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609912AA: Biomek® 2000. Tutorial Guide

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1. Table 1 P20 MP20 Wash 1 P200L MP200 Wash 8 P1000L The HDR tool does not contain any modifiable parameters An HDR gel matrix is controlled under Labware Edit HDR Gel For specific instructions regarding modifying Wash Tools refer to the BioWorks Software Reference Manual Biomek 2000 7 9 Tutorial Guide Chapter 7 Document 609912 AA Click the Edit menu and click Tools The following window will appear Edit Tools Author Keyword Last Madified Filter Al E 811 h Tool Name Type Description OpY Gripper GRIPPER e HDRT HDRT Edit HDRT384 HDRT384 MP20 deliver MP20 Rename MP20 repeat MP20 MP20 MP20 Delete MP200 blowout MP200 MP200 deliver MP200 Prnt MP200 repeat MP200 em MP200 Soln 3 MP200 MP200 MP200 Import P1000L deliver P1000L P1000L repeat P1000L P1000L P1000L P20 deliver P20 Export All P20 repeat P20 P20 P20 P200L deliver P200L Close P200L repeat P200L P200L P200L xl Help In this exercise you will copy and create a new P200L tool for a viscous liquid Click P200L and click Copy The following window will appear Copy From P200 Type P200 PEE ddi New Name Help Author E eckman Instruments Keyword P200L Description 7 10 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA On the following screen type P200L Viscous and click OK Copy From pon Ds pon 7 Cancel New Name P200
2. Chapter Five Exercise 4 SS Exercise 4 Pipette Transfer with Pauses Loops and Marks In this exercise you will modify Method 1 that you created in Exercise 3 You will use two different modes of pause beginning and ending loops and marks The objectives of this exercise are to Identify and open a saved method Access a function in a method list e Use Internal Delay in the advanced section of the Pipette Transfer window Use the Pause Labware icon button on the Function palette e Use the Begin Loop icon button on the Function palette Use the End Loop icon button on the Function palette e Use marks on the Pipette Transfer window Task Modify Method 1 to pause one minute between each dispense and save the method as Method 2 Modify Method 1 to pause five minutes between each dispense and save the method as Method 3 Biomek 2000 5 1 Tutorial Guide Chapter 5 Document 609912 AA Pipette Transfer with Pauses Loops and Marks Click the Method menu and then select Open The following window will appear Open Method Author Keyword Filter X Date Created LastModified Date Time Last Run 02707738 02707788 Method Name Description hax 0 BB Default Confi Click Method 1 and select Open Biomek 2000 Chapter 5 Tutorial Guide Document 609912 AA Double click on Pipette 50 uL from A4 to A5 using P200L P250 on th
3. The tool holder with tools will appear in position A1 on the Worksurface Biomek 2000 Worksurface Side Loader Top View E Disposal B Port Valve Use the same procedure to place a Reservoir Holder located above the tool rack on the Other drop down menu at Worksurface position A4 To configure the Reservoir Holder as shown below scroll through the reservoir list and place two quarter horizontal reservoirs in the first two positions Then place two quarter vertical reservoirs in the last two positions of the reservoir holder Click OK Biomek 2000 2 7 Tutorial Guide Chapter 2 Document 609912 AA Reservoir Holder Reservoir List To add Labels use right Mouse Button quarter horizontal 4 quarter single quarter vertical Cancel Help You can add labels to a reservoir by clicking on it with the right mouse button then entering a label in the dialog The Reservoir Holder will appear in position A4 on the worksurface Biomek 2000 Worksurface Side Loader Top View 2 8 Biomek 2000 Chapter 2 Tutorial Guide Document 609912 AA Next place plates on the worksurface by selecting plates on the Labware Bar scrolling to 96 well flat selecting it then clicking on locations B4 B5 and A5 Biomek 2000 Worksurface Side Loa
4. Method 2 The Save As window will appear as follows Method Save As Author Cancel Keyword Help Description Save Unvalidated Click OK to save the method B2KEDIT Windows Application Eg N Method validation complete Click OK when the Method Validation Complete screen appears Close the method by clicking on the Method menu and then click Close Biomek 2000 5 5 Tutorial Guide Chapter 5 Document 609912 AA Move back to Method and Open and select Method 1 and then click Open Open Method Author Keyword Filter M v Date Created Last Modified Date Time Last Run 02707738 02 07 98 Method Name Description Method 1 Double click on Pipette 50 00 uL from A4 to A5 using P200L P250 on the Method list You may need to move the Workstation and the Palette out of the way lt TUTORIAL gt Method 1 Biomek 2000 Tutorial Guide Document 609912 AA Chapter 5 For Method 3 you must disable the Repeat Pipetting option so that the five minute pause can be placed between each dispense The Internal Delay feature of Repeat Pipetting only allows up to a 100 second delay so it cannot be used in this method Click Repeat Pipetting Enabled to remove the checkmark and disable it Change the Source Labware End Action to Stop Pipette Transfer Source Labware Destination Labware Tool
5. 1 00 Lid Height E 327 mm Grip Type Below bottom Lifter Height F 0 003 mm Grip at top Height 0 00 mm Grip Lid Depth G 300 mm FREE Cancel Help Note that you can hold the mouse over any of the numeric fields to display the allowable range of values for that parameter Click OK You have now created the Uniwell Plate labware definition as part of the labware library In the Edit Labware menu click Close to return to the BioWorks Edit window 7 8 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA Click Plates on the Labware Bar scroll down the menu and click Uniwell Plate Make sure the With Lid option is not enabled Click Worksurface position A6 The Worksurface will appear as follows Biomek 2000 Worksurface 00000000 00000000 00000000 00000000 6 Port Valve Tool Edit Tool editing allows you to modify tool parameters and define a new tool with a specific set of parameters In a method you may have several tool names based on a single tool type For example you may have a P200L tool on the Worksurface tool rack and use several different tool names based on that type The tool names appear in the tool list on the Pipette Transfer and Mix windows When working with liquids of varying viscosities optimizing pipette delays and overages increases pipetting accuracy Tool definitions can be copied modified and renamed for the following tools
6. Location faa P200L Location 5 Label VE Label S6 well flat Name Reservoir Holder Name 96 well flat 50 00 yl per tip j Aspirate Liquid Level m Dispense Heighd 0 00 x Fixed Repeat Pipetting Height 50 0025 Type Rate 10 Depth T Enabled Rate 102 To Deliver 0 mm Repeat Ex Prewet Blowout M Tip Touch IV Tip Touch Hiv Values Mix Hi falls m Intemal Delay I fie Pit d Source Labware Action 0 000 sec Destination Labware Action Range Range Replicates 13 C Pattern Local Pattern m Tip Handling Pattern Local Pattern Direction By Row y Tip Change Direction By Row No Tip Change Discard Tips End Action tp El End Action E Clear Zoom Marks Tip Source 11800000000000 pao z 990000000000 000000000000 BO00000000000 EO00000000000 Basic FO00000000000 81000000000000 Le 6600000000000 Cancel Clear Zoom Marks This will permit only one aspiration from the source for every dispense at the destination Since the Pause Labware function will be used for the five minute pause a mark must be placed after each destination dispense to identify its place Each successive pipetting step will dispense to the marked well on the destination plate and then move the mark to the next well in preparation for the next step Biomek 2000 Tutorial Guide Chapter
7. have been exposed to hazardous solutions Maintenance Turn the POWER off and UNPLUG the Biomek before changing fuses or performing any maintenance Do NOT autoclave Pipetting or Wash tools autoclaving may cause damage to the internal parts Perform only the maintenance described in this manual and in the Biomek 2000 Maintenance and Troubleshooting Guide Mainte nance other than specified in these manuals should be performed only by Beckman trained qualified personnel It is your responsibility to decontaminate components of the Biomek before requesting service by a Beckman Field Service Representative or returning parts to Beckman for repair Beckman will NOT accept any items which have not been decontaminated where it is appropri ate to do so If any parts are returned they must be enclosed in a sealed plastic bag stating that the contents are safe to handle and are not contaminated e Do not replenish bleach in a sterilization reservoir using the aspirate and bulk dispense transfers as the bleach may damage the Wash tool Accessory Safety Follow the appropriate safety instructions for the accessories listed below in addition to the standard safety precautions for the Biomek 2000 Biomek 2000 vii Safety Side Loader SL Verify that the voltage selector is set for current voltage by a Beckman Representative at the time of installation During method operation DO NOT touch change or otherwise interfere wi
8. m Automatic data display in SOFT max at Run View Protocol in SOFT max now Cancel Click on View Protocol in SOFTmax now button Click OK when you re finished The SOFTmax screen is displayed similar to the one shown on the next page Biomek 2000 6 11 Tutorial Guide Chapter 6 Document 609912 AA as SOFTmax le x File Edit Setup Display Control Mode Kinetics Microplate Chamber Run Time 1 00 00 SetPoint S Wavelength 340 Protocol Select File Open from the SOFTmax window Click Protocol Files at the bottom of the Open dialog to display the protocol files then select a protocol from the list shown The files on your system may vary Then click Open Open File Name SMPROTO PRO Files in c bioworks ik Cancel C Data Files Protocol Files Analysis Parameters Only 6 12 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA From the SOFT max screen select the File Return to BIOMEK option as SOFTmax BEE ES cs Setup Display Control New Open lose Save Save As Ctrl N Ctrl O ily Ctrl S Microplate Chamber Preferences Summary Page Print Batch fant mds stro Set Password Review Protocol Selection Return to BIDMEK The selected protocol file and data file will be shown in the SOFTmax Review Selected Protocol dialog Review Selected Protocol Protocol
9. you to set up labware tip racks and tools on the worksurface You will be prompted to accept the worksurface configuration When you have set up your worksurface appropriately click on the Accept All button to accept the worksurface configuration Biomek 2000 Configuration 3 16 Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA M Save Log to Disk 03 02 98 13 50 17 Method My Method begins Biomek S N Pilot 81 Ver 3 0 12 03 02 98 13 50 19 Light turned on 03 02 98 13 50 28 Pipette 200 00 pl To Deliver by P200L Tool P250 Tips From Microfuge 24 at A2 By Row Range A1 Tip Touch Aspirate Height Fixed at 25 00 Rate 10 To 96 well flat at B2 By Column Range A1 H12 4 Replicates Tip Touch Dispense Height 50 00 Rate 10 Change Tips on Replicate 03 02 98 13 50 39 Attaching tip 1 of rack at A3 03 02 98 13 50 53 From Al to Al The method will begin and the Method Run screen will be displayed as shown above showing a list of actions performed during the method run Once the run is completed you will have successfully completed exercise 2 Biomek 2000 3 17 Tutorial Guide Chapter 3 Document 609912 AA 3 18 Biomek 2000 Chapter 4 Tutorial Guide Document 609912 AA Chapter Four Exercise 3 OOOO Exercise 3 Pipette Transfer In this exercise you will perform a liquid transfer from a source to a destination using the Pipette Transfer icon button and window The objectives of
10. 08 Type al ia i To Contain Y 0 n mm P20 deliver Prewet Blowout E TipTouch P200L deliver E Tip Touch TET Mix lida P200L repeat T Mis 1 Source Labware Action Destination Labware Action z Range Range heplicates 13 C Patter Local Pattern r Tip Handling C Pattern Local Pattern Tip Change Direction Box by Column No Tip Change End Action Stop Direction Box by Column End Action Stop Discard Tips iem 1000000000000 n 4090000000000 21000000000000 BOSOOC0000000 B000000000000 Advanced ODooOooOoOoOOOO 900000000000 EA 6000660600000 Clear Zoom a Marks Cancel Clear Zoom Marks Click the volume bar either position the cursor or highlight the area and type in a volume of 50 uL Left Section In the Source Labware section set the Aspirate Height to 0 0096 so that the pipette tip will go to the bottom of the reservoir Click Tip Touch 4 4 Biomek 2000 Chapter 4 Tutorial Guide Document 609912 AA Since liquid will be aspirated from only one horizontal quarter reservoir click on that horizontal quarter reservoir position Click the End Action arrow and select Repeat Same Labware Repeat Same Labware tells the system to repeat the range at the source or destination until the other range is fille
11. 200 00 ul per tip Aspirate Liquid Level m Dispense Fixed Height 50 002 Type Depth To Deliver y mm mm r Prewet Blowout u Tip Touch TTE I E Touch aa Mix VII BEST VIR Ma aile Source Labwere Action Destination Labware Action Range Range Replicates C Patten Local Pattern Tip Handing Patten Local Pattern Direction ByRow y Tip Change Direction Ey Column y End Action to H At New Replicate End Action to y Discard tips Tip Source P250 y Advanced Help Clear Zoom Marks Cancel Clear Zoom Marks Lo Um 0O m p In this function the Biomek pipettes 200uL from location A2 to B2 on the worksurface using the P200L tool When you have finished viewing the configuration click Cancel to exit the dialog without making any changes Next we will modify the configuration of the second transfer function 3 8 Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA Double click on the second function the third line of the method to display the Pipette Transfer dialog Pipette Transfer Source Labware Location 82 Label S6 well flat Name 96 well flat Aspirate Liquid Level Height 50 00 Fixed Depth 0 mm Prewet Tip Touch Source Labware Action Range Pattern Local Pattern Directi
12. 4 appears The completed window appears as shown on the next page 4 6 Biomek 2000 Chapter 4 Tutorial Guide Document 609912 AA Pipette Transfer m Source Labware Destination Labware Tool Location z P200L Location ps Label Label S6 well flat Dispense Volume Name Reservoir Holder 50 002 ul per tip Name S6 well flat Aspirate Liquid Level Dispense Height Ez Fixed sil pee Estr Height 50 002 Type Rate 105 Depth v Enabled Rate 10 To Deliver 0 mm mm Repeat 45 Prewet T Blowout Tip Touch Iv Tip Touch TETE Mix MI vales Internal Delay T fiy e ari des Source Labware Action 000 sec Destination Labware Action a Range Range heplicates U Pattern Local Pattem Tip Handling Pattem Local Pattern Direction e y Row End Action Repeat Same Labware Y Tip Change Direction e y Row No Tip Change y End Action Stop Discard Tips Tip Source A 400000000000 p z 9900000000000 HOOSCOCOCOCO0SO HOOCOOSCOOC00S EOO00000000000 Basic FOOOOOOOOOOOO 000000000000 AA o o00000000000 Clear Zoom Marks Cancel Clear Zoom Marks Click OK to complete this function The following transfers will occur e 50uL of liquid is dispensed four times from a single 200 uL aspiration using a
13. 5 Document 609912 AA Click the Marks button on the bottom right hand corner of the Destination Labware section The window will appear as follows Marks Usage C Use no Marks C Seta New Mark o se an existing Mark Click Use then set new mark on the Marks Usage window and click OK The pipette transfer window will look like this Pipette Transfer Source Labware Destination Labware Tool Location A4 P200L Location P5 Label i Label S5 well flat Volume Name Reservoir Holder 50 00 pl per tip Name S5 well flat Aspirate Liquid Level Dispense Height 0 00 Fixed Repeat Pipetting Height 50 00 Type Rate 10 Depth T Enabled Rate 10 To Deliver y D nm mm Repeat 4 Prewet I Blowout Iv Tip Touch v Tip Touch Mix Mig Values r Internal Delay E My TEM BIUES Source Labware Action j 0 000 ES em Destination Labware Action Range Range Replicates U C Patten Local Pattern r Tip Handling Patten Local Pattern Direction By Row y Tip Change Direction By Row End Action Stop No Tip Change y End Action Stop Discard Tips Bones 200000000000 mo z 900000000000 000000000000 1900000000000 E000000000000 Basic FH000000000000 8000000000000 Help OOO0000000000 OK Cancel Clear Zoom M
14. Path Filename C BIOWORKS SMPROTO PRO Data Path Filename CABIOWORKS dat Automatic data display in SOFTmax at Run View Protocol in SOFT max now DK Cancel Click OK to accept the settings and return to BioWorks Biomek 2000 6 13 Tutorial Guide Chapter 6 Document 609912 AA Resume here if you don t have SOFTmax You can now specify a move of the 96 well flat plate from the Plate Reader to the disposal by clicking the Move Labware icon clicking on location A1 then clicking on the disposal Your worksurface should look like the one shown below Biomek 2000 Worksurface Q Ho io O O io io io io R 00000000 0000000017 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 OODODODO Disposal The Method Window should look like the one shown below lt BOOK1 gt Method 3 Initial Configuration Gripper Move B6 Lid to Disposal Gripper Move A5 Lid to Disposal Gripper Move B4 Vacuum Collar Std to A4 Gripper Move B5 Filter Plate to A4 retain lid present Gripper Move A4 Lid to Disposal if you Pipette 2 00 pl from B6 to A4 using MP20 P20 skipped the acuum Control Open SOFTmax System Pause for 00 01 00 Message steps acuum Control Closed Gripper Move 44 Filter Plate to Disposal Gripper Move A4 Vacuum Collar Std to B4 Gripper Move A4 96 well flat to Al Execute P
15. Purification 8 columns Version 2 0 Plasmid 96 Semi automated Plasmid Purification 12 columns Version 2 0 y Open Cancel Help Click Open to proceed 3 4 Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA BioWorks loads the method then displays the Method Function Palette and Worksurface windows as shown below Method Function window Palette BOO Demo BioWo ethod E d ZI X Method Edit View Configure Transfer rol Device Options Window Help pele e fal ajaja viz S vive Pipette 200 00 pil from A2 to B2 using P200L P250 Pipette 5 00 ul from B2 to B3 u Mg P200L P250 END Plates AA C Tips C Tubes P he dej Devices T E C Other a 8 2 wl with Lid SS o 000 o pese ooog tels ODD 000001 0000 pagoa 0956 B5 6596 6506 or Help press reni A Worksurface window Before we begin editing the method let s review some important features of the Edit window and its child windows Make sure that the Initial Configuration line in the Method window is highlighted before you begin placing or moving labware on the worksurface The labware and locations set when the Initial Configuration line is highlighted will be used as the starting point BioWorks prompts you to verify that labware is arranged properly when you start a method Biomek 2000 3 5 Tutorial Guide Chapter 3 Document 609912 AA e To p
16. necessary They may already be displayed from the previous exercise Pipette Transfer Source Labware Took Destination Labware Location pa P200L w Location 5 Label Label S5 well flat Volume Name F eservoir Holder 50 0054 ul per tip Name S5 well flat Aspirate Liquid Level Dispense Height 0 002 Fixed Repeat Pipetting Height 50 004 Type Rae 102 Depth v Enabled Rate 1024 To Deliver 0 mm Repeat 4 Prewet I Blowout v Tip Touch v Tip Touch Mix Min Valles Internal Delay la M i idi Values Source Labware Action oo can Destination Labware Action Range Range Replicates U C Patter JiLocal Pattern Tip Handing Pattem Local Pattern Tip Change Direction By Row Direction e y Row No Tip Change End Action Stop End Action Repeat Same Labware Discard Tips Tip Source A B00000000000 p El H000000000000 2000000000000 BIO00000000000 B000000000000 Basic HOG0000000000 81000000000000 DB 660000000000 Clear Zoom Marks Cancel Clear Zoom Marks Enter an Internal Delay of 60 00 seconds This delay will cause a 60 second pause between each dispense Biomek 2000 Chapter 5 Tutorial Guide Document 609912 AA Click OK to save the change Go to the Method menu and select Save As Type in
17. 00 Chapter 2 Tutorial Guide Document 609912 AA You have successfully edited the default configuration Close the method by clicking Method then clicking Close Now when you open a new method in this lab book the configuration that you just created will be used for the default configuration To open a new method click Method then click New amp amp lt TUTORIAL gt BioWorks Method Edit ajaja v 21x Method Edit View Options Help 1 lt TUTORIAL gt Default Config 2 lt BSPBOOK gt Demo NUM Z You will be prompted to select the Initial Configuration for the new method Biomek 2000 2 11 Tutorial Guide Chapter 2 Document 609912 AA New Method Initial Configuration Cancel Help C Clear Configuration C Use Curent Configuration When you select Use Default Configuration the labware and tools you just configured are automatically used US lt TUTORIAL gt Method 2 BioWorks Method E dit Method Edit View Configure Transfer Control Device Options Window Help lt TUTORIAL gt Method 2 C Plates Initial Configuration Tips C Tubes C Devices C Other with Lid Biomek 2000 Worksurface Side Loader Top View Disposal O i Qu 0000000015 00000000 000000004 000000007 00000000 00000000 00000000 jooooooooP 00000000 00000000 00000000 0000000 You have now successfully completed exercise 1 2 12 Biomek 2000 Chapter
18. 0L P250 Click the Edit Menu and select Labware The window will appear as follows 7 2 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA Edit Labware Author Keyword Filter All z 811 h Library Labware Last Madified E Modular Reservoirs Labware Name Labware Type l i apy 1 0 Minitubes Tube Module small Edit 1 4 Minitubes Tube Module small 10 75 160 Tube Rack large Hename 10 x 75 24 Tube Module small 12 x 75 128 Tube Rack large m 12 x 75 24 Tube Module small 13 x 100 24 Tube Module small 13 x 100 96 Tube Rack large 384 well flat Titerplate or similar 384 well square Titerplate or similar 48 well Titerplate or similar B well Titerplate or similar 96 well deep Titerplate or similar 96 well flat Titerplate or similar 96 well square Titerplate or similar 96 well u bottom Titerplate or similar SB well v bottom Titerplate or similar 96 well vinyl flat Titerplate or similar 96 well vinyl u bot Titerplate or similar x Help In this exercise we will modify a 96 well plate From the Edit Labware window click the labware name 96 well flat then click Copy Biomek 2000 7 3 Tutorial Guide Document 609912 AA Chapter 7 Edit Labware Author Keyword Filter Beckman Instruments 96 well flat Library Labware Last Madified C Modular Reservoirs 0710736 La
19. 2000 6 9 Tutorial Guide Chapter 6 Document 609912 AA Vacuum Valve Close M Timed zem Lose EUR C Open 00 01 0 7 Help Click OK when done Remove Filter Plate Now we will use the move icon button to remove the filter plate from the manifold and put it in the Disposal Cir Click the Move Labware icon click at location A4 then click the Disposal This will use the Gripper to dispose of the filter plate The worksurface should now look like the one shown below Biomek 2000 Worksurface Disposal OOOOOOOO OOOODODOOR 00000000 00000000 pD OOOODODO 00000000 00000000 00000000 00000000 00000000 00000000 j oooooooo Setup Flask Move the Plate to the Plate Reader and Run Plate Reader Protocol The final portion of the exercise will move the 96 well flat plate from the Vacuum Manifold to the Plate Reader and take a reading on the plate using the Plate Reader icon button on the Function Palette shown on the next page 6 10 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA T Click the Move Labware icon click at position A4 then click the Plate Reader at A1 as the destination This moves the plate to the Plate Reader Next click the Plate Reader icon to start the SOFT max software for control of the Plate Reader Review Selected Protocol Protocol Path Filename m Data Path Filename
20. 3 Tutorial Guide Document 609912 AA Chapter Three Exercise 2 DR Exercise 2 Editing and Running a Method This section will guide you through the basics of editing by changing an initial configuration and a transfer function using the Demo method To begin double click on the Edit icon in the BioWorks program group This displays the Edit window as shown below d lt BOOK1 gt BioWorks Method E dit Method Edit View Options Help csse ala aa ales vis 5 218 The name of the current lab book is shown in angle brackets at the top of the window If the BOOKI lab book is currently the default skip to the next step in the middle of page 3 4 Otherwise change the lab book to BOOKI by selecting Options Select Lab Book from the Menu bar Biomek 2000 3 1 Tutorial Guide Document 609912 AA Chapter 3 Select Lab Book KE lt BOOK1 gt BioWorks Method Edit Method Edit View EMEA Help Dist x de Ajajo 2 8 BioScript Pro Lab Book Manager Select Lab Book Default Configuration Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA This displays the Select Lab Book dialog Select Lab Book Current Lab Book BOOK NAME PATH LABIO DORESABODETA CBI DORES ANE BODE Highlight the BOOK 1 lab book then click on the Select button When the Edit window displays BOOK as the current lab book select Method Open from the Menu Bar of the Edit window This wil
21. 5 Document 609912 AA 5 14 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA Chapter Six Exercise 5 SS Exercise 5 BioWorks Device Functions In this exercise you will use BioWorks Device Functions to control a Vacuum Valve Unit and to operate a Biomek Plate Reader You will also use the Gripper Tool to handle labware and lids on the worksurface Note This exercise utilizes the following accessories i e Gripper Tool Plate Reader and 96 Filtration System vacuum manifold If you don t have all of this equipment you may practice this exercise in the BioWorks Edit mode but you will not be able to run the method created Task In this exercise you will create a method to do the following Remove the lids from the labware and tip racks on the worksurface e Place a Vacuum collar and a filter plate on the Vacuum Manifold Perform a pipette transfer to the filter plate on the vacuum manifold e Aspirate the filter plate to collect sample into a 96 well flat plate Move the 96 well flat plate to the Plate Reader and take readings Open a New Method and Set the Initial Configuration Begin by closing any open methods Then select Method New from the command bar Select Clear Configuration to start with a clear worksurface for this method then click OK Biomek 2000 6 1 Tutorial Guide Chapter 6 Document 609912 AA New Method Initial Configuration OK Clear Configuratio
22. A ET and select the labware A5 with the stopwatch The following window will appear m Pause Location Location ps Label B amp well flat Cancel Name 96 well flat Help OK y m Pause Duration gir s 00 05 00 24 C Until operator cancels Click Duration and highlight the Duration field Type 00 05 00 use left and right arrows to select digits Click OK to insert the function in the Method list The Method list will appear as follows lt TUTORIAL gt Method 1 Initial Configuration Clear Marks at Ab Pipette 50 00 il from A4 to A5 using P200L P250 Pause Labware A5 00 05 00 5 10 Biomek 2000 Chapter 5 Tutorial Guide Document 609912 AA To specify the transfer from the reservoir to the first twelve wells of the 96 Well Flat plate you can use a loop to repeat the Pipette Transfer function and the Pause Labware function This can be achieved by inserting a Loop before the Pipette Transfer function with a count of 12 and inserting an End Loop before End on the method list Do this as follows e To insert a loop first highlight the pipette function on the method list to insert the loop before that function Now click the Begin Loop icon button on the Function Palette E3 Specify the loop in the dialog as follows Begin Loop v Loop for count 14 T Loop for time 00 00 00 Cancel Loop until operator cancels Help Loop until all labwa
23. Beckman Part No 609912 AA April 1998 Tutorial Guide BECKMAN Beckman Instruments Inc 2500 N Harbor Blvd Fullerton CA 92834 3100 Copyright 1998 Beckman Instruments Inc Printed in U S A Copyright Licenses and Trademarks Copyright Beckman Instruments Inc 1998 All rights reserved No part of this publication may be reproduced transcribed transmitted or translated into any language in any form by any means without the written permission of Beckman Instruments Inc The product warranty does not apply to software which is warranted on an as is basis without fitness for any specific purpose with the exception of the media which is warranted against defects in materials and workmanship for a period of one year The software is copyrighted and may not be altered or given to a third party without the written authorization from Beckman Instruments Tutorial Guide Document 609912 AA Notice Safety Notice Safety During Installation 12 eren eee eene teet e ette eec re be eonun V Electrical Satin uei e tue ene v Safety Against Risk of Fire uec eR aaa vi Chemical and Biological Safety innsir tiesne eneret a e a nen vi Moving Parts e Ad vi Cleaning on rci tein etd testet ueste ERI RE Ina da pat tear reete vii Maintenance onere ii tapia vii Ve aeri nm E X vii Side Eoader SI iie te Vtt eek acere a eee ee Here as HERI las vili SLE TU Bator sca 2 4 ipeo e HE PUO adas diste viii High
24. DRAKSABSPBOOKA NEW BOOK Set as Current Lab Book Help Biomek 2000 Chapter 2 Tutorial Guide Document 609912 AA When the Copy Lab Book dialog is displayed enter the name Tutorial for the New Name and specify a path as shown Copy Lab Book Copy From NEWBDOK New Name TUTORIAL New Path CABIOWORKSNTUTORIALN Cancel Help Click OK The contents of the source lab book is then copied into the new lab book and the new lab book Tutorial is shown in the list of lab books Select Tutorial as the Current Lab Book by highlighting Tutorial from the list then clicking the Set as Current Lab Book button EDITORES BODE TS CMW OR ES Ewa ODE pai fe C pingit 1 15 PECA Sat arr Curl Lait Back Hain Cima Close the Lab Book Manager by clicking the Close button Now that we have a new Lab Book to work in we will use the Edit module to build a method Double click on the Edit icon button to access BioWorks Method Edit Biomek 2000 2 3 Tutorial Guide Chapter 2 Document 609912 AA S Bioworks File Edi View Help Wo X BioScript BioWorks Advisor Diagnostics Lab Book Manager Af 8 Readme Workstation System Config Server Click Options in the menu bar then select Default Configuration EE TUTORIAL Biota es Metal EA E yew 2 4 Biomek 2000 Tutorial Guide Chapter 2 Document 609912 AA When the Default Configuration is displayed click the Setup b
25. Density Replicating System sess enne ix Plate Reader dinero a a ix Wash SysStem i e eee itll edere ete tue tiere te rei tin re re pad te ea oe ede redes X Heater Cooler Block sien o eee in X Biomek 2000 Safety Feat res einer tite iiie erred er na n aer Daba erae PL ea Tode e X Summary of Warning Information eese enne nennen eren X Introduction PHETACE ERR 1 1 Exercise 1 Exercise 1 Creation of a Default Configuration rr 2 1 Exercise 2 Exercise 2 Editing and Running a Method seen 3 1 Changing the Initial Configuration sess 3 6 Viewing and Editing a Transfer Function eese 3 7 Adding Transfer Function orte ertet ee ete Idee tete er eie re tectae 3 10 Inserting Messages and Pauses esses eerte nennen enne 3 12 Saving Method suciedad 3 15 Runinga Method rre Erster te deter ei ele Cb quina e etn deren aee 3 16 Biomek 2000 i Table of Contents Tutorial Guide Document 609912 AA Exercise 3 Exercise 3 Pipette l ransfer eerie ee den t dte e De eo eter etes 4 1 UL E 4 1 Pipette Trastero antes adeb ee osos 4 1 Center SectIOn oic epe Leiden e net cett gebe ere erbe o eene nee bt eg boc cd 4 4 Left Section ica 4 4 Right Section ii ia Last eere rd 4 5 Center Section Advanced aisne eerren in Ee ter eei R e dee rer eda 4 6 Exercise 4 Exercise 4 Pipette Transfer with Pauses Loops and Ma
26. Display message until canceled moro E Display message for tne 00 01 00 EN Click OK when you are finished 3 14 Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA BOOK1 Demo A E Initial Configuration Pipette 200 00 ul from A2 to B2 using P200L P250 System Message until cancelled Alarm System Pause until 00 01 00 i from B2 to B3 using P200L P250 Saving a Method Before proceeding you should save your edited method under a different file name To do so select Method Save As then enter a file name of your choice in the dialog Method Save As Author Ceres K d EVIWIDT Help Description Save Unvalidated Note that when you save a method it is automatically validated unless you request otherwise A method must be validated before it can be run Biomek 2000 3 15 Tutorial Guide Chapter 3 Document 609912 AA Running a Method Before you run a method for the first time on a new Biomek you must perform an alignment check and re align the Biomek and Side Loader if necessary Refer to the Biomek 2000 Hardware and Software Installation Guide for alignment instructions If the Biomek has already been aligned and been in use you can run your new method now To run the method click on the Run icon in the icon bar of the BioWorks Edit window Bel The Biomek 2000 Configuration screen will appear This screen will serve to remind
27. Edit Biomek 2000 1 1 Tutorial Guide Chapter 1 Document 609912 AA 1 2 Biomek 2000 Chapter 2 Tutorial Guide Document 609912 AA Chapter Two Exercise 1 SS Exercise 1 Creation of a Default Configuration In this exercise you will become familiar with the method build window of BioWorks Edit You will build validate and save a Default Configuration that contains tools reservoirs tip racks and plates on the worksurface The objectives of this exercise are to e Identify the components of the BioWorks Method Edit window e Modify the worksurface Setup e Place tools and labware on the worksurface e Save a method as the Default Configuration Locate the BioWorks Program Group then double click on the Lab Book Manager icon Biomek 2000 2 1 Tutorial Guide Chapter 2 Document 609912 AA Biow orks A ES File Edit View Help W ogg BioScript Bio orks Aun Advisor Diagnostics E dit Lab Book Manager Readme Workstation System Config Server 1 abject s selected 338 bytes This displays the Lab Book Manager window To create a new lab book for use in this tutorial select Newbook from the list of installed lab books then click Copy From List Lab Book Manager x Current Lab Book Copy From List Delete Recover PSPBOOK Copy From Other Source Rename Resize NAME PATH Print List CABIDWORKSSBODKTS LSBICWDOBKSSNEWB LCOKS CABIOW
28. L Viscous Bun Author Beckman Instruments Keyword ppt Description In the Edit screen click the new tool name P200L Viscous and click Edit The following window will appear P200L Viscous Tool Type P200L earns Source Destination Channels 1 Prewet Minimum Volume 5 00 pl Aspirate Maximum Volume 200 00 p Dispense n Maximum Capacity 250 00 ul DLE 3 JV Liquid Level Sensing Tip Touch Tips y Bverages r Calibration Prewet 10 00 Slope 008475 mm ul 1 p Blowout 100024 Offset 0 024 mm To Deliver 10 00 E pl Bias 10 00 Help The tool type number of channels minimum and maximum volume and maximum capacity are predefined values specific to that tool The Tips field includes all possible tip choices for that tool You can choose a specific tip to be used with that tool definition if applicable In this case however both tips are acceptable The Tool Delays are used to optimize the performance of a tool Overages are volumes of liquid or air that assist in the transfer of a liquid Definitions of these fields are found in the Bio Works Software Reference Manual Biomek 2000 7 11 Tutorial Guide Document 609912 AA Chapter 7 To improve the pipetting performance for a viscous liquid in this example you will enter values for Aspirate Dispense and Blowout delays and a Blow
29. P200L tool and Repeat Pipetting e One horizontal quarter reservoir is used as Source Labware e Liquid is aspirated from the bottom of the reservoir with a tip touch after each aspiration e The same source is revisited after the four dispenses since the source end action is Repeat Same Labware e 12 wells in a row on a 96 Well Plate are used as Destination Labware Liquid is dispensed at 50 of the well s height with a tip touch after each dispense e The pipette transfer function ends after the 12 wells receive liquid since the destination end action is Stop Biomek 2000 4 7 Tutorial Guide Chapter 4 Document 609912 AA The Method List window will appear as follows lt TUTORIAL gt Method 1 A x Initial Configuration Pipette 50 00 ul from A4 to A5 using P200L P250 Click the Method menu and then click Save Save Method Method Name Method 1 EE 4 8 Biomek 2000 Chapter 4 Tutorial Guide Document 609912 AA Type in the name Method 1 then click OK to save the method as Method 1 The method will be validated and saved and the following window will appear B2KEDIT Windows Application N Method validation complete Click OK Close the method by selecting Method Close You have successfully completed Exercise 3 Biomek 2000 4 9 Tutorial Guide Chapter 4 Document 609912 AA 4 10 Biomek 2000 Chapter 5 Tutorial Guide Document 609912 AA
30. Stop so that only these wells receive liquid Biomek 2000 4 5 Tutorial Guide Chapter 4 Document 609912 AA Pipette Transfer r Source Labware Took Destination Labware Location pa P200L Location ps Label 3 Label S6 well flat Tae Dispense Volume Name eservoir Holder 50 00 ul per tip Name S5 wel flat Aspirate Liquid Level Dispense Height 0 00 EA Fixed Height 50 00 Type Depth To Contain y 0 00 mm Prewet Blowout M Tip Touch Iv Tip Touch Mix Min elves Mix Miralles Destination Labware Action r Source Labware Action Range Pattern Local Pattern Direction Box by Column End Action Repeat Same Labware Range Replicates 1 Tip Handling C Pattern Local Pattern Tip Change Direction e y Row No Tip Change End Action stop Discard Tips Tip Source A 00000000000 m sif eoooooooooo ejoDooooooOOOO BO000000000000 E000000000000 Advanced FH000000000000 siODOOOOOOOOOO E Re 1550666000000 Clear Zoom Marks Cancel Clear Zoom Marks Center Section Advanced Go to the center section of the Pipette Transfer window and click the Advanced button located in the lower portion of the window section to show Repeat Pipetting further up Click Enabled for Repeat Pipetting Click the Repeat up arrow until
31. acking parameters will be utilized for purposes of creating a new labware definition For more information on utilizing Liquid Level Tracking please refer to the BioWorks Software Reference Manual 7 6 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA To create a new labware definition you must measure the labware s inner well depth top height including labware holder and inner top diameter of the well Assume that the following dimensions were obtained by measuring the plate Well Depth 11 1 mm Top Height 20 17 mm Top Diameter 7 0 mm If you are using a Gripper tool or Side Loader to automate lid and labware handling you must also measure the dimensions for the grip parameters and edit them as needed Lip Height 2 6 mm Because the plate has a thin base and ridges at the sides we will keep the Grip Type as Below Bottom Note The height of the labware includes the height of the labware holder Beckman Labware Holder Part No 609120 has a top height of 5 37 mm If you use a custom labware holder you must measure the height of the holder and include it in the top height field The sum of the Zones under Liquid Level Tracking equal the maximum volume of a well of the new labware definition Each well of the Uniwell Plate has two zones a conical shaped zone with a flat bottom for the bottom third of the well and a cylindrical shaped zone for the top two thirds of the well It is extremely important to c
32. ameters Take a moment to review this window and consider the task identified at the beginning of this exercise Direction Box by Column End Action Step e Pipette 50 uL from the first top left quarter horizontal reservoir into the first 12 wells row of the 96 Well Flat plate in position A5 Perform a tip touch at source and destination labware There is more than one way to write a method for pipetting 50 uL from one reservoir location to 12 wells of a 96 Well Flat plate In order to perform this task in relatively few steps while maintaining an accurate transfer Repeat Pipetting will be utilized Using a P200L tool four dispenses of 50 uL each can be made from one liquid aspiration Therefore it will take only three aspirations to fill 12 wells of the 96 Well Flat plate Biomek 2000 4 3 Tutorial Guide Chapter 4 Document 609912 AA Configure the Pipette Transfer window as follows Center Section To choose a P200L tool to pipette in a single row click the arrow on the Tool menu and then click on the P200L tool Pipette Transfer r Source Labware Tod Destination Labware ool Location im MP20 repeat Location ps Label Tipa Label S5 well flat Name Reservoir Holder eire blowout Name S5 well flat Aspirate Liquid Level MP200 deliver Dispense 3 21552 P MP200 repeat 7 7 Height 21 55 Fixed b4 MP200 Soln 3 Height 17
33. ar j Clear Zoom zu Marks 5 8 Biomek 2000 Chapter 5 Tutorial Guide Document 609912 AA Click OK to save the Pipette Transfer window Since a mark is set on the Pipette Transfer window a Clear Marks function should be inserted before the pipette transfer function in the Method List to erase any existing marks on that labware location Highlight the line in the method which specifies the Pipette Transfer then click the Clear Marks icon button on the Function Palette A and move the cursor to position A5 Click position A5 The Clear Marks window appears as follows Clear Marks Clear all marks Single labware AS Cancel Label 8 well flat Help Meme 26 wel flat EE Choose Single labware to clear marks only on this piece of labware and click OK Selecting Clear all marks clears marks on all locations The Method list will appear as follows Note that the new line is inserted above the highlighted line lt TUTORIAL gt Method 1 OF ES After completion of the clear marks one 50 uL transfer will be made and the system will stop In order to pause five minutes after the transfer a Place a Hold Until on a Piece of Labware function should be added to the Method list Highlight End on the Method list Click the Pause Labware icon button on the Function Palette shown on the next page Biomek 2000 5 9 Tutorial Guide Chapter 5 Document 609912 A
34. as follows Make sure the Tool is set to P200L Set the volume to 100ul per tip Set the Source Labware Action to Range and the Direction to By Row Use the cursor to highlight the top row of wells on the source plate Set the Destination Labware Action to Pattern and Direction to By Row Use the cursor to highlight at least 6 wells of the destination plate in any pattern you choose Note that if you select more than 6 wells only the first six will be used because there are only 6 source wells selected If you want to fill more than 6 wells on the destination plate you could either select more source wells to fill each with a different source or change the Source End Action to Repeat Same Labware which would reuse the source wells until all of the destination wells were filled Select a Tip Touch at the source and at the destination Select Fixed for Liquid Level Biomek 2000 3 11 Tutorial Guide Chapter 3 Document 609912 AA The dialog should look like the one shown on the following screen patterns for the destination plate may be different Pipette Transfer Source Labware Tod Destination Labware Location E P200L Location ps Label M icrofuge 24 Label S5 wel flat Wolume Name Microfuge 24 100 a deu Name S5 well flat Aspirate Liquid Lewel Dispense Height 0 00 Fixed y Height 0 003 Type Depth To Contain y 0 00 mm P
35. ble the Message Alarm and set the Interval if you wish The dialog should look like the one shown System Pause Message Edit System Activity r System Actions Pause System eset clact 00 01 00 El v Message C Pause until clack reads E C Pause system Far 00 01 00 C Pause system until cancelled Display message until cancelled p C Display message for time 00 01 00 mil Message Message Alarm 1 v Enable Interval 10 sec Cancel Help Click OK to add the Message step to the method Note that we have not yet added the pause itself Biomek 2000 3 13 Tutorial Guide Chapter 3 Document 609912 AA Now insert the system pause between the message and the next pipette transfer Highlight the second pipette transfer line in the method note that new method steps are always inserted before the highlighted line in a method Click on the Pause System button again This displays the System Pause Message dialog Specify a pause by selecting the dialog items as follows Set System Activity to Pause System Set System Actions to Pause system for then set the timer to 1 00 minute The dialog should look like the one shown below System Pause Message Edit System Activity r System Actions v Pause System C Reset clack E Message C Pause until clock reads 00 01 00 E Pause system for 00 01 00 E C Pause system until cancelled C
36. bware Name Labware Type 96 well flat Titerplate or similar Copy 1 0 Minitubes Tube Module small Edit 1 4 Minitubes Tube Module small 10 x 75 160 Tube Rack large 10 x 75 24 Tube Module small 12 x 75 128 Tube Rack large 12 x 75 24 Tube Module small 13 x 100 24 Tube Module small 13x 100 96 Tube Rack large 384 well flat Titerplate or similar 384 well square Titerplate or similar 48 well Titerplate or similar B well Titerplate or similar Export 96 well deep Titerplate or similar 96 well square Titerplate or similar 96 well u bottom Titerplate or similar 96 well v bottom Titerplate or similar 96 well vinyl flat Titerplate or similar 96 well vinyl u bot Titerplate or similar y Help a Rename Delete Print Import Export All Pell lee You will add a new style of 96 well plate to the Labware Library The Uniwell MicroPlate has flat wells with conical sides and a slightly larger maximum value than the standard 96 well flat plate In the Copy Labware window type Uniwell Plate as the new name Copy Labware Copy From S6 well flat Type fr iterplate or similar Cancel New Name Uniwell Plate Help Author Beckman Instruments Keyword 36 well flat Click OK when done Uniwell is a trademark of Elkay Products Inc 7 4 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA The newly named labware is now part
37. by qualified service personnel Safety During Installation Do not lift the Biomek 2000 by the bridge Two people are needed to lift the Biomek grasping the front rail and the back support Do not connect the Biomek to an electrical outlet until it is positioned properly on the bench Electrical Safety To reduce the risks of electrical shock this equipment employs a three wire electrical cord and plug to connect the equipment to earth ground To preserve this safety feature Make sure the matching wall outlet receptacle is properly wired and earth grounded e Never use a three to two wire plug adapter e Never use a two wire extension cord or a non grounding type multiple outlet receptacle strip e Any servicing of this equipment which requires removal of any covers or panels can expose parts which involve the risk of electric shock or personal injury Refer such servicing to Beckman trained qualified personnel e Do not use any power supply other than the type supplied for the accessory for the Biomek 2000 as appropriate for the country where it is installed Biomek 2000 V Safety Safety Against Risk of Fire Certain electrical circuits within this equipment are protected by fuses against over current conditions For continued protection against risk of fire replace fuses only with the same type and rating specified Chemical and Biological Safety Normal operation of this equipment sometimes involves the use of r
38. d Pipette Transfer m Source Labware Toot Destination Labware Location pa P200L Location ps Label Label S5 well flat Dispense Volume Name Reservoir Holder 50 00 ul per tip Name S5 well flat Aspirate Liquid Level Dispense Heighd 0 00 Ea Fixed y Height 0 00 Type Depth To Contain y 0 a mm Prewet v Tip Touch Mix Im ales hie Wales Source Labware Action m Destination Labware Action Range Range Replicates 1 C Pattern Local Pattern Tip Handling C Pattern Local Pattern Tip Change Direction Box by Column Direction Box by Column y No Tip Change y End Action Stop End Action Repeat Same Labwart eee MOOCOCOOCOO0OO p a ooooooooooo 2000000000000 000000000000 E000000000000 Advanced H000000000000 8000000000000 LL 4060000000000 Clear Zoom Marks Cancel Clear Zoom Marks Right Section In the Destination Labware section set the Dispense Height to 50 00 so that liquid will be dispensed at 50 of the well s height Click Tip Touch Range will automatically be selected for the Destination Labware Action Since the dispense will be to 12 wells in one row click the Direction arrow and click By Row Click and drag from well A1 to A12 on the 96 Well plate diagram Ensure that the End Action is on
39. der Top View 00000000 00000000 00000000 00000000F Disposal B Port Valve Next select tips on the Labware Bar scroll to P250 tips and click on positions A2 A3 and B3 Biomek 2000 Worksurface Side Loader Top View 000000000000 000000000000 000000000000 000000000000 000000000000 0000000047 00000000F Disposal 00000000 00000000 00000000 Biomek 2000 Tutorial Guide Chapter 2 Document 609912 AA Place P20 tips at B1 and B2 Biomek 2000 Worksurface Side Loader Top View a 0000000 0000000 0000000 0000000 0000000 00000000 0000 0000 000 0000 0000000000 00000000000 00000000000 000000000000 00000000 Disposal 00000000 00000000 00000000 00000000 00000000 6 Port Valve To save this configuration as the Default Configuration go to the Method menu and choose Save As Verify that the method name is specified as Default Config The name must be typed exactly as shown for BioWorks to recognize this as a default configuration Method Save s Name Default Config Author FETU Keyword I Comcel Help Description Save Unvalidated Click OK The default method is automatically validated and the Method Validation Complete screen appears B2KEDIT Windows Application Eg Method validation complete Click OK to acknowledge the prompt 2 10 Biomek 20
40. drag selection was done for wells A1 through H12 Click OK to accept the transfer configuration Controlling the Vacuum Manifold with a Device Function Now insert a control function in the method to turn on the Vacuum Manifold and aspirate the filter plate For this you will use the Device Control icon button on the Function Palette shown below AS Click the Device Control icon button then click location A4 Because there is a Vacuum Manifold device at this location the Vacuum Control dialog appears Select Open to open the valve and begin aspiration then click OK 6 8 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA Vacuum Valve C Close Timed OUI E Cancel Open 00 01 04 Bessa Help Next insert a pause in the method to control the timing of the aspiration step Click the Pause icon button on the Function Palette Set the Pause parameters as shown below System Pause Message Edit System Activity m System Actions IV Pause System Reset clack M Message Pause until clock reads 00 01 00 Pause system for 0001 00 Pause system until cancelled E Display message until cancelled C Disc message for time 00 01 00 E Message wee Please wait while filter plate is aspirated Enable Internal Click OK Then use the Device Control icon to insert another Vacuum Control step to close the Vacuum Valve Biomek
41. e Labware icon click position B6 then click the Disposal Because the Gripper can move either the lid or the plate with the lid the following dialog appears so you can provide specific instructions Move Labware Move Type E E A can OK Move Lid Only Lx C Move Plate and Lid Cancel Help C Device Labware anda Select Move Lid Only then click OK Then move the Tip Rack Lid at A5 to the Disposal as well You will see the following message because the Gripper cannot be used to move a Tip Rack but it can be used to move the lid Click OK Edit Worksurface Warning Ed Gripper cannot move tip rack Do you want to move the tip rack lid Then click the Disposal The Method window now looks like this lt BOOK1 gt Method 3 Initial Configuration Gripper Move B6 Lid to Disposal Gripper Move A5 Lid to Disposal Use the Move Labware icon button to move the collar at location B4 to the manifold at position A4 Biomek 2000 6 5 Tutorial Guide Chapter 6 Document 609912 AA The worksurface window now looks like the following screen Biomek 2000 Worksurface 000 30000000000 00000 00000 00000 OOOOOL 00000 00000 00000 00000 00000 000000 O i i i Q o i i i i 000000000000 000000000000 Disposal Setup Flask Move the Filter Plate at location B5 to the Vacuum Manifold at location A4 Move the lid o
42. e Method list lt TUTORIAL gt Method 1 This will display the Pipette Transfer dialog Pipette Transfer m Source Labware Location a Label Name F eservoir Holder Aspirate Liquid Level Height Ma Z Fixed Rate 10 Depth 0 a mm Prewet Tool P200L z Volume 50 00 gl per tip m Repeat Pipetting v Enabled Repeat 4 v Tip Touch L Mix hl Iz wales Source Labware Action Range C Patter Local Pattern Direction E y Row End Action Repeat Same Labware Clear Zoom ul Marks Internal Delay 0 000 sec m Tip Handling Tip Change No Tip Change Discard Tips Tip Source P250 hM Basic Help Cancel Destination Labware Location 5 Label S5 well flat Name S5 well flat m Dispense Height 50 00 Type Rate 10 To Deliver E Blowout Iv Tip Touch ale Destination Labware Action I Values Range Replicates 12 C Pattem Local Pattern Direction ByRow y End Action Stop 4800000000000 H000000000000 000000000000 000000000000 E000000000000 F000000000000 8 000000000000 M000000000000 Clear Zoom Marks Biomek 2000 5 3 Tutorial Guide Chapter 5 Document 609912 AA Click the Advanced button in the center section to display the Advanced options if
43. eagents which are toxic flammable or biologically harmful When using such reagents observe the following precautions Infectious samples must be handled according to good laboratory procedures and methods to prevent the spread of disease Observe all cautionary information printed on the original solution containers prior to their use All waste solutions must be disposed of according to your facility s waste disposal procedures Liquid transfers may generate aerosols Operate the Biomek in an appropriate enclosure and take all necessary precautions when using biohazardous pathologic toxic or radioactive materials Objects dropped onto plates accidental tool release or other accidental collisions may result in splashing of liquids therefore take appropriate safety precautions such as the use of safety glasses when working with potentially hazardous liquids Use an appropriate containment environment when using hazardous materials Observe the appropriate cautionary procedures as defined by your safety officer when using flammable solvents in or near a powered up instrument Make sure that the vacuum is attached prior to any method that contains any wash or aspirate functions Moving Parts The bridge and head assembly may suddenly move To avoid injury due to moving parts you must observe the following Never attempt to exchange labware reagents or tools while the instrument is operating as indicated by the amber safety light at the
44. el Help When you are done click on OK to exit this dialog then click on OK again from the Pipette Transfer window Note that the Edit Window will not reflect changes made to a transfer function when they involve parameters not included in the descriptor line Adding a Transfer Function Now you will add a new transfer function to the method Highlight the last transfer function in the Method window then click on the Pipette button on the Function Palette 3 10 Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA as lt BOOK1 gt Demo BioWorks Method Edit Method Edit View Configure Transfer Control Device Options Window Help oleja see ajaja v amp ep lt BOOK1 gt Demo Initial Configuration Pipette 200 00 ul from A2 to B2 using Function Palette Labware Bar DE 96 well flat 000000000000 loooooooooooo loooooooooooo 000000000000 with Lid O O i O O i i O O i 000000 00000 Jb well fla Jb well fla 090000000000 focoo00000000 oooooooooooo 500990000090 loooooooooooo loooooooooooo loooooooooooo 9900000000 loooooooooooo 0990000090 990000000 000000000000 000000000000 Reset cursor to pointer The cursor s shape changes to a pipette symbol Click on location A2 to designate the source then click on location B4 for the destination The Pipette Transfer dialog is displayed Set the options on the dialog
45. end of the bridge When the light is on the workstation is in operation and may move suddenly and rapidly at any moment A beep sounds just prior to initial movement to provide additional warning Never attempt to physically restrict the movement of the head and bridge assembly Use the Stop switch at the base of the workstation if an emergency stop is required Pressing this switch will freeze the workstation but not the Side Loader Click on the Stop button on the Run window to stop the instrument 1f the stop is not an emergency vi Biomek 2000 Safety e Because the parts of the Biomek move automatically keep clear of the head assembly during operation Also keep the area around the workstation clear including the expansion area to prevent obstructing the movement of the instrument e Always check the position of the tools and labware before beginning any stage of the method to ensure that their locations on the worksurface match those given on the window Also check that the labware is properly seated on the worksurface before beginning an operation Cleaning You may clean the spill trays of the Biomek worksurface and the nozzles of the Wash tools Please observe the following precautions e Be careful when handling the Wash tools as the nozzles are sharp e Contact your laboratory safety officer and refer to the guidelines in the section titled Chemical and Biological Safety if you will be cleaning spill trays that may
46. essure to the SL Incubator is 5 psig 34 5 kPa When cleaning the incubator wear protective gloves and eyewear viii Biomek 2000 Safety High Density Replicating System The High Density Replicating HDR System is not autoclaveable nor should you use organic solvents to clean the system However you can autoclave the pins of the HDR Tool and use organic solvents to clean the pins If you are using the bleach tray within the tool holder remove the HDR Tool from the bleach tray and rinse thoroughly after each session Do NOT store or let the HDR Tool stand in the tool holder with its pins immersed in bleach when not in use Extended contact with bleach will result in corrosion of the metal pins Plate Reader Refer to the Plate Reader User s Manual from the original manufacturer Molecular Devices Corp for maintenance and service information There are no user serviceable components under the cover Change lamps only with the power off Never touch any of the fiber optic cables or their housing manifold or rotor connections These fibers are extremely delicate and critical to the performance of the Plate Reader Use only the tools described to perform the steps defined in the Plate Reader user s manual Do not touch or loosen any screws or parts other than those specifically designated in the instructions of the Plate Reader user s manual Doing so could cause misalignment and possibly void warranty Never perform any
47. ette tip will go to 5046 of the height of the reservoir Click the vertical quarter reservoir to the far right of the reservoir holder Click Repeat Same Labware as the Source Labware End Action At the destination labware set the Dispense Height to 50 0096 and the Type to To Contain Select Blowout and Tip Touch Set the Dispense Height to 50 00 In the Center Section click Advanced to display extra menu items To decrease the dispense rate from 10 to 5 click the Dispense Rate down arrow in the Right Section under Dispense until you reach 5 Click Range for the Destination Labware action Select By Row for the Destination Labware Direction Click and drag from well A1 to H12 so that the entire plate will receive liquid Click Stop as the Destination Labware End Action 7 14 Biomek 2000 Tutorial Guide Document 609912 AA Chapter 7 The window will appear as follows Pipette Transfer r Source Labware Toot r Destination Labware Location faa Label Name Reservoir Holder Aspirate Liquid Level Height 50 00 Fixed Rate 103 Depth P200L Viscous Dispense Volume 1003 yl per tip gt Repeat Pipetting I Enabled Repeat 1 E 0 ma mm Iv Prewet M Tip Touch D Mix Min Values Source Labware Action Range Pattern Local Pattern Direction Box by Column z End ction Repeat Same Labware Clear Click OK 7 Interna
48. g a Wash tool make sure a quarter reservoir is installed properly in the support block under the tool Heater Cooler Block Failure to provide cooling water to the Heater Cooler Block HCB will cause excessive and potentially dangerous heating of the assembly DO NOT operate the assembly without adequate water flow 1 to 2 liters minute Full power time out faults may be caused by loss of cooling water Should this occur the Heater Cooler Block assembly may be hot e Always be sure to shut down the HCB as the last command of each heating cooling sequence Include a shut down command in all Biomek routines Provided water cooling is maintained extended cooling operations do not adversely affect block life span The TEMP command may not permanently turn off the block if a programmed event list is executing Biomek 2000 Safety Features The Biomek 2000 workstation is equipped with several safety features A Stop switch is located on the front of the instrument Press this switch to stop the Biomek Also the warning light at the top of the bridge warns you that the instrument is operating and emits a beep before the initial movement in a method When this light is on do NOT attempt to change labware Summary of Warning Information This manual is provided to help you establish safe conditions for performing the maintenance and servicing of your equipment Specific considerations and precautions are also described in the manual but appea
49. ic functionality of the Biomek 2000 provides a solid foundation for solving your own laboratory automation challenges Tutorial Guide Chapter 8 Document 609912 AA 8 2 Biomek 2000
50. ick the Reservoir in position A4 and click the Uniwell Plate in position A6 The Pipette Transfer screen will appear Source Labware Too Destination Labware Location z MP20 Location RE Labet Labet Uniwell Plate E E Volume Name eservoir Holder E Name Uniwell Plate 0 253 ul per tip i m Liquid Level r Dispense Fixed m Height 170 X Type Depth To Contain E 0 ma mm Fa rewet lowou Tip Touch E Tip Touch Hz Value Mix Mix ES a aba AER Destination Labware Action Range Range Replicates 1 C Patter Local Pattern Tip Handling C Patter Local Pattern Direction Box by Column Tip Change Direction Box by Column O stop No Tip Change z End Action Stop gt ME Discard Tips om 9000000000000 m H 000000000000 H000000000000 7 000000000000 E000000000000 Advanced FO000000000000 000000000000 Ee 1000566605000 Clear Zoom Marks Cancel Clear Zoom Marks Click the Tool field and click the P200L Viscous Tool Click the Volume field and type in a volume of 100 per tip Choose the appropriate source and destination parameters to utilize the delays and overages chosen for this tool Just above the source labware action section click Prewet and Tip Touch Set the Aspirate Height to 50 00 so that the pip
51. ips The Pipette Transfer dialog should look like the one shown on the next page Biomek 2000 6 7 Tutorial Guide Document 609912 AA Chapter 6 Pipette Transfer r Source Labware Toot r Destination Labware Location PE Meo y Location pa Label S6 well flat RECIPE Label Filter Plate Name pwet 203 Name FiterPlate Aspirate m Liquid Level A Dispense Height 0 003 Fixed Height 50 003 Type Depth fr Contai 0 ma mm em Prewet v Blowout M Tip Touch M Tip Touch Bo Mig values T Mix Mir Values pu A r Destination Labware Action Rue ware Action Range _Replicates 13 Pattern Local Pattern r Tip Handling Pattern Local Pattern Direction Box by Column Tip Change Direction Box by Column End Action Stop ater Transfer End Action Stop J M Discard Tips 1900000000000 Tip Source 800000000000 1000000000000 Po HM 900000000000 e 000000000000 csioooooooooooo 000000000000 1000000000090 soooooooooooo E000000000090 roooooooooooo H000000000000 8000000000000 000000000000 1000000000000 1900000000000 Clear Zoom Marks OK Cancel Clear Zoom Marks After selecting the parameters for the Source Labware and Destination Labware click and drag on the wells in which the pipetting should take place In the example above the click and
52. king Well Top Circular Zone 1 0 00 E ul WelBotom Flat a Height 0 00254 mm Maximum Volume 362 76 yl Zone 2 0 0024 pl Rows 8 x Columns 12 Height 2 0 00 a8 mm 2 g Ta szal Well Depth mm 3 ES 362 76 ul Top Height 20 17 m Top Diameter 6 60 dies M Gan Have lid m Grip Parameters E AS Al Lid Length 127 3574 mm pa E Lid Width 4 85402 mm C E Top Width B 82 10 mm hi p Lid on Height C 16302 mm Labware End View Lip Height DJ 6 05 E mm Acceleration 1 005 Lid Height E 3 27 mm Grip Type Below bottom Y LifterHeight F 0 00 mm Grip at top Height 0 00 m Grip Lid Depth G 3 00 mm Cancel Help As shown in the window Labware Edit serves two functions defining dimensions for gripping plates and setting parameters for Liquid Level Tracking Liquid Level Tracking LLT is an automatic calculation of aspirate height based on an initial height and the liquid volumes subsequently removed from the wells LLT is compatible with all Biomek 2000 pipetting tools including tools with Liquid Level Sensing Liquid Level Sensing LLS automatically detects the meniscus of the liquid with the sonic detector in the tool Since LLS is available only in the P200L and P1000L Biomek 2000 tools LLT offers the advantage of tracking liquid levels in non sensing tools such as the P20 MP20 and MP200 Biomek 2000 tools e In this exercise the Liquid Level Tr
53. l Delay 0 00 sec Location 5 Label p niwell Plate Name p niwell Plate Dispense Height 50 002 Type Rate 53 To Contain r Tip Handling Tip Change No Tip Change Discard Tips Tip Source P250 al Y Blowout Y Tip Touch Mix Destination Labware Action Range heplicates 13 C Pattern Local Pattern Direction By Row s End Action Stop al Min Values The Method window will appear as follows lt BOOK1 gt Method 1 Initial Configuration Pipette 50 00 Pipette 100 00 from A4 to A5 using 41800000000000 1000000000000 1000000000000 1000000000000 1000000000000 1000000000000 soo0000000000 11000000000000 Clear Zoom Marks P200L P250 from A4 to A6 using P200L Viscous P250 Biomek 2000 Tutorial Guide Chapter 7 Document 609912 AA Click the Method Menu and select Save As Type in Method 1A Method Save s Name Method 1a Author nem K Do Cancel eyword E Description EM Save Unvalidated Click OK The method will be validated and saved B2KEDIT Windows Application EA AN Method validation complete Click OK You have now successfully completed Exercise 6 7 16 Biomek 2000 Tutorial Guide Document 609912 AA Chapter Eight Congratulations you have completed all of the tutorial exercises Your familiarity with the bas
54. l display a list of available methods Select the Demo method from the list Biomek 2000 3 3 Tutorial Guide Chapter 3 Document 609912 AA Open Method Author Keyword Filter smith demo M Date Created LastModified Date Time Last Run 05 25 94 n 23 95 Method Name Description Demo p emonstrates the Biomek 2000 Auto Plasmid 32C amp utomated Plasmid Purification 4 columns Version 2 0 Auto Plasmid 484 Automated Plasmid Purification 6 columns Yersion 2 0 Auto Plasmid 48B Automated Plasmid Purification 6 columns Yersion 2 0 Auto Plasmid 644 Automated Plasmid Purification 8 columns Version 2 0 Automated Plasmid Purification 8 columns Version 2 0 Automated Plasmid Purification 12 columns Version 2 0 Demonstrates the Biomek 2000 Demo R DNA Method for DNA sample preparation Elisa Example of an Elisa assay using the Side Loader HDR Method Example for using the High Density Replicating System Plasmid 324 Semi automated Plasmid Purification 4 columns Version 2 0 Plasmid 32B Semi automated Plasmid Purification 4 columns Version 2 0 Plasmid 32C Semi automated Plasmid Purification 4 columns Version 2 0 Plasmid 484 Semi automated Plasmid Purification 6 columns Version 2 0 Plasmid 48B Semi automated Plasmid Purification 6 columns Version 2 0 Plasmid 644 Seim automated Plasmid Purification 8 columns Version 2 0 Plasmid B4B Semi automated Plasmid
55. lace labware on a worksurface location first you select the item from the Function Palette Labware Bar window Use the round buttons to select the type of labware then scroll to select a specific item Then place the labware on the desired location on the Worksurface window To delete an item of labware from the Worksurface click on the item then press the Delete key You will be prompted for confirmation e When adding or placing labware on the worksurface you may receive a Possible Collision error message If this occurs this does not necessarily mean that you cannot use that position for that labware However you should carefully consider whether or not the adjacent labware will cause a conflict based on the information in the warning message If in doubt consider using another arrangement e If you add delete or remove labware when any other line of the method is highlighted BioWorks will consider this a labware move and will function accordingly e If you add delete or move labware during a method you will notice that the labware displayed on the Worksurface window changes as you increment through the steps in the Method window This will allow you to verify labware positions as the method progresses Changing the Initial Configuration To change the Initial Configuration for this method first make sure that the Initial Configuration line of the Method is highlighted Then click on the Plates button of the Labware ba
56. late Reader Protocol C1SOFTMAXASMPROTO PRO Gripper Move Al 96 well flat to Disposal This step will not be Select Method Save 6 14 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA Method Save s Method 3 Author Cancel Keyword Help Description Name Save Unvalidated Enter your preferred method name and click OK The file will be automatically validated B2KEDIT Windows Application E3 Method validation complete Click OK This completes Exercise 5 Biomek 2000 6 15 Tutorial Guide Chapter 6 Document 609912 AA 6 16 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA Chapter Seven Exercise 6 SS Ul Exercise 6 Labware and Tool Edit In this exercise you will copy and edit labware and tool definitions from their respective libraries Labware Edit allows you to choose a piece of labware from the Labware Library and modify it to match specific labware that is not currently defined in the library Tool Edit allows you to modify the pipetting delays and overages for aspiration and dispense The calibration slope and offset are also found on the Tool Edit window Once a labware or tool definition is copied edited and named the new labware or tool definition becomes part of its respective library The objectives of this exercise are to e Copy and edit a labware definition and place it on the Worksurface in the initial configura
57. nly for the filterplate at A4 to the disposal You can click location A4 with the right mouse button to display a list of the labware layered at this location You should now have the following labware at this location e Filter Plate e Vacuum Collar Std e 96 well flat e Vacuum Manifold The method screen should look like this lt BOOK1 gt Method 3 Gripper Move B6 Lid to Disposal Gripper Move A5 Lid to Disposal Gripper Move B4 Vacuum Collar Std to A4 Gripper Move B5 Filter Plate to 44 retain lid Gripper Move 44 Lid to Disposal END Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA Pipette Transfer Now use the Pipette icon button to add a Pipette Transfer from the plate at B6 to the filter plate at A4 ES Click the Pipette icon button click position B6 for the source then click position A4 as the destination When the Pipette Transfer dialog is displayed verify that the correct tool and tips are selected then configure the transfer as follows Select all wells in source and destination Select Tip Touch at the source and destination Set the Volume to 2 00 Select Blowout at the destination Select a Dispense Height of 50 for the destination to ensure that the tips do not go too deeply into the filter plate Select the source and destination Labware Action as a Range and an end action of Stop Setthe Tip Handling to Tip Change After Transfer and enable Discard T
58. of the library From the Edit Labware window highlight Uniwell Plate the numerically named labware appear first the rest of the labware is in alphabetical order Edit Labware Author Keyword Filter Beckman Instruments y 96 well flat Library Labware Last Madified C Modular Reservoirs 0210788 Labware Name Labware T ype Uniwell Plate Titerplate or similar Copy SB well vinyl v bot Titerplate or similar Beckman ElA Titerplate or similar BreakawayS6 Titerplate or similar Rename Coming 12 Titerplate or similar Costar 24 Titerplate or similar Crvo v bot Tube Module small Falcon 24 Titerplate or similar gt Filter Plate Titerplate or similar Print FlashPlate TM Titerplate or similar Full Reservoir Titerplate or similar HDR Bleach Titerplate or similar HDR Ethanol Titerplate or similar HDR Gel 384 HDR Gel or Membrane HDR Gel HDR Gel or Membrane HDR Water Titerplate or similar Microfuge 24 Tube Module small PES600 Titerplate or similar Sagian 4 Well Titerplate or similar Uniwell Plate Edit Delete Import Export Export ll Close Help duda iterplate for similar Click Edit Biomek 2000 7 5 Tutorial Guide Chapter 7 Document 609912 AA Now you may customize the parameters of the Uniwell Plate Uniwell Plate Labware Type Titerplate orsimla Liquid Level Trac
59. on By Row End Action Stop 00000000000 1000000000000 1000000000000 2000000000000 000000000000 9000000000000 000000000000 1000000000000 Clear Zoom Marks Tool P200L Y Volume 5 00 gl per tip Tip Handling Tip Change No Tip Change Discard Tips Tip Source P250 Advanced Help Destination Labware Location 3 Label S6 well flat Name SE wel flat m Dispense Height 50 00 EX Type To Deliver F Blowout Tip Touch His Destination Labware Action Mi BUS Range Replicates C Pattern Local Pattern Direction By Row End ction Stop 1800000000000 1000000000000 1000000000000 1000000000000 soooooooooooOo 000000000000 soo0000000000 1000000000000 Clear Zoom Marks To add a Mix function to this step click on the Mix option box for the source Then click on the Mix Values button to display the Mix Values dialog Edit the Mix Values dialog as follows Change the Mix Cycles to 3 Change the Aspirate and Dispense Rates to 5 Change the Aspirate and Dispense Heights to 50 Biomek 2000 Tutorial Guide Chapter 3 Document 609912 AA Mix Values Mix Volume 5 00 yl per tip Mix Cycles 33 Mix at Sides Aspirate Rate 54 Height 5 0024 x Dispense Rate Sim Hen 50 00 Canc
60. onsider the number of wells well bottom type and well top shape when choosing a labware definition to copy In this example a 96 well flat definition was chosen because the Uniwell plate has 96 wells 8 rows x 12 columns a circular well top and a flat bottom All labware definitions can accept different volumes by defining the heights and zones You can determine the zone volume by pipetting up to each zone with a hand held pipettor Some labware manufacturers may have this information available on request Biomek 2000 7 7 Tutorial Guide Chapter 7 Document 609912 AA The volume and height for each zone of the Uniwell Plate is Zone 1 0 Height 1 0 mm Zone 2 260 Height 2 3 6 mm Zone 3 121 Type the zone and height values listed above and the other labware measurements mentioned earlier in the appropriate fields on the Edit Labware window Uniwell Plate Labware Type Titerplate or similar Liquid Level Tracking Well Top Circular Zone 1 0 00 a pl pce FFlat x Height 1 0 0024 A Maximum Volume 381 00 p Zone 2 260 00 pl Rows 8 x Columns 12 R Heicht 2 mo a eight 2 B0 WelDepth 11105 mm Zoe3 1210024 ul Top Height 201728 mm 3 a Top Diameter 6 60 E mm JM Gan Have lid M Grip Parameters EA Ay Lid Length 127 36 mm peu Lid Width 4 503 mm CT E Top Width B 82102 mm li D Lid on Height C 16 90 Aj mm Labware End View Lip Height D 2 60 a E Acceleration
61. operation on the Plate Reader in an environment where damaging liquids or potentially damaging gases are present Never touch the surfaces of the interference filters or optical lenses DO NOT install the Plate Reader in a stack location that could inhibit access to the Stop Switch of the SL in the event of an emergency Use only locations 1F1 or 2F1 on the SL To prevent fluid from dripping off the microplate when it is in the reading chamber onto any sensitive optical elements and to minimize potential biohazard exposure to other Plate Reader users observe the following precautions When reading microplates that may have fluid on the underside of the microplate damp dry the underside using a dry paper towel or equivalent before putting the microplate on the drawer Alternatively place a clear sheet such as a Molecular Devices blanking template underneath the microplate when inserting it in the drawer Biomek 2000 ix Safety Wash System Never run the 6 Port Valve dry Liquid should always run through the 6 Port Valve Failure to do so can result in damage to the valve e Strong acids strong bases oxidizers radioactive and biohazardous liquids should not be run through the Wash Unit Each laboratory must qualify this instrument with its unique application s e Plug any unused port with the plugs provided with the 6 Port valve Otherwise liquid may spill through exposed ports when the 6 Port valve is used e When usin
62. out overage Insert the following delays in milliseconds and overage in appropriate fields Table 2 Parameter Source Destination Prewet 200 Aspirate 500 Dispense 500 Blowout 200 Tip Touch 350 350 Overages Blowout 40 Note These values are for illustration only For practical purposes it is best to test each liquid and make the necessary modifications in Tool Edit 7 12 Biomek 2000 Chapter 7 Tutorial Guide Document 609912 AA The window will appear as follows Tool Type Channels Minimum Volume Maximum Volume P200L m 59 20000 yy Maximum Capacity 250 00 ul Iv Liquid Level ensino Prewet Aspirate Dispense Blowout Tip Touch Delays milliseconds P200L Viscous Destination Source 203 1 2001 1 500 4 203 350 1 Tips P250 P250 with Barrie Overages Prewet Blowout To Deliver Bias 350 E Calibration Slope 0 0847 mm Offset 0 02 mm Click OK then click Close in the Tool Edit screen You are now ready to create a pipette transfer function using the new tool name into the new labware Highlight the last command End in the Method Window of the method Biomek 2000 7 13 Tutorial Guide Chapter 7 Document 609912 AA From the Function Palette click the Pipette icon Cl
63. r then scroll through the list and select the 96 well flat bottom plate The cursor becomes a rectangle to represent the plate Place the rectangle on position B4 to add a third plate to the initial configuration The new configuration with the 96 well plate located in position B4 of the worksurface is shown on the following screen Biomek 2000 Tutorial Guide Chapter 3 Document 609912 AA Workstation Surface Setup Select your Workstation accessories Worksurface Side Loader r Plate Reader Iv Disposal v Plate Reader present v Left Side Module Location M Right Side Module Side Loader Section v Areal Side Loader Section E Side Loader Area 2 Left Expansion Area Zeas v Wash Unit High Density Replicate Syster Six Port Valve Vacuum Manifold Cont lt Back Cancel Viewing and Editing a Transfer Function Familiarize yourself with a basic Pipette Transfer function by viewing the first transfer function in the Demo Method To do this double click on the second line in the Method window This displays the Pipette Transfer dialog for this step Biomek 2000 3 7 Tutorial Guide Chapter 3 Document 609912 AA m Source Labware Toot r Destination Labware Location E P200L Location 2 Label Microfuge 24 Label S5 well flat Volume Name Microfuge 24 Name S5 well flat
64. r in the form of Warnings Cautions and Notes It is important that you service your equipment in accordance with this instruction manual and any additional information which may be provided by Beckman Address any questions regarding the safe and proper maintenance and servicing of your equipment to your nearest Beckman Sales and Service Center Biomek 2000 Chapter 1 Tutorial Guide Document 609912 AA Chapter One Introduction ER Preface Welcome to the tutorial phase of the Beckman Training Program for the Beckman 2000 By now you should have been introduced to the basic instrument functions by a Beckman field engineer during the installation of the Biomek 2000 The purpose of the tutorial is to help you to become comfortable with the basic functions of the Biomek 2000 and to introduce you to some of the more advanced functions This tutorial comprises five 5 self paced exercises that increase in their level of difficulty Do not proceed to the next exercise until you are comfortable with all of the functions that are covered in the current exercise as each successive exercise builds on the knowledge gained in the preceding exercise The exercises are as follows Exercise One Creation of a Default Configuration Exercise Two Pipette Transfer Exercise Three Pipette Transfer with Pauses Loops and Marks Exercise Four BioWorks Device Functions Vacuum Manifold and Plate Reader Exercise Five Labware and Tool
65. re used Click Loop for Count and click the up arrow to a count of 12 Alternatively you could type in the number 12 Click OK to insert this function into the Method list To end the loop after the count of 12 highlight End on the Method list Click the End Loop icon button on the Function Palette a Biomek 2000 5 11 Tutorial Guide Chapter 5 Document 609912 AA R TUTORIAL Method 1 BioWorks Method Edit Method Edit View Configure Transfer Control Device Options Window Help DER x x Sal ej 9 v amp 2 4 lt TUTORIAL gt Method 1 OY x Pause Labware A5 00 05 00 Function Palette Labware Bar Plates Tips C Tubes C Devices Other with Lid 0000000015 0000000017 00000000E 000000007 00000000 00000000H 00000000 00000000 00000000 00000000 00000000 00000000 Disposal 6 Port Valve To save the method click the Method menu and then select Save As Method Save As Name Method 3 Author Cancel Keyword Help Description Save Unvalidated Type in Method 3 and click OK The method will be validated and saved 5 12 Biomek 2000 Chapter 5 Tutorial Guide Document 609912 AA Click OK on the Method Validation Complete window B2KEDIT Windows Application EA N Method validation complete You have now successfully completed Exercise 4 Biomek 2000 5 13 Tutorial Guide Chapter
66. rewet Blowout v Tip Touch v Tip Touch Mix fle alus Mix ie Vales an Destination Labware Action Range C Range Replicates ires C Patter Local Patter r Tip Handling Pattem Local Pattern Direction e y Row Tip Change Direction e y Row End Action Stop No Tip Change End Action stop Discard Tips Tip Source A 9400000000000 m 9990000000000 009000000000 1900000000000 9090000000000 Advanced FHO00000000000 siODOOOOOOOOOO E Re 5eoooooooooo Clear Zoom Marks Cancel Clear Zoom xu Marks E Click OK to add this step to the method Inserting Messages and Pauses You can also insert messages to the operator and system pauses in a method Using the same method now add a pause before the second pipette transfer to display a message to the operator We will display a message to inform the operator that the system will pause for one minute after the message is acknowledged From the Edit Window highlight the second pipette transfer in the Method Window then click on the Pause System button on the function pallette 3 12 Biomek 2000 Chapter 3 Tutorial Guide Document 609912 AA 3 This displays the System Pause Message dialog Select the dialog items as follows Set System Activity to Message Set System Actions to Display message until canceled Type a message in the Message box Ena
67. ri mnm C se Current Contiguration Cancel y C Use Default Gontiquration Help Click the Setup button on the worksurface to display the Setup dialog Select the following options Disposal unit enabled Left Side Module not present Right Side Module present Plate Reader installed on the Left Expansion Area Wash Unit present The Setup dialog should look like the one shown below Biomek Setup Worksurface Side Loader r Plate Reader v Disposal v Plate Reader present Left Side Module Location v Right Side Module Left Expansion Area Areal Side Loader ies2 Area 3 Y Wash Unit Six Port Valve Cancel Help Click OK when done Highlight the Initial Configuration line in the method list window and establish the configuration as follows Select the Tool Rack from the Other option on the Labware Bar and click position A2 Place a Gripper Tool and an MP20 tool in the rack as shown on the next page 6 2 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA Tool Change Tool List Tool Rack a L Q 2 za gt Bleach Tray Cancel Help Disposal Next select the following devices from the Devices list in the Labware Bar and place them on the worksurface Vacuum Manifold at position A4 Collar Holder at position B4 Vac
68. rks esee 5 1 I PLE 5 1 Pipette Transfer with Pauses Loops and Marks eee 5 2 Exercise 5 Exercise 5 BioWorks Device Functions sessssssesseeeeeeeeee eene nere 6 1 ASK m 6 1 Open a New Method and Set the Initial Configuration ees 6 1 Remove Lids to the Disposal er eren 6 4 Pipette Transfers i veo ola dbi einen 6 7 Controlling the Vacuum Manifold with a Device Function eese 6 8 Remove Filter Plate tii dtd o e Er d ce UE 6 10 Move the Plate to the Plate Reader and Run Plate Reader Protocol 6 10 Exercise 6 Exercise 6 Labware and Tool Edit ccscccsssssssssssnseceececesscessccsencsesnsecenascssaecenaceonsooes 7 1 Task is desti alii etse ete tedesco hel He hee OTS 7 1 Labware Edit re ette ter there ete estie oet teret d do tias Pikes 7 2 Tool Bdit inp int oad hut esas ced e D Pe iet dere pedet rodeos siete i EE od eoo 7 9 Summary Biomek 2000 ij Notice Notice CRER This equipment has been tested and found to comply with the limits for a Class A digital device pursuant to part 15 of the FCC rules These limits are designed to provide reasonable protection against harmful interference with the equipment is operated in a commercial environment This equipment generates uses and can radiate radio frequency energy and if not installed and used in accordance with the in
69. struction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the used will be required to correct the interference at his own expense This manual is copyrighted and all rights are reserved This document may not in whole or in part be copies photocopied reproduced translated or reduced to any electronic medium or machine readable form without prior consent in writing from Beckman Instruments Inc Biomek and Beckman are registered trademarks of Beckman Instruments Inc BioWorks and BioScript are trademarks of Beckman Instruments Inc Microsoft and MS DOS are registered trademarks and Windows is a trademark of Microsoft Corporation Biomek 2000 iji Notice iv Biomek 2000 Safety Safety Notice The exclamation mark contained in a triangle is an international symbol displayed to indicate to the user that all safety instructions should be read and understood before installation and operation are attempted When you see the safety notice symbol on the instrument or on one of its accessories you should refer to this manual for specific safety information that applies If the product is used in a manner other than specified in the manual the safety and performance of the equipment could be impaired Any installation or service procedures not described in this manual must be performed
70. te tip will fill with liquid Move the pipette tip to the destination the 96 Well Flat plate in position A5 and click The following Pipette Transfer window will appear 4 2 Biomek 2000 Chapter 4 Tutorial Guide Document 609912 AA Pipette Transfer r Source Labware Tos r Destination Labware Location faa Meo y Location p5 Label a Label SE wel flat Dispense Volume Name Reservoir Holder BEE rey Name SE wel flat Aspirate Liquid Level Dispense Height 21 252 Es Fixed al Height 0 003 Type Depth To Contain 0 003 mm o Prewet E Blowout T Tip Touch I Tip Touch m Mix Mig Values gt Mix Mir values Source Labware Action Destination Labware Action Range Range Replicates 13 C Pattern Local Pattern C Pattern Local Pattern Y r Tip Handling Tip Change Direction Box by Column No Tip Change End Action Step T Discard Tips Tip Source A 000000000000 m 929000000000 900000000000 1900000000000 goooooooooooOo H000000000000 8000000000000 900000000000 Clear Zoom Marks DK Clear Zoom Marks The Pipette Transfer window is divided into three vertical sections The middle section identifies the tool pipette tips and volume The far left section identifies the pipetting source and parameters The far right identifies the pipetting destination and par
71. th labware on the worksurface stacks or in the SL hand unless the system tells you to The arm can move suddenly Stay clear of the arm and hand during operation Keep the area around the SL clear of any obstructions to avoid collisions There is a Stop switch at the base of each Stack Area If an emergency stop is required pressing this on each stack area of your SL switch will freeze the SL instantly CAUTION The Stop switch on the SL will not stop the workstation nor will the Stop switch on the workstation stop the SL NOTE You may lose data and be forced to quit the run in progress if you press the SL Stop switch Use of the SL stop switch may result in spill age or splattering of liquids in transit Click on the Stop button on the BioWorks Run window to stop the instrument if it is not an emer gency SL Incubator Operating the incubator at 4 C for longer than twenty four hours may result in ice formation within the chamber adversely affecting temperature equilibrium and assay results Do NOT place the incubator in stack location C as the incubator may inhibit access to the Stop switch of the SL in the event of an emergency Allow enough time for the incubator to reach the desired temperature to ensure reliable assay results typically less than one hour depending on the circulator and desired temperature Use 50 polyethylene glycol and 50 water as the conductive fluid in the water circulator Maximum inlet pr
72. this exercise are to Use the Function Palette and identify the Pipette icon button e Identify a source and destination for a liquid transfer e Identify the components of the Pipette Transfer window e Access the advanced pipetting options e Use Repeat Pipetting Task Pipette 50 uL from the first top left quarter horizontal reservoir into the first 12 wells row of the 96 Well Flat plate in position A5 Perform a tip touch at source and destination Pipette Transfer If you do not have the method open from Exercise 2 then you should open a new one as follows From the BioWorks Method Edit window click Method and then New Click Use Default Configuration and then OK Hew Method OF Initial Configuration C Clear Configuration ES Cancel E Se Curent Coniguratior You should see the Default Configuration you prepared in Exercise 1 Biomek 2000 4 1 Tutorial Guide Chapter 4 Document 609912 AA 42 lt TUTORIAL gt Method 3 BioWorks Method E dit Method Edit View Configure Transfer Control Device Options Window Help Dos ta ve see exem v x 8 lt TUTORIAL gt Method 3 E Initial Configuration Biomek 2000 Worksurface Side Loader Top View Disposal B Port Valve Click on the Pipette icon button on the function palette ES The mouse cursor turns into a pipette tip Move the pipette tip to the reservoir source at A4 The pipet
73. tion of Method 1 e Copy and edit a tool definition then add it to Method 1 Note In order to protect the integrity of existing methods and the labware and tool libraries you must copy labware and tools before you edit them If you rename edit without first copying or delete any lab ware or tool that is used in any method a list of affected methods is displayed If you choose to edit the labware or tool before copying it will be changed in all the affected methods If you delete or rename labware without first copying the methods containing the labware are displayed BioWorks will not permit you to delete or rename lab ware or tools until the affected methods are deleted or modified so they do not include the labware Task Create a new 96 well plate and a P200L tool definition for use with viscous liquids Modify a method to perform a pipette transfer using the new tool and labware Biomek 2000 7 1 Tutorial Guide Chapter 7 Document 609912 AA Labware Edit From the Method Menu click Close to close any opened methods Repeat as necessary Click Open on the method menu click Method 1 then click Open Confirm that Initial Configuration is highlighted on the Method List Since you will create a new piece of labware and a tool definition in the libraries they must be created and utilized as part of the initial configuration The method list will appear as follows lt BOOK1 gt Method 1 from A4 to A5 using P20
74. utton on the Worksurface window to configure the Worksurface B TUTORA Deia Er m Worksurface Window Select the options indicated below and then click OK Worksurface Side Loader Plate Reader v Disposal i lv Left Side Module locaton v Right Side Module Side Loader rea Y v Areal Side Loader Area2 Area 3 IV Wash Unit IV Six Port Valve From the Function Palette Labware Bar click the Other button and then select the Tool Rack from the drop down menu Move the cursor to Worksurface position A1 and click Biomek 2000 2 5 Tutorial Guide Chapter 2 Document 609912 AA A lt TUTORIAL gt Def Cady Moa a Heihi E di Meco di es Compas jeum oval Devis poe indios jju aa TRE a ER uton Valni Labesara Dm Vp ea ES RE LES x Function i js ms eg ae IES Palette E Pim 4 n B Labware Bar Dn ml c Ht ET op Vira Tool Change Tool List Tool Rack Bleach Tray coca to 2 6 Biomek 2000 Chapter 2 Tutorial Guide Document 609912 AA Click the P20 tool and then click the left most tool holder position position 1 to place the tool Place the P200L MP20 WASH8 and MP200 tools in the same manner If you click on the wrong tool simply click on the correct tool then proceed with placing it in the tool holder After the appropriate tools have been placed in the holder click OK Tool Change Tool List Tool Rack Bleach Tray Cancel Help
75. uum Collar std on top of the Collar Holder at B4 Tip Rack Holder at position A5 Biomek 2000 6 3 Tutorial Guide Chapter 6 Document 609912 AA Biomek 2000 Worksurface 000000 000000 000000 000000 000000 000000 000000 000000 000000008 00000000 00000000 00000000 00000000 00000000 Disposal Setup Flask Next select the following plates from the Plates list in the Labware Bar and place them on the worksurface 96 well flat plate at position A4 on the Vacuum Manifold 96 well flat plate with lid check the With Lid box on the Labware Bar at position B6 Filter Plate with lid at position B5 Select the P20 Tip Rack with lid checked from the Tips list in the labware bar and place it on the worksurface at position A5 This configuration is shown below Biomek 2000 Worksurface Disposal Note that the star to the left of the labware and tip rack names means a lid is present You have now established a new Initial Configuration Highlight the End command in the Method Window to begin adding moves and transfer steps to the method Remove Lids to the Disposal Use the Move Labware icon on the Function Palette shown below to perform each of the labware moves required for the method 6 4 Biomek 2000 Chapter 6 Tutorial Guide Document 609912 AA E To move the lid on the 96 well flat plate to the Disposal click the Mov

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