 1 Open BenchCel Diagnostics dialog box to access the Controls page 2 Click Go Home Note If you have cleared one or more On check boxes or have clicked Disable all to disable the servos for robot axes a dialog box will display Some of the Robot s servos are inactive Enable servos You must click Yes to enable the servo motors so the robot can go home For
181. formation is stored in the BenchWorks database and is used by the robot to perform tasks with the object Labware parameters may be entered into BenchWorks by two methods Q Using the Labware Editor dialog box in the labware diagnostics to add new or edit existing labware types Q Using the Labware Parameters group box in the BenchCel robot diagnostics to edit existing labware definitions Each method has its own purpose Q Use the Labware Editor dialog box to add new or to edit labware definitions in the database Q Use Labware Parameters group box when you want quick access to basic labware parameters to edit existing labware definitions For information about See Using the labware editor About the labware editor on page 215 Labware parameters group box About the Labware Parameters group box on page 236 Opening the labware editor Opening the labware editor on page 219 Chapter 10 Defining labware 215 BenchCel User Guide About the labware editor Labware editor defined Types of information stored About labware properties About labware classes Related information The labware editor is the BenchWorks interface through which users enter information about labware Note The labware database cannot be used by other companies systems into which Velocity11 devices are integrated You must be logged on with an administrator or technician user account to use the labware editor Tw
182. four quadrants of a 384 well plate and 16 quadrants of a 1536 well plate A 384 well head can dispense into a 384 well plate or the four quadrants of a 1536 well plate The distance that the tips should move upwards per unit volume of liquid being dispensed This value allows the tips to move upwards during dispensing to maintain a certain height above the surface of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use You might want this value to be the same as the Tip Retract Distance for the Aspirate pipette task The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel Whether you want the tips to touch the sides of the plate wells or not When the value for this parameter is zero the tips will move horizontally one well radius The well radius is defined in the labware database for the type of plate you are using If you want the tips to touch harder increase this value If you want the tips to touch more lightly enter a negative value 184 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Property Data type Task parameters Comments task tiptouchRiseHeight Float Tip touch rise height The height that the tips should move upwards before touching the side of the
183. g a run and there must be at least two racks available for this operation If you have added more than one rack you can change the order in which particular racks are used a Selecta rack b Click Use earlier to increase the priority of the rack or Use later to decrease the priority of it In the Store up to text box type a number equal to the number of plates you intend to incubate This value is important because it can affect the timing of the incubation For example if the time taken to move all plates to the first restack rack is greater than the time specified for the incubation the first plate cannot be moved to the next task in time This problem can be resolved by lowering the number of plates in a restack operation and adding more racks In the Incubate plate for text box type the time interval between when a plate enters the first restack rack and leaves the second restack rack IMPORTANT When you start a run that includes a Restack task you must type in a number that is equal to the total number of plates you want to restack in the Number of Runs dialog box The following screen shot shows one example of how to use the Restack task The plates are first downstacked and delivered to a VPrep fora pipette process After the pipette process is completed the plates are restacked to their original order ready for the next step in the assay protocol f g Jo Costar 96 pp black Downstack fr
184. g and configuring a Pipette Process task on page 140 Setting Dispense pipette task parameters About this topic Dispense pipette task defined Dispense value limits Before you start This topic describes how to set the Dispense pipette task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Dispense task A Dispense pipette task is used with a VPrep to dispense liquid into a plate You cannot dispense more volume than you aspirated If you enter a total dispense volume that is greater than the total aspirate volume you will get an error message when you compile the protocol More specifically the Aspirate Volume Pre Aspirate Volume Post Aspirate Volume must be greater than or equal to the Dispense Volume Blowout Volume Post Dispense Volume Before you can set the Dispense pipette task parameters you need to associate a VPrep shelf with the labware type from which you will aspirate Procedure Chapter 7 Setting pipette task parameters BenchCel User Guide To set Dispense pipette task parameters 1 2 In the pipette process window click the Dispense pipette task icon If you have defined a liquid class for the liquid you intend to dispense select it from the Liquid class list box at the bottom of the Pipette Task
185. g file Pipettor transfer log file The protocol log file records all available event and error information The information recorded in the protocol log file cannot be modified A protocol log Monday May 9 2005 4_38_58 PM txt Notepad ile Edit Format Help im 5 9 05 4 39 06 69 PM Into Banchworks Creating OriginalvcodeDevice 5 9 05 4 39 06 70 PM Info Benchworks Creating PipettorFiltershelfbevi 5 9 05 4 39 06 70 PM Info Benchworks Creating PipettorReagentshelfbev 5 9 05 4 39 06 71 PM Info Benchworks Creating PipettorservoshelfDevic 57 9 05 4 39 06 71 PM Info Benchworks Creating PipettorshakeshelfDevic 5 9 05 4 39 06 81 PM Info Benchworks Creating Pipettorstandardshelfpe 5 9 05 4 39 06 81 PM Info Benchworks Creating PipettorTipchuteshelfbpe 5 9 05 4 39 06 81 PM Info Benchworks Creating PipettorTipboxshelfpevi 57 9 05 4 39 06 81 PM Info Benchworks Creating Pipettorvacuumshelfbevi 57 9 05 4 39 06 81 PM Info Benchworks Creating PlateLocDevice 57 9 05 4 39 06 92 PM Info Benchworks Creating PlatePierceDevice 65 9 05 4 39 06 95 PM Info Benchworks Creating QFillDevice 57 9 05 4 39 07 29 PM Info Benchworks Creating RempcsPDevice 57 9 05 4 39 07 40 PM Info Benchworks Creating RobotDevice 57 9 05 4 39 07 61 PM Info Benchworks Creating sT 6 stackerDevice 57 9 05 4 39 07 66 PM Info Benchworks Creating shuttleRobotDevice 5 9 05 4 39 07 73 PM Info Benchw
186. g the protocol on page 59 14 Preparing plates instruments and accessories on page 61 15 Setting up a VSpin counterweight plate on page 63 16 Installing a rack on page 64 Related information For information about See Protocols About protocol files on page 84 BenchWorks About BenchWorks on page 27 BenchWorks components Relationships of BenchWorks components on page 30 Turning on the BenchCel About this topic Procedure Related information Chapter 3 Preparing for a run 33 BenchCel User Guide This topic describes how to turn on the BenchCel and integrated instruments if they are not already on To turn on the BenchCel and configured instruments 1 Make sure that the main power line air line and Ethernet or serial cables are plugged into the connection panel INJURY HAZARD Keep your fingers hair clothing and jewelry away from the machine while it is in motion 2 Power on any connected instruments See their respective user guides for power switch locations 3 On the connection panel press the power switch to the on 1 position The robot homes Note If the BenchCel robot does not home or if the power indicator lights do not come on turn off the BenchCel check the connections and turn it on again For information about Indicator lights Where this step fits in to the preparing for a run process The next step See Connect
187. gainst the problem of a full waste container or empty reservoir container the protocol writer can incorporate User Message tasks into the protocol to remind the operator at the appropriate steps in the protocol Alternatively operators can set timer alarms to remind them to fill reservoirs and empty the waste container at the appropriate time Monitoring overall progress Closing unneeded toolbars Related information Chapter 4 Performing a run TL BenchCel User Guide You can monitor overall progress of the run on the Progress page of BenchWorks Protocol Progress Elapsed protocol time 0 20 31 sec Plates left to process 516 Tasks remaining 4014 Tasks defined in protocol 4140 3 04 You can close unneeded toolbars to create more room on the screen for you to monitor a run by clicking the close box For information about See Pausing a run Pausing or stopping a run on page 74 Starting a run Q Starting a run from BenchWorks on page 70 Q Starting a run from a command line on page 73 What to do when you get an error Maintenance and troubleshooting on page 299 Working with the Log toolbar About this topic This topic gives an overview of what the Log toolbar does and how to use its features Event and error messages are displayed in the BenchWorks Log toolbar of the BenchWorks window With all message options turned on a large number of messages are displayed du
188. ge 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting Pierce task parameters About this topic This topic describes how to set the Pierce task parameters for the BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the Pierce task Q An operator who needs to specify parameters for the Pierce task Pierce task defined The Pierce task pierces a plate seal using a PlatePierce Procedure To set the Pierce task parameters 1 Add the Pierce task to a protocol process 2 Inthe Task Settings page of the Protocol Task Parameter toolbar enter a value in the Pierce Pressure text box If you are unsure of the best piercing pressure to use for your application contact the Velocityl1 Service Center Related information For information about Adding tasks to protocols Pipette tasks Other tasks See Adding and deleting tasks and pipette tasks on page 92 About setting pipette task parameters on page 96 About setting task parameters on page 95 ne Chapter 6 Setting task parameters BenchCel User Guide Setting Place Labware task parameters About this topic When to use Usage example This topic describes how to set the Place Labware task parameters The Place Labware task is designed for labs that use multiple types of labware for a protocol It
189. group box 236 labware classes Sub page 234 labware database 152 156 161 183 186 191 208 labware editor classes page 217 entries page 216 opening 220 relationship with other configurations 192 LabwareSelector plug in setting up 764 length of filter tip pin tool property 228 Liconic STR see StoreX Liconic STX StoreX see Storex lid departure height property 228 241 lid gripper offset property 227 241 lid resting height property 227 241 lidded stacking thickness property 227 lidded thickness property 227 lights connection panel 22 linking a pipette process 147 liquid class 151 liquid library adding an entry 248 calibrating VPrep 244 changing database 208 classes defined 244 database defined 244 editor defined 244 opening the editor 246 liquid library editor about 245 248 opening 246 relationship with other configurations 192 loading a rack 265 log file bar code 53 107 importing into Excel 57 pipette 52 protocol 52 58 searching 78 setting options for 55 types 57 Log toolbar 29 72 77 adding a note 79 message display 55 options for 78 log txt file about 52 adding a note to 79 logging out of BenchWorks 87 Loop pipette task defined 153 JavaScript properties 787 setting parameters 154 lower plate at VCode property 228 maintenance routine 300 manifold of MicroWash tray 162 Materials Safety data Sheet see MSDS Matrix WellMate s
190. gt About BenchWorks To find the diagnostics version number 1 Start BenchWorks 2 Open BenchCel Diagnostics 3 Read the version number on the title bar From the files You can look at the version information in the executable files To find the BenchWorks or diagnostics version number 1 Navigate to C Program Files Velocity11 BenchCel 2 Right click BenchWorks exe or BenchCel3 ocx diagnostics and select Properties 3 Click the Version tab Related information For information about See Getting help About Velocity11 user guides on page 3 Opening Diagnostics Opening BenchCel Diagnostics on page 253 Finding firmware version About general settings on page 277 Starting BenchWorks Starting BenchWorks on page 34 Chapter 1 Introduction BenchCel User Guide Reporting BenchCel problems About this topic If you find a bug in the software or have a technical or hardware problem that you can t resolve after reading the chapter on maintenance and troubleshooting read the information in this topic for how to report problems Reporting software If you find a problem in the Velocity11 software let us know by problems Q Sending a bug report from within BenchWorks Q Sending an email to service velocity11 com or euroservice velocity11 com Q Calling the Velocity11 Service Center at 1 800 979 4811 or 1 650 846 6611 Reporting hardware If you have a problem with a hardware component of
191. hCel ReleaseStack 0 Description Method to release a stack To downstack from or upstack to a stack the stack must be loaded A loaded stack is locked into the stacker head and cannot be freely taken from the device The stack number is 0 based 334 Chapter 14 BenchCel ActiveX controls BenchCel User Guide LONG MoveToHomePositio n LONG ShowLabwareEditor BOOL bModal BSTR bstrLabware Parameters Argument Argument Range Description Type Name SHORT sStack 0 to n l The stack to be loaded where n is the number of stacks Returns S_OK if successful other value otherwise Example Visual C Visual Basic 1Result 1Result BenchCel1 LoadStack 0 m_BenchCel LoadStack 0 Description Method to move the device to the origin This method is not commonly used Parameters None Returns S_OK if successful other value otherwise Example Visual C Visual Basic 1Result 1Result BenchCel MoveToHomePositionQ BenchCell MoveToHomePositionQ Description Method to display the labware editor graphical user interface Through this interface dialog the user can specify labware parameters that will be used by the device to handle the plates Parameters such as plate height and notch information will be associated with a labware name which can be used by SetLabware to indicate to the device how to handle the next plate Parameters Argument Argument Range Description Type Name BOOL bModal TRUE Whether to
192. hanges and close the dialog box 14 In the Device Properties window select the new profile from the list box next to the Profile name property 284 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Related information Device Properties E General Device name Device type E BenchCel Robot properties Automatically find and add BenchCel stacks For information about Profiles Teachpoint files Managing profiles BenchCel1 BenchCel Robot Benchcel2 Benchcell BenchCel3 See Q Relationships of BenchWorks components on page 30 Q About profiles on page 282 Managing teachpoint files on page 274 About this topic After creating a profile you can edit delete or rename it This topic describes how to do these tasks Procedure To edit a profile 23 3 toolbar Option Description In the BenchWorks main window click the Device Manager tab Select the desired BenchCel from the Device List Click Device Diagnostics located at the bottom of the Device List In the Device Diagnostics window click the Profiles tab Select one of the options using the following table as a guide Create a copy Click to create a copy of the profile currently displayed of this profile in the Profile name field Rename this Click to rename a profile profile Type in the desired name in the Rename Profile dialog box Related information Chap
193. hapter 14 BenchCel ActiveX controls 323 BenchCel User Guide BenchCel ActiveX controls This chapter gives integrators the ActiveX control they need to integrate another company s lab automation device into the BenchCel The ActiveX has been verified to work with both Visual Studio 6 and Visual Studio NET v 7 1 324 Chapter 14 BenchCel ActiveX controls BenchCel User Guide Setting up properties About this topic IPictureDisp ControlPicture SHORT Speed BOOL Blocking Properties are variables whose values can be set or retrieved by the container application Description Read only property that the client can use to get an icon to represent the ActiveX control This example paints a VSpin bitmap over a button Visual C Visual Basic The CPicture class is imported Assume that there is a button into your project when the Activex is installed CButton button Create a button CPicture VSpinPic VSpinPic m_CVSpin GetControlPictureQ Retrieve the picture button SetBitmap HBITMAP Vsp inPic GetHandle Q Paint the bitmap onto the button named Command on the current form You must set the style property of Command to Graphical Command1 Picture VSpin1 ControlPicture Description Property to specify how fast the BenchCel should move 0 slow 1 medium 2 fast This property should not be changed during an operation Setting this property to an invalid
194. have bar codes on south side Set ne O Incoming plates have bar codes on west side Bar Codes NOT in file z O Incoming plates have bar codes on north side Bar Codes NOT i 1 Me O Incoming plates have bar codes on east side Bar Codes NOT in file ha Q Specify each field of a bar code that is printed on a plate Field 1 FILE I How they are created Bar code input files are typically generated by a LIMS system although you can create them manually Viewing a bar code file in BenchWorks Chapter 8 Creating a protocol advanced topics BenchCel User Guide File structure Bar code input files contain lists of bar code fields or parts of fields that are grouped together in series In the following example there are two series Q Setl L Set2 PB BarcodelInputFile bar Notepad Eel E3 File Edit Format view Help lt name gt SsetL NAWLOOL NAWLOO2 NAWwLOO3 NAWLOO4 NAWLOOS NAWLOO6 NAWLOO NAWLOOS NAWwLOOS NAWLOLO lt name gt Set2 IGEN20021 IGEN20022 GEN2 0023 Each series could be used to label a different side of the same plate or label plates during different runs You can view the bar code file that is currently associated with BenchWorks as follows To view the associated bar code input file 1 Select Tools gt Show Bar Code File This opens a view of the bar code input file C WWorks Workspace B arCodeD ata Files B arCodeFile1 bar SourcePlate DestinationPlate
195. he same time New tab on Task Parameters Toolbar of plate instance Renamed to Apply label task If a deadlock occurs the plates are moved to the positions they would be in at the end of a successful protocol run New task performs replicate dispense operations See Using WellMate Diagnostics on page 293 Using QFill2 Diagnostics on page 291 Using Multidrop diagnostics on page 285 Using Nanodrop Diagnostics on page 288 The JavaScript task object and properties on page 178 Setting pre protocol rules on page 48 BenchCel ActiveX controls on page 323 Setting up a pre protocol or post protocol process on page 87 Device Driver User Guide Setting up a plate instance on page 88 Setting Apply Label task parameters on page 102 Setting general error handling options on page 44 Setting Change Instance pipette task parameters on page 146 7 Chapter 1 Introduction BenchCel User Guide Related information For information about See Overview of the BenchCel BenchCel overview on page 13 Finding your software versions About this topic This topic shows you some ways to find out your versions of BenchWorks and BenchCel Diagnostics From the software You can open the software to find the version of BenchWorks or BenchCel Diagnostics To find the BenchWorks version number 1 Start BenchWorks 2 Navigate to Help
196. he Use single instance of plate check box For example you may have one source plate from which you want to repeatedly aspirate a given volume and dispense it into a different receiving plates 89 90 Chapter 5 Creating a protocol basics BenchCel User Guide Related information 6 5 Inthe Bar code control sub page a a If the incoming plates have bar codes select the appropriate Incoming plates have bar codes check box If you want to check the bar codes on the incoming plates against a series of bar codes in a bar code input file select the name of the bar code series you want to use Incoming plates have bar codes on south side Bar Codes NOT in file Bar Codes NOT in file Seti Set2 A For more information about bar codes input from file see Related information at the end of this topic In the Special error handling sub page Select one or more devices that you want to use as quarantine stations and click Add The device names are moved to the bottom quarantine list A quarantine station is a place that plates will be placed if the plate has a bar code mismatch error Check or leave clear the Quarantine plate after process completed check box based on the following descriptions If the check box is left clear a plate that gives a bar code misread error is immediately moved to a quarantine station and a new plate takes the place of the quarantined plate in the processing sequence
197. he online help 1 If you are currently using BenchWorks press F1 2 Ifyou are not currently using BenchWorks open help html in C Program files Velocity 1 1 BenchWorks HelpSystem benchworks_ug Place a shortcut to this file on your desktop for future use Main features The online help includes a navigation pane content pane and navigation buttons 3 Chapter 1 Introduction BenchCel User Guide Navigation pane Introduction Who should read this guide About Velocity11 user guides Supported software versions Finding your software versions Reporting VWorks problems VWorks overview Basic description Instruments you can use with VwWorks Overview of the VWorks user interface Showing and hiding tabs and toolbars in VWorks Relationships of configuration VWworks Content pane Navigation buttons Main Page Mm lt gt E O D lt lt ff gt About Velocity11 user guides Introduction Each Velocity11 user guide is delivered to you as gt Online help gt A PDF file gt A printed book The information in each format is the same but each has different strengths To work most components Preparing for a run workflow for preparing a run Starting VWorks Logging in to VWorks and changing your password About tasks processes and protocols Opening a protocol in Yorks Setting general options About setting error handling options Sattina aonoral orrnr handlina antiane PDF user guide
198. he plate is in the correct orientation check the notch setting in the labware parameters a b Open the Controls page of the BenchCel Diagnostics dialog box In the Labware group box select the Show parameters check box In the Labware Parameters dialog box verify that the correct notch position is selected 312 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Plate presence and orientation sensors conflict 3 Check the orientation sensor offset a Open the Labware Editor dialog box and click the Stacker tab b Verify the value in the Orientation sensor offset This is the distance from the bottom of the plate to the middle of the sensor window 4 Check the orientation plate notch sensor readings See Checking the stacker sensors on page 314 for a procedure 5 If readings do not detect the correct orientation see Resetting the orientation sensors for a plate on page 313 for a procedure on how to adjust the sensors This error is generated when the plate presence sensor and the orientation sensors disagree as to whether there is a plate present or not The problem is usually resolved by adjusting the plate presence sensor threshold and or the orientation sensor offset To resolve plate not present error 1 Check the orientation sensor offset a Open the Labware Editor dialog box and click the Stacker tab b Verify the value in the Orientation sensor offset This is the distan
199. he robot If homing fails contact Velocity11 Service Center Click retry If that doesn t work turn the BenchCel off and then on If you continue to experience this problem contact Velocity11 Service Center Click retry If retrying does not work turn the BenchCel off and then on If problem continues contact Velocity11 Service Center Close and restart BenchWorks Turn the BenchCel off and then on Check the communication cables Verify that the Ethernet hub has power If the problem continues contact Velocity11 Service Center Re examine the protocol with the aid of the Log toolbar and run simulator to determine why the deadlock is occurring Check to be sure that the number of simultaneous plates is not too high See Wait for the head to cool and retry Error Message Timeout on theta axis Timeout on x axis Timeout on z axis Timeoout on grippers Chapter 13 Maintenance and troubleshooting 309 BenchCel User Guide Possible Cause Recommended Actions The motor s controller did not Home the robot and then move the respond as expected robot in the same axis If the robot moves continue on If the robot does not move shut down the application and turn the BenchCel off and then on Contact Velocity11 Service Center if problem continues The motor controller did not Home the robot and then move the respond as expected robot in the same axis If the robot move
200. he same information from a different perspective The following diagram explains how information flows from the various data stores in BenchWorks into a single Aspirate pipette task that is stored as part of a protocol file Four main kinds of information are associated with a pipette task in a protocol file These are Q General task properties set in the Pipette Task Parameters toolbar Q Device information Q Labware information Q Liquid properties information This information is included in the pipette task through a cascade of associations In the Aspirate pipette task example the association between the type of liquid and the pipette task is made by selecting a liquid class for the pipette task Chapter 8 Creating a protocol advanced topics 193 BenchCel User Guide All of the settings from the three data categories are stored in their respective databases and entered through their respective interface Data categories Databases Data interfaces device files device manager device manager plate types labware database labware editor liquid classes liquid library liquid library editor When a protocol is saved the names of the three data categories that it uses are saved and associated with it so that you don t have to select them every time During a run these data categories are referenced from the protocol they were associated with 194 Chapter 8 Creating a protocol advanced topics BenchCel User Guide devic
201. height 8 Departure height i5 237 238 Chapter 10 Defining labware BenchCel User Guide Related information For information about See The BenchCel Controls page About the Controls page on page 254 Opening BenchCel Diagnostics Opening BenchCel Diagnostics on page 253 Changing labware parameters Changing labware parameters on page 238 Changing labware parameters About this topic When adding new labware or troubleshooting existing labware you may need to make adjustments to the labware parameters This topic describes how to edit labware parameters using the Labware Parameters group box Procedure To change labware parameters 1 Ensure that you select the desired plate type from the list box 2 Enter new values or edit existing values for the Plate Dimensions using the following table as a guide Parameter Comment Stacking thickness The thickness in millimeters of two stacked plates minus the thickness of one plate Measure using calipers Example Thickness of two stacked plates x 23 14 mm Thickness of one plate 14 14 mm Stacking thickness 23 14 mm 14 14 mm 9 00 mm c X Plate Thickness 5 Stacking Thickness c Plate thickness The distance in millimeters from the bottom surface of the plate to the top surface of the plate Measure using calipers Chapter 10 Defining labware 239 BenchCel User Guide 3 Enter
202. hen to redefine or If you are sure the teachpoint is off then either redefine the teachpoint adjust the or make an adjustment in the software as described below teachpoint If Then You have moved the BenchCel Redefine the teachpoint You have changed the stage height Redefine the teachpoint on the VCode You have moved an external Readjust the device and recheck the teachpoint slightly teachpoint If it is very close you can make a slight adjustment Adjusting the To adjust the teachpoint you will measure the difference between the teachpoint marks left on a plate by the grippers after picking the plate from an internal teachpoint and external teachpoint To adjust a teachpoint 1 Open the Controls page of BenchCel Diagnostics dialog box 2 Place a new plate in a stacker rack and click on the stacker teachpoint in the animated display 3 Using the pick from command in the animated display command the robot to pick the plate Note the marks on the plate left by the grippers Place the same plate on the teachpoint you want to adjust Select the teachpoint in the animated display and click pick from to command the robot to pick up the plate The marks on the plate left by the grippers this time will be in a different place 6 Measure the distance between the gripper marks in the x and y direction and incorporate those differences in the teachpoint definition Chapter 13 Maintenance and troubleshooting 317 BenchC
203. his task moves a plate to an Access2 and centrifuges it To set VSpin with Access2 task parameters 1 Add the VSpin with Access2 task to a protocol process 2 Inthe Task Settings page of the Protocol Task Parameter toolbar select a VSpin from the Select a VSpin with Access2 to use list box 3 Set the desired options in the Load Plate group box a Enter the Gripper Z offset mm for the plate you are using This value is the distance from the bottom of the plate to where the Access2 grippers will grab the plate Typically this value is the same as the robot gripper offset b Ifyou don t want to use the plate sensor on the Access2 select the Ignore optical plate sensor check box Related information Chapter 6 Setting task parameters 131 BenchCel User Guide c Ifyou are using flexible plates such as PCR plates select the Grip gently check box Set the spinning parameters in the Spin Plate group box Enter a value for the Velocity Acceleration and Deceleration These parameters are calculated as a percentage of the maximum value possible Maximum speed is 3000 rpm For more information see the VSpin User Guide Set the spin duration a Choose a Timer mode option Total time includes the time it takes the VSpin to accelerate to the target speed and decelerate to a stop Time at speed only includes the time that the rotor is at the target speed b Enter the spin duration The format for the time
204. hpoint name Valid teachpoint name VARIANT_TRUE VARIANT_FALSE 0 2 Visual Basic PlateLoc FALSE 2 Description 329 BenchCel User Guide Description Destination to pick from Destination to place to Whether the plate is lidded 0 Do nothing 1 Retract arms normally 2 Retract arms only in Z 0 clearance that is specified in teachpoint detail 3 Retract arms so they are vertical 1Result BenchCel1 PickAndPlace Stacker 1 Method to retrieve the teachpoints known to the device This method must be called after initialization is complete and it returns an array of available teachpoints including the stackers Parameters None Returns A safe array of teachpoint names 330 Chapter 14 BenchCel ActiveX controls BenchCel User Guide LONG ProtocolStart LONG ProtocolFinish Example Visual C Visual Basic VARIANT vTeachpoints teachpointNames m_BenchCel GetTeachpointName BenchCel GetTeachpointNames sO For i LBound teachpointNames To SAFEARRAY psa UBound teachpointNames vleachpoints parray MsgBox teachpointNames i BSTR bstrArray Next if FAILED SafeArrayAccessData ps a reinterpret_cast lt void gt amp bstrArray VariantClear amp vTeachpoints return for ULONG i 0 i lt psa gt rgsabound 0 cElements i MessageBox CString bstrAdday i SafeArrayUnaccessData psa Vari antClear amp vTeachpoints Description Method to
205. ice on page 142 142 Chapter 7 Setting pipette task parameters BenchCel User Guide Configuring a VPrep shelf as a device About this topic All VPrep shelves have to be configured in BenchWorks as devices before they can be used in a protocol All shelves on your VPrep were set up as devices at the factory This topic shows you how to modify the existing settings for a shelf Read this topic if you are an administrator or technician who writes protocols that uses a VPrep Use this procedure when creating a protocol that uses a type of reservoir on the VPrep that is not currently set up or when a new type of shelf device is used in a protocol for the first time When you set parameters for some pipette tasks you have to select the type of labware or device used in the task The following screenshot shows both a plate and a device in the list box of an Aspirate pipette task Plate to aspirate from Plate A E shelfl The plate in the list box refers to Plate A in the associated process Costar 96 well o Y plate called 4 Plate A i i With Plate A selected the robot will move the plate to the VPrep and liquid will be aspirated from it Costar 96 well Dor plate called Plate A The device in the list box refers to a reagent shelf on the associated VPrep With shelf 1 selected the VPrep head will move to shelf 1 and the VPrep will aspirate from whatever type of labware sits on the shelf Before you can run the pr
206. ile that is read by the FileReader plug in Read this topic if you are a technician or administrator who writes protocols with Apply Label VCode tasks and who want to use the FileReader plug in to read and process the label text The first row in the text file must contain a header row The header row is a human readable guide to show where the contents of each column will print The FileReader plug in will assume that the rest of the text contains the same text separation method as the header row For example if the header row uses a CSV format but the rest of the file uses a tab delimited format the FileReader plug in expects commas to separate the values in the file Having found none it assumes that the entire text for each row after the header row is one field A screenshot of a FileReader plug in text file is shown below This example is a tab delimited text file but a CSV text file could also be used West4 West5 West6 Northl ricio ricil rici2 ricl3 r2c10 r2c11 r2cl2 r2cl3 r3c10 r31 r3cl2 r3cl3 r4c10 r4c11 r4cl2 r4cl3 r5c10 r5c11 r5c12 r5c13 r6clo r c11 r6cl2 r6cl3 r7c10 rza r7c12 r7c13 r8c10 r8c11 r8c12 r8c13 r9c10 r9c11 r9cl2 r9cl3 r10c10 r10c11 r10c12 r10c13 rliclO rilicll ritci2 riicl3 rl2c10 ril2cill ri2ci2 ri2ci3 r13cl0 ri3cll risa rizez r1 14c10 r14c11 r14c12 ri4cl3 ri5c10 riscl riicl2 ri5cl3 r16c10 ri6cll ri16cl2 r16ci3 The order of the columns Note how the order of the columns references
207. ill begin to fall to its lowest z axis position when the On check box is cleared 3 Move the robot s x z and theta axes manually Any subsequent commands will trigger a dialog box that states Some of the Robot s servos are inactive Enable servos You must click Yes before the robot can move autonomously again For information about See Teachpoints About teachpoints on page 269 Opening diagnostics Opening BenchCel Diagnostics on page 253 Chapter 12 Using BenchCel Diagnostics 259 BenchCel User Guide Jogging the robot About this topic Jogging the robot in the zaxis Jogging is the process of moving the robot in small increments You can jog the robot head in the z x or theta axes and jog the grippers open and closed Jog the robot when you need to move it in small increments Jogging is useful when creating teachpoints For example you could move the robot manually to a position you want to set as a teachpoint After you have re enabled the robot s servos you can fine tune the robot s position by jogging it DAMAGE HAZARD Before you jog the robot make sure that there is nothing that the robot can crash into Move the robot slowly and keep the jog increment small until you are certain that there is no obstruction To jog the robot in the z axis 1 Open BenchCel Diagnostics dialog box to access the Controls page 2 Select the increment that you want the robot to move by
208. ing a device file A device is an item on the BenchCel that has an entry in the device manager A device can be an instrument or a location on the BenchCel that can hold a piece of labware Examples of devices Q Platepad Q VPrep shelf Q Stackerrack Every device on your BenchCel system has been properly configured for you by Velocity11 personnel However if you have a VPrep integrated with your BenchCel system and want to add a shelf or if you wish to add new instruments to your BenchCel system administrators in your organization need to configure the relevant device settings The data entered into the device manager and saved as a device file contains the configuration information for your devices Device files have the file name format lt file name gt dev and are stored in the folder location that you specify when saving the file After you make changes in the device manager you must save the changes for them to be available the next time the protocol is opened To save a device file 1 Make sure you are logged in as an administrator 2 Select File gt Device File gt Save As 3 Navigate to the folder in which you want to save the file If you want to save the file in the current folder skip this step 4 Click Save The path of the device file specified in the protocol file and Protocol Options dialog box is changed to reflect the different location The next time you compile or run a protocol that references the d
209. ing task parameters on page 95 Setting Multidrop task parameters About this topic This topic describes how to set the Multidrop task parameters for the BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the Multidrop instrument Q An operator who needs to specify parameters for the Multidrop task Multidrop task The Multidrop task moves a plate to a Thermo Labsystems Multidrop 384 defined or 96 dispenser and instructs the dispenser to fill the plate You can specify whether to include prime shake or purge operations The Multidrop is capable of dispensing up to eight different liquids into one plate During a dispense the plate stage moves in the left right axis and the wells are filled in columns starting with column 1 In a 96 well plate there are eight rows so every well in a column is filled at the same time In a 384 well plate there are 16 rows requiring two dispense passes During the first pass every second well in a column is filled The plate stage then moves over by one well so that the dispensers sit above empty wells In the second pass the stage returns to the starting position and the remaining wells are filled Procedure Rows Chapter 6 Setting task parameters BenchCel User Guide Columns To set Multidrop parameters l 2 Add a Multidrop task to a protocol process If the BenchCel has more than one Multidrop select the
210. int marker in the BenchCel animated display Load all stacks Load Stack 1 Load Stack 2 Release all stacks Retract Clamps Retract Clamps Li ove to Stacker 1 Pick from Stacker 1 Stacker 2 teachpoint marker not selected Transfer to Stacker 1 Pick from test1 Test1 teachpoint marker selected In this illustration there are three available teachpoints There is a teachpoint for each of the two stackers and one teachpoint called Test1 Both Stacker and test1 teachpoints are selected as indicated by the enlarged border around each teachpoint marker Up to two teachpoint markers can be selected at one time To move the robot using teachpoint control l Make sure you have selected the desired Plate Type from the Labware list box Click once on a teachpoint marker Several boxed command buttons appear See the test1 teachpoint marker in the illustration above Click a button using the following table as a guide Command button Description Move to teachpoint Move the robot to the teachpoint Pick from teachpoint Pick or place a plate at the teachpoint Delid from teachpoint Tells the robot to delid This option is not available for stacker teachpoints Transfer to teachpoint Transfer from the currently selected teachpoint to another selected teachpoint This command only becomes available after you have selected two teachpoints DAMAGE H
211. ion 267 jogging the robot theta axis 260 jogging the robot X axis 260 jogging the robot Z axis 259 minimum system requirements 27 monitoring a run 76 moving between teachpoints 275 moving the robot manually 258 network cards 27 pausing a run 74 performing a run 31 67 performing a run overview 68 performing pre run checks 69 preparing for a run workflow 32 preparing instruments for a run 67 robot axes 256 routine maintenance 300 setting error options 43 setting general options 47 setting simultaneous plates 97 shutting down 87 space setup requirements 79 stacker controls 264 stacker gripper controls 24 starting 33 starting run from command line 73 temperature range 20 using the robot slider controls 263 utility and environment requirements 20 BenchWorks control toolbar 28 finding the version number 5 8 introduction and overview 27 logging out 87 new features 7 protocol definition 30 starting 34 Bio Tek ELx405 Washer see Bio Tek Bio Tek supported instrument 78 blowout volume 752 156 160 Cc calibration file Nanodrop 290 can be mounted property 228 can be sealed property 227 can have lid property 227 240 can mount property 228 Change Instance pipette task defined 146 setting parameters 147 Change Instance process task 146 Change Tips pipette task defined 148 requirements for 148 using 148 check orientation property 237 chimney see MicroWash tray class la
212. ion in order for it to indicate the current number Parameters Argument Argument Range Description Type Name LONG pCount Valid If successful the value pointed pointer to to by pCount should indicate the receive the number of stacks the device has stack count Returns S_OK if successful other value otherwise 332 Chapter 14 BenchCel ActiveX controls BenchCel User Guide Example Visual C Visual Basic 1Result 1Result m_BenchCel GetStackCount amp nu BenchCel1 GetStackCount numStacks mStacks LONG Description IsStackLoaded SHO Method to test whether a stack has been loaded The stack number is 0 RT sStack in out based This method should be called after a successful connection VARIANT_BOOL pLoaded Parameters Argument Argument Range Description Type Name SHORT sStack 0 to n l Which stack to check where n is the number of stacks VARIANT_ pLoaded Valid On a successful call the value BOOL pointer to pointed to by pLoaded should receive indicate whether the stack is whether or loaded or not not the stack is loaded Returns S_OK if successful other value otherwise Example Visual C Visual Basic 1Result 1Result m_Benchcel IsStackLoaded 1 amp bS BenchCell IsStackLoaded 1 bStackLoa tackLoaded ded LONG Description IsPlatePresent SHO Method to test whether a stack has a plate and is loaded If the stack is RT sStack in out not loaded the result returned through pPresent will not be meaningful
213. ion panel description on page 22 Workflow for preparing for a run on page 32 Logging into the operating system on page 34 34 Chapter 3 Preparing for a run BenchCel User Guide Logging into the operating system About this topic Procedure Related information After turning on the BenchCel you may log in to the Windows operating system on the computer This topic describes how to do that To log in to the Windows operating system 1 At the Welcome to Windows screen press CTRL ALT DELETE 2 At the Log On to Windows screen type your user name and password 3 Ifnecessary in the Log on to text box type the name of the network domain to which your BenchCel is connected Contact your network administrator if you do not know your network domain name You should only need to type in this name once because the system will remember it 4 Click OK For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Starting BenchWorks on page 34 Starting BenchWorks When to start BenchWorks Starting BenchWorks Start BenchWorks after you have turned on the BenchCel and computer and logged on to the computer operating system To start BenchWorks 1 Make sure that everyone is clear of the BenchCel and that there are no objects that could obstruct the robot INJURY HAZARD When BenchWorks starts robot and i
214. ipper holding stack position mm Sensor offset correction mm Property Robot gripper offset Gripper open position Gripper holding plate position Gripper holding lidded plate position Gripper holding lid position el Ei 4 00000 4 00000 i 0 00000 Description The distance in millimeters from the bottom of the plate to the point where the grippers grip the plate Typically this value is 6 10 mm Note The robot gripper offset that appears on the Plate Properties page applies to Velocity11 robots used in BioCels not BenchCel robots Distance between the widest possible robot gripper position and the position at which the grippers are considered to be open Distance between the widest possible robot gripper position and the position at which the grippers hold a plate This value is currently not used if you enter a value it will have no effect Distance between the widest possible robot gripper position and the position at which the grippers close to hold a lid 229 230 Chapter 10 Defining labware BenchCel User Guide Property Gripper holding stack position Sensor offset correction Defining stacker properties Description Distance between the widest possible robot gripper position and the position at which the grippers close to when they are holding a stack of plates Leave this value at 0 zero About this topic This topic describes how to define the stacker
215. ipper offset is incorrect for the plate type Stacking thickness for the plate type is incorrect Plate thickness for the plate type is incorrect Recommended Actions Open the Labware Editor dialog box and click the BenchCel tab Check the value for the Robot gripper offset This value is the distance from the bottom of the plate to the point where the grippers grab the plate This should be the middle of the plate Open the Labware Editor dialog box and click the Plate Properties tab Check the Stacking Thickness value See Defining plate properties on page 226 for a procedure Open the Labware Editor dialog box and click the Plate Properties tab Check the Thickness value See Defining plate properties on page 226 for a procedure Open the Labware Editor dialog box and click the BenchCel tab Adjust the values for the Gripper open position Open the Labware Editor dialog box and click the Stacker tab Check the Stacker gripper offset value This value is the distance from the bottom of the plate to the center of the stacker gripper The gripper should grab the plate midway Open the Labware Editor dialog box and click the Plate Properties tab Check the Stacking Thickness value See Defining plate properties on page 226 for a procedure Open the Labware Editor dialog box and click the Plate Properties tab Check the Thickness value See Defining plate properties on page 226
216. is specified by the value in the Length of incubation text box Using this function plates can leave the plate hotel and delivered to the pipettor every minute instead of every 10 seconds An alternative way to control the time at which plates are delivered to an instrument is to use the Release a new plate every x seconds parameter for the Downstack task If you want to restrict a device so it is not used as the place where the incubation takes place in the Available devices box select the device and click Exclude This may be useful if a particular platepad is used during multiple steps of the protocol Protocol Task Parameters Task Settings Advanced Settings Length of incubation sec O Start timer when previous plate finishes incubating Available devices Devices that will be excluded from this task Platepad3 The name of the platepad moves to the lower box 113 114 Chapter 6 Setting task parameters BenchCel User Guide Example In the following example a plate is downstacked moved to an incubator and then upstacked ey Greiner 384 Black Downstack from Incubate for 600 Upstack to Stack TC 781091 called Stack sec using relative unnamed 1 timing Related information For information about See Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About sett
217. ispense tab Wellmate Diagnostics ersion 1 2 2 Eg Profile Command Dispense 500 Prime volume Abort dispense 0 2499 pL Dispense Abort dispense 250 Dispense volume 0 2499 pL Dispense to whole plate 1000 Purge volume Dispense to columns 0 2499 pL Z ai 100 to iaig Check all 1 tick 0375 mmi Return home after dispense Column mask 0 CTT Enter in the appropriate values using the table below as a guide Property Description Prime Volume with which to prime the lines before dispensing Dispense Volume to dispense into the wells Chapter 12 Using BenchCel Diagnostics 297 BenchCel User Guide Property Description Offset The distance in ticks where 1 tick 0 0375 millimeters from the center of the well you want to dispense Move to a column Enter the column number you want to move to in the Column number field and then click Move to Column 3 Select the wells of the plate to which you want to dispense a To dispense to the whole plate click Dispense to whole plate b To dispense to a specific column or columns click Dispense to columns and then click the button s corresponding to the column number When selected the button changes its appearance 4 To dispense click Dispense To stop the dispense process before it is finished click Abort dispense Related information For information about See Diagnostics About diagnostics on page 252 Using the WellM
218. ity of task icons L Release of BenchCel stackers Review general options after you open a protocol but before starting a run IMPORTANT Protocols do not store Options dialog box settings as part of the protocol This means that all protocols use the settings that are currently selected in the Options dialog box You may decide to keep all or many of the options the same for every run IMPORTANT If you use bar code data files remember to select the correct file for every run To set general options 1 Select Tools gt Options 2 Make sure that the Options page of the BenchWorks Options dialog box is selected 3 Ifyou are using a bar code file select its location a Inthe Bar Code Settings group box click the ellipsis button next to the appropriate type of bar code file b Inthe Open dialog box navigate to the folder that contains the bar code file c Select the file with a bar filename extension for an input file and a dat filename extension for a database file and click Open 42 Chapter 3 Preparing for a run BenchCel User Guide 7 Related information In the Robot Settings group box select the desired maximum speed of the robot movement If the plate specific robot speed set in the Maximum Robot Handling Speed group box of the Labware editor is different from the general robot speed the slower of the two speeds is used DAMAGE HAZARD If you are testing a new prot
219. just the sliders controls for each axis you want to change INJURY HAZARD Make sure everyone is clear of the BenchCel before you command the robot to move 4 Click Move robot The robot axes will move to their commanded positions 5 To close the dialog box click Exit For information about See Animated display About the Controls page on page 254 263 264 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide About stacker controls Stacker clamps Plate present indicator Related information The stacker controls are located in the BenchCel animated display Each stacker has two clamps that perform two functions Q Anchor the stacker rack to the stacker head U Grip and release plates You can command the BenchCel stacker clamps to grip plates or release plates with the Extend Clamps and Retract Clamps controls You can command the BenchCel stack clamps to load and release stacker racks with the Load Stack and Release Stack controls Release Stack 1 Load Stack 2 Retract Clamps Retract Clamps The plate present indicator above each stacker teachpoint marker will change color depending on the presence of a stack with plates Color Meaning Green A stack with plates is loaded correctly and the BenchCel is ready for you to start a protocol Yellow A stack with plates is present but the robot grippers are blocking the stacker sensor Blank There are no plates p
220. k Initialize device using profile 7 Click OK To manage profiles 1 Open WellMate Diagnostics 2 Click the Profile tab Wellmate Diagnostics ersion 1 2 2 xi Profile Command Dispense Profile Operations WellMate profile hd Create a new profile Pump speed 500 fast 1000 slow Create a copy of this profile Stage speed 1700 fast 15000 slow Rename this profile Volume to prime on initialization 0 2499 pL Delete this profile Update this profile Initialize device using profile 2 3 Select the profile to manage from the Profile Operations list box Make changes to the profile if desired 4 Atthis point you may perform any of the operations displayed in the Profile Management group box by clicking the appropriate button Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Moving the plate To move the plate stage stage 1 Open the WellMate Diagnostics 2 Click the Command tab Profile i Profile WellMate profile z Initialize selected profile Commands Guery plate type Column number Current plate type unknown 1 12 96 1 24 384 a o Offset 100 to 100 ticks Pine Pirce 1 tick 0375 mm 3 Perform the desired task using the following table as a guide To Then Home the WellMate Click Move to home Move the stage to the priming Click Move to prime area a
221. k of plates harder than a single plate to support the weight of the stack 6 If your plates can be lidded select the Can be lidded check box You can now configure the lid parameters using the following table as a guide Parameter Comment Can be lidded Select if the plate can be lidded The following settings are only available if this setting is selected Stacking thickness Stacking thickness of the plate with a lid in place Thickness The distance in millimeters from the bottom surface of the of a lidded plate to the top surface of the lid Measure using calipers Parameter Resting height Gripper offsets Gripper position Departure height Chapter 10 Defining labware 241 BenchCel User Guide Comment Height in millimeters above the bottom of the plate at which the bottom ofa plate lid rests a Height in millimeters above the lid resting height at which to grip the lid A b t T Adjusts the distance between the robot grippers when holding a lid Height above the bottom of the plate to which the lid is lifted 7 Click Apply parameters for the changes to take effect Related information For information about The BenchCel Controls page Opening BenchCel Diagnostics See About the Controls page on page 254 Opening BenchCel Diagnostics on page 253 242 Chapter 10 Defining labware Be
222. ked for most protocols When to clear the rule If your protocol has all of the following attributes consider clearing this check box Q The protocol has more than one pipette process that uses the same VPrep L The duration of one of the pipetting operations is much longer than another Explanation Consider an example in which a protocol has two processes and both have a pipetting operation that uses the same VPrep When the check box is selected the pipetting operations for one process are completed before the pipetting operations begin for the other process Now consider what happens when the first pipetting operation takes significantly longer to complete than the second operation and the protocol is run several times in succession The overall time taken for the protocol to complete is much greater than it needs to be because during each cycle the system had to wait for the slower pipetting operations to complete for all the plates in the process before it could continue If the rule is turned off a plate from the fast pipetting process can be delivered to the VPrep after a plate from the slow pipetting process followed by another plate from the slow pipette process and so on This reduces the bottleneck at the VPrep because it allows the faster process to continue and its second cycle in the series to start before the first cycle is complete 50 Chapter 3 Preparing for a run BenchCel User Guide Handle plates
223. ker s regulator in pounds per square inch Notches The far left plate sensor is called Al because that corner is intended for the Al well of the microplate Values that are less than the Sensor threshold indicate the presence of a notch Values that are greater than the Sensor threshold indicate the absence of a notch To set the Sensor threshold or Sensor intensity see Changing general settings on page 278 Resolving teachpoint problems About this topic Once set properly you should never need to adjust or redefine a teachpoint unless you do one of the following L Move the BenchCel U Change settings on external devices such as the Z height on a VCode Q Move one of the external devices accidently Symptoms of a The symptoms of a teachpoint error are the following teachpoint error Q Robot is not placing the plate properly at an external teachpoint Q Robot is not picking the plate properly from an external teachpoint Note If the robot is not picking or placing a plate properly from an internal teachpoint one of the stacks then you most likely have a gripper alignment problem and not a teachpoint error Before changing the Before you adjust or redefine a teachpoint always check to be sure that teachpoint the grippers are aligned See Checking the arm alignment on page 309 for a procedure to check the gripper alignment 316 Chapter 13 Maintenance and troubleshooting BenchCel User Guide W
224. l In general one simultaneous plate can be used for every task in the protocol This is because in general each task uses one plate position As an example a protocol with three tasks can have three plates on the table at once There are exceptions to this though such as cases where the same plate position is used for more than one of the tasks and when a VPrep is used Several plates can be positioned on a VPrep at the same time Q Positions there are in the system that will incubate plates Q Plates there are in a restack task If the protocol includes a restack task the number of simultaneous plates must be equal to or greater than the number of plates in the restack task If the number of simultaneous plates is set too high the protocol may be slowed down because the robot will move around to avoid a deadlock In cases where too many plates are in the system and there is no way to move plates around further this can result in a deadlock at which point the protocol stops If the number of simultaneous plates is set too low the time for the protocol run could be extended Optimizing the number of simultaneous plates is therefore critical for maximizing efficiency A typical BenchCel protocol has 5 30 simultaneous plates but it could be many more than that A safe number to start with when testing a new protocol is 1 2 Run the protocol in simulation to optimize the number of simultaneous plates 92 Chapter 5 Cr
225. l Microplate Handling Workstation and the VStack Labware Stacker use labware racks to store the stacks of labware microplates tipboxes and tube racks that are processed during a protocol run Figure BenchCel Workstation with front load labware racks All the rack models have the following basic parts e Carrying handle The standard rack has a polished top bar that can be used as a carrying handle The top load and front load racks have fold down carrying handles Rack e Tabs A pair of vertical tabs are located at the bottom sides of the rack The tabs insert into slots on the device when you mount the rack e Stacker grippers A gripper is located on the interior bottom of each tab The pair of grippers hold a microplate during the labware loading unloading downstacking and upstacking processes A clamp in the device opens and closes the grippers Figure Standard rack containing labware Stacker head Handle Tab A stacker gripper hidden is located on interior of each tab Labware For a description of the BenchCel device or VStack device see the BenchCel User Guide or VStack User Guide The labware racks are available in three models standard rack top load rack and front load rack 22825 00 00 00_RackHandlingGuide_June08 Copyright 2008 Velocity11 An Agilent Technologies Company 4 VELOCITY 1 1 All rights reserved An Agilent Technologies Company Carrying the ra
226. l To set up the outgoing email server 1 Select Tools gt Options 2 Inthe BenchWorks Options dialog box click the Email Setup tab 3 Inthe Mail Server Setup group box enter the name of your SMTP server name outgoing email server 4 If the server requires a user name and password a Select the Server requires authentication check box b Enter the User name and Password that you use to access email on the network Error Notifications Recipient list for error notifications Mail Server Setup SMTP server name M ainServer Server requires authentication abc wigit com User name XXXXXXXX This information only needs to be set up once provided the email account remains active All email sent from BenchWorks is authenticated using this account Related information For information about See The workflow that this procedure Workflow for preparing for a run on belongs to page 32 The next step Setting protocol errorhandling options on page 47 How to setup the outgoing mail Setting up email on page 206 server How to send a bug report using Sending a bug report on page 321 email Chapter 3 Preparing for a run 47 BenchCel User Guide Setting protocol error handling options About this topic This topic describes the errorhandling options available in the Protocol Options dialog box There are four groups of protocol options Protocol Option See Device File Wo
227. lick button Which location atthis device would you like tc to create a Default Location X new process What labware do you wantto place atthis loc Plate type C321 p Procedure Related information Set labware 2 for protocol B r Set labware for Place Plate type protocol B D698 at Prep Standard Shelf Remove Chapter 6 Setting task parameters 119 BenchCel User Guide tocol Tas Pa Task Settings Advanced Settings Which device would you like to use VPrep Standard Shelf v Click button to create a new process Which location at this device would you like tc Default Location x What labware do you wantto place atthis loc Plate type D698 bd To set task parameters for the Place Labware pre protocol task 1 Click on the Place Labware icon and drag it from the pre protocol task list to the protocol editor window until a vertical dashed line appears In the Task Settings page of the Pre Post Protocol Task Parameters toolbar select items from appropriate boxes The device you want to use with this task The location of the labware on the device you are using Labware type you are using in this protocol For information about Working with device files Pre protocol and post protocol processes Creating protocols See Working with device files on page 195 Setting up a pre protocol or post protocol process on page 87 Workflow for
228. liquid type here Copy values to dispense tab See page 246 40 r Z axis Aspirate Parameters E Velocity into wells 1 250 mm s Acceleration into wells 1 2000 mm s Velocity out of wells 1 250 mm s Acceleration out of wells 1 2000 mm3 Opening the liquid library editor on Creating a liquid class on page 248 245 246 Chapter 11 Setting liquid handling definitions BenchCel User Guide Opening the liquid library editor About this topic This topic explains how to open the liquid library editor You open the liquid library editor when you want to U View the properties that are defined for a liquid class Q Edit the properties that are defined for a liquid class Q Add new liquid classes You must be logged on with an administrator or technician user account to open the liquid library editor Procedure To open the liquid library editor from BenchWorks 1 Click the Device Manager tab 2 Inthe Device List select the VPrep device 3 Click Device Diagnostics The VPrep Diagnostics dialog box opens Click the Processes tab Click on one of the Process buttons r Select Process Aspirate Dispense Wash tips Tip attach i z mj ka Chapter 11 Setting liquid handling definitions BenchCel User Guide 247 6 Inthe Configuration group box which in this case is Aspirate click Edit liquid type Aspirate Configuration
229. ly starts adjusting to that temperature 3 Select the PlateLoc to use for the sealing operation from the Select PlateLoc to use list box If you are using more than one PlateLoc make sure that you select the device with the correct seal type temperature and time for the plate Chapter 6 Setting task parameters 125 BenchCel User Guide Related information For information about See Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting User Message task parameters About this topic This topic describes the parameters for the User Message task Read this topic if you are Q An administrator or technician who writes protocols for the BenchCel Q An operator who runs protocols and may need to set the parameters for this task User Message task The administrator or technician who creates a protocol can add User defined Message tasks to provide reminders to the operator The reminders are in the form of messages that appear on the screen at the appropriate time and pause the protocol until acknowledged by the operator User message tasks can for example be used to remind the operator to empty the waste container fill a reservoir or remove plates IMPORTANT Remember to remove all user messages from protocols that you intend to run unattended
230. m and 10 ul are dispensed into it from the mother Procedure Related information Chapter 7 Setting pipette task parameters 147 BenchCel User Guide plate This loop repeats until all 10 daughter plates have been dispensed into To set Change Instance pipette task parameters l Set up a protocol and pipette processes following the example shown above In the Pipette Task Parameters toolbar from the list box select the first daughter plate for the plate icon to change instance on Task Settings Advanced Settings Select the plate to change instance on f Jaughter Plate 1 Spawn Control O Spawn plate only when needed In general you should do this only when running a script that uses the skip command If you are using a JavaScript in the protocol that involves task skipping check the Spawn control check box to force BenchCel to only bring in the next plate when the Change Instance task is reached The script may otherwise override this flow For information about Setting up a plate instance Setting Loop task parameters Configuring a pipette process See Setting up a plate instance on page 88 Setting Loop pipette task parameters on page 153 Q Configuring a pipette process example on page 136 Q Adding and configuring a Pipette Process task on page 140 148 Chapter 7 Setting pipette task parameters BenchCel User Guide Setting Change Tip
231. mber of sides of the wells that you want the tips to touch The volume of liquid to be aspirated and dispensed to each plate well Property task numberOfLoops Property task action task howOften task maxLevel task minLevel task plateName task shelf task speedPercent Chapter 8 Creating a protocol advanced topics 187 BenchCel User Guide Loop task These properties are the same as the properties described for the Loop task Data type Task parameter Comments Integer Number of times to Number of times to loop loop Pump Reagent task These properties are the same as the properties described for the Pump Reagent task Data type Task parameter Comments Integer Q Fill reservoir The Fill reservoir and value 0 Empty reservoir values determine whether the Q Empty reservoir pumps will fill or empty value 1 the reservoir To empty the reservoir you must complete the Autofill Configuration information on the Shelves tab of the VPrep Diagnostics software For more information see the VPrep User Guide Integer Every The number that controls how frequently the liquid is pumped For example if you type 3 the pump will run every third time the task runs Integer Max level The maximum percentage of liquid that you want the reservoir to contain Integer Min level The minimum percentage of liquid that you want the reservoir to contain String Plate name The name of the plate S
232. n page 278 282 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide About profiles Profiles defined Stored settings Related information A profile contains the initialization settings associated with a particular BenchCel The data in a profile is used by BenchWorks to identify each BenchCel on the network A profile can also contain other basic settings that you are unlikely to change once set up Because profiles identify each BenchCel device every BenchCel on the network must have its own profile You can create modify and delete profiles as needed Profiles are stored in the Windows registry The settings stored in a device driver profile include Q Whether the BenchCel is connected using serial or Ethernet U If the BenchCel is connected using Ethernet the Device ID of the BenchCel on the network Q Ifthe BenchCel is connected using serial the COM port that the controlling computer uses for communication For information about See Creating a profile Creating a BenchCel profile on page 283 Managing profiles Managing profiles on page 284 Chapter 12 Using BenchCel Diagnostics 283 BenchCel User Guide Creating a BenchCel profile About this topic Procedure Your BenchCel was delivered to you with the correct profiles already created However at times you may need to create a new profile if for example to set up unique communications settings or use a different teachpoint
233. n you should become familiar with when running a protocol What you should At a minimum you should be familiar with the following know Q Which instruments you need to prepare Q Where you need to position the plates before the run and where they are moved to during the run Q Whether User Message tasks prompt you to perform certain actions after you start the run or whether you need to perform the actions on your own initiative before you start the run Q Whether you need to replace fluids and empty waste during the run Q Whether you need to remove and add plates during the run Q Which liquids you need to prepare where they should be placed and in what kinds of reservoir Related information For information about See Where this topic fit into the Workflow for preparing for a run on workflow page 32 The next step Preparing plates instruments and accessories on page 61 Printing a protocol Printing a protocol on page 60 60 Chapter 3 Preparing for a run BenchCel User Guide Printing a protocol About this topic Printing a protocol Related information You can print a description of a protocol which will help you to analyze the sequence of tasks This topic describes how to print a copy of the protocol It may help you to refer to a printout of the protocol steps as you analyze the protocol To set up the printer 1 Select File gt Print Setup 2 Select the printer you wa
234. nce for the Aspirate pipette task 151 152 Chapter 7 Setting pipette task parameters BenchCel User Guide 5 Field Description Blowout volume The volume of air to blow out when the tips are in the liquid This is typically the same as the pre aspirate volume Note Blowout only occurs in the last quadrant dispensed into for a given Dispense task Post dispense volume The volume of air to blow out when the tips are out of the liquid If the VPrep head has fewer tips than the plate has wells select a quadrant configuration from the Quadrant s diagram to indicate which well quadrant of the plate you want to dispense to To select a quadrant click a representative well Two possible examples are shown below Quadrant s Quadrant s ooo d oooc ooodc ogo ooo oooc oooc o0o o0 0 If you want the tips to touch one or more sides of the plate wells a Select the Enable tip touch check box b Type a value for the tip touch rise height This is the height that the tips should move upwards before touching the side of the wells c Type a value for the Tip touch horiz distance When the value for this parameter is zero the tips will move horizontally one well radius The well radius is defined in the labware database for the type of plate you are using If you want the tips to touch harder increase this value If you want the tips to touch more lightly enter a negative value d Inthe Number of sides t
235. nchCel User Guide Chapter 11 Setting liquid handling definitions 243 BenchCel User Guide Setting liquid handling definitions This chapter is for people with administrator or technician login privileges It describes the liquid library editor which is used to set parameters that affect pipetting speed accuracy and precision and to save the parameters as classes for convenient reuse 244 Chapter 11 Setting liquid handling definitions BenchCel User Guide About the liquid library editor Accessing the liquid library editor Liquid library editor defined Liquid classes defined Liquid library database defined Using a liquid class Calibrating the VPrep The liquid library editor is only available when you have a VPrep or other liquid handling device connected to the BenchCel When you have a liquid handling device connected to the BenchCel you can access the liquid library editor through the diagnostic page of the VPrep or liquid handling device The liquid library editor is a dialog box through which users with technician or administrator privileges can enter values for properties that affect pipetting speed accuracy and precision The values entered into the liquid library editor can be saved as a collection known as a liquid class Using liquid classes saves time when writing protocols because you do not have to enter values for the liquid properties every time you create a protocol The data that represe
236. nd BenchCel Stack 3 black called gt gt j unnamed 2 d The order in which plate 1 and plate 2 are processed is selected by the scheduler program Without the Waitfor and Signal tasks this would also be the case for the bar coding operation However in this protocol the Waitfor task called Label Me Second is included for Plate 2 and this causes the process to wait until it receives an instruction to continue Meanwhile the bar code is applied to Plate 1 Costar 96 pp black Downstack from Incubate for 10 Label me second Fopply label Upstack to called unnamed 2 BenchCel Stack 2 sec BenchCel Stack 4 After the bar code has been applied to Plate 1 the Signal task called Label Me Second releases the wait condition on Plate 2 and the bar code is applied Related information For information about Workflow for creating protocols Adding tasks to protocols Pipette tasks Other tasks Chapter 6 Setting task parameters 133 BenchCel User Guide See Workflow for creating a protocol on page 85 Adding and deleting tasks and pipette tasks on page 92 About setting pipette task parameters on page 96 About setting task parameters on page 95 134 Chapter 6 Setting task parameters BenchCel User Guide Chapter 7 Setting pipette task parameters 135 BenchCel User Guide Setting pipette task parameters This chapter gives the procedures for configuring the param
237. nents used in combination with the BenchCel If you are the person in your organization responsible for training others on the BenchCel and you have a safety question please take the time to ask us Pay attention to any safety labels printed on your BenchCel A safety label shown below consists of a warning symbol A description of the warning and information that will help you to avoid the safety hazard is located in the general hazard warning section of the user guide A Some chemicals used when working with the BenchCel may be hazardous Make sure that you follow the recommendations in the MSDS Material Safety Data Sheet for every chemical that you plan to use The manufacturer of the chemical should provide you with the MSDS Remember to dispose of chemicals in accordance with local state and federal regulations Velocity 1 s products must only be used in the manner in which we intend as described in our user guides Any other use may damage the product or injure you Velocity11 is not responsible for damages caused in whole or part by unauthorized modifications or by procedures that are not explicitly described in our user guides Any modifications or changes to products not expressly approved in Velocity 1 user guides could void the warranty Related information Chapter 1 Introduction 11 BenchCel User Guide For information about See General hazard warnings BenchCel hazard warnings on page 11 Who sh
238. neral name of the device if necessary gt Labware 3 BenchCel Stack 3 BenchCel Stack1 3 BenchCel stack2 Multidrop Ej F PlateLoc Thermal Plate Sealer H 8 BenchCel Robot 3 Click Device diagnostics located at the bottom of the Device List toolbar The device drivers Diagnostics dialog box opens For information about See Diagnostics About diagnostics on page 252 Controls page About the Controls page on page 254 General Settings page About general settings on page 277 Profiles page About profiles on page 282 254 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide About the Controls page Contents of the The Controls page is the first page displayed when you open the Controls page BenchCel Diagnostics dialog box It provides Q An interface for controlling the robot and defining teachpoints Q An interface for creating and loading teachpoint files Q Controls for homing the robot sending it home and adjusting its speed Q Controls for moving the robot incrementally in each of its axes Q Stacker sensor readouts Q An interface for changing labware settings Release all racks Release Stack 1 Release Stack 2 Release Stack 3 Release Stack 4 Retract Clamps Retract Clamps Extend Clamps Extend Clamps i Move to Stacker 1 Pick from Stacker 1 Transfer to Stacker 4 Speed Medium Lidded plates O Sealed plates
239. nerated stating Could not read side bar code on plate at device 318 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Bar code mismatch errors Recovering from bar code errors Related information When the plate that is picked up does not match the bar code that BenchWorks expects in that position an error message is generated stating Scanned side bar code scanned bar code does not agree with expected expected bar code for plate at location Bar code confirmation xi Scanned south side bar code MPOM does not agree with expected SD0001 00 05 for plate at Stack01 Please enter the corect bar code To recover from a bar code error 1 Enter the correct bar code in the text box of the Bar code confirmation dialog box 2 Click OK The run continues For information about See Resolving VCode errors Resolving VCode bar code reader errors on page 319 Setting the error options About the Controls page on page 254 About setting error options on page 43 Chapter 13 Maintenance and troubleshooting 319 BenchCel User Guide Resolving VCode bar code reader errors About VCode errors VCode errors which include bar code errors are generated by VCode devices and displayed in BenchWorks An example VCode error is shown below i failed to apply the label Ill Ignore and continue using the barcode value below mn For more information about
240. new instruments Check with Velocity11 for the most recent information Instrument ABgene SEAL IT 100 Bio Tek ELx405 Washer Genetix aliQuot Genetix QFill2 Dispenser Innovadyne Nanodrop Labcyte Echo 550 Liconic STX StoreX and STR series Matrix Wellmate Molecular Devices instruments using SoftMax Pro software PerkinElmer FlexDrop PerkinElmer ViewLux Description Adhesive plate sealer Microplate washer Low volume liquid dispenser Liquid dispenser Liquid dispenser Compound reformatter Plate incubators Liquid dispenser Plate readers Liquid dispenser Microplate imager Chapter 2 BenchCel overview 19 BenchCel User Guide Instrument Description Thermo Electron Multiskan Ascent Plate reader Thermo Electron Multidrop Microplate dispenser Laboratory setup requirements General bench Ensure that the bench for the BenchCel has the following requirements Q Proximity to utilities Q Enough space to accommodate the complete configuration of your BenchCel which includes the number and size of stacks computer and any instruments Q Enough strength to support the BenchCel and instruments without excessive shaking or movement Q A fixed position no wheels Q Proper height for any users to comfortably operate the BenchCel and instruments BenchCel space The minimum space requirements for your BenchCel depends on its requirements stack and instrument configuration The following table gives dimensions
241. nformation about See The loop task in an example Setting Change Instance pipette task parameters on page 146 Configuring a pipette process Q Configuring a pipette process example on page 136 Q Adding and configuring a Pipette Process task on page 140 Chapter 7 Setting pipette task parameters 155 BenchCel User Guide Setting Mix pipette task parameters About this topic This topic describes how to set the Mix pipette task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Mix task Mix pipette task The Mix pipette task is used with a VPrep to mix reagents by aspirating defined and then dispensing Before you start Before you start you must associate a VPrep shelf with the labware you will be using for the aspiration step of the mixing Procedure To set Mix pipette task parameters 1 Add the Mix pipette task to the pipette process 2 If you have defined a liquid class for the liquid you intend to mix select it from the Liquid class list box at the bottom of the Pipette Task Parameters toolbar 3 Complete the following properties Property Description Mixing volume The volume of liquid to be aspirated and dispensed to each plate well Number of mixing cycles The number of aspirate dispense operations
242. ng Q Device file U Profile Q Teachpoint file Device file dev Q Profile Q Teachpoint file Profile None Teachpoint file you are prompted Teachpoint file xml Teachpoint definitions Chapter 3 Preparing for a run 31 BenchCel User Guide Preparing for a run This chapter describes how to setup the BenchCel and its instruments within BenchWorks to run an existing protocol All of the procedures in this chapter can be performed by someone with operator privileges Chapter 3 Preparing for a run BenchCel User Guide Workflow for preparing for a run About this topic This topic gives the order of recommended tasks before performing a run and tells you where to look for information and procedures for each task Workflow The general workflow for starting the BenchCel and preparing for a run is listed in the following table Step Topic 1 Turning on the BenchCel on page 33 2 Logging into the operating system on page 34 3 Starting BenchWorks on page 34 4 Logging in to BenchWorks on page 36 5 Opening a protocol in BenchWorks on page 40 6 Setting general options on page 41 7 Setting general error handling options on page 44 8 Setting up email error notification on page 45 9 Setting protocol error handling options on page 47 10 Setting pre protocol rules on page 48 11 Setting protocol rules on page 49 12 Setting log options on page 54 13 Understandin
243. ng general settings About this topic Procedure This topic describes how to edit the general settings IMPORTANT Be very careful making changes to the general settings Incorrect settings can cause robot crashes resulting in gripper misalignment If you are unsure consult with a Velocity11 engineer before changing these settings to ensure that you input them correctly Velocity11 keeps records of the settings that were factory set for your machine To change general settings 1 Click the General Settings tab The BenchCel Diagnostics General Settings dialog box appears 2 Configure the Stack Settings Stack Settings Gripper delay time ms Plate presence threshold Rack sensor threshold Additional release height mm Low pressure threshold psi IV Enable tilt margin value o Type the new value into the text box for the parameter you want to change using the following table as a guide Setting Gripper delay time Plate presence threshold Rack sensor threshold Additional release height mm Low pressure threshold psi Comment The length of time the robot pauses to wait for the stacker gripper to open or close Any value at or higher than this means a plate is present Below this value means there is no plate Similar to the Plate presence threshold but higher because the sensor is closer to the metal rack which reflects more light than the plates do This setting lets y
244. nly applies when the robot is carrying a plate When the robot is not carrying a plate it will approach the teachpoint along the x axis at the height of the teachpoint unless the Respect clearance both ways check box is selected This height is the same as the clearance above the teachpoint and is measured in millimeters Specifies the height above the normal grip height that the robot must grip the plate Some platepads prevent the robot from gripping a plate at the normal grip height The cavity depth is measured in millimeters When selected the robot moves to and from the teachpoint at the approach height even if it is not carrying a plate If not selected the robot approaches and retreats from the teachpoint at the height of the teachpoint when it is not carrying a plate Prevents the robot from moving in the space above the teachpoint 3 Click Save and exit to save the teachpoint and close the Teachpoint Dialog box For information about Teachpoints Editing teachpoints Deleting teachpoints Managing teachpoints See About teachpoints on page 269 Editing a teachpoint on page 272 Deleting a teachpoint on page 273 Managing teachpoint files on page 274 Moving between teachpoints Moving between teachpoints on page 275 Selecting teachpoints Selecting two teachpoints on page 276 272 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Editing a te
245. nobs that regulate grippers the stacker grippers Refer to the diagram and table below fora description Stacker head Air pressure regulator _Close gripper flow 00069 Open gripper flow Item Description Air pressure Controls the air pressure to the stacker head regulator Gripper flow Controls the air flow to the grippers to regulate the speed control they grip and retract Connecting the controlling PC and BenchCel About this topic The con following topic describes how to connect the BenchCel and trolling PC to a main power line and to each other with a serial or Ethernet connection Connecting to power To connect the BenchCel and PC to power 1 Plug one end of the power cord into the power entry on the back of the BenchCel and the other end into an appropriate electrical outlet Plug one end of the power cord into the power entry on the back of the operating computer and the other end into an appropriate electrical outlet Connecting by serial cable Connecting by Ethernet cable Chapter 2 BenchCel overview 25 BenchCel User Guide To connect the computer to the BenchCel with a serial cable 1 Plug in a standard 9 pin male serial cable to the RS 232 port on the BenchCel Plug the other end of the cable into one of the computer s serial ports To connect the computer to the BenchCel with an Ethernet cable 1 Connect one end of an Ethernet cable to
246. not be edited here The distance between the bottom of the pipette tips and the bottoms of the MicroWash tray chimneys The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated This value allows the tips to move upwards or downwards during dispensing or aspirating to maintain a certain height below or above the surface of the liquid You will need to determine an appropriate value by trial and error The volume of air to be drawn up before the pipette tips enter the liquid and before mixing begins The volume of air to blow out when the tips are in the liquid once the mixing is complete This is typically the same as the pre aspirate volume If the VPrep head has fewer tips than the plate has wells select a quadrant configuration from the Quadrant s diagram to indicate which well quadrant of the plate you want to dispense to To select a quadrant click a representative well Two possible examples are shown below Quadrant s 2000 1oeo0oe 90005 OOOO Quadrant s 0000 0000 2000 000o Chapter 7 Setting pipette task parameters 161 BenchCel User Guide Type a value for the Inflow pump which is the relative rate of liquid flow into the MicroWash tray manifold This value should be high enough for the washing liquid to just bubble over the tops of the chimneys Type a value for the Outflow pump which is the relative rate of liquid
247. nput file The robot moves the plate to a VCode The bar code that was read is used as a key to look up the bar code fields to print on the other sides of the plate using the bar code data file as the lookup table 5 The VCode prints a bar code on the north side east side and west side of the plate Bar code data files can also be used with incoming plates that have west side bar codes In this case the bar code must be read at the VCode or platepad and not by the robot s bar code reader File structure Related information Chapter 8 Creating a protocol advanced topics BenchCel User Guide IMPORTANT Bar code data files cannot currently be used with incoming bar codes on the north or east sides Bar code data files can still be used if the downstacked plate has no bar code provided that incoming bar code verification is turned off The plate could be moved to the VCode and labelled on its south or west side That label could then be read and used with a bar code data file to specify the labels to be printed on the other sides of the plate Where they are specified The use of bar code data files is specified when configuring task parameters for an Apply Label task Field 1 DB An example of a bar code data file is shown below The columns are separated by tabs IMPORTANT The columns must be in the order north east south and west from left to right Ph barcodedata dat Notepad iof x File Edit Fo
248. ns Action Meaning Prime Priming clears air bubbles from the syringe path tubing Prime the Nanodrop if it has been left idle for more than two hours Dispense Delivers liquid into the plate wells Wash Cleans the insides and outsides of the tips The operation is performed with the tips immersed in the wash station Rinse Cleans the insides of the tips The operation is performed above the wash station in the park position Purge Purging clears air bubbles from the pressure path and syringe path Purging is often performed after priming to make sure that the valves contain no air 290 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide About calibration files About QRM files Related information The actions use the settings in the selected QRM file and any calibration corrections from the selected calibration file To perform an individual operation 1 From the Files group box of the Actions page select a QRM file and calibration file Files QRM TestQRMFile grm Calibration TestCalibration cal bd Click a button to start an action To stop the action click Abort Calibration files contain the results of gravimetric calibration tests and are used to adjust the volume delivery process to make sure that volumes delivered are accurate Calibration files are initially provided by Innovadyne but you can perform your own calibrations the results of which are stored in a file Calibrations are perform
249. nstrument parts may unexpectedly move to their home positions 2 Double click the shortcut to BenchWorks on the Windows desktop Note If the shortcut has been deleted open the folder C Program Files Velocity11 BenchWorks and create a new shortcut from the executable file BenchWorksversion exe The BenchWorks splash screen opens Related information Chapter 3 Preparing for a run 35 BenchCel User Guide BENGHGEL AUTOMATION SOFTWARE PRODUCT VERSION 3 0 0 COPYRIGHT 2005 VELOoOcITY11 BenchWorks opens at the Progress tab and you are logged in with guest privileges BenchWorks Untitled Ele Edt View Tools Help 1 bed 6 O Dla 9 g te EE conte set roe Hp stance Y voon Progress Protocol Edtor Pipette Process Editor Device Manager 12355 02 52 PM 12255 02 57 PM BenchWorks BenchWorks BenchWorks BenchWorks BenchWorks Qvevcociryi Creating ViciValveDevice Creating WeighPadDevice Creating WellMateDevice Creating ZeissReaderDevice Finished preparing device drivers Time w BenchWorks Loading pl BenchWorks BenchWorks BenchWorks lugins Plugin loaded FileReader dll Plugin loaded LabwareSelector dll f Finished loading plugins Time was 460 m gt For information about See The workflow this procedure belongs to Workflow for preparing for a run on page 32 The next step Logging in to BenchWorks on
250. nt to print to and configure the print dialog box as required To print a protocol 1 Navigate to File gt Print Preview 2 View the preview and if it is satisfactory click Print Note If you try to print a protocol before a network printer driver is installed on the BenchCel computer you will receive an error If this happens contact your network administrator for help An example of a printed process that includes a pipette process is shown here BenchyYorks 6 5 03 9 42 30 48 AM 384 ABGene deepwell called Test Plate Pipet process 1 Downstack from Stacker 2 Pipet Process 1 Aspirate 10 0 uL from Test Plate quadrant 1 Dispense 10 0 uL to VPrep 1 Shelf 3 quadrant 1 using 384 Disposable Tip O1ul O5ul Mix 10 00 uL 3 times at VPrep 1 Shelf 5 quadrant 1 For information about See Information you should know Understanding the protocol on about protocols page 59 Chapter 3 Preparing for a run 61 BenchCel User Guide Preparing plates instruments and accessories About this topic Set up order PlateLoc set up process VCode set up process This topic provides a quick reference for use when preparing instruments and accessories for use on the BenchCel Do not use this topic as a substitute for the manuals for the individual instruments This topic is intended for quick reference only The procedures in this topic assume that the instruments are already turned on and that you are familiar with
251. nt to use vacuum filtration your QFill2 must include the vacuum station option developed by Velocity11 For more information about setting up vacuum filtration as a separate task contact the Velocity11 Service Center To set the QFill2 task parameters 1 Add a QFill2 task to a protocol process 2 Inthe Task Settings page of the Protocol Task Parameter toolbar enter the volume of liquid that you want to dispense into each plate well 3 Inthe Available devices box select the QFill2 that you want to use for this task and click Add The name of the device moves to the Devices to use list 4 Ifyou want to use vacuum filtration in the Filtration group box a Select the Use filtration check box 122 Chapter 6 Setting task parameters BenchCel User Guide Related information b Complete the Begin filtration sentence specifying how long before or after filling you want the filtration to start c Type a filtration duration in the Filter for text box If you want to add a post iltration delay type the delay time in the remaining text box The delay is the time that elapses before the robot will pick up the plate allowing the vacuum under the plate to dissipate IMPORTANT If this value is too small the robot may not pick up the plate correctly causing a robot crash For information about See Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks Abo
252. ntains the file to load 4 Click Open Note The file path displayed in the Protocol Options dialog box is updated if you save a protocol to a different folder For information about See Modifying the device file fora Configuring a VPrep shelf as a device VPrep shelf on page 142 Chapter 8 Creating a protocol advanced topics 197 BenchCel User Guide For information about See How the device file relates to other Relationships of BenchWorks BenchWorks components components on page 30 About bar code reading and tracking About this topic This topic gives an overview of the bar code reading and tracking abilities of the BenchCel Read this topic if you are a technician or administrator who writes protocols with bar code reader tasks or Apply Label tasks Bar code readers A customized BenchCel can have bar code readers installed that can read bar codes on one side of a plate the side varies depending on your application needs These may be installed on VPrep shelves or platepads Every time a plate is moved to one of these devices the bar code is read Note To read a bar code at a platepad bar code reader or VCode use the Place Plate task VCode bar code If your BenchCel has a VCode you have the ability to print and apply bar printer and optional code labels reader If the VCode includes an optional reader bar code labels can be read on any side of the plate because the VCode can rotate the pl
253. nts Selecting two teachpoints on page 276 Deleting a teachpoint Chapter 12 Using BenchCel Diagnostics 273 BenchCel User Guide About this topic Occasionally you may need to delete a teachpoint For example if you want to replace one of your modules with another you would first delete the teachpoint for the old module and then add a teachpoint for the new one Procedure To delete a teachpoint 1 Double click the teachpoint marker that represents the teachpoint you want to delete The Teachpoint Details dialog box is displayed Click Delete Your current teachpoint file will automatically be updated when you delete a teachpoint Related information For information about Teachpoints Editing Adding Managing teachpoints Moving between teachpoints Selecting teachpoints See About teachpoints on page 269 Editing a teachpoint on page 272 Adding a teachpoint on page 270 Managing teachpoint files on page 274 Moving between teachpoints on page 275 Selecting two teachpoints on page 276 274 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Managing teachpoint files About this topic Creating a new teachpoint file Loading a teachpoint file Related information Teachpoint files store teachpoint parameters for all of the defined teachpoints using the Teachpoint Details dialog box This includes all of the teachpoints that are visible as tea
254. nts a liquid class is saved to the liquid library database which is maintained in the Windows registry When preparing for a protocol run you select the liquid class that you want to use Then during the run the liquid class values are referenced for pipetting operations The liquid library editor also has an equation editor that can be used to calibrate the VPrep Liquid Library Editor dialog box Related information Chapter 11 Setting liquid handling definitions BenchCel User Guide Ascreenshot of the liquid library editor is shown below MB Liquid Library Editor v5 0 3 Please select a liquid entry from the list below in Use this box to enter a description of the liquid entry and any notes pertaining to order to view and edit its properties 384 disposable tip 0 5ul 1 0ul 384 disposable tip 1 1ul SOul 384 disposable tip 1ul 2ul 384 disposable tip 3ul 6ul 384 disposable tip 6ul 10ul 384 disposable tip Wash 384 fixed tip 0 01ul 0 05ul 384 fixed tip prime 96 disposable tip 11 60ul 96 disposable tip 11ul 50ul 96 disposable tip S1ul 200ul 96 disposable tip wash Fixed Tip 0 005 0 010ul Fixed Tip 0 05ul 1ul Fixed Tip O2ul 10ul Fixed Tip 11ul SOul Fixed Tip Prime Fixed Tip Wash H20 Mix Rename liquid entry Delete liquid entry Saye changes as For information about Opening the liquid library editor Creating a new liquid class its use Enter description of new
255. o Access2 Automated Microplate Loader Automated Centrifuge Loader Element Automation System BioCel 900 System IWorks Device Driver Programming Interface PlatePierce Seal Piercing Station VWorks Device Driver Interface Microplate Seal Piercer VCode Barcode Print and Apply Station Microplate Barcode Labeler Velocity11 Robot 3 Axis Robot VHooks Integration Interface VPrep Pipetting System VWorks Hooks Interface Vertical Pipetting Station VSpin Microplate Centrifuge Microplate Centrifuge VStack Labware Stacker Labware Stacker New contact information Documentation feedback documentation automation agilent com Technical Support 1 800 979 4811 or 1 408 345 8011 service automation agilent com Customer Service 1 866 428 9811 or 1 408 345 8356 orders automation agilent com European Service 44 0 1763853638 euroservice automation agilent com Web www agilent com lifesciences automation Letter to our Customers 2 Agilent Technologies Inc Automation Solutions Division Labware Rack Handling Guide This guide explains how to handle the labware racks Figure Three models of labware racks safely The topics are Standard Top load Front load e About the labware racks e Carrying the racks e Lifting the racks e Loading labware into the racks e Accessing product user documentation e Contacting Velocity11 About the labware racks The BenchCe
256. o be executed before the protocol runs See Setting up a pre protocol or post protocol process on page 87 Protocol Editor Create and edit protocols and processes See the following topics Q Creating a protocol basics on page 83 U Creating a protocol advanced topics on page 163 Log toolbar Page Post Protocol Editor Pipette Process Editor Device Manager Chapter 2 BenchCel overview 29 BenchCel User Guide Use to Create a process to be executed after the protocol run is completed See Setting up a pre protocol or post protocol process on page 87 Create and edit pipette protocols and processes This is only used if a VPrep is one of the configured peripheral devices See Adding and configuring a Pipette Process task on page 140 Manage and configure devices Every device that is added to the platform must be added to the device file See Working with device files on page 195 The Log toolbar can display different subsets of log data or display all log data You can also add a note to a log There are five pages in the Log toolbar for different data The five tabs to access these pages are in the lower left corner of the page All Process Fluid Transfers Errors Notes Page All Process Fluid Transfers Errors Notes Description Displays all logs Displays BenchCel process logs Displays VPrep fluid transfer logs Displays run errors Lets
257. o log in to BenchWorks Your user account is associated with a user role that determines the privileges you have to perform particular functions This topic describes the privileges associated with different user roles The effect of Privileges have the following effects privileges Q Ifyou do not have the privilege to perform a function associated with a particular menu command the text of the command is gray Q If you do not have the privilege to perform the functions accessed from a particular tabbed page the tab is not visible to you Q Insome cases if you do not have the privilege to perform an operation when you attempt the operation you get an error message telling you that your privileges are insufficient User roles and User roles enforce the following privileges privileges User role Has privileges to Guest Run existing protocols Operator Q Perform guest functions see above Q Operate devices in real time using diagnostics software Technician Q Perform operator functions see above Q Create and save protocols Q Edit the labware database and liquid library database Administrator Perform technician functions see above Q Manage devices through the device manager Q Create and delete user accounts Q Run a protocol that contains compiler errors Velocity11 Perform any function Used by Velocity 1 personnel only Related information Chapter 9 Administrator procedures 205 BenchCel User Guide
258. o main types of information are stored in the labware database Q Information about the labware properties L Information about labware classes Labware has physical properties such as width length and number of wells as well as non physical properties such as robot handling speed offsets and plate handling options Without the labware editor you would have to enter values for the many properties associated with a plate each time you set up a protocol With the labware editor all you have to do is select the type of labware to use Labware classes are sets of labware entries grouped so they are easier to manage than many individual labware entries Labware classes are used in combination with the device manager of BenchWorks to restrict which types of labware can be used on which devices during a protocol run This helps to prevent wasted runs and damage to the devices on the platform An example of how damage can be prevented by labware restriction is where a tipbox that is too tall fora device crashes into the device as the robot delivers it For information about See Moving the labware database to Moving or sending a registry file on another computer page 208 Defining labware About the defining labware process on page 218 Opening the labware editor Opening the labware editor on page 219 Editing labware parameters Changing labware parameters on page 238 216 Chapter 10 Defining labwar
259. o network cards addresses 1 In BenchWorks click the Device Manager tab 2 Select a stack from the Device List 3 Click Device Diagnostics 4 In the Discovered BioNet Devices dialog box click the drop down arrow for the Select the Ethernet adapter to use list box IMPORTANT Make sure that you do not change the selected IP address when you do this VStacks should always be connected to the LAN network with the 192 168 0 1 IP address Related information For information about See Sending a bug report Sending a bug report on page 321 Setting up email for error Setting up email on page 206 notification Users and privileges About user accounts and privileges on page 204 212 Chapter 9 Administrator procedures BenchCel User Guide Chapter 10 Defining labware 213 BenchCel User Guide Defining labware This chapter is for people with administrator or technician login privileges It describes the use of the labware editor dialog box and the labware parameters group box which are used to enter information about labware 214 Chapter 10 Defining labware BenchCel User Guide About defining labware in BenchWorks Labware defined Labware entry defined Entering labware parameters Related information Labware is a physical object such as a plate lid or tip box A labware entry is the collection of property values used to describe the properties of a piece of labware This in
260. o or from Teachpoints also represent physical objects This is very important for collision avoidance After you create a teachpoint the robot will automatically navigate around the teachpoint during a run If you tell the robot to move and the teachpoint is in the robot s path the software will ask you before moving the robot through it Teachpoints are shown graphically as square dots called teachpoint markers They are displayed and manipulated in the BenchCel animated display on the Controls page of the BenchCel Diagnostics dialog box For information about See Teachpoints About teachpoints on page 269 Editing a teachpoint on page 272 Deleting a teachpoint on page 273 Managing teachpoint files on page 274 Moving between teachpoints on page 275 mE mE maa ma m Selecting two teachpoints on page 276 270 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Adding a teachpoint About this topic This topic describes how to add a new teachpoint A teachpoint is a set of coordinates that the robot can move its grippers to for the purpose of picking up or dropping off plates Each teachpoint is represented by a teachpoint marker in the BenchCel animated display New teachpoints are automatically saved to your current teachpoint file Add a new teachpoint to define where the robot can pick up and drop off plates on an instrument or platepad You can also add tea
261. o touch text box type a value for number of sides of the wells that you want the tips to touch In the Plate to dispense to list box select the plate or device to dispense to If you do not want to record this dispense in the transfer log clear the Record in transfer log check box You might do this for example if you are running a casual test protocol Related information For information about Configuring VPrep shelves Defining liquid handling parameters Labware editor Configuring a pipette process Chapter 7 Setting pipette task parameters 153 BenchCel User Guide See Configuring a VPrep shelf as a device on page 142 About the liquid library editor on page 244 About the labware editor on page 215 Q Configuring a pipette process example on page 136 Q Adding and configuring a Pipette Process task on page 140 Setting Dry Tips pipette task parameters Special note The Dry Tips task is associated with the VPrep tip dryer This tip dryer hardware is no longer available If you have a tip dryer contact the Velocity 1 Service Center before using the Dry Tips task Setting Loop pipette task parameters About this topic Loop task defined Read this topic if you are This topic describes how to set the Loop task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep and is illustrated with an example in which an Aspirat
262. ocesses that is performed one or more times in a series When you start a run you are prompted to enter the number of cycles that you want to run The value that you enter represents the number of times the protocol executes before the run ends For example a value of four means that the protocol runs four times in the series The pipette process link icon is always the first icon in a pipette process The icon performs a similar function to a plate icon in that it does not represent a task itself but is the first icon in a pipette process The pipette process link icon s function is to link a pipette process task in the protocol editor to a pipette process in the pipette process editor a X Pipette process 1 A pipette task is an operation that is performed on one or more plates by a VPrep or a Multimek It is represented by an icon in the pipette process editor The following diagram shows a pipette task It Mix 10 00 pL 3 times at Plate 1 quadrant 1 40 Chapter 3 Preparing for a run BenchCel User Guide Pipette process defined Related information A pipette process is a sequence of pipette tasks that is performed ona specific plate as defined in the process editor It is a subroutine of a pipette process task The following diagram describes the relationship between a task pipette process task and a pipette process Hes Task Black 6007270 called Plate 1 Pipette process Pipette Process
263. ocol or learning to use the BenchCel run the robot at a slow or medium speed to reduce the risk of damage in the event of a crash Select an option in the Protocol Editor Settings group box if desired It is strongly recommended that you select the Hide icons for non configured device types check box This makes sure you choose the right icons for the devices available to you This is especially important where similar icons are used for different tasks In the BenchCel Settings group Box select Release BenchCel stackers when filled during run to be able to remove the stackers after they have been filled Click OK to close the BenchWorks Options dialog box For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step About setting error options on page 43 About setting error options About this topic Chapter 3 Preparing for a run 43 BenchCel User Guide This topic provides an overview the types of error handling options available when running a protocol with the BenchCel Review error options after you open a protocol and review general options before starting a run You may not need to do this for every run What error handling General error options options include Related information Error reporting Choose from a list of error types that you want reported Error handling Direct the BenchCel on how to handle errors
264. ode control Special error handling Incoming plates have bar codes on south Bar Codes NOT in file he O Incoming plates have bar codes on west si Bar Codes NOT in file r O Incoming plates have bar codes on north s Bar Codes NOT in file Z O Incoming plates have bar codes on east si Bar Codes NOT in file nf 4 Inthe Task Settings page of the Protocol Task Parameters toolbar a b Type a name for the plate in the Plate name text box In the Plate type list box select the type of plate you want to use If you want to add or modify a plate definition click Edit labware settings to open the labware editor If you are using a plug in select it from the Plug in list box If the plug in is not available for selection it may be because the file_name dll file is not in the plug ins folder in the same folder as the BenchWorks executable In the Simultaneous plates text box type the maximum number of plates of this type that the system is allowed to operate on at any given time If the plates entering the system have lids select the Plates have lids check box Note This option is only available if the plate you selected is capable of using a lid as defined in the labware editor If the sample plates in the protocol have seals when they are loaded onto the BenchCel select the Plates enter the system sealed check box If you have only one instance of a plate type and want it to be used repeatedly select t
265. ode modifiers on page 106 Using bar code input files on page 198 Using bar code data files on page 200 Setting general options on page 41 Setting up a plate instance on page 88 About the FileReader plug in on page 164 About log and data files on page 51 106 Chapter 6 Setting task parameters BenchCel User Guide About combining bar code modifiers About this topic This topic describes how to combine bar code modifiers for the Apply Label task Bar code modifiers are text numerical strings that are appended to the bar code Typically they are used to add a readable text numerical string to a bar code which increments for each plate giving each plate a unique label Read this topic if you are Q An administrator or technician who writes protocols that uses a VCode Q An operator who needs to specify parameters for one or more of the Apply Label tasks Before you start Before you modify the bar codes read the VCode User Guide to become familiar with bar codes and label formats Combining barcode You can combine bar code modifiers with text in a single field This modifiers section shows how to do this by using an example The example has five fields and for each field the symbology or font used has been defined as follows in the VCode Format field BenchWorks Symbology Font valid for pre VCode field 2003 VCodes Field 0 Field 1 Swiss Mono 721 Bold Field 1 Field 2 Code
266. og files Attachments e Email Velocity11 322 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Related information 2 Type a description of the error in the text box In your description provide a summary of the error and in the case of a software bug a description of how we can reproduce it 3 Attach the following files which can help us to troubleshoot the problem File Protocol file you were running when the problem occurred Device file Protocol log file Velocity11 registry file aT Click the ellipsis button Find in The location set by your administrator when saving protocols The default location is C BenchWorks Workspace protocols The location set by your administrator when saving device files The location set in log file options The Windows registry HKEY_LOCAL_MACHINE SOFTWAR E Velocity11 Select the Attach log files check box c Browse to one of the files listed above and click Open d Repeat this step to attach each remaining file appears For information about Locating the protocol file Locating the device file Locating the log files Exporting a registry file Click Email Velocity11 and wait until a Message Sent message box See Opening a protocol in BenchWorks on page 40 Working with device files on page 195 Setting log options on page 54 Moving or sending a registry file on page 208 C
267. ol that would otherwise report errors Select from the following options in the Error Handling group box Option Send Email when errors occur Halt on barcode misreads Halt on barcode database lookup errors Launch program if error occurs Halt if available disk space falls below Sound alarm on output When checked The people listed in the Email Setup tab of the BenchWorks Options dialog box will receive an email for every error notification The robot will halt the run if it encounters a bar code misread The robot will halt the run if the bar code found in the database does not match the plate bar code A program that you specify is launched You must specify the program by clicking the ellipsis button and browsing to the program s executable With the appropriate script this function can be used to send a page or an email If you want to pass the text of the error message to the program select the Add error text as command line argument check box The robot completes the currently scheduled step and then stops if the percentage of available hard disk space is less than the percentage specified in the text box Not for use with the BenchCel Related information Chapter 3 Preparing for a run 45 BenchCel User Guide 5 Inthe Scheduler Error Behavior group box select one of the following options Option When selected in the event of an error Process as many platesas A
268. om Pipette process 1 Restack up to 50 called unnamed 1 Stack1 plates per stack over 180 seconds 123 124 Chapter 6 Setting task parameters BenchCel User Guide Related information For information about See Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting Seal task parameters About this topic Seal task defined Procedure This topic describes how to set the Seal task parameters for the BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the Seal task Q An operator who needs to specify parameters for the Seal task The Seal task places a seal on a plate using a PlateLoc If you are sealing more than one type of plate that requires different sealing temperatures we recommend that you use a separate PlateLoc for each temperature This avoids time delays as the PlateLoc heats and cools between different plate types When you open a protocol containing one or more Seal tasks the PlateLoc immediately starts adjusting to the temperatures defined in the task parameters To set Seal task parameters 1 Add the Seal task to a protocol process 2 Inthe Protocol Task Parameters toolbar enter a seal time and seal temperature When you enter a seal temperature the PlateLoc immediate
269. on page 299 Global settings Making global general settings changes on page 281 Chapter 12 Using BenchCel Diagnostics 281 BenchCel User Guide Making global general settings changes About this topic Button descriptions Related information In the bottom right of the General Settings page are three buttons that affect changes to the whole page This topic provides a description of these buttons You should rarely need to use these buttons Use default settings Record settings to file For information about each button consult the following table Button Description Refresh Pressing the refresh button does not change any settings but verifies that your computer is displaying the correct values This is useful when you have lost connection to the machine or you want to make sure your settings are reflecting the settings that the BenchCel is currently using Use default settings This will restore the factory default values This is useful if you have made changes that do not work correctly and you want to get back to normal functionality Record settings to file This creates an XML file with the current general settings values This is used for sending information to a Velocity11 service engineer to help diagnose problems on your machine For information about See Adjusting labware settings Maintenance and troubleshooting on page 299 General settings Changing general settings o
270. on about See Cleaning Cleaning up after a run on page 80 Gripper pressure Adjusting the stacker gripper pressure on page 320 Chapter 13 Maintenance and troubleshooting 301 BenchCel User Guide About error handling About this topic The BenchCel is a complex instrument that requires the interaction of hundreds of parameters configurations and operator setup tasks for a protocol to run successfully Causes of errors Errors have many causes including poor protocol writing incorrect operator setup variation in plates hardware failure and software failure Handling errors It is important to understand that error handling is a normal part of during normal operating the BenchCel and that when errors occur it does not operation necessarily mean that the BenchCel has malfunctioned Related information For information about See Initialization errors Resolving device initialization errors on page 302 Compiling errors Compilation warnings and errors on page 303 Error messages Resolving common problems and error messages on page 304 Labware problems Resolving labware problems on page 310 Sensors U Resetting the orientation sensors for a plate on page 313 Q Checking the stacker sensors on page 314 Teachpoint problems Resolving teachpoint problems on page 315 Bar code reader errors Q Resolving non VCode bar code reader errors on page 317 Q
271. one you want to use for the task from the Select the Multidrop to work with list box If you want to prime the Multidrop enter the volume of liquid to prime with in the Prime volume text box Priming moves liquid through the dispensing system into waste to make sure that there is no air in the lines In the Dispense volume text box enter the volume of liquid that you want to dispense into each well To shake the plate after the dispense enter a value into the Shake time text box To purge the lines after the dispense select the Purge x times when complete check box and enter the number of times to purge Purging moves liquid back into the liquid reservoir or reservoirs If you want to return all liquid the value of x may need to be greater than one To dispense into all wells make sure that the Entire plate option is selected To only dispense into some of the wells a Select the Selected columns option b Click Select none c Inthe number matrix click the numbers corresponding to the columns to dispense into In the following example liquid will be dispensed into columns 2 4 6 and 8 of a 384 well plate Entire plate Specific columns Select All 1 Clear All 2 314 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 115 116 Chapter 6 Setting task parameters BenchCel User Guide Related information For information about Adding tasks to protocols Pipette ta
272. ont view Stacker rack Stacker head PlateLoc VCode Robot Head Plate Gripper PlateLoc veode F i integration integration plate BenchCel integration plate plate Rear view Connection panel Stacker head ote BB 00042 umd 13v oun pia Len Air pressure regulator 00069 Chapter 2 BenchCel overview 17 BenchCel User Guide BenchCel accessories and integration options About this topic If an instrument is not listed here Compatible accessories Accessories provide a function without performing tasks themselves For example a platepad provides a temporary holding place for a plate Individual instruments that are mounted on integration plates on either side of the BenchCel can be used by the BenchCel robot to perform tasks with microplates This topic lists the accessories that are currently available for the BenchCel If there is a product not listed here that you would like to add to your lab automation system please contact your Velocity11 sales representative or email your regional sales contact for customization information Regional sales contact Asia Europe MidAtlantic Midwest Northeast Southeast Southwest West Accessory Stacker racks Laptop computer Platepad Plate hotel Auxiliary bar code reader Email address asiansales velo
273. opics This chapter is intended for people with technician or administrator privileges It provides the background information necessary to set up certain tasks Before reading this chapter you should be familiar with the concepts presented in the following chapters Q Creating a protocol basics on page 83 U Setting task parameters on page 99 U Setting pipette task parameters on page 135 Note This chapter is not a tutorial on writing protocols it provides the basic reference information you will need to write protocols 164 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Setting up the LabwareSelector plug in About this topic Procedure Related information The LabwareSelector plug in allows you to assign a plate type at the time you start your run Use this plug in if your laboratory is using many plate types with the same protocols To set up the LabwareSelector plug in 1 Select the plate icon the first icon in a protocol process 2 Inthe Task Settings page of the Protocol Task Parameters toolbar select LabwareSelector dll from the Plugin list box 3 Select lt From Plugin gt from the Plate type list box Note The software defaults to whatever is selected in the Plate type field For example if you have the LabwareSelector dll selected as a Plugin and Costar 99 pp black selected as the Plate type the software will execute the run with Costar 99 pp bl
274. or approximately 7 minutes the third plate for approximately 9 minutes and so on To avoid these different incubation times you could downstack one plate every 2 minutes The plates are then incubated sequentially and not simultaneously 6 Ifyou want to dynamically assign an upstacking stacker racks click Add dynamically assigned stacker Note This option is only available for upstacking tasks With dynamic assignment you do not have to specifically assign every stacker rack that will receive plates because assignments are made automatically When stacker racks are dynamically assigned the text TBD meaning To Be Determined is added to the stacker task icon Note When using dynamically assigned stackers you need to have a dynamic stacker in the Device Manager for each stack you expect to require You can determine which stackers contain which plates at the end of the run by consulting the run log For information about See Adding and deleting tasks Adding and deleting tasks and pipette tasks on page 92 Creating a protocol process Setting up a plate instance on page 88 Specifying task order Specifying task order across processes on page 132 Restacking Setting Restack task parameters on page 122 Me Chapter 6 Setting task parameters BenchCel User Guide Setting Incubation task parameters About this topic This topic describes how to set the Incubation task parameters Rea
275. orks Creating SpectrafluorDevice 5 9 05 4 39 07 74 PM Info Benchworks Creating StackerDevice 57 9 05 4 39 07 80 PM Info Benchworks Creating StandardPlatePadbevice 5 9 05 4 39 07 80 PM Info Benchworks Creating StorexDevice 5 9 05 4 39 07 85 PM Info Benchworks Creating StorexIoPadDevice 5 9 05 4 39 07 85 PM Info Benchworks Creating TeleshakeDevice 5 9 05 4 39 07 89 PM Info Benchworks Creating TeleshakeHighSpeedpevic 5 9 05 4 39 07 96 PM Info Benchworks Creating TrashDevice 5 9 05 4 39 07 98 PM Info Benchworks Creating UltramarkDevice 5 9 05 4 39 08 07 PM Info Benchworks Creating vCode3kDevice 57 9 05 4 39 08 17 PM Info Benchworks Creating vLidDevice 57 9 05 4 39 08 20 PM Info Benchworks Creating vLidstationDevice 57 9 05 4 39 08 20 PM Info Benchworks Creating vMixDevice 57 9 05 4 39 08 25 PM Info Benchworks Creating vPrepDevice F5 Q NG A 2Q NR 24 PMY Tnfn Ranchitarbe Creating vWeaninaccass neavice During a run you can type notes that are added to this log file The pipettor transfer log file is a tab delimited text file that records VPrep pipetting information on a BenchCel that has a VPrep Note This log is not the same as the log generated by the VPrep Part of a pipettor transfer log file opened in Notepad is shown in the following diagram y3 12 53 56 60 PM vPrep 1 96 channels alsource 1 Master agod4 No bar code No bar code N al 57 22 03 12 54 04 71
276. ort LONG Ignore LONG PickAndPlace BSTR PickFrom BSTR Place To VARIANT_BOOL bLidded LONG nRetractionCode Example Visual C Visual Basic m_BenchCel RetryQ BenchCell Retry Description Method to clear an error and state information Parameters None Returns None Example Visual C Visual Basic m_BenchCel AbortQ BenchCell Abort Description Method to ignore the previously issued error This is not a recommended course of action as the errors are issued for a reason However ignoring some errors such as Plate is rotated can be appropriate if the operator understands the implications Parameters None Returns None Example Visual C Visual Basic m_BenchCel IgnoreQ BenchCell Ignore Description Method to transfer a plate Stacker locations are called Stacker 1 Stacker 2 etc Downstacking can be specified by using a stacker location for PickFrom and upstacking can be specified by using a stacker location for PlaceTo bLidded indicates whether the robot should treat the plate as if it has a lid nRetractionCode should be 3 reserved for future options Visual C 1Result m_BenchCel PickAndPlace Stacker 1 PlateLoc FALSE 2 VARIANT GetTeachpointName s Parameters Argument Argument Type Name BSTR PickFrom BSTR PlaceTo VARIANT_ bLidded BOOL LONG nRetractioCode Returns None Example Chapter 14 BenchCel ActiveX controls Range Valid teac
277. otocol you have to associate a type of labware with the VPrep shelf You do this in the device manager Procedure To configure a VPrep reagent shelf as a device 1 Click the Device Manager tab 2 Select a reagent shelf in the Device List Shelf Reagent reservoir reservoir2 reservoir3 Chapter 7 Setting pipette task parameters 143 BenchCel User Guide 3 Make sure that The Parent device is the VPrep you intend to use The Shelf number is the shelf you intend to use reagent shelves have odd numbers with shelf 1 being at the top left E General Device name reservoirl Device type Shelf Reagent Approach height mm 12 7 Allowed prohibited labware E Shelf Reagent properties Shelf number 1 Parent device VPrep2 Vil MicroWash 384 B If these are not correct select another reagent shelf in the Device List 4 Optionally change the Device name to one that describes the type of liquid being used by typing over the existing name 5 Select the type of labware that will contain the reagent from the Labware list box 11 MicroWash 384 New plate Renamed new test entry Polyfiltronics 384 filter plate Test plate Tip Box Lid 11 Autofiling Reservoir 384 11 Autofiling Reservoir 96 11 Manual Reservoir 384 411 Microwash 384 6 Click the blank column to the right of Allowed prohibited labware 7 Click the ellipsis button The Labware Classes dialog
278. ou compensate for the stacker grippers if they grip the plates too low The setting is adjusted in millimeters Sets the threshold for the low pressure warning This value is usually 50 psi Chapter 12 Using BenchCel Diagnostics 279 BenchCel User Guide Setting Comment Enable tilt margin value When checked the sensors will check for plate tilt using the value entered 0 5 mm as the amount of allowable tilt If tilt is detected the BenchCel will automatically restack the plates Configure the X Margin Settings x Margin Settings Empty mm 109 973 Full mm 149 981 Stay within unit Type the new value into the text box for the parameter you want to change using the following table as a guide If Then Empty The distance the robot needs to travel from its farthest horizontal points to safely move its arms when not holding a plate Full The distance the robot needs to travel from its farthest horizontal points to safely move its arms when holding a plate Stay within unit This button restores the default values to the previous settings Check the Homing Offsets Homing Offsets Theta X mm Z mm Gripper mm Home unit after releasing stacks IMPORTANT These offsets are set at Velocity11 and should not need to be changed They are used to calibrate all axes relative to their true home position Type the new value into the text box for the parameter you
279. ou create labware classes and assign page defined labware to a labware class Labware Editor 12 0 6 Uses Filter Platepad Uses Standard Platepad Uses Vacuum Platepad 24 Matrix Glass Tube Rack 384 BD Biocote Plate Black 354663 384 Costar Square Wells Clear w Lid 384 Falcon TC Plate Black 353962 384 Greiner Low Volume Black 788076 384 Greiner PP Bottom 781280 384 Greiner PP Bottom w Greiner Lid 7 384 Matrical Low Volume Black MCR101 384 Matrix PP ScreenMates 384 Matrix PP ScreenMates w Greiner 384 Matrix PS ScreenMates 4331 96 Costar Flat Bottom w Lid 3628 96 Costar U Shaped wyLid 96 Matrix Tube Rack w abgene septur Corning 384 Black TC 3712 384 Round Bottom Black 3676 Falcon 96 Microtest w Lid 353072 Falcon 96 Microtest w Lid 353077 Greiner 1536 Hi Base White 782075 Greiner 1536 HiBase White w Greiner L Greiner 384 Black TC 761091 Greiner 384 Low Vol Black PS 784076 Greiner 384 Low Vol Black PS w Greiner Greiner 384 Low Vol White PS 784075 Greiner 384 Low Vol White PS w Greine Greiner Lid 656191 LIL 384 Half Height White Low volume Nunc 1536 Short White 253607 218 Chapter 10 Defining labware BenchCel User Guide Related information For information about See Moving the labware database to Moving or sending a registry file on another computer page 208 Defining labware About the defining labware process on page 218 Opening the labware editor Opening the labware editor on page 219
280. ould read this guide Who should read this guide on page 2 Reporting a problem to Velocityl11 Reporting BenchCel problems on page 9 Using the guide About Velocity11 user guides on page 3 BenchCel hazard warnings About this topic Intended use Moving parts injury hazard This topic gives more information for some hazard warnings found in this guide Be aware of these hazards at all times when using the BenchCel INJURY HAZARD The BenchCel must be used for its intended purpose as specified in this user guide Failure to do so will compromise the BenchCel safety features INJURY HAZARD Never attempt to touch any of the moving parts or attempt to remove plates while the BenchCel is in operation Possible pinching piercing or bruising can occur INJURY HAZARD Do not launch software while touching the machine Automatic motion begins if the machine is turned on and connected to the PC INJURY HAZARD Keep your fingers hair clothing and jewelry away from the machine while it is in motion It is possible to be hit by the robot head when it is moving If this happens the robot head is designed to immediately stop minimizing injury and the likely outcome is minor bruising However the robot is particularly powerful in the vertical z axis and could pierce a hand with one of its grippers Not all circumstances can be foreseen and more serious injury is possible It is the responsibility of
281. out the Controls page on page 254 Changing the robot speed About this topic It is useful to change the robot speed when creating new protocols or teachpoints For example change the robot speed to Slow when you are experimenting with new teachpoints and protocols so that you can monitor the robot s accuracy more closely After you have observed the robot move to a new teachpoint or complete a protocol without errors change the robot speed to Medium Change the robot speed to High when the robot is able to perform a protocol without errors and you have eliminated inaccuracies in new teachpoints and protocols If the robot starts to have errors set the robot speed lower until you can diagnose the problem Note It is safe to move at high speed with default Velocity11 teachpoints and protocols because they have been extensively tested for accuracy 262 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Procedure Related information To change the robot speed l Open BenchCel Diagnostics dialog box to access the Controls page Click the down arrow of the Speed list box in the Options group box Options Speed Medium v oO Lidded plates Select a speed from the drop down menu Slow Medium Fast Click OK at the bottom of the Controls page for the changes to take effect For information about See Opening diagnostics Opening BenchCel Diagnostics on page 253 Chapte
282. parameters parameters on page 146 Change tips pipette task Setting Change Tips pipette task parameters on parameters page 148 Dispense pipette task Setting Dispense pipette task parameters on parameters page 150 For information about Dry tips pipette task parameters Loop pipette task parameters Mix pipette task parameters Pump reagent pipette task parameters Wash tips pipette task parameters Chapter 5 Creating a protocol basics 97 BenchCel User Guide See Setting Dry Tips pipette task parameters on page 153 Setting Loop pipette task parameters on page 153 Setting Mix pipette task parameters on page 155 Setting Pump Reagent pipette task parameters on page 157 Setting Wash Tips pipette task parameters on page 159 Simulating a run About this topic Simulating the run This topic provides suggestions on how to check for errors in a protocol after it is compiled After making sure that there are no compiler errors in the protocol you can check for other types of problems by running the protocol through the simulator The simulator allows you to confirm that steps are done and sequenced correctly and to find problems such as Q Deadlocks U Periods of inefficiency such as when the robot is not being used Q Plates spending different times at critical steps when they should be run under identical conditions Q A number of simultaneous plates
283. perating speed of the robot If your assays require greater precision in plate incubation times than this method supports you can adjust the rate at which plates enter the system Procedure To set incubation parameters 1 Add the Incubate task to a protocol process window 2 Inthe Task Settings page of the Protocol Task Parameter toolbar type the length of time for which you want the plate to incubate on the platepad 3 Chapter 6 Setting task parameters BenchCel User Guide If you need to control the rate at which plates are delivered to a particular instrument incubate the plates on a plate hotel or similar short term storage device and select Start timer when previous plate finishes incubating A situation can arise in which plates move through a protocol too fast for one of the steps An example is a pipetting step in which a reagent that starts a timed reaction is added to the plate The result is that plates queue up at the pipettor Without selecting the Start timer when previous plate finishes incubating check box plates are delivered to the plate hotel as fast as the robot can deliver them are incubated for the time specified in the Length of incubation text box and then leave as fast as the robot can remove them The robot may remove the plates as frequently as every 10 seconds With the Start timer when previous plate finishes incubating check box selected the time separation between each plate being picked up
284. pic Above each stacker teachpoint marker in the BenchCel animated display there is a button for extending or releasing the clamps Release Stack 2 Retract Clamps Extend or release clamps button Stacker teachpoint It is important to understand the difference between extending and releasing stacker clamps and loading and releasing a stack Unlike the load and release stack commands the extend and retract stacker clamp commands do not use the robot The clamp actuators are the only mechanisms commanded to move Q Extending clamps moves them away from the walls of the stacker head Q Retracting clamps draws them in against the walls of the stacker head 268 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide When to use Extending clamps Retracting clamps Related information Extend or retract clamps when you need to diagnose a problem you have performing a run For example if you want to load a stack but the clamps are retracted use the Extend Clamps command to extend the clamps If there is a single plate in the stacker grippers which you are using to diagnose the BenchCel with it may be faster to Retract Clamps and catch the plate with your hand than to wait for the robot to move the plate after you issue the Release Racks command Do not use the extend and retract clamps controls to load or release a stack To load and release stacks use the Load Racks and Release Racks commands
285. protocol workflow 32 68 S safety interlock circuit 23 labels 10 training 10 saving protocols 94 scheduler behavior options 45 screen message options 78 Seal task defined 124 setting parameters 124 sealed stacking thickness property 227 sealed thickness property 227 SEAL IT Adhesive Sealer see ABgene SEAL IT 100 send the robot home 255 257 sensor intensity property 231 serial connecting 25 interface on connection panel 22 shaking 287 shelf VPrep configuring 142 shutting down 81 Signal task example 132 setting parameters 127 simulating a protocol 97 simultaneous plates 89 91 SoftMax Pro supported instrument 18 software versions 5 space requirements 19 speed 255 stacker adjusting clamp pressure 320 adjusting gripper pressure of 320 configurations 15 controls 264 defining properties for labware 230 extending and retracting clamps 267 head pressure control 24 plate present indicator 264 settings 278 stacker gripper control 24 offset property 230 BenchCel User Guide stacker sensors 255 checking 314 list of 374 Stacker task defined 709 setting parameters 110 stacking thickness property 227 238 starting a run from a command line 73 BenchWorks 34 runs 70 the BenchCel 33 stopping a run 74 Storex supported instrument 78 system requirements 27 T task object JavaScript 174 properties 178 task parameter setting 95 Task Parameters toolbar see
286. ps enter the liquid Post aspirate volume The volume of air to be drawn up after the liquid is drawn up If the VPrep head has fewer tips than the plate has wells select a quadrant configuration from the Quadrant s diagram to indicate which well quadrant of the plate you want to aspirate from To select a quadrant click a representative well Two possible examples are shown below Quadrant s Quadrant s ooo ooc ooc ooo gt 0000 o IOO iOO 0o00 In the Plate to Aspirate from list box select the type of labware or device from which to aspirate If you do not want to record this dispense in the transfer log clear the Record in transfer log check box You might do this for example if you are running a casual test protocol For information about See Configuring VPrep shelves Configuring a VPrep shelf as a device on page 142 Defining liquid handling About the liquid library editor on page 244 parameters Labware editor About the labware editor on page 215 146 Chapter 7 Setting pipette task parameters BenchCel User Guide For information about See Configuring a pipette Q Configuring a pipette process example process on page 136 Q Adding and configuring a Pipette Process task on page 140 Setting Change Instance pipette task parameters About this topic Change Instance pipette task defined This topic describes
287. question for help amp f X Del ara Eo BIU x E a A a ta y anaal ahga v Reply with Changes End Review q Nhe X Fe 2 12 04 6 32 21 28 PM E a 412 04 6 32 21 26 PM I Scheduler 7326MB 41 89 of disk space remains on volume c 2 12 04 6 32 21 63 PM Scheduler Checking that all stackers are properly loaded 2 12 04 6 32 28 95 PM Administrator Starting protocol 2 12 04 6 32 26 99 PM Stacker Source 1 Downstack Costar 384 polypro round bottom 2 12 04 6 32 31 70 PM Stacker1 Source 1 Downstack complete 2 12 04 6 32 31 75 PM Prep Starting pipette process 1 2 12 04 6 32 31 75 PM Wash Shelf Wash Shelf Aspirate 40uL from 1 quadrant s 2 12 04 6 32 31 78 PM Shelf 2 Source 1 Transfer 2 12 04 6 32 31 81 PM Robot Source 1 Fetching plate from Stackerl and placing at Shelf 2 2 12 04 6 32 36 83 PM Prep Aspirate 40 00pL from row 1 column 1 Shelf 5 2 12 04 6 32 38 61 PM Wash Shelf Wash Shelf Completed Aspirate 40pL from 1 quadrant s 2 12 04 6 32 38 63 PM Shelf 2 Source 1 Dispense 10pL into 4 quadrant s 2 12 04 6 32 43 36 PM VPrep Dispense 10 00pL to row 1 column 1 Shelf 2 2 12 04 6 32 45 83 PM Prep Dispense 10 00pL to row 1 column 2 Shelf 2 2 12 04 6 32 46 36 PM VPrep Dispense 10 00uL to row 2 column 1 Shelf 2 2 12 04 6 32 50 88 PM VPrep Dispense 10 00uL to row 2 column 2 Shelf 2 2 12 04 6 32 52 88 PM Shelf 2 Source 1 Completed Dispense 10pL into 4 quadrant
288. r The volume of air to blow out when the tips are in the liquid This is typically the same as the pre aspirate volume The name of the liquid class Change Tips task These properties are the same as the properties described for the Change Tips task Property Data type Task parameter task plateName String Plate name task quadrants An array of Quadrants diagram pairs of integers task action Integer Q Press On New Tips integer 1 Q Tips off integer 2 Dispense task These properties are the same as the properties described for the Dispense task Property Data type Task parameters task plateName String Plate name task acceleration Float Dispense acceleration task blowoutVolume Float Blowout volume task liquidClass String Liquid class list box task postDispenseVolume Float Post dispense volume The volume of air to blow out when the tips are out of the liquid Property Data type task quadrants An array of pairs of integers task retract Float task tipOffset Float task tipTouch Boolean task tipTouchHorizontalDi Float stance Chapter 8 Creating a protocol advanced topics 183 Task parameters Quadrants diagram Retract distance Distance from well bottom Enable tip touching Tip touch horizontal distance BenchCel User Guide Comments A quadrant is an evenly spaced array of locations that is addressable by the tips ona pipette head A 96 well head can dispense into a 96 well plate
289. r 12 Using BenchCel Diagnostics BenchCel User Guide Using Move To Position commands About this topic Procedure Related information The BenchCel Move to Position commands let you quickly move the robot to a set of x z and theta coordinates that you can specify with sliders Each slider control represents a point on a spectrum that spans the full range of movement for a robot axis The Move to Position commands can be accessed from the Move to button displayed in the upper left corner of the BenchCel animated display After you have become familiar with jogging the robot and you have a sense for how the robot moves use the Move to Position commands to move the robot much more quickly than you can with jogging commands DAMAGE HAZARD Make sure the robot is clear of any obstacles that you have not defined BenchWorks will display a dialog box warning you of a possible collision if the requested movement overlaps a known teachpoint The Move to Position commands present a higher damage risk to the robot because you command it to move in large increments To move the robot with the Move to Position command 1 Make sure that you have selected a Plate Type to use from the Labware list box 2 Inthe BenchCel animated display click Move to The BenchCel Move to Position dialog box appears x Coordinate x 0 01501 eae eee 183 z 0 019c 9 Aca Theta 0 09001 pic i ven Move robot Exit 3 Ad
290. r 384 11 MicroWash 384 11 MicroWash 96 W11 Tip Box 384d30 V11 Tip Box 384d40 For information about See Opening the labware editor Opening the labware editor on page 219 Defining general properties Defining general properties on page 225 of your new labware entry Defining the Plate Properties Defining plate properties on page 226 Defining BenchCel Defining BenchCel properties on page 229 properties 222 Chapter 10 Defining labware BenchCel User Guide Deleting a labware entry About this topic If there is a labware entry that you no longer need you can delete it This topic describes how to delete a labware entry You must be logged on with an administrator or technician user account to perform this procedure Before you start Make sure that the entry you are deleting is not referenced in protocols IMPORTANT If you delete a labware entry that is already referenced in protocols the link between the protocol and the labware data will be broken and the protocol will not run Procedure To delete a labware entry 1 Open the labware editor 2 Inthe labware selection box on the left of the window select the labware entry to be deleted Click Delete labware entry In the V11Labware dialog box click Yes to delete the entry Related information For information about See Opening the labware editor Opening the labware editor on page 219 Defining labware Q
291. r is hours minutes seconds For information about See Setting up counterweights Setting up a VSpin counterweight plate on page 63 Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 132 Chapter 6 Setting task parameters BenchCel User Guide Specifying task order across processes About this topic If you are running more than one process in a protocol you may want to specify that a particular task in one process is performed before a particular task in another process You do this when creating a protocol by using the combination of Waitfor and Signal tasks This topic describes how to use this task by providing an example Read this topic if you are Q An administrator or technician who writes protocols for the BenchCel Q An operator who runs BenchCel protocols Example In this example the administrator or technician creating the protocol wants to make sure that a bar code is applied to plate 1 before plate 2 The operator creates the protocol shown in the following diagram Waitfor task Signal task Costar 96 pp q black called Vi 1 VW unnamed 4 Costar 96 pp gt Costar 96 pp black Downstack from Incubate for 10 Foply label Signal Label me Upstack to called unnamed 4 BenchCel Stack 1 e seco
292. rameters for it Most tasks require you to set parameters The parameters specify the details of the task As you set the parameters the text underneath the task icons change to reflect the new parameters For information about the specific types of tasks see the following topics For information about Pipette task parameters AliQuot task parameters Apply Label task parameters Delid Relid task parameters Downstack and Upstack task parameters Incubate task parameters Multidrop task parameters Nanodrop task parameters Pierce task parameters Place Plate task parameters QFill2 task parameters Restack task parameters Seal task parameters User Message task parameters See About setting pipette task parameters on page 96 Setting AliQuot task parameters on page 100 About setting Apply Label task parameters on page 101 Setting Delid Relid task parameters on page 108 Setting Downstack and Upstack task parameters on page 109 Setting Incubation task parameters on page 112 Setting Multidrop task parameters on page 114 Setting Nanodrop task parameters on page 116 Setting Pierce task parameters on page 117 Setting Place Plate task parameters on page 120 Setting QFill2 task parameters on page 121 Setting Restack task parameters on page 122 Setting Seal task parameters on page 124 Setting User Message task parameters
293. re e PDF files on the software CD e Printed books You can also search the online help or download the latest version of any PDF file from the Velocity11 website at http www velocity11 com support knowledge_base Contacting Velocity11 e Technical Support 1 800 979 4811 or 1 650 846 6611 e Customer Service 1 866 428 9811 or 1 650 846 6601 e Email info velocityl1 com e Web http www velocityl1 com Velocity11 an Agilent Technologies Company 3565 Haven Avenue Menlo Park CA 94025 USA 1 650 846 6600 esa The Speed of Discovery BenchCel User Guide January 2006 BenchWorks version 24 x 16967 00 00 00_ BenchCelUG_Jan06 Copyright 2006 Velocity11 The information provided in this guide is intended to be accurate and reliable However Velocity11 does not assume responsibility for its use or for any infringements upon the rights of third parties that may result from its use The transfer of this guide in any manner or form to a representative of another company is strictly forbidden BenchCel PlateLoc VCode Velocity11 VPrep and VStack are registered trademarks of Velocity11 BenchWorks PlatePierce VersaScan and VSpin are trademarks of Velocity11 Microsoft and Windows are registered trademarks of the Microsoft Corporation in the United States and other countries All other trademarks are the sole property of their respective owners Velocity11 3565 Haven Avenue Menlo Park CA 94025 USA Phone
294. rea Move the 384 plate offset Click Move to 384 plate offset The stage moves to the end of its travel and then shifts to the next stage for dispensing on a 384 well plate Move to a column Enter the column number you want to move to in the Column number field and click Move to column Change the offset Enter a value in the Offset field and the desired column in the Column number field and click Move to column This works in conjunction with the Move to Column command Offset defines how far away from the center of the well to dispense 295 296 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide Querying the plate type Priming and purging Executing dispense commands To query the plate type l 2 Open the Command page To determine the plate type 96 or 384 well that the WellMate is set for click Query plate type The plate type is displayed next to Current plate type text Priming moves the fluid from the reservoir to the tips and purging moves the fluid from the tips to back to the reservoir To prime or purge l 2 Open the Command page Click and hold the mouse on the Prime or Purge button Fluid is pumped at the Pump Speed set in the Profile page until you release the mouse Use the Dispense page to set the prime dispense and purge volumes and to initiate the dispense To execute dispense commands l 2 Open the WellMate Diagnostics dialog box and click the D
295. reference to more information Property Data type Task parameter Comments task plateName String Plate name The name of the plate Read only task acceleration Float Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor task liquidClass String Liquid class list box The name of the liquid class task postAspirateVolume Float Post aspirate volume The volume of air to be drawn up after the liquid is drawn up task preAspirateVolume Float Pre aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid task quadrants An array of Quadrant selection A quadrant is an evenly pairs of diagram spaced array of locations that integers is addressable by the tips ona pipette head A 96 well head can dispense into a 96 well plate four quadrants of a 384 well plate and 16 quadrants of a 1536 well plate A 384 well head can dispense into a 384 well plate or the four quadrants of a 1536 well plate Property task retract task tipOffset Distance from well bottom task velocity task volume Data type Float Float Float Float Chapter 8 Creating a protocol advanced topics 181 Task parameter Tip retract distance Distance from well bottom Aspirate velocity Aspirate volume BenchCel User Guide Comments The distance that th
296. resent at the stacker sensor level regardless of the presence of a stack For information about See Teachpoints About teachpoints on page 269 The animated display About the Controls page on page 254 Chapter 12 Using BenchCel Diagnostics 265 BenchCel User Guide Loading and releasing stacks About this topic This topic describes when and how to load and release BenchCel stacks When to use Stacker rack loading and unloading normally take place automatically in the course of performing a run After you place the stacker racks onto the stacker heads and start a run the stacker racks are automatically secured After the run has completed the software asks if you want to release the stacks When diagnosing problems you may want to manually load and release stacker racks at your convenience Do this from the BenchCel animated display Loading and The process of loading stacker racks is the securing of the stacker onto a releasing defined stack head so that the BenchCel robot can access the stack of plates When you start a run the BenchCel automatically secures the stack and prepares the plates This process involves both the stacker clamps and the robot The BenchCel stacker will not operate until the stacker rack is loaded The process of releasing involves the BenchCel repositioning the stack of plates so that the stack is free to move and the plates are secured within the stack The stack becomes free to move
297. reservoir Offset Offset defines how far away from the center of the well to dispense To dispense into all wells make sure that the Dispense to entire plate option is selected To only dispense into some of the wells a Select the Dispense to selected columns option b Click Clear All c Inthe number matrix click the numbers corresponding to the columns to which you want to dispense In the following example liquid will be dispensed into columns 2 4 6 and 8 of a 384 well plate 129 130 Chapter 6 Setting task parameters BenchCel User Guide Related information Dispense to selected columns Check all Clear all EEEE 22j 23 24 For information about See Workflow for creating protocols Workflow for creating a protocol on page 85 Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Pipette tasks About setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting VSpin with Access2 task parameters About this topic VSpin with Access2 task defined Setting VSpin with Access2 task parameters This topic describes how to set the Access2 task parameters Read this topic if you are Q An administrator or technician who writes protocols Q An operator who may need to change the Access2 task parameters T
298. ring a run For ease of use you can hide types of messages that are not important to you The messages displayed during a run are controlled by Q Selecting Screen Setting options in the Log Options dialog box before a run Q Clicking tabs at the bottom of the display during a run 78 Chapter 4 Performing a run BenchCel User Guide Viewing the Log toolbar 1 Log To view the Log toolbar If the toolbar is not showing from the View menu select Toolbars gt The toolbar opens at the bottom of the screen 2 Refer to the table below to view different kinds of log data Log toolbar options BenchWorks log tab All Process Pipettor Fluid Transfers Errors Notes Searching the Log toolbar The following options are available for displaying screen messages Displays All event and error messages This is the data that is recorded in the log txt file Event messages including fluid transfer messages Event messages reported by VPrep This is the same data that is recorded in the pipettor transfer log file but is presented in sentence rather than tab delimited format Event messages can be disabled by deselecting the Record in transfer log option in the aspirate and dispense pipette task parameters Error messages that appear as alert boxes on the screen This data is not saved in a separate log but is included in the log txt file Notes that you add You can search for specific
299. ring for a run BenchCel User Guide Plate orientation Always place plates so that the Al well is in the far left corner as viewed with stacker by someone standing in front of the BenchCel Note With some VPrep integrations this orientation may be shifted such that Al will be located on the lower right corner 7 A1 well Related information For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 Extending or retracting clamps Extending and retracting stacker clamps on page 267 Chapter 4 Performing a run 67 BenchCel User Guide Performing a run A run is a single protocol that is performed one or more times in a series This chapter describes how to run an existing protocol on the BenchCel All of the procedures in this chapter can be performed by someone with operator privileges 68 Chapter 4 Performing a run BenchCel User Guide About performing a run About this topic Ways to set up a run Tasks associated with a run This topic tells you where to find the information about starting a run and performing tasks associated with running a protocol There are two ways to start a run Method Set up a single protocol run and manually start it by clicking the Start button in the BenchWorks Set up a single protocol in advance and manually start it from a command lin
300. ript prints the word hello to the log toolbar and log txt file print hello Example 2 This one line script opens an external file that could contain another script The new script is run immediately open C scripts scriptl txt Example 3 This script prints a list of the properties for the task to the log toolbar It is an essential part of determining the names of properties when creating JavaScripts for x in task print task x task x Velocity 1 offers a custom script writing service for BenchWorks and other applications Please contact us for more information For information about See The properties for each available The JavaScript task object and task in BenchWorks version 18 properties on page 178 The workflow that this procedure Workflow for creating a protocol on belongs to page 85 178 Chapter 8 Creating a protocol advanced topics BenchCel User Guide The JavaScript task object and properties About this topic Task properties The BenchWorks JavaScript interpreter includes a task object that is defined by Velocity11 This topic lists the properties for the Velocity11 JavaScript task object One of the properties is for the Apply Label task The other properties are all for pipette tasks Properties available to all tasks The following properties can be used for any task Property Data type Description task name String Name of the task for
301. rked instrument s software This is because BenchWorks and instrument software run on the same controlling computer and access the same databases If you make a change to the labware or liquids database you can use a two step process to propagate the change to another computer 1 Export the Windows registry key containing the data to a file 2 Import the file to the other computer s registry IMPORTANT Making a mistake when editing the registry may cause critical failures with your operating system To export a registry key 1 From the Windows Start menu select Run 2 Inthe Open text box type regedit 3 Click OK The Windows registry editor opens 4 Expand folders to display the following folder HKEY_LOCAL_MACHINE SOFTWARE Welocity11 Shared 5 Expand the Shared folder and select either Labware Liquid Library 6 From the Registry or File menu select Export The Export Registry File browser box opens Navigate to the folder in which you want to save the file 8 Inthe File name text box type a name of your choice for the file Importing a registry key Emailing a registry file Related information Chapter 9 Administrator procedures 209 BenchCel User Guide 9 Ifyou are moving the file to a computer with a different Windows operating system select the appropriate recipient operating system from the Save as type list box if one is available 10 Click Save 11 Select Registry gt Exit or File gt E
302. rking with device files on page 195 Description Notes Compiling and saving protocols on page 93 Rules Using JavaScript in BenchWorks on page 171 Setting pre protocol rules on page 48 Setting protocol rules on page 49 Error Handling This topic Setting protocol To set protocol error handling options error handling 1 Select Tools gt Protocol Options options 3 pt 2 Inthe Error Handling group box select any or all of the following options Option Description Attempt to put plates away if If a deadlock occurs any lids are replaced and the plates are moved to the positions they would be in at the end of a successful protocol run deadlock occurs Abort run if stacker runs out of If the stacker runs out of plates before plates the run is finished the run is aborted Aborting a run permanently terminates the run Related information For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Setting pre protocol rules on page 48 i Chapter 3 Preparing for a run BenchCel User Guide Setting pre protocol rules About this topic Pre protocol rules include Reset script context Automatically load stacker racks Related information This topic describes the pre protocol rules available in the Protocol Options dialog box There are two rules in the Pre Protocol Rules group box U Reset script context
303. rmat View Help eastoool southoool westoool eastood2 southood2 westood2 east0003 southooo3s west0003 eastooo4 southooo4 westooo4 northooos eastooos southooos westooos northooo6 eastooo6 southooo6 westoood6 eastooo 7 southooo 7 westooo eastooos southooos westooos eastooo9 southooos westooos eastoolo southoolo westoolo eastooll southoo11 westooll northoo12 eastool2 southool2 westool2 northoo1l3 eastool3 southool3 westool3 eastoold southool4 westool4 eastools southoo1ls westooLls eastoole southool6 westool6 eastool southool westool northoo1s eastools southools westools For information about See Selecting bar code data files Setting general options on page 41 Bar code input files Using bar code input files on page 198 Applying bar codes Setting Apply Label task parameters on page 102 201 202 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Chapter 9 Administrator procedures 203 BenchCel User Guide Administrator procedures This chapter is for people with administrator login privileges It describes assorted administrative tasks that include how to Q Administer user accounts Q Import and export BenchWorks data from the registry of your computer Q Set up email so that you can send bug reports from within BenchWorks 204 Chapter 9 Administrator procedures BenchCel User Guide About user accounts and privileges About this topic You must have a user account t
304. rmation about See Defining labware U Labware editor overview on page 216 Q About the defining labware process on page 218 Editing labware parameters Changing labware parameters on page 238 Chapter 10 Defining labware 271 BenchCel User Guide Adding a labware entry About this topic Procedure Related information The first step in defining a new piece of labware is to add a labware entry for it You must be logged on with an administrator or technician user account to perform this procedure To add a labware entry 1 Open the labware editor 2 Under the labware selection box on the left of the window click New labware entry New labware entry 3 Inthe New Labware Entry dialog box enter a name for the plate and click OK The entry appears in the labware selection box 384 ABGene deepwell 1384 ABGene short well plate 384 Matrix clear polystyrene 384 REMP micro tube rack 384 REMP square well 96 ABGene deepwell block 96 ABGene tube rack TRIPOS 96 Matrix clear polystyrene 96 Matrix tube rack 196 Micronics tube rack ALSB Costar 384 black flatbottom Costar 384 polypro round bottom Costar 96 well plate Falcon 384 clear bottom Falcon 384 clear polystyrene Matrix 96 well Block Polypro MJ Research 384 well plate Polyfiltronics 384 filter plate Test plate Tip Box Lid W11 Autofilling Reservoir 384 11 Autofilling Reservoir 96 v11 Manual Reservoi
305. rocedure This topic describes how to set the Waitfor and Signal task parameters for the BenchCel Read this topic if you are Q An administrator or technician who writes protocols for the BenchCel Q An operator who runs protocols and may need to set the parameters for this task The Waitfor task and a Signal task work together to specify the order in which tasks are performed across processes You must first set the Waitfor task and then set the Signal task To set Waitfor task parameters 1 Add a Waitfor task to a protocol process 2 Inthe Protocol Task Parameters toolbar type a name for the task To set Signal task parameters 1 Add a Signal task to a protocol process 2 Inthe Available waitfors text box of the Protocol Task Parameters toolbar select the Waitfor task that you want to reference 128 Chapter 6 Setting task parameters BenchCel User Guide Related information 3 Click Add The task moves to the lower box For information about See Example usage of Waitfor and Specifying task order across Signal tasks processes on page 132 Adding tasks to protocols Adding and deleting tasks and pipette tasks on page 92 Specifying task order Specifying task order across processes on page 132 User message tasks Setting User Message task parameters on page 125 Setting WellMate task parameters About this topic WellMate task defined This topic describes how to set
306. rotocol advanced topics 175 BenchCel User Guide Methods The task object has the following methods Method Comments task skipQ Skips execution of the current task Use this function to conditionally execute a task such as in this example which skips the task if the simulator is not running if isSimulatorRunning task skip task pauseQ Pauses the protocol and opens a dialog box that asks you whether you want to continue or abort the run Use this function if you need to pause the protocol to for example replenish the fluid in a static reservoir You could use the printQ function to add a note to the log toolbar describing the action to take when the BenchCel has paused task isSimulatorRunning Returns true if this is a simulated run Has no arguments task repeat Schedules the task to be repeated None of the task object methods accept any parameters These are generic methods that are the same regardless of the task that is executing them The properties of these methods are specific to the current task The default behavior of BenchWorks JavaScript is that the values of all variables are cleared set to undefined before the next protocol is run You have the option to change this so that the value of a variable assigned in a script is held in memory until BenchWorks is closed This means that if you assign the value to a variable in one protocol the same value will be used in the next protocol with the
307. rotocol Task Parameters Task Settings Advanced Settings South West North East Printing Option Use this label M Format to use 1 Number of Fields 2 Field 1 NAWIINC Field 2 FILE Field 3 FILE Field 4 from South x side Field 5 Field 6 use South f side i m Increment Chars From user plugin Starting Increment 1001 Numeric 0 3 Alphanumeric 0 2 O Verify bar codes and reapply up to 0 times Bar Code File Entry 4 Bar Codes NOT in file The FileReader plug in allows BenchWorks to input the data in the label fields from a text file Functionally the text file is similar to a label data file except that it includes data for all fields in a label instead of just one field This allows two fields on the same label to contain different data from the same file in the same run without using prefixes and suffixes For information about See Setting up the file reader plug in Using the FileReader plug in in a protocol on page 168 Using JavaScript with BenchWorks Using JavaScript in BenchWorks on page 171 The workflow that this procedure Workflow for creating a protocol on belongs to page 85 166 Chapter 8 Creating a protocol advanced topics BenchCel User Guide About the FileReader file format About this topic The header row P TestData txt Notepad File Edit Format View Help This topic describes the format of the text f
308. rotocol that you created to use the FileReader plug in 2 Click Start from BenchWorks to start the protocol 3 Select the plug in text file from the dialog box that opens Look in jo FileR eaderPluginD ata gt Q si w E My Recent Documents Desktop S My Documents a My Computer aderData txt EL a My Network File name Testo ata txt Places Files of type Text Documents txt X Cancel VA Encoding Jans z 170 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Related information 4 Inthe FileReader dialog box that opens check the list of names of the columns of the text file and the total number of rows in the file x South field 1 Plate Name South field 2 Barcode South field 3 Plate ID South field 4 User South field 5 Date west field 1 Barcode West field 2 Plate ID West field 3 Destination There are 7 lines 5 Click OK The Number of Cycles dialog box opens x Number of times to run protocol i 6 Enter the number of cycles to run If the file is not the one you intend to use you can cancel the run If the number of rows in the file is greater than the number of cycles that are run the extra rows will be unused If the number of rows is less than the number of cycles that are run an error occurs when the rows are executed If the error is ignored additional labels are left blank The input file does not change during a run
309. rs The After filtration delay is the time after the filtration has stopped before the plate can be picked up DAMAGE HAZARD Ifthe After filtration delay is too short the robot may crash Related information For information about See Adding and deleting tasks Adding and deleting tasks and pipette tasks on page 92 Pipette task parameters About setting pipette task parameters on page 96 Creating protocols Workflow for creating a protocol on page 85 Chapter 6 Setting task parameters 101 BenchCel User Guide About setting Apply Label task parameters About this topic Apply Label task defined Bar code labelling decisions Bar code format Related information This topic provides some information about the Apply Label task to help you make choices about bar code labeling The Apply Label task uses a VCode to print a bar code label and apply it to a plate Before you add an Apply Label task to a protocol consider your record keeping and automation needs For example Q Q Q Q Do you need each bar code label to be unique within a run but not from run to run Do you need each bar code label to be unique across all runs Will you be using a Laboratory Information Management System LIMS for barcoding information and record keeping What human readable fields do you want to include on the label Do you want to use a bar code input file Do you want to use a bar code d
310. rsion information Parameters none Returns none Example Visual C Visual Basic BenchCell AboutBoxQ m_BenchCel AboutBox Description Method to programmatically retrieve the version of the ActiveX Parameters None Returns None Example Visual C Visual Basic CString strVersion Version BenchCel1 GetVersionQ m_BenchCel GetVersionQ 326 Chapter 14 BenchCel ActiveX controls BenchCel User Guide LONG lnitialize BSTR Profile LONG ShowDiagsDialog BO OL bModal SHORT iSecurityLevel Description Method to connect to the BenchCel device A BenchCel profile specifies how to connect to the device serial or Ethernet if Ethernet which device on the network and if serial which port to use and which teachpoint file to use If this is called in non blocking mode the client application should wait for InitializeComplete before calling other methods This method should be called before most other methods Parameters Argument Argument Range Description Type Name BSTR Profile Valid profile The name of the profile to be name used for initialization Returns S_OK 0 on success other value otherwise Example Visual C Visual Basic LONG 1Result LONG 1Result m_BenchCel Initialize ethernet BenchCell Initialize ethernet Description Method to show the graphical diagnostics menu that allows the user to troubleshoot and correct problems This method can be called before Initialize to creat
311. run Procedure To clean up after a run 1 Click Yes in the dialog box that prompts you to release all stacker racks Protocol Complete i x 2 Release stacker racks used in protocol Remove used sample plates from the racks Remove manually placed plates from platepads VPrep module shelves and VSpin 4 Wash items such as reservoirs tubes and manifolds that were contacted by liquid 5 If necessary use the VPrep diagnostics software to remove pipette tips 6 Check run logs for errors 7 If you have administrator or technician privileges and you have modified the protocol including selected options you can save the protocol Log out of BenchWorks Optionally shut down the BenchCel Related information For information about See Run logs About log and data files on page 51 Protocols Workflow for creating a protocol on page 85 Logging out Logging out of BenchWorks on page 81 Using the Log toolbar Working with the Log toolbar on page 77 Shutting down Shutting down the BenchCel on page 81 Chapter 4 Performing a run 81 BenchCel User Guide Logging out of BenchWorks About this topic This topic describes how to log out of BenchWorks Logging out of BenchWorks ensures that unauthorized users do not use your account to control the BenchCel or its devices For example an administrator should log out after making changes in the plate editor Procedure To log out
312. run 59 what you should know 59 Protocol Task Parameters toolbar 766 pump inflow 767 outflow 767 Pump Reagent pipette task defined 157 JavaScript properties 787 setting parameters 158 purging 285 287 Q QFill2 diagnostics using 297 dispensing 292 filtration port 292 identifying 297 QFill2 task defined 127 setting parameters 127 QFill2 supported instrument 78 QRM file Nanodrop 290 quadrant 145 152 156 160 quadrant representation in JavaScript 776 rack loading and releasing 265 loading and releasing all racks 267 registry file 322 registry key emailing 209 exporting 208 importing 209 releasing a rack 265 Relid task defined 708 renaming a labware entry 223 reporting errors 9 requirements space 19 system 27 utility and environment 20 reservoir filling see VPrep reset all robot servos 255 Restack task setting parameters 123 retract distance 151 156 160 robot changing the speed 262 homing 257 jogging 259 jogging the gripper position 267 jogging the theta axis 260 jogging the X axis 260 jogging the Z axis 259 limits 280 moving manually 258 preventing crashes 47 sending home 257 slider controls 263 routine maintenance 300 run aborting 74 defined 39 monitoring 76 performing overview 68 Index 345 BenchCel User Guide performing pre run checks 69 protocol until done 72 starting 70 starting from command line 73 what happens after 72 running a
313. s 323 Setting UP Propels We ose Goad ek eek oa he Ve bara aes 324 Setting up methodS 2 a ea a eee 325 V vi Table of Contents BenchCel User Guide Chapter 1 Introduction BenchCel User Guide Introduction This chapter introduces the BenchCel User Guide To operate the BenchCel become familiar with the procedures in this guide as well as the guides for the devices installed on your BenchCel 1 Chapter 1 Introduction BenchCel User Guide Who should read this guide Job roles This user guide is for people with the following job roles Job role Responsibilities Integrator Someone who configures software and hardware to allow integration of the BenchCel into a larger lab automation system Installer Someone who unpacks puts together and tests the BenchCel before it is used Lab manager administrator or Someone who is responsible for technician Q Managing the BenchCel Developing the applications that are run on it problems that may arise Q Q Solving the more challenging Q Developing training materials and standard operating procedures for Operators Operator Someone who performs the daily production work on the BenchCel and solves routine problems Your organization may choose to create its own procedures for operators based on the information in this guide Related information For information about See Using Velocity11 user guides About Velocity11 user guide
314. s Aspirate property Definition Velocity Specifies the speed of the aspiration stroke in microliters per second Acceleration VPrep only Specifies acceleration during the aspiration stroke in microliters per second squared Z axis velocity into wells Specifies how fast the pipettor moves as the tips enter the wells in millimeters per second Chapter 11 Setting liquid handling definitions Aspirate property Z axis acceleration into wells Z axis velocity out of wells Z axis acceleration out of wells Post aspirate delay 249 BenchCel User Guide Definition VPrep only Specifies the acceleration of the pipettor as the tips move into the wells in millimeters per second squared Specifies how fast the tips leave the wells in millimeters per second VPrep only Specifies the acceleration of the pipettor as the tips move out of the wells in millimeters per second squared Specifies the time the pipettor waits after aspiration is complete before moving the tips out of the wells in milliseconds 7 Enter values for the dispense properties The following table describes these properties Dispense property Velocity Acceleration Z axis velocity into wells Z axis acceleration into wells Z axis velocity out of wells Z axis acceleration out of wells Post dispense delay 8 Click OK Definition Specifies the maximum speed of the dispensing stroke in microliters per second VPrep only
315. s For information about See BenchCel Diagnostics About the Controls page on page 254 Labware parameters Q Opening the Labware Parameters group box on page 237 Q Changing labware parameters on page 238 Chapter 10 Defining labware BenchCel User Guide Opening the Labware Parameters group box About this topic This topic describes how to access the Labware Parameters group box so you can make changes to some of the labware settings Procedure To show the Labware Parameters group box 1 Open BenchCel Diagnostics 2 Inthe Controls page of the BenchCel Diagnostics dialog box select a labware type from the list box Labware Costar 96 pp black Show parameters 3 Select the Show parameters check box The Labware Parameters group box is displayed on the right side of the Controls page The values displayed in the Labware Parameters group box are for the plate selected Labware Parameters Plate dimensions mm Plate offsets mm Stacking thickness 13 Robot gripper Plate thickness 143 Stacker gripper Sensor Sensors Error correction Sensor threshold 20 Sensor intensity 90 Gripper positions mm 10 1 Check plate notches Open 4 AL O Top right Holding plate i f Bottom left C Bottom right Holding stack 45 Can be lidded Lid Parameters mm Stacking 13 i 3 Ey Gripper offset Thickness 14 3 Gripper position i Resting
316. s l 2 Add the Apply Label task to a protocol process In the Protocol Task Parameters toolbar click a tab corresponding to a side of the plate The options are South West North and East Protocol Task Parameters x Task Settings Advanced Settings South West North East Printing option Use this label ha Format to use 1 From file Number of fields 2 neremen l Date Feld Bes Field 3 risting bal Field 4 from South Field 5 text date Field 6 South Increment chars 3 m user phi Starting increment 1 Numeric 0 9 Alphanumeric OZ O O Verify bar codes and reapply up to 1 tim Bar code file entry Bar Codes NOT in file Chapter 6 Setting task parameters 103 BenchCel User Guide 3 Select one of the options in the Printing Option list box 4 If Then You do not want to place a label Select No Label and return to step 2 on this side of the plate You want to define a bar code Select Use this label and continue label and place it on this side of with step 4 the plate You want to print a label thatis Select Use side label and continue the same as a label already set with step 4 up for another side of the plate All other parameters on the page are ignored In the Format to use text box type a number that corresponds to the bar code format that you want In the Number of Fields text box type the number of fields that you want to prin
317. s effectively it helps to know when it is best to use each format Where to get the online help and PDF Online help The VWorks online help file is installed separately from the software from the VWorks Help CD_ROM The file that launches the help is called help html and is located in this directory C WWorks Workspace docs helpsystem PDF file of the user guide C MWorks Workspace docs The VWorks user manual in PDF format is located on the software CD ROM as a file that you need to The content pane displays the online help topics Navigation buttons in the content pane allow you to navigate through the pages Computer requirements To open a user guide in PDF format you need an Acrobat viewer You can either use the viewer that is built into Adobe Acrobat or you can download the free Adobe Reader application from http www adobe com support downloads main html Printing and searching We provide user guides in PDF format mainly for printing additional copies You can use them for simple searches from the Find button although these searches are much slower than online help searches More information For more information about using PDF documents see the Adobe Acrobat PDF help system that can be accessed from your Acrobat viewer Related information For information about Who this guide is for What this guide covers Finding firmware version Starting BenchWorks What this guide covers
318. s on page 3 Finding firmware version About general settings on page 277 What this guide covers What this guide covers on page 5 Starting BenchWorks Starting BenchWorks on page 34 Chapter 1 Introduction BenchCel User Guide About Velocity11 user guides About this topic This topic describes the different formats of Velocity11 documentation Each Velocity11 user guide is delivered to you as Q Online help Q APDF file U A printed book The information in each format is the same but each format has different benefits Where to find the Online help user guides The online help is automatically added to your computer with the software installation PDF The BenchCel User Guide and Device Driver User Guide in PDF format are located on the software CD ROM as a files named BenchCelUserGuide_Jan2006 pdf and DeviceDriverUserGuide_Dec2005 pdf You will need to copy the files onto your computer They are not automatically installed with the software Velocity11 website You can download the latest version of any PDF file from our website at www velocity11 com techdocs docdownloadpage html All of Velocity11 user documentation can be searched from the website at www velocity11 com support support html Online help The online help is the best format to use when you are working at the computer and when you want to perform fast or advanced searches for information It is also the only format in color To open t
319. s but you need to make sure that shelf 1 where you want to place the buffer reservoir is configured correctly Again looking at the device manager you see that there are two shelves configured as reagent shelves which can hold reservoirs El Shelf Reagent reservoirl reservoir2 On selecting reservoir 1 you see that it is assigned to shelf 1 of VPrep 2 which is what you want However the labware associated with the shelf is the wrong type E General Device name reservoirl Device type Shelf Reagent Approach height mm 12 7 Allowed prohibited labware E Shelf Reagent properties Shelf number 1 Parent device VPrep2 11 MicroWash 384 138 Chapter 7 Setting pipette task parameters BenchCel User Guide Adding the Aspirate pipette task If you leave it as V11 MicroWash 384 the pipette tips may crash into the reservoir because the task will be performed on the assumption that the tips are moving into a 384 V11 Reservoir manual fill 21 5 deep reservoir So you change the labware association to 384 V11 Reservoir manual fill 21 5 deep Note To save the changes in the device manager you need to have administrator login privileges 384 11 Reservoir Manual fill 21 5 deep Note that when you associate a type of labware with the VPrep shelf you are also associating all of the parameters for that type of labware stored in the labware database The VPrep references the labware database parameters so
320. s continue on If the robot does not move shut down the software and turn the BenchCel off and then on Contact Velocity11 Service Center if problem continues Checking the arm alignment About this topic When to check the arm alignment Who should adjust the alignment The gripper arms of the BenchCel robot must be in alignment that is level with each other in all planes If the arms become misaligned the robot will have difficulty placing and picking labware Under normal working conditions the arms should not become unaligned Usually misalignment is the result of a physical collision of the robot with a peripheral device or other object This topic describes when and how to check the arm alignment Q When teachpoints appear to be off and nothing was changed on the BenchCel system Q When a plate being held by the grippers appears tilted in any direction U Any time the robot is not picking up or placing labware properly Adjusting the gripperarm alignment is a tedious process and should be performed by Velocityl1 Service Center personnel If you suspect the arms are out of alignment you should follow the procedure in this topic to check their alignment If they are found to be out of alignment contact Velocity11 Service Center to set up a service visit 310 Chapter 13 Maintenance and troubleshooting BenchCel User Guide Procedure To check the arm alignment 1 Open the Control page in the Bench
321. s with the exception of the use of diagnostics software that is developed by Velocity11 for other companies devices For more information about these topics see the user guides for the relevant instruments Because the BenchCel is available in different configurations and can be customized your BenchCel may not be exactly as described in this guide For information about See Starting BenchWorks Starting BenchWorks on page 34 Finding firmware version About general settings on page 277 What s new in this version About this topic Chapter 1 Introduction BenchCel User Guide The following table describes the main new features of BenchWorks version 24 x and the BenchCel hardware that it supports since the last BenchCel User Guide was released New features Feature WellMate QFill2 MultiDrop Nanodrop JavaScript methods Reset script context protocol rule ActiveX controls Pre and post protocol processes Save All command Bar code error handling Bar code task Attempt to put plates away if deadlock occurs Change Instance pipette task Description Newly supported device Newly supported device Newly supported device Newly supported device task repeat method added New rule that changes the context of global variables New Ability to add a pre and or a post protocol process to the run New ability to save the current protocol file and device file at t
322. s 100 About setting Apply Label task parameters 0 0000 eee eee eee 101 Setting Apply Label task parameters 000 eee ee ee 102 About combining bar code modifiers 0 0 cece es 106 Setting Delid Relid task parameters 0 0 00 es 108 Setting Downstack and Upstack task parameters 00 0 cee eee eee 109 Table of Contents BenchCel User Guide Setting Incubation task parameters 0 00 cc es 112 Setting Multidrop task parameters 0 0 aaa es 114 Setting Nanodrop task parameterS 0 0 0 ees 116 Setting Pierce task parameters 0 0 cee es 117 Setting Place Labware task parameters 0 00 cee ee ees 118 Setting Place Plate task parameters a nn naaa aaa es 120 Setting QFill2 task parameters 2 0 es 121 Setting Restack task parameterS 000 ee es 122 Setting Seal task parameterS naunan aaan es 124 Setting User Message task parameters 000 cee es 125 Setting Waitfor task and Signal task parameterS 000 eee eee ee 127 Setting WellMate task parameters 0 0 cee es 128 Setting VSpin with Access2 task parameters 0 0 0 00 ee ee es 130 Specifying task order across PrOCESSES 1 es 132 Chapter 7 Setting pipette task parameters 135 Configuring a pipette process example 00 0 eee eee 136 Adding and configuring a Pipette Process task 2 0 00 cee eee eee 140 Configuring a VPrep shelf aS a device
323. s many tasks as possible given the error possible are completed Continue processing Tasks involving plates that are currently in without starting any new the system continue Other tasks are not plates scheduled Stop scheduler The scheduler stops scheduling new tasks even if plates are currently available to the robot The current task continues to completion 6 Click OK to close the BenchWorks Options dialog box For information about See The workflow this procedure Workflow for preparing for a run on belongs to page 32 The next step Setting up email error notification on page 45 Protocol error handling options Setting protocol errorhandling options on page 47 Error options About setting error options on page 43 Setting up email error notification About this topic Requirements for email setup This topic describes how to add an email address to BenchWorks so you can be notified by email or pager when there is a run error Email setup in BenchWorks enables you to do the following tasks Q Automatically be notified by email or pager when errors occur during a protocol run Q Send a bug report to Velocity11 Before you can send an email from BenchWorks Q The BenchCel computer must be connected to a network with internet access Q The outgoing email server must be set up on the system s computer 46 Chapter 3 Preparing for a run BenchCel User Guide Setting up emai
324. s of BenchWorks components 0 0000 e cece eee e anaes 30 Chapter 3 Preparing for arun 31 Workflow for preparing for a run uaaa 32 Turning on the Bencheels reglada e eaa e e A ees 33 Logging into the operating SySteM Tewa tia eoa O Era E ees 34 starting BBenchWOrkS i 6 2s oseks FG a i ae eee Dae ae ee ee 34 Logging in to BenchWorkS 00 e ee ees 36 About tasks processes and protocolS 0 2 00 ee 37 Opening a protocol in BenchWorkS 000 es 40 Setting general OptionS aana ees 41 About setting error options 0 6 ees 43 Setting general error handling OptionS 2 0 0 ce ees 44 i Table of Contents BenchCel User Guide Setting up email error notification ssi noera ere ngae a eee 45 Setting protocol error handling optionS 2 0 0 ce ee ee 47 Setting pre protocol ruleS arre eaa E E ee eee 48 Setting protocol ruleS oer ieee e e E eee 49 A out log and data files ech ares eee ee yee esis eea E ER ee ee ee Y 51 Seung logc oplilons aee bea aa a a fe reed adi Moa ote th at Soa ore fh i ee EO oe 54 Importing a log Tile to ExC l c ew on ta ee ow ea eG Oe Be eR bea 57 Understanding the protocol 1 cc ees 59 Printing a protocol snas seird a eee 60 Preparing plates instruments and accessories aaae eee 61 Setting up a VSpin counterweight plate 2 aaa aaa ee 63 Installingsasraek oe eaa nad awh bl dad bie add wae Gia weet we at
325. s pipette task parameters About this topic Change Tips pipette task defined Before you start Overall process This topic describes how to set the Change Tips task parameters This task is used when creating a BenchWorks protocol that uses a Velocity11 VPrep Read this topic if you are Q An administrator or technician who writes protocols Q An operator who needs to specify parameters for the Change Tips task The Change Tips pipette task uses the robot to apply or remove VPrep pipette tips Pairs of Change Tips pipette tasks are usually used together For example if the protocol starts with tips already on the VPrep the first Change Tips pipette task would remove the tips and the second Change Tips pipette task would install new tips Change Tips pipette tasks are always entered in a process created solely for changing tips an example is described in this topic Before you start you need to configure a shelf on the VPrep to use tip boxes and have ready a tip box containing tips with the tip box lid removed and placed in a robot accessible position Also if you are removing tips first you need an empty tip box on the tip box shelf of the VPrep that you intend to use for the operation Changing tips with a VPrep requires you to create the following processes 1 In the protocol editor create a process for the tip box such as in the following example werd V1 96ST Q1 Tip Downstack from Pipette process 1
326. show the editor FALSE modally or not LONG Pause LONG Unpause LONG OpenClamp Chapter 14 BenchCel ActiveX controls 335 BenchCel User Guide Argument Argument Range Description Type Name BSTR bstrLabware Valid The labware to be selected when labware the editor is displayed name Returns S_OK if successful other value otherwise Example Visual C Visual Basic m_BenchCel ShowLabwareEditor BenchCel ShowLabwareEditor 1 MyPlateType 1 MyPlateType Description Method used to pause the BenchCel movement Parameters None Returns S_OK if successful other value if there was an error Description Method used to unpause the BenchCel movement The BenchCel will continue any remaining movements before the call to pause the device Parameters None Return S_OK if successful other value if there was an error Description Method used to open the stacker grippers of a given stack Parameters Argument Argument Range Description Type Name SHORT Stack 0 number of Specify which stack s gripper Stacks 1 to open Returns S_OK if successful other value if there was an error 336 Chapter 14 BenchCel ActiveX controls BenchCel User Guide IsConnected LONG Delid LONG Relid Description Method used to check whether a connection to the BenchCel is established The BenchCel is ready to process commands from the BenchCel Active X driver when a connection has been established
327. sing the correct plate type check the notch setting in the labware parameters a b Open the Controls page of the BenchCel Diagnostics dialog box In the Labware group box select the Show parameters check box In the Labware Parameters dialog box verify that the correct notch position is selected Check the Number of wells value in the labware entries page of the Labware Editor dialog box a b Open the Labware Editor dialog box and check the value in the Number of wells entry field Make sure that the displayed value matches the number of wells in the plate you are using Check the orientation sensor offset a b Open the Labware Editor dialog box and click the Stacker tab Verify the value in the Orientation sensor offset This is the distance from the bottom of the plate to the middle of the sensor window Check the orientation plate notch sensor readings See Checking the stacker sensors on page 314 for a procedure If readings do not detect the correct orientation see Resetting the orientation sensors for a plate on page 313 for a procedure on how to adjust the sensors This error is generated when the notch sensors located in the stacker head detect a plate notch pattern consistent with the correct plate type placed in the wrong orientation To resolve a plate is rotated type error l Check to ensure that the plate is in the correct orientation in the stacker rack If t
328. sks Other tasks See Adding and deleting tasks and pipette tasks on page 92 About setting pipette task parameters on page 96 About setting task parameters on page 95 Setting Nanodrop task parameters About this topic This topic describes how to set the Nanodrop parameters on a BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the Nanodrop instrument Q An operator who needs to specify parameters for the Nanodrop task Nanodrop task The Nanodrop task moves a plate to a Nanodrop liquid dispenser and defined runs a pre defined program using a calibration file for more accurate dispensing Procedure To set Nanodrop task parameters 1 Add the Nanodrop task to a protocol process 2 Inthe Task Settings page of the Protocol Task Parameter toolbar select the following from the list boxes a The program to run b The calibration file to use c The Nanodrop to use if your BenchCel is connected to more than one The name of the Nanodrop is defined in the device manager Task Settings Advanced Settings Select program to run TestQRMFile grm Select calibration file to use TestCalibration cal Select Nanodrop to use Nanodropt Chapter 6 Setting task parameters 117 BenchCel User Guide Related information For information about See Adding tasks to protocols Adding and deleting tasks and pipette tasks on pa
329. so if you perform another run with the same file the same labels will print If a power outage occurs during a run and you are unable to resume the run delete the first few rows after the header row Then run the protocol again 7 Click OK For information about See Using JavaScript with BenchWorks Using JavaScript in BenchWorks on page 171 The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Chapter 8 Creating a protocol advanced topics 171 BenchCel User Guide Using JavaScript in BenchWorks About JavaScript in BenchWorks About JavaScript JavaScript resources Examples of use In BenchWorks JavaScript programs scripts can be used to Q Configure tasks in ways that task parameters do not allow Q Change the parameters of a protocol task immediately before it is scheduled This extends the capability of BenchWorks because the parameters can be changed dynamically during a run based on Q Information passed from an external source such as a database Q The number of times the protocol has cycled Q Feedback on changing conditions during the run Scripts can be run as part of pre protocols protocols and post protocols JavaScript is a general purpose programming language that requires an interpreter to run its programs You are probably most familiar with JavaScript where it is used to create dynamic effects in Web pages This form of Jav
330. ss task to the Protocol Process window Set the Pipette Process task parameters Add any other tasks that you want to for the tip box You could for example add an Apply Label task to place a bar code on the tip box After you have created a process for the tip box create a pipette process for the Change Tips pipette task To create a pipette process for changing tips 1 2 3 Click the Pipette Process Editor tab Add a Change Tips pipette task to the pipette process window In the Pipette Task Parameters toolbar select either Option With this option during the protocol Q Press On New Tips Puts tips on to a VPrep head Q Tips Off Removes tips from a VPrep head From the Select the tip box to use list box select the name of the tip box that you have assigned to the tip box process 150 Chapter 7 Setting pipette task parameters BenchCel User Guide Related information 5 Add other pipette tasks including a second Change Tips pipette task as required For information about See How to set the number of Setting the number of simultaneous simultaneous plates plates on page 91 Configuring VPrep shelves Configuring a VPrep shelf as a device on page 142 Labware editor About the labware editor on page 215 Applying labels Setting Apply Label task parameters on page 102 Configuring a pipette process Q Configuring a pipette process example on page 136 Q Addin
331. ss2 task defined 130 setting parameters 130 W Waitfor task example 132 setting parameters 127 warnings hazard 11 warranty 10 Wash Tips pipette task defined 159 JavaScript properties 788 wash volume 159 washing pipette tips 759 waste disposal 10 WellMate creating profiles 293 diagnostics using 293 execute commands 296 moving plate stage 295 priming and purging 296 querying plate type 296 supported instrument 78 Index 347 BenchCel User Guide WellMate task defined 128 setting parameters 129 Windows logging on 34 Windows registry key copying 208 X X margin settings 279 XML schema 84 Z z axis acceleration into wells property 249 z axis acceleration out of wells property 249 z axis speed into wells property 248 z axis velocity into wells property 249 z axis velocity out of wells property 249 348 Index BenchCel User Guide oes Agilent Technologies User Guide G5400 90002
332. sual C Visual Basic VARIANT vPRofiles profileNames m_BenchCel EnumerateProfilesQ BenchCel EnumerateProfilesCQ SAFEARRAY psa For i LBound profileNames To vProfiles parray UBound profileNames BSTR bstrArray MsgBox profileNames i if Next FAILED SafeArrayAccessData psa reinterpret_cast lt void gt amp bstrArray VariantClear amp vProfiles return for ULONG i 0 i lt psa gt rgsabound 0 cElements i MessageBox CString bstrArray i SafeArrayUnaccessData psa VaraintClear amp vProfiles Index Index 339 BenchCel User Guide Note You can also search our technical documentation on our website at wwwvelocity 1 com support support html Symbols bar filename extension 47 bwl file format 30 dev file format 30 xml file format 30 A ABgene SEAL IT 100 supported instrument 78 aborting a run 74 acceleration property 248 249 Acrobat Reader 4 Acrobat viewer 4 adding labware entries 227 new teachpoint 255 user accounts 205 administrator privilege 85 204 Advanced Settings tab 172 air connecting 26 input on connection panel 23 pressure control stacker head 24 required pressure 20 26 stacker gripper flow control 24 Aliquot task defined 700 setting parameters 100 AliQuot supported instrument 78 Apply Label task 164 defined 101 JavaScript properties 178 setting parameters 102 aspirate acceleration 155 160
333. t on the bar code The maximum number of fields you can print is limited by the number of fields in the format you selected For example if the format specifies three fields you cannot print a bar code with four fields In this example if you do enter the number four into the text box the last field is ignored Click in the Field text box for the first field that you want to use and enter one or more of the following types of information that you want to print in that position on the label If you want to print Text field that does not increment A field that is identical to a bar code field on another side of the plate Then Type the text in the text box To use this option your VCode must have an attached bar code reader a Select the side of the plate from the from side side list box below the Use existing bar code button b Click Use existing bar code This places the code BC in the text box Note This option copies a single field from another side of the plate The similar option selected in the Printing Options list box copies an entire bar code from another side of the plate 104 Chapter 6 Setting task parameters BenchCel User Guide If you want to print A series of bar codes from a bar code input file A series of bar codes by referencing bar codes on another side of the plate using a bar code data file Then a Make sure that you have set up a bar code input file and selec
334. task tipTouchHorizontalDi stance task tiptouchRiseHeight task tipTouchSides task volume Data type Float Float Boolean Float Float Integer Float Task parameters Retract distance Distance from well bottom Enable tip touching Tip touch horiz dist Tip touch rise height Number of sides to touch Mixing volume Comments The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated This value allows the tips to move upwards or downwards during dispensing or aspirating to maintain a certain height below or above the surface of the liquid You will need to determine an appropriate value by trial and error for each type of plate you use The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel Whether you want the tips to touch the sides of the plate wells or not When the value for this parameter is zero the tips will move horizontally one well radius The well radius is defined in the labware database for the type of plate you are using If you want the tips to touch harder increase this value If you want the tips to touch more lightly enter a negative value The height that the tips should move upwards before touching the side of the wells The nu
335. te object has the following methods available on those systems with the volume tracking database option Method Comments plate setUserData string key string Stores value under the key key ina value database record associated with this plate plate getUserData string key Returns the value stored earlier using plate setUserData The task object is a BenchWorks defined generic object that refers to the currently executing task It allows the properties of the task to be accessed using a standard syntax Depending on which task is executing a different set of properties may be available Properties The task object provides a comprehensive set of properties that can be read write or read only These properties specifically affect the behavior of the task that is about to be executed by the BenchWorks scheduler For example the Aspirate task has a property called volume To store this property in a variable you would write x task volume To set the volume property of the Aspirate task to the value stored in the variable x you would write task volume x In this example the run time interpreter determines through the context that task refers to the currently executing Aspirate task Attempting to access properties that are inappropriate for the current task will result in a scripting syntax error but will not halt the execution of your protocol About variables Chapter 8 Creating a p
336. ted it in BenchWorks general options b Make sure that the number of bar codes specified in the series of the bar code input file that you want to use is equal to or greater than the number of labels that you want to print c Select the series in the Bar code file entry list box at the bottom of the toolbar Note If there are no entries in the Bar code file entry list box other than the default text you need to set the location of the bar code input file d Click From File This places the code FILE in the text box IMPORTANT If you use this option in two fields the same data will be printed in both fields You cannot enter different data into fields using this method a Make sure that you have created a bar code database file and selected it in BenchWorks general options b Make sure that the incoming plates have bar code labels on the south or west side or a previous Apply Label task is set up to print labels on the south or west side c Ifthe incoming plates are labelled make sure that the system verifies the labels by setting up bar code control on the plate icon d Click From text database This places the code DB in the text box e Inthe use side side list box under the From text database button select the side of the plate that has the bar codes you want to use as a reference IMPORTANT Although you can select any side only the south and west sides can currently be use
337. ter 12 Using BenchCel Diagnostics 285 BenchCel User Guide Option Description Delete this Click to delete a profile profile A dialog message appears asking if you are sure you want to delete this profile Update this Click to save changes made to a profile for example if profile you have changed the Teachpoint file for that profile Initialize this Click to instruct the software to connect to the profile BenchCel using the current profile For information about See Profiles Relationships of BenchWorks components on page 30 Creating a profile Creating a BenchCel profile on page 283 Using Multidrop diagnostics About this topic Terms defined Before you start The Thermo Electron Multidrop microplate dispenser can be used either in stand alone mode or as a device within a protocol using the BenchCel This topic explains how to manipulate the dispenser independently of BenchWorks using Multidrop diagnostics software created by Velocity11 To use the dispenser within a BenchWorks protocol set the Multidrop parameters in the Protocol Task Parameter toolbar The Multidrop has priming and purging functions that can be controlled through the Multidrop Diagnostics Priming Priming moves liquid through the dispensing system into waste to make sure that there is no air in the lines Purging Purging moves liquid back into the liquid cassettes Before you can manipulate a Multidrop make sure that it is corr
338. text in the Log toolbar To perform a search in the Log toolbar 1 Select the appropriate tab in the Log toolbar 2 Click in the toolbar pane 3 Click CTRL F3 or CTRL FE The Find dialog box opens Find Find what l Eind Het I Match whole word only I Match case Direction Cancel C Up Down Adding a note Message color coding Related information Chapter 4 Performing a run 79 BenchCel User Guide You can type notes into the message display pane during a run Any notes that you type are also incorporated into the log txt file To add a note to the Log toolbar and log txt file 1 At the bottom of the message display pane click the Notes tab Click in the display pane wherever you want to add the note 2 3 Type the note 4 Press ENTER on the keyboard A timestamp is appended to the note The BenchWorks log colorcoding scheme is listed here Color Black Blue Red Lime green For information about Setting screen message options before a run Importing a log file Meaning Standard events with a date stamp or user added notes Liquid transfer events Warnings General information See About log and data files on page 51 Importing a log file to Excel on page 57 Chapter 4 Performing a run BenchCel User Guide Cleaning up after a run About this topic This topic describes the tasks you should perform when you have finished a protocol
339. that is too high or too low The simulator does not move any instruments It performs a virtual run based on the estimated task execution times displayed for each task You can change the execution times for tasks to make the simulation more accurate for your protocol One approach you can use for testing is the following 1 Run the simulator with the default task execution times and the same number of plates expected for a run to identify deadlocks and rate limiting tasks Resolve any major problems with the protocol Perform a real dry run with a plate Use the times recorded in the Log toolbar to edit the task execution times for each task 98 Chapter 5 Creating a protocol basics BenchCel User Guide Running the simulator Changing execution times Related information 5 Run the simulator with the more accurate task execution times 6 Fine tune the protocol based on the results of the simulation To run the simulator 1 Turn the Simulator on by clicking the Simulation is off button on the toolbar iG Simulation is off The button changes to read Simulation is on cy Simulation is on 2 Click the Start button to run the protocol Not all tasks have adjustable execution times but for those that do follow this procedure to change them To change the default task execution times 1 Select a task in a protocol sequence 2 Inthe Protocol Task Parameters toolbar click the Advanced Settings ta
340. that the pipette tips move to the right depth position and so on as they enter the reservoir After configuring a VPrep shelf compile the current protocol to check for errors The next step is to add the Aspirate pipette task Pipette Process 1 on VPrep1 W It if Associating the task with a liquid class on VPrep1 from Plate A quadrant 1 In the Pipette Task Parameters toolbar of the Aspirate pipette task you need to tell the system what class of liquid it is aspirating The system then uses the parameters stored in the liquid library database for that class during the aspiration operation In this case you select the class 1XTE Liquid class You can see the parameters used for the class by clicking the Edit button which opens the liquid library editor Associating the task with the VPrep shelf In the Pipette Task Parameters toolbar of the Aspirate pipette task you need to tell the system from what type of labware to aspirate In this case there are two choices If you select Plate A the Costar 96 well plate you downstacked will be moved to the VPrep and the volume aspirated from it Instead you select reservoirl which is the name of the device that holds the buffer reservoir Plate to aspirate from Plate A Adding a Dispense task Related information Chapter 7 Setting pipette task parameters 139 BenchCel User Guide Finally you specify that we want to aspirate 20 uL Aspir
341. the BenchCel Adjusts the height at which the orientation checking sensors view the plate with respect to the bottom of the plate If the orientation sensor offset is 0 mm the bottom of the plate should be in the same plane as the orientation sensors Determines the highest intensity of the detected light at which the stacker senses a notch when the plate stage is in the orientation sensor position If the stacker does not sense a notch when it should adjust the sensor threshold value The maximum value is 255 Determines the lowest intensity of the detected light at which the stacker senses a notch when the plate stage is in the orientation sensor position If the stacker does not sense a notch when it should adjust the sensor threshold value Sets the percentage of maximum sensor intensity for all sensors If the sensor intensity is set too low a plate will not be detected even though one is present If it is set too high the sensors may become saturated causing failure to detect the orientation of a plate This property adjusts for the fact that clear black and white plates reflect light differently For example white plates generally reflect more light so the sensor intensity should be set lower Obsolete With the Al well of your plate positioned in the far left corner as you face the BenchCel select the corresponding notch or notches for your plate in the Notch Locations group box When
342. the Ethernet port on the BenchCel Connect the other end of the Ethernet cable to your computer hub or switch IMPORTANT To connect the computer directly to the BenchCel use a crossover Ethernet cable If you are connecting the computer to a hub or switch use a straight through Ethernet cable After you connect the BenchCel to power and to the computer and turn the BenchCel on verify the connections by checking the status lights Light Color Activity Meaning PWR Red Light turns on The system has power ACT Yellow Light is blinking There is Ethernet activity LNK Green Light turns on An Ethernet link has been established Serial port o 2 I d gt Q pi rc Zz A um Ethernet port _ status lights 26 Chapter 2 BenchCel overview BenchCel User Guide Connecting the BenchCel to compressed air About this topic This topic describes the information needed to connect the BenchCel to compressed air Air pressure The following table lists the air pressure range required for the BenchCel and associated instruments Unit Air Pressure psi Air Pressure MPa BenchCel 50 90 0 34 0 62 VPrep 90 95 0 62 0 65 PlateLoc 85 90 0 56 0 62 VCode 70 75 0 56 0 62 VSpin with Access2 80 90 0 55 0 59 Procedure To connect the BenchCel to the compressed air 1 Connect one end of the air supply tubing to the source of compressed air 2 Connect the other end to the air intake
343. the Log Options tab 3 Inthe Screen settings group box select one or more of the following options as needed Log Option Writes to screen and file Log task begin events on screen Messages at the time that process tasks are scheduled not at the time that they are performed This applies only to the protocol log file Log task complete events on Messages that confirm when process screen tasks are completed This applies only to the protocol log file Log robot motions on screen Robot motion events as they happen This applies only to the protocol log file Log pipettor debug messages Event messages that are generated by VPrep pipettors This applies only to the protocol log file 4 Inthe File Settings group box a Inthe Max number of each log file to maintain text box type the maximum number of log files that you want to store IMPORTANT After this number has been reached each new log file replaces the oldest existing log file 56 Chapter 3 Preparing for a run BenchCel User Guide b Select one or more of the following options as needed Log options Description Create new logs for every run A separate log file is created for every run If the check box is cleared each run appends data to the same log file and a new log file is created when BenchWorks is started This affects all log files Append timestamps to log file The date and time of the run is names appende
344. the WellMate task parameters in BenchWorks Read this topic if you are Q An administrator or technician who writes protocols for the BenchCel Q An operator who runs protocols and may need to set the parameters for this task For general information about using the WellMate see the Matrix Technologies WellMate user documentation The WellMate task moves a plate to a Matrix Technologies WellMate and dispenses liquid into the plate Procedure Chapter 6 Setting task parameters BenchCel User Guide To set the WellMate task parameters l 2 3 Add the WellMate task to a protocol process If your system has more than one WellMate in the Available Wellmates list box select the one you want to use Protocol Task Parameters x Task Settings advanced Settings Available Wellmates Wellmate ha 0 Prime volume 0 2499 pL 0 Dispense volume 0 2499 uL 0 Purge volume 0 2499 uL 0 Offset 100 to 100 ticks 1 tick 0375 mm Dispense to entire plate Dispense to selected columns Column mask 0 CEEEEEELELT EEE Enter values for one or more of the following parameters Parameter Description Prime volume The volume of liquid to move through the tubing cartridge before dispensing liquid into a plate Dispense The volume of liquid to dispense into a plate volume Purge volume The volume of liquid to move through the tubing from the tips back to the
345. the operation of the individual instruments connected to your BenchCel Prepare instruments and accessories after you have become familiar with the protocol You would typically prepare the BenchCel instruments and accessories in the order presented in this topic Using this order you first set up instruments and accessories that have no time sensitive elements and can therefore be set up the night before the run Leave the more complex preparations which may use expensive and unstable reagents until last Note If the protocol includes User Message tasks to prompt you to perform some setup steps such as placing counterweight plates don t include these steps in the setup The general process of preparing a PlateLoc is described here For more detailed procedures see the PlateLoc User Guide 1 2 Make sure that there is enough seal stock on the roll for the run Make sure that the right support insert is installed for the plates you are using Select the profile that you want to use from the PlateLoc Diagnostics software The general process for preparing a VCode for a run is described here For more detailed procedures see the VCode User Guide 1 2 3 Make sure that there is enough label stock in the label source roll Make sure that there is enough media stock in the media source roll If the radius width of the label backing on the take up roll is more than 1 inch 2 5 cm wide remove the label backing from
346. the plate To understand this think of the columns as occurring in six column sets If there are fewer than six columns the remaining columns will be left blank If there is only one set in the file the set is repeated for the other sides of the plate where you have selected Use this label from the list box For information about See Setting up the file reader plug in Using the FileReader plug in in a protocol on page 168 Using JavaScript with BenchWorks Using JavaScript in BenchWorks on page 171 168 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Using the FileReader plug in in a protocol About this topic The FileReader plug in is installed and registered during the standard BenchWorks installation You should see the FileReader dll file in your Velocity 1 1 BenchWorks plugins directory This topic describes how to modify the task parameters in the protocol so that the Apply Label task uses the FileReader plug in Read this topic if you are a technician or administrator who writes protocols with Apply Label VCode tasks and who wants the FileReader plug in to read and process the label text Setting up the Create a protocol and then modify the plate icon and Apply Label task protocol parameters as described here To set up the protocol to use the File Reader plug in 1 Select a plug in to use a Click the plate icon in the Protocol Editor b Select FileReader dll from the
347. the take up roll cut it and reattach the end Too much label backing on the take up roll can interfere with the operation of the VCode Use VCode Diagnostics software to perform a plate labelling test label For more information see the VCode User Guide Chapter 3 Preparing for a run BenchCel User Guide VPrep set up The general process for preparing a VPrep for a run is described here process For more detailed procedures see the VPrep User Guide The BenchCel robot has access to VPrep shelves 2 4 6 and 8 meaning that only these shelves can hold sample plates Shelves 1 3 5 and 7 are reserved for reservoirs and tipboxes 1 Ifyou are changing the reagent type in a particular reservoir Remove and wash any reservoirs Detach and wash reservoir tubing a b c Replace the tubing and reinstall the reservoir d Remove and wash any MicroWash trays e Detach and wash MicroWash tray tubing f Replace the tubing and reinstall the tray 2 Make sure that the reservoir and tray tubing allows the shelves to move to their fully engaged position Install tubing into the correct pumps Fill the fluid reservoir bottle replace the cap and attach the fluid line to the cap connector Make sure you attach the fluid line that pumps towards the VPrep 5 Empty the waste container replace the cap and attach the fluid line to the cap connector Make sure that you attach the fluid line that pumps away from the VPrep
348. ties on page 226 BenchCel properties Defining BenchCel properties on page 229 Defining labware classes About this topic Two places to define classes About the Labware Classes page This topic explains how to set up labware classes Labware classes contain labware entries When you set up a device you can associate labware classes with the device to indicate what labware can and cannot be used with the device Before you create labware classes consider what labware you want used or prohibited on each of your devices Out of the box BenchWorks is provided with three labware classes already defined Q Uses Filter Platepad Q Uses Standard Platepad Q Uses Vacuum Platepad You can view and define which plate types are associated with which labware classes in U The Labware Classes page Q The Labware Classes sub page of the Labware Entries page These views present the same information in different ways In the Labware Classes page if you select a class in the labware selection box on the left the plate types that are members of that class are displayed in the far right hand column 234 Chapter 10 Defining labware BenchCel User Guide About the Labware Classes sub page Labware Entries Labware Classes Please select a labware class from the list below in order to view and edit its properties Intermediate Height TallPlates TipBoxes Uses Filter Platepad Uses Standard Platepad Us
349. to use a slightly different procedure from the one below To see the network connections in Windows 1 In Windows from the Start menu select Settings gt Control Panel 2 Double click the Network and Dial Up Connections icon The Network and Dial up Connections window opens J Network and Dial up Connections OF x File Edit View Favorites Tools Advanced Help Ei Back eq seach Gyrokders AE GE XxX A Ed Address ja Network and Dial up Connections gt Go al g cH eB ee WAN LAN Network and Dial up Connections This Folder contains network connections For this computer and a wizard to help you create a new gt Re Fin LAN network card The LAN network card is used for communication between the computer and devices that use Ethernet communication cable This network is considered to be the local area network The LAN network card has a fixed IP address which is 192 168 0 1 WAN network card The WAN network card is for networking with your organization s network The settings for this card should be configured by your network administrator in the same way that any PC would be configured to make it available to your network The WAN network card has an IP address that is dynamically assigned by your domain name server when you start you BenchCel s computer Chapter 9 Administrator procedures 211 BenchCel User Guide Obtaining network IP To see the IP address of the tw
350. tocol basics BenchCel User Guide Related information For information about See Creating a protocol process Q Setting up a plate instance on page 88 U Setting the number of simultaneous plates on page 91 Q Adding and deleting tasks and pipette tasks on page 92 Compiling a protocol Compiling and saving protocols on page 93 Running a protocol in simulation Simulating a run on page 97 mode The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Setting up a plate instance About this topic Procedure This topic describes how to set up a plate instance when creating a protocol See Related information at the end of this topic for where to find a definition of plate instance To set up a plate instance 1 Click the Protocol Editor tab This page is referred to as the protocol editor 2 Click Add Click button to add a new plate A plate icon appears in the protocol editor window 3 Ifthe Task Parameters toolbar is not showing select View gt Toolbars gt Protocol Task Parameters Task Settings Advanced Settings Chapter 5 Creating a protocol basics BenchCel User Guide aram Plate name Unnamed 3 Plate type Costar 96 pp black h Edit labware settings Plugin lt no plugin gt z Simultaneous 1 plates O Plates have lids O Plates enter the system sealed O Use single instance of plate Bar c
351. tocol basics 85 BenchCel User Guide Related information For information about See Workflow for creating a protocol Workflow for creating a protocol on page 85 Using JavaScript in protocols Using JavaScript in BenchWorks on page 171 Workflow for creating a protocol About this topic This topic gives the steps used to make a protocol and a cross reference to the topic that describes each step Who creates People who have technician and administrator level user accounts have protocols the necessary privileges to create protocols Workflow Step Topic See 1 Preparing back end bar code label data to use Q About the FileReader plug in on with a plug in optional page 164 Q Using the FileReader plug in in a protocol on page 168 2 Writing JavaScript scripts to dynamically set task J Using JavaScript in BenchWorks on parameters optional page 171 Q The JavaScript task object and properties on page 178 3 Creating a pre protocol process optional Setting up a pre protocol or post protocol process on page 87 86 Chapter 5 Creating a protocol basics BenchCel User Guide Step Topic 4 Creating a protocol process which includes Setting up a plate instance Deciding the number of simultaneous plates to set Adding tasks Setting task parameters Optionally entering JavaScript scripts to dynamically set task parameters See Setting up a
352. tring unnamed list box The shelf on which the reservoir is located Integer at The percentage of maximum pumping rate 188 Chapter 8 Creating a protocol advanced topics BenchCel User Guide Property Data type Task parameter Comments The time in seconds that the pumps pump task time Integer for Wash Tips task These properties are the same as the properties described for the Wash Tips task Property task plateName task aspirate Velocity task aspirateAcceleration task blowoff task cycles task dispenseAcceleration task dispenseToWaste Data type String Float Float Float Integer Float Boolean Task parameters Plate name Aspirate velocity Aspirate acceleration Last cycle blowout volume Number of wash cycles Dispense acceleration Dispense to waste at height of check box Comments The name of the plate The rate at which to draw up liquid If you selected a liquid class this value is entered automatically from the liquid library editor The rate of increase in velocity before the maximum aspirate velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor The volume of air to blow out when the tips are in the liquid This is typically the same as the pre aspirate volume The number of aspirate dispense operations The rate of increase in velocity before the Dispense Velocity is r
353. ts own profile Once created you will probably not need make changes to the profile A profile for your WellMate was created at the factory However if you need to create a new profile you can do so Managing profiles To create a WellMate profile 1 Open WellMate Diagnostics 2 Click the Profile tab Wellmate Diagnostics ersion 1 2 2 Eg Profile Command Dispense Profile Operations _ _ Profile Options ka COM 1 v COM port i Pump speed Create anew eR 500 fast 1000 slow Create a copy of this profile ss Stage speed 700 fast 15000 slow fl Rename this profile Volume to prime on initialization 0 2499 uL Update this profile Kier ae EES ee 3 Click Create a new profile enter a name for the device in the New Profile dialog box and click OK 4 Set the Profile Options a From the COM port list box select the port that the WellMate uses to communicate with the controlling computer b Enter a value for the Pump speed using the range shown as a guide c Enter a value for the Stage speed using the range shown as a guide 294 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide d Enter a volume in the Volume to prime on initialization field to prime the lines when the profile initializes 5 Click Update this profile 6 To open communications to the WellMate and send the profile settings immediately clic
354. uctions for using this software are given in this guide 252 Chapter 12 Using BenchCel Diagnostics BenchCel User Guide About diagnostics Background Types of diagnostics software Related information The BenchCel can be controlled in real time directly through the BenchWorks diagnostics software using simple commands Diagnostics software is used for Q Troubleshooting Q Setting teachpoints Q Performing manual operations outside a protocol For example if an error occurs during a run that leaves a plate and the robot where they should not be you can use BenchCel Diagnostics to move the plate and return the robot to its home position Instruments and robots manufactured by Velocity11 include their own diagnostics software You can find instructions for using this software in the relevant user guide For information about See Opening diagnostics Opening BenchCel Diagnostics on page 253 Controls page About the Controls page on page 254 General Settings page About general settings on page 277 Profiles page About profiles on page 282 Chapter 12 Using BenchCel Diagnostics 253 BenchCel User Guide Opening BenchCel Diagnostics About this topic Procedure Related information This topic describes how to open BenchCel Diagnostics To open BenchCel diagnostics 1 Click the Device Manager tab 2 Select the BenchCel robot from the Device List toolbar Expand the ge
355. using samples to be switched around For information about Starting a run Monitoring a run Using the Log toolbar See Q Starting a run from BenchWorks on page 70 Q Starting a run from a command line on page 73 Monitoring a run on page 76 Working with the Log toolbar on page 77 76 Chapter 4 Performing a run BenchCel User Guide Monitoring a run About this topic What to monitor This topic describes what operations you need to monitor and how to view the progress of a run After starting a run monitor the operation of the BenchCel Exactly what you do to monitor a run depends on the protocol that you are using For example you might need to Q Compare the motions of the robot to the protocol tasks being completed You can identify the task that is currently being performed from the position of the green ball in the process panes Because BenchWorks can schedule more than one task at a time there may be more than one green ball displayed 1 Dispense 50 0 pL to 03SandFuture quadrant 1 using 384 Disposable Tip Add and remove labware Empty liquid waste containers Fill liquid reservoirs DODO Replace an empty roll of PlateLoc seal or bar code labels IMPORTANT No errors are reported when a liquid waste container becomes full or a liquid reservoir becomes empty Exceptions to this are reservoirs on a VPrep Weigh Shelf To guard a
356. using the InitializeQ method Parameters None Returns 1 if there is a connection and 0 if disconnected Description Method used to remove a lid from a plate You will need to specify where the plate is located and where to place the lid once it is removed from the plate The DelidTo parameter is optional The BenchCel robot will hold onto the lid if the DelidTo parameter is empty The third argument RetractionCode specifies how to position the arms after delidding the plate l retract normally 2 retract only in Z to clearance that is specified in the teachpoint details 3 retract so that arms are vertical Parameters Argument Argument Range Description Type Name BSTR DelidFrom Available Name of teachpoint where the teachpoints plate with the lid is located Returns S_OK if successful other value if there was an error Description Method used to put a lid on a plate You will need to specify where the lid is located and where the plate is located If the first RelidFrom argument is blank then it is expected that the robot is holding the lid The third argument RetractionCode specifies how to position the arms after relidding the plate l retract normally 2 retract only in Z to clearance that is specified in the teachpoint details 3 retract so that arms are vertical VARIANT GetLabwareNames Chapter 14 BenchCel ActiveX controls 337 BenchCel User Guide Parameters Argument Argument Range Description T
357. ut setting pipette task parameters on page 96 Other tasks About setting task parameters on page 95 Setting Restack task parameters About this topic Restack task defined This topic describes how to set the Restack task parameters on the BenchCel Read this topic if you are Q An administrator or technician who writes protocols using the Restack task Q An operator who needs to specify parameters for the Restack task The Restack task collects plates in a stack moves them to another stack in a definable time and in a way that maintains the proper order of the plates so that they are ready to be passed to another task The Restack task can be used as part of a larger process that carries out simultaneous timed incubations of more than one plate where the goals are the following Q Time between the start of the incubation and the reading of the plate to be approximately the same for each plate Q Evaporation from the plates is to be minimized Note Two or more racks are required to use the Restack task Procedure Usage example Chapter 6 Setting task parameters BenchCel User Guide To set Restack task parameters l 2 Add the Restack task to a protocol process In the Protocol Task Parameters toolbar either Select the empty racks that you want to use for the task and click Add Click Add dynamically assigned stacker With this option the scheduler automatically assigns racks durin
358. ve lid is selected Height above the lid resting height at which to grip the lid Shown as b below Height above the bottom of the plate at which the bottom of a plate lid rests Shown as a below 228 Chapter 10 Defining labware BenchCel User Guide Property Lid departure height Lower plate at VCode Can mount Can be mounted Maximum robot handling speed Length of filter tip pin tool Related information Description Height above the bottom of the plate to which the lid is lifted Oo l Select if the plate has a thick skirt and must be lowered when on the stage of the VCode This allows the VCode to place the label above the thick skirt Select if the plate can be placed on top of another plate This property is for filter plates that are placed on top of waste plates during filtration steps of a protocol Select if another plate can be placed on top of this plate This property is for collection plates that collect filtrate from filter plates during the filtration steps of a protocol Many different plates may be able to fit under any one type of filter plate IMPORTANT The wells of the waste plate must have a large enough diameter that the filter plate does not stick on the waste plate The robot must be able to pick up the filter plate without the waste plate lifting
359. ver again select the Use single instance of plates check box in the Task Setting page of the plate icon If the plate is a tip box when this option is selected the tips will be picked up and the tip box will be moved from the VPrep At the end Chapter 7 Setting pipette task parameters 141 BenchCel User Guide of the pipetting series the tip box will be returned to the VPrep and the tips replaced in it Associating the link Because you can have more than one VPrep on a lab automation icon system you must link each pipette process link icon with one or more VPreps that you want the pipette task to be able to use You do this by setting the parameter for the pipette process link icon To link a Pipette Process task to a pipette process 1 Inthe Pipette Process Editor select the Pipette process link icon w k Pipette process 1 2 Inthe Available pipettors list of the Pipette Task Parameters toolbar select one or more pipettors to link to and click Add Available pipettors VPrep1 VPrep2 Pipettors that this task will use The selected pipettors move to the lower box and become available for the pipette task to use Related information For information about See Creating a pipette process Configuring a pipette process example on page 136 The workflow that this procedure Workflow for creating a protocol on belongs to page 85 Configuring VPrep shelves Configuring a VPrep shelf as a dev
360. w Agilent disclaims all warranties either express or implied with regard to this manual and any information contained herein including but not limited to the implied warranties of merchantability and fitness for a par ticular purpose Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing use or perfor mance of this document or of any information contained herein Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms the warranty terms in the sep arate agreement shall control Technology Licenses The hardware and or software described in this document are furnished under a license and may be used or copied only in accordance with the terms of such license Restricted Rights Legend If software is for use in the performance of a U S Government prime contract or sub contract Software is delivered and licensed as Commercial computer soft ware as defined in DFAR 252 227 7014 June 1995 or as a commercial item as defined in FAR 2 101 a or as Restricted computer software as defined in FAR 52 227 19 June 1987 or any equivalent agency regulation or contract clause Use duplication or disclosure of Software is subject to Agilent Technologies standard commercial license terms and non DOD Departments and Agencies of the U S Gov ernment will re
361. wells task tipTouchSides Integer Number of sides to The number of sides of the touch wells that you want the tips to touch task velocity Float Dispense velocity The rate at which to dispense the liquid If you selected a liquid class this value is entered automatically from the liquid library editor task volume Float Dispense volume The volume of liquid to be moved out of each pipette tip task enableShake Boolean Enable shaking Turns on shelf shaking during dispense task shakeRPM Integer Shake RPM Shaking speed in RPM task shakeDelay Integer Post dispense delay Wait time in milliseconds before shaking starts task shakeTime Integer Shake time Duration in milliseconds of shaking Mix task These properties are the same as the properties described for the Mix task Property Data type Task parameters Comments task plateName String Plate name The name of the plate task aspirateAcceleration Float Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached If you selected a liquid class this value is entered automatically from the liquid library editor task aspirateVelocity Float Aspirate velocity The rate at which to draw up liquid If you selected a liquid class this value is entered automatically from the liquid library editor Property task blowoff task cycles task dispenseAcceleration task dispenseVelocity task liquidClass task preAspirateAirGap task quadr
362. when there is power to the BenchCel Q Communication indicator light flashes yellow when communicating to the software Q Ethernet indicator light is green when there is an Ethernet connection Item Safety interlock circuit Fuse holder AC power entry On Off switch Air input Chapter 2 BenchCel overview 23 BenchCel User Guide Description The BenchCel is equipped with a safety interlock circuit that must be closed for the system to operate Normally the BenchCel is shipped with a relay jumper which allows the BenchCel to function without an interlock An external circuit may be added to provide full ESPTOP emergency stop safety Contact Velocity 1 to obtain an ESTOP and connector This circuit can also be fitted with a light curtain to shut off power to the BenchCel if the light boundary is breached Light curtains are not currently available from Velocity11 Contains the main fuse Use two 250 VAC 5 A fast acting fuses Used to connect a power cord Switches main power on I or off O Used to connect a 1 8 inch air hose to supply the BenchCel with 28 Lpm at 6 bar 1 0 cfm at 80 psi Note Required air pressure depends on your platform configuration a Chapter 2 BenchCel overview BenchCel User Guide Stacker gripper control description About this topic This topic describes the control knobs for the stacker grippers Controls for stacker On the back side of every stacker head are control k
363. xit to close the registry editor Before you start You must have Windows Administrator access to perform this task To import a registry key 1 Copy the registry file to any location on the recipient computer 2 On the recipient computer double click the registry file The information in the file will be written automatically to the registry Occasionally you may be asked to send a registry file to Velocity11 To email a registry file 1 Export the Windows registry key containing the data to a file 2 Zip the file or change its extension to re_ This is necessary because many Exchange servers do not allow reg files to be emailed 3 Email the file For information about See Sending a bug report Sending a bug report on page 321 Setting up email for error Setting up email on page 206 notification 210 Chapter 9 Administrator procedures BenchCel User Guide Obtaining information about the BenchCel network cards About this topic BenchCel computer network connections You may need to provide some of the information to your network administrator for your BenchCel to be connected to your organization s network Your BenchCel has two network cards The network connections for these cards are named WAN and LAN This topic describes the BenchCel network cards and how to obtain their network IP addresses Note Depending on how you have personalized your operating system you may need
364. ype Name BSTR DelidFrom Available Name of teachpoint where the teachpoints or plate with the lid is located blank string BSTR DelidTo Available Name of teachpoint to place teachpoints the lid after it has been removed from the plate Int nRetraction 1 3 Specify the retraction position Code of the BenchCel robot arms Returns S_OK if successful other value if there was an error Description Method to retrieve a list of defined labware The strings in this array are the options that should be used for SetLabware Parameters None Returns An array of labware names Example Visual C VARIANT vLabware m_BenchCel GetLabwareNames J SAFEARRAY psa vLabware parray if FAILED SafeArrayAccessData ps a reinterpret_cast lt void gt amp bstrArray VariantClear amp vLabware return for ULONG i 0 i lt psa gt rgsabound 0 cElements i MessageBox CString bstrArray i D SafeArrayUnaccessData psa VariantCLear amp vLabware Visual Basic LabwareNames BenchCel GetLabwareNames For i LBound labwareNames To UBound labwareNames MsgBox labwareNames i Next 338 Chapter 14 BenchCel ActiveX controls BenchCel User Guide VARIANT EnumerateProfiles Description Method to retrieve a list of defined profiles The strings in this array are the options that should be used for Initialize Parameters None Returns An array of profile names Example Vi
365. ys a log of BenchWorks actions 28 Chapter 2 BenchCel overview BenchCel User Guide Control toolbar There are seven buttons on the Control toolbar e Log In z Compile Start JJ Pause C simuiation is off E Diagnostics Button Use to Log In Logs a user into BenchWorks This provides a level of security by controlling access to software security levels See Setting protocol rules on page 49 Log Out Logs a user out of BenchWorks See Logging out of BenchWorks on page 81 Compile Checks the protocols for errors See Compilation warnings and errors on page 303 Start Begins a protocol or run See Starting a run from BenchWorks on page 70 Pause Interrupts a protocol or run after it has been started See Pausing or stopping a run on page 74 Simulate Helps you find errors that you would encounter during an actual run See Simulating a run on page 97 Diagnostics Displays the BenchWorks Device list providing access to diagnostics for all of the installed devices See Using BenchCel Diagnostics on page 251 BenchWorks pages Each BenchWorks page is accessed from a tab in the upper left corner of the page Progress Pre Protocol Editor Protocol Editor Pipette Process Editor Post Protocol Editor Device Manager Page Use to Progress Display the status of the current protocol See Monitoring overall progress on page 77 Pre Protocol Editor Create a process t

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