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Concert - TRIAD Series Software User`s Manaul

1. Figure 7 6 Viewing kinetic measurement graphs Detailed graphs for individual samples all samples in a column or row or all samples on the plate may be viewed and printed To view detailed graphs for e an individual sample click in the desired well Depending on measurement type a two or three dimensional graph of the selected result appears refer to Section 7 2 4 1 Viewing Two Dimensional Graphs or Section 7 2 4 2 Viewing Three Dimensional Graphs Note Detailed graphs for individual samples may be viewed for all measurement types even when the graphs displayed appear to be empty e arow or column click in the desired row or column header A three dimensional graph of results for the row or column appears refer to Section 7 2 4 2 Viewing Three Dimensional Graphs Note Rows and columns may not be selected for multiwavelength and area scan measurement results e all samples on the plate click in the upper left corner of the plate layout Figure 7 6 A three dimensional graph of all results on the plate appears refer to Section 7 2 4 2 Viewing Three Dimensional Graphs Note All samples may not be selected for multiwavelength and area scan measurement results Concert TRIAD Series Software User s Manual 7 8 Viewing Measurement Results 7 2 4 1 Viewing Two Dimensional Graphs Results for individual single point kinetic and linear scan measurements are displayed in two
2. 1 3 2 Installing Concert TRIAD Series Software on Windows 2000 or XP On a Windows 2000 or XP system the Concert TRIAD Series Software installer uses a simple interface to guide the installation of the software and required components To install the verification plate software 1 Exit all Windows programs before running the setup program 2 Make sure the current user account has Administrator privileges Accounts with Standard or Restricted access are not permitted to run the setup program Contact the site system administrator for more information about account privileges W Insert the installation CD into the CD ROM drive and browse to the contents of the CD D In the contents of the CD open Begin here for XP or W2K systems Nn In Begin here for XP or W2K systems double click Installer exe Concert TRIAD Series Software Installer appears Figure 1 3 All components required to successfully install the software are listed The current status of each required component is listed e a check icon indicates the correct version of the component is already installed on the system e a caution icon indicates that an older version of the component is installed and must be updated before the software may be installed A 8 e an X icon indicates that the component must be installed before the software may be installed x Concert TRIAD Series Software User s Manual 1 8 Installing Settin
3. In Account Management choose the Settings tab In Settings choose Set Admin Password and enter a new administrator password Refer to the Account Management online help for more information Note Account Management online help may be accessed by pressing F1 or choosing the help button in the lower right corner of the window Figure 3 1 Close Account Management Follow the steps in Section 3 2 2 Setting the Signet Support Level to set the level of support provided by Signet 3 2 2 Setting the Signet Support Level Signet provides three support levels e No Support Signet is disabled user accounts are not required e Signet User accounts are required to log into the software but passwords are not required to sign items Note Signet without password checks may not provide adequate support to comply with 21 CFR Part 11 or other regulations Each site must evaluate the level of support required for a given system e Signet with password checks for signing and check in User accounts are required to log into the software and passwords must be entered for confirmation when prompted Note Compliance with regulations such as 21 CFR Part 11 requires implementing site processes beyond the control of the software To set the level of support 1 2 3 Log off and close all software applications using Signet Place the Signet CD in the drive and browse to the contents of the CD Double cl
4. Es Show Result viewer Variables LW Perform after completing measurement s Measurement result Transformation HE Create XML and dat data files H Concentration Perform after completing measurements output options H Print options v Perform after completing measurements Cutoff validation Output Settings gt Execute program Run protocol Run this protocol now Run this protocol now Execute a program after protocol executes Figure 6 28 Configuring output settings To configure Output Settings 1 Choose export view and print output options as desired Table 6 3 describes the options available 2 Choose Run protocol now to run the protocol Refer to Section 6 3 Running ie Protocols for more information about running protocols Note When creating or editing a protocol the protocol must be saved before it can be run After saving the protocol Run Protocol appears for protocols that were edited new protocols must be selected in the Protocol Selection List before they may be run 3 Choose Execute a program after protocol executes to display options for configuring an external software application to run after the protocol run is completed Refer to Section 6 2 11 1 Configuring a Program to Execute after a Protocol Run Completes for more information DYNEX Technologies Inc Creating Protocols 6 43 Table 6 3 Output Options Output Option Export to
5. 7 2 Viewing Measurement Results Measurement results selected from the list are viewed in the Result Viewer which depending on measurement type displays raw data from each measurement technique measurement cycle or point reduced data and graphs Results calculated using a data reduction method may be reevaluated using different parameters When the optional Concert TRIAD Series Analysis Software module is installed results may be reevaluated by editing analysis parameters configured in the protocol Result actions covered in this chapter include e Viewing Measurement Results in the Result Viewer Section 7 2 e Viewing and Reevaluating Results from an Analysis Application Section 7 3 e Viewing Exported Measurement Results Section 7 4 Note This section includes viewing measurement results exported to Microsoft Excel from the Result Viewer and results exported to XML or data files at the completion of a protocol run e Signing Measurement Results Section 7 5 e Deleting Measurement Results Section 7 6 e Printing Measurement Results Section 7 7 To view measurement results 1 From the navigation pane choose Results The Results Selection List appears Figure 7 1 i 2 In the Results Selection List select the desired results and from the toolbar choose View the selected result The Result Viewer appears Figure 7 2 OR Use the search options to locate specific results Tab
6. 1 Select the type of filter slide to add Excitation or Emission The list of filter slides displays all slides of the selected type currently stored in memory 2 Choose Add Slide A new filter slide is added to the list of filter slides 3 Configure the slide following the steps in Section 2 3 2 2 Configuring Filter Slides 2 3 2 2 Configuring Filter Slides The filter slide configuration includes a name and ID for the slide and information about the filters installed on the slide When a new slide is added or the filter configuration on a slide changes the slide must be configured To configure a filter slide 1 Select the type of filter slide to configure Excitation or Emission The list of filter slides displays all configured slides of the selected type 2 Select the desired filter slide to configure from the list Filter Slide Properties displays information about the selected slide Figure 2 3 3 In Slide ID enter the identification number printed on the slide 4 In Slide Name enter a name to identify the filter slide 5 In the list of filter slides click the to the left of the filter slide name to display the list of filters installed on the slide 6 Select a filter to configure Filter Properties for the selected filter is displayed on the right side of the screen Figure 2 4 a gt Instrument Settings Basic Settings Fl Selected filter Excitation C Emissidn Add Slide B Fi
7. To configure a linear scan click anywhere on the center row or column inside the well boundary and drag towards the boundary until the desired number of measurement points is selected Figure 6 13 Note The type of scan that may be configured is determined by the Reading Direction Settings in Layout Settings refer to Section 6 2 4 Configuring Labware Layout Settings For example horizontal linear scans along the center row may be configured only when Read by row is selected while vertical linear scans along the center column may be configured only when Read by column is selected Read by well allows area and vertical linear scans to be configured Scan Selection Editor Select the scan resolution and measurement points to read The type of linear scan that may be configured is determined by which reading direction is configured in Layout Settings When Read by row is selected a horizontal linear scan may be configured When Read by column is selected a vertical linear may be configured When Read by well is selected only area scans may be configured Resolution mm Selected Scan Points 0 2810 Points X 22 Points Y 1 Well boundary Measurement points Click on the center row or column and drag until the desired number of points is selected OK Cancel Figure 6 13 Configuring a linear scan 5 Choose OK to save the scan configuration and close the Scan Selection Editor OR Choose
8. e Section 6 2 9 Configuring Cutoff Values Concert TRIAD Series Analysis Software only e Section 6 2 10 Configuring Validation Rules Concert TRIAD Series Analysis Software only ae Result Viewer 20050321 135246 DTX 880 Transformation Variables Data Concentration Layout View List View Parameters Edit Cutoff Report Options validation m Transformation View transformed measurement results or edit the transformation formula if reevaluating the results is desired eA SSS Name of x Transformation Figure 7 16 Editing transformation parameters in the Results Viewer 5 Edit additional analysis options if desired 6 From the toolbar choose Reevaluate current measurement results to recalculate the results using the edited parameters Note The Reevaluate button appears on the toolbar only when a parameter in the results such as the transformation formula has been changed 7 Optionally save the reevaluated results with a different name to preserve a record of changes made to the parameters refer to Section 7 2 7 Saving Measurement Results DYNEX Technologies Inc Viewing Measurement Results 7 19 7 4 Viewing Exported Measurement Results Measurement results may be exported manually from the Results Viewer or automatically at the end of a protocol run when export options are configured in Output Settings Two file export and save options are av
9. 2 In Open browse to and select the desired xml file to import 3 Choose Open The filter slides defined in the xml file are imported into the filter slide list and replace all existing filter slides 2 3 2 5 Exporting and Importing Individual Filter Slide Configurations Configuration information for a single filter slide may be exported to an XML file and imported to restore that configuration or share the configuration with another instrument To export a filter slide configuration 1 In the list of filter slides choose the slide desired to export 2 Choose Export This Slide Save As appears 3 In Save As select the desired directory and enter a file name 4 Choose Save Slide information is saved as an xml file with the specified path and file name To import a filter slide configuration 1 If the list of filter slides contains a slide with the same ID as the slide configuration desired to import delete that slide Every filter slide ID stored in the software must be unique 2 Choose Import Single Slide Open appears 3 In Open browse to and select the desired xml file to import 4 Choose Open Concert TRIAD Series Software User s Manual 2 12 Setting Up and Controlling Instruments DYNEX Technologies Inc 2 3 3 Manually Controlling the Instrument The Manual Control tab Figure 2 5 provides options to control the actions of the connected instrument such as shaking microplates and ejecting
10. 7 3 Viewing and Reevaluating Results from an Analysis Application When the optional Concert TRIAD Series Analysis Software module is installed the Result Viewer displays measurement results transformed data from the analysis options configured in the protocol and the parameters currently configured for each analysis option Multiple what if analyses on transformed data may be performed by editing the parameters configured for an analysis option and then reevaluating the data with the new parameters This section covers e Viewing Results From an Analysis Protocol Section 7 3 1 e Reevaluating Results from an Analysis Protocol Section 7 3 2 Note Refer to Section 7 2 Viewing Measurement Results in the Result Viewer for information about viewing results reported in the Data screen recalculating data reduction and exporting and saving results 7 3 1 Viewing Results From an Analysis Protocol All analysis options configured in the protocol appear in the navigation pane of the Result Viewer Figure 7 14 Transformed data and parameters for the selected analysis option appear in a series of tabs To view analysis results and parameters 1 In the navigation pane choose the desired analysis option Only analysis options configured in the protocol are listed A series of tabs with results from the selected analysis option appears Figure 7 14 a Result Viewer 20050329 101737 DTX 880 Transformati
11. Concert TRIAD Series Software User s Manual 4 6 Creating and Editing Detection Methods a5 Method 4 2 3 Defining Method Parameters Detection method properties such as filters and integration time are defined in Method Parameters The parameters available for configuration depend on the technique selected in Method Technique refer to Section 4 2 1 Selecting a Method Technique Use Method Parameters for e Defining Absorbance Method Parameters Section 4 2 3 1 e Defining Luminescence Method Parameters Section 4 2 3 2 e Defining Fluorescence Intensity Top Method Parameters Section 4 2 3 3 e Defining Fluorescence Intensity Bottom Method Parameters TRIAD only Section 4 2 3 4 e Defining Fluorescence Polarization Method Parameters TRIAD only Section 4 2 3 5 e Defining Time Resolved Fluorescence Method Parameters TRIAD only Section 4 2 3 6 4 2 3 1 Defining Absorbance Method Parameters A monochromatic absorbance method performs an absorbance measurement at a single wavelength A bichromatic method performs a second measurement at a reference wavelength This measurement is subtracted from the first to calculate the final result Editor Method Parameters Method Technique Method Type Method Name Jabs405 Bichromatic Method Parameters gt DYNEX Technologies Inc Excitation Filter nm 405 SL2 X Reference Excitation Filter nm Date created Reference
12. Contact a DYNEX Technologies Service Engineer 417 Z transport commanded to move to a position greater than maximum travel Contact a DYNEX Technologies Service Engineer 419 LED transport initialization failed Contact a DYNEX Technologies Service Engineer 420 Shutter transport initialization failed Contact a DYNEX Technologies Service Engineer 421 Z transport initialization failed Contact a DYNEX Technologies Service Engineer 423 LED transport lost steps Contact a DYNEX Technologies Service Engineer 424 Shutter transport lost steps Contact a DY NEX Technologies Service Engineer 425 Z transport lost steps Contact a DYNEX Technologies Service Engineer 427 LED transport is not energized Initialize the instrument refer to Section 2 2 3 Initializing the Instrument 428 Shutter transport is not energized Initialize the instrument refer to Section 2 2 3 Initializing the Instrument 429 Z transport is not energized Initialize the instrument refer to Section 2 2 3 Initializing the Instrument 431 LED transport error while positioning Contact a DY NEX Technologies Service Engineer 432 Shutter transport error while positioning Contact a DY NEX Technologies Service Engineer 433 Z transport error while positioning Contact a DY NEX Technologies Service Engineer 440 LED nu
13. Entering simulation mode Don t show this message again Figure 1 7 Warning Instrument is not connected 3 If the instrument was not detected configure the communications settings following the steps in Section 1 4 1 Configuring Communication Settings 4 Configure system settings such as printing options following the steps in Section 1 4 2 Configuring Software Settings Concert TRIAD Series Software User s Manual 1 14 Installing Setting Up and Using the Software 1 4 1 Configuring Communication Settings After physically connecting the instrument to a serial communications port on the host computer the selected serial port and communication speed must be configured correctly before Concert TRIAD Series Software can control instrument actions Communication settings are configured in Instrument Settings Before communication with an instrument is configured a simulated instrument appears in the Instrument Selection List Figure When communication is configured correctly and the instrument is detected by the software the simulated instrument is replaced in the list by the connected instrument Note When Signet is enabled on the system only users assigned a role containing the Instrument Settings permission may configure instrument settings Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To confi
14. Export Export records currently displayed in the Audit Viewer to an XML file Search Criteria Enter the desired search term s and choose Go All records containing matching terms are listed Searching for term s within records may also be limited to specific dates configured in Date from to Date from to Limit the records displayed to those falling between the specified dates Searching for records by date may also be combined with term s entered in Search Criteria 3 4 4 Reactivating Disabled Message Boxes Message boxes that have been disabled by users may be reactivated Note Message boxes are disabled by choosing Don t show this message again when the message box is displayed To reactivate disabled dialog boxes 1 In the navigation pane choose Users to access the User Selection List if necessary 2 From the toolbar choose Reactivate Disabled Message Boxes Message appears Figure 3 12 confirming that the message boxes have be reactivated OR From the Actions menu choose Reactivate Disabled Message Boxes OR Right click in the User Selection List and choose Reactivate Disabled Message Boxes from the menu All disabled messages are now activated Figure 3 12 Activating disabled messages Setting Up and Using Signet 3 17 3 4 5 Adding Electronic Signatures and Comments to Items Protocols measurement results detection methods and labware types may signed be by users assigned a role w
15. Note Depending on how Print Settings are configured Print and or Print Preview may appear before the protocol configuration prints Refer to Section 1 4 2 1 Configuring Print Settings for more information about enabling and disabling Print and Print Preview 3 If Show Printer Settings and Print Preview are not enabled in Print Settings no additional configuration is required OR If Print appears configure printing options as desired and choose OK Note Print is the dialog box that appears when Show Printer Settings is selected OR If Print Preview appears use the toolbar controls to change the magnification layout view or page s displayed if desired Figure 6 38 Concert TRIAD Series Software User s Manual Creating Protocols M Print preview Piste Sunday March 13 20 Change layout view mode Detector Protocol national Laboratories PrniOuUser Beteley Rattan Change view magnification Dave Boned Date Last Used Notes efinition Fluorescein Top Read 96 Fuuoresosin Top Read 96 Basic Row Monday May 03 2004 9 08 AM Thursday May 08 2004 1 28 PM Monday May 03 2004 0 09 AM Fuuorescein top read with Sence pro read shake Auto export data to Excel Tabeware Name Wells X Y count Used Wells Labware Created Labware Edited Notes Lot Lot Greated Lot Optimized Notes Standard 98 128 98 96 Monday February 28 2005 3 06 PM Monday Feb
16. configured To configure a program to run after a protocol is executed 1 In Output Settings choose Execute a program after protocol executes Two configuration fields appear Figure 6 29 4 Create Protocol Kinetic 340 Output Settings General Settings Select data output and printer options Technique Type Labware Selection Layout Settings Export to Microsoft Excel lv Perform after completing measurement s Es Show Result Viewer LY Perform after completing measurement s Transformation HE Create XxML and dat data files Concentration Perform after completing measurements Cutoff H Print options v Perform after completing measurement s Validation Output Settings gt Method Selection Variables Execute program Run this protocol now VY Execute a program after protocol executes Execute program ue Command line parameter Figure 6 29 Configuring an external software application in Output Settings 2 In Execute Program enter the complete path of the program to run for example C Windows System32 Net exe Net exe is a small utility supplied with Windows operating systems that sends messages to computers on the same network OR Select Choose an external program to run at the end of measurement Open appears 3 In Open browse to the location of the desired application and select it 4 Choose Open to return to Output Settings The selected path appears in Execute Program
17. the software may have been installed for a single user account on the system instead of all accounts Check with the site system administrator or login to the user account with permission to access the software Refer to Section 1 3 2 Installing Concert TRIAD Series Software on Windows 2000 or XP for more information about installing the software for a single or multiple user accounts d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 File Actions Help Protocol Selection List Application Type Created Last Edited Last Executed NewProtocoll Analysis 2 28 2005 3 13 PM 2 28 2005 3 23 PM 2 28 2005 3 13 PM Abs 340 single point Basic 2 28 2005 3 08 PM 2 28 2005 3 08 PM 2 28 2005 3 08 PM NewProtocol2 2 28 2005 3 28 PM 2 28 2005 3 29 PM 2 28 2005 3 29 PM CheckPlate Validation CheckPlate 2 28 2005 3 07 PM 2 28 2005 3 07 PM 2 28 2005 3 07 PM Figure 1 6 Concert TRIAD Series Software main screen DYNEX Technologies Inc Installing Setting Up and Using the Software 1 13 2 If the Protocol Selection List Figure 1 6 appears immediately the instrument was automatically detected by the software Proceed to Section 1 4 2 Configuring Software Settings to configure system settings OR If Warning appears Figure 1 7 the instrument was not detected by the software Choose OK to work in simulation mode until the communications settings are configured properly Warning Instrument is not connected
18. 2 28 2005 3 06 PM 2 28 2005 3 06 PM Labware Figure 5 1 Accessing labware actions DYNEX Technologies Inc Creating and Editing Labware 5 3 5 2 Creating Labware New types of labware are created in the Labware Editor which guides the creation process with a wizard type interface Creating labware includes e Defining Labware Information Section 5 2 1 e Configuring Offsets and Well Dimensions for the Default Labware Lot Section 5 2 2 e Optionally Signing Labware Section 5 2 3 to prevent labware from being edited or deleted Labware may be signed only when Signet is enabled on the system Note When Signet is enabled on the system only users assigned a role containing the Create permission may create new labware definitions To sign labware users must be assigned a role containing the Sign permission Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To create and define new labware From the toolbar choose Create a new labware type The Labware Editor appears Figure 5 2 OR From the Actions menu choose Create a new labware type OR Right click in the Labware Selection List and choose Create a new labware type from the menu Concert TRIAD Series Software User s Manual 5 4 Creating and Editing Labware 5 2 1 Defining Labware Information Use Labware Information to define lab
19. 2 3 e Configuring Labware Layout Settings Section 6 2 4 e Configuring Detection and Preparation Methods Section 6 2 5 e Configuring Output Settings Section 6 2 11 When the optional Concert TRIAD Series Analysis Software module is installed several analysis options may be selected and configured to transform measurement data as desired e Configuring Variables Concert TRIAD Series Analysis Software only Section 6 2 6 e Configuring a Transformation Formula Concert TRIAD Series Analysis Software only Section 6 2 7 e Configuring Concentration Concert TRIAD Series Analysis Software only Section 6 2 8 e Configuring Cutoff Values Concert TRIAD Series Analysis Software only Section 6 2 9 e Configuring Validation Rules Concert TRIAD Series Analysis Software only Section 6 2 10 Concert TRIAD Series Software User s Manual 6 4 Creating Protocols To create and configure a new protocol 1 From the toolbar choose Create a new protocol Select Application Type appears Figure 6 2 OR From the Actions menu choose Create a new protocol OR Right click in the Protocol Selection List and choose Create a new protocol from the menu Select Application Type ApplicationT ype Basic o YX Analysis Basic applications allow you to quickly set up and read plates Figure 6 2 Selecting the application type 2 Choose the Application Type The t
20. 21 2008 Time 54500 PM Change view magnification Pratccal Nae Application Type Date Measured Usar Measured Date Evaluated User Evalusted Vaid Tateware Name Lot Created Lot Optimized Nates tesult Multiwavelenght Kinetic 340 405 20050318 154720 Muttiwavelenghs Kevetic 340 405 Analysis Wednesday March 16 2008 3 47 PM Barkaley Ractan Wednesday March 16 2008 348 PM Berkeley Rattar inana CUE 12x8 96 Wednesday March 18 2008 10 58 AM Wednesday March 16 2008 10 58 AM None Dotauittot Wednesday March 18 2008 10 58 AM Wednesday March 16 2008 10 58 AM None Measurement Method 1 Excitation Filter am Measuramen Technique Excitation Filter am UnieName Measurement Technique Kinetic Cycles Kinetic interval Date Reduction RETENI 340 SL2 o Avsorbance 9 7 Deta aBSg405 405 SL2 00 Absorbance a 7 Dolta Thternational Laboratones Change page s displayed Detection Results International Laboratories E Waray March 37 2008 Time 54500 PM ratOumUser Berkeley Ratan Result Multiwavelenght Kinetic 340 405 Matrix Legend Allocation Transformation Qualification nar Lime 586 jes j 537 336 amp sao 0524 0575 Lite Uninet in 549 s50 s51 s53 855 856 s7 osas oosa aeza oss 1495 1124 2552 Lior Umi inder ma Undor anid Limit Under timi Breder Limi tor uni pdr nt erie se7 py a
21. 263 393 OK Ol OK OK GES 543 239 av Figure 7 5 Viewing mean data for a fluorescence polarization measurement To view mean data 1 Select the Mean Data tab if necessary 2 Choose Show Status to show the measurement status for each well if desired Table 7 2 describes the status indicators that may be displayed 3 Choose Show Well Identifier to show identifiers for each well if desired 4 To reject a well as an outlier right click on the desired well and select Reject Well A red X appears over the well and the Reevaluate current measurement results button appears on the toolbar Note Multiple wells may be rejected as outliers Rejected wells may be included in the measurement results again by right clicking on each well desired and selecting Accept Well 5 Choose Reevaluate current measurement results to recalculate the results with outliers removed Note The Reevaluate button appears on the toolbar only when a parameter in the results such as an outlier has been changed DYNEX Technologies Inc Viewing Measurement Results 7 7 7 2 4 Viewing Graphs The Graphs tab displays graphs for all measured wells on a plate Figure 7 6 The detection method s configured in the protocol determine the types of graphs displayed a Result Viewer 2005031 6 110303 DTX 880 Click here to view a 3 D graph of all results ea 3 4 5 6 7 8 9 10 AAAA AAAA LLAZA AE
22. 4 e Copying Protocols Section 6 5 e Deleting Protocols Section 6 6 e Printing Protocol Configuration Information Section 6 7 e Exporting and Importing Protocols Section 6 8 Concert TRIAD Series Software User s Manual 6 2 Creating Protocols To select protocols and access protocol functions From the navigation pane choose Protocols The Protocol Selection List appears Figure 6 1 d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 DEAR Fie Actions Help Protocol actions Protocol Selection List Application Type Created Last Edited Last Executed FloTopkinetic 01 2 28 2005 3 13 PM 3 8 2005 2 33 PM 3 2 2005 9 56 AM FloTopkinetic 12 cycle Analysis 2 28 2005 3 13 PM 3 8 2005 2 34 PM 3 2 2005 9 56 AM Rhodamine Bottom Read 96 Basic 5 6 2004 11 48 4M 5 6 2004 11 48 AM 5 6 2004 11 48 An Rhodamine Top Read 384 Basic 5 3 2004 9 09 AM 5 6 2004 11 51 AM 5 3 2004 9 09 AM Rhodamine Top Read 96 Basic 5 3 2004 9 09 AM 5 6 2004 11 47 AM 5 3 2004 9 09 AM Protoc ol s parked Top Read 384 Bask 5 3 2004 9 09 AM 5 6 2004 1 29 PM 5 3 2004 9 09 AM luorescein Top Read 96 Basic 5 3 2004 9 09 4M 5 6 2004 1 28 PM 5 3 2004 9 09 4M Fluorescein Bottom Read 96 Basic 5 4 2004 3 18 AM 5 6 2004 11 46 AM 5 4 2004 3 18 AM Basic TRF Europium 96 Basic 5 3 2004 9 02 AM 5 6 2004 12 01 PM 5 3 2004 9 02 AM YY Bradford Protein Assay 96 Basic 5 6 2004 10 52 4M 5 6 2004 12 08 PM 5 6 2004 10
23. 5 Viewing mean data for a fluorescence polarization measurement e cesses 7 6 Figure 7 6 Viewing kinetic measurement graphs c cccercssccesescucesasceveccesssdecresaueesseevsueeeuseeveeneeeens 7 7 Figure 7 7 Viewing a two dimensional absorbance graph ou eee eeeeeseeeeneceeeeeeeeeeseeeeeeeeeeeeaees 7 8 Figure 7 8 Viewing a three dimensional area scan graph eeeeeeceeeseeeseceeeeeseeceaeeeseeeeneeenees 7 9 Figure 7 9 Changing data reduction parameters in the Results Viewer 0 0 0 ceeeeeeeeeseeeneeees 7 10 Figure 7 10 Selecting a data reduction method for the sequence eee eeeeeseeeeeeereeeneeeneeetees 7 11 Figure 7 11 Choosing to overwrite existing measurement results 0 ee eee eeeeeeeeeeneeeneeeees 7 12 Figure 7 12 Entering a new name for saved results eee eeeseeeseeesseceeeeeeeeeeseecsaeceaeenseeenaeenes 7 13 Figure 7 13 Saving parameters edited in the Result Viewer to the protocol eee 7 13 Figure 7 14 Viewing existing transformation parameters in the Results Viewet 0 7 14 Figure 7 15 Viewing existing transformation parameters in the Results Viewet 0 7 17 Figure 7 16 Editing transformation parameters in the Results Viewer ceeseeseesseeeeeeeees 7 18 Figure 7 17 Viewing protocol information in the General worksheet excerpt 0 0 0 0 eee 7 20 Figure 7 18 Viewing raw data CXCS0 0 ocescscce cde cchoceues thea teeedaniesadesaie event oteddeegaacned ences 7 21 Figu
24. 52 AM OS Software Settings Basic FP Fluorescein 96 Basic 5 3 2004 9 37 AM 5 6 2004 12 07 PM 5 3 2004 9 37 AM Basic Luminescence 96 Basic 5 3 2004 9 04 AM 5 6 2004 12 02 PM 5 3 2004 9 04 AM AE Users Basic Absorbance Multiwavelength 96 Basic 4 7 2004 10 28 AM 5 6 2004 12 10 PM 4 7 2004 10 28 Ab Basic Absorbance Kinetic 340 96 Basic 4 7 2004 9 09 AM 5 6 2004 12 12 PM 4 7 2004 9 09 AM Basic Absorbance Linear Scan 96 Basic 5 6 2004 11 00 AM 5 6 2004 12 10 PM 5 6 2004 11 00 AM Basic Absorbance Area Scan 96 Basic 5 3 2004 9 05 AM 5 6 2004 3 45 PM 5 3 2004 9 05 AM Basic Absorbance DNA Quantitation 96 Basic 5 6 2004 11 38 AM 5 6 2004 12 11 PM 5 6 2004 11 38 Ab Absorbance ELISA 405 96 Basic 4 7 2004 8 50 AM 5 6 2004 12 11 PM 4 7 2004 8 50 AM Absorbance ELISA 450 96 Basic 5 6 2004 11 30 AM 5 6 2004 12 12 PM 5 6 2004 11 30 4h Absorbance 405 96 Basic 5 4 2004 3 42 AM 5 6 2004 5 50 PM 5 4 2004 3 42 AM Abs 340 single point Basic 2 28 2005 3 08 PM 2 28 2005 3 08 PM 2 28 2005 A Instruments Figure 6 1 Protocol Selection List DYNEX Technologies Inc Creating Protocols 6 3 6 2 Creating Basic and Analysis Protocols New protocols are defined in Create Protocol which guides the creation process with a wizard type interface Creating a new protocol requires e Configuring General Settings Section 6 2 1 e Selecting the Technique Type Section 6 2 2 e Selecting the Labware Type Used in the Protocol Section 6
25. Cancel to close the Scan Selection Editor without updating changes Concert TRIAD Series Software User s Manual 6 22 Creating Protocols H 6 In Method Properties click in Data Reduction and choose the configuration button Data Reduction Method appears Figure 6 14 a Data Reduction Method Method Peak Value Used to detect the highest value per sample within a Smoothing Points 5 sequence of measurements Figure 6 14 Selecting a data reduction method for a scan method 7 In Data Reduction Method select the desired Method If required by the selected method additional parameters such as smoothing points appear 8 Configure additional parameters for the selected data reduction method if required Note Refer to Table A 1 in Appendix A Data Reduction Techniques for details about the data reduction methods available for scan measurements 9 Choose OK to confirm the selection of the data reduction method DYNEX Technologies Inc Creating Protocols 6 23 6 2 5 2 Configuring a Method in Advanced Mode Configuring a method in advanced mode allows multiple detection methods and preparation methods such as microplate shaking and temperature control TRIAD only to be arranged as desired in a linear execution sequence Kinetic and scan methods may also be configured Protocols that require multiple measurements at different wavelengths such as a multiwavelength absorbance measurement must be c
26. Data tab Simulated Data appears Figure 1 12 2 In the desired field enter the full path to the new simulated data file for example c detection software templates DefaultSimulatedData dat Any data file with a dat extension may be selected including prior measurement results Proceed to step 5 OR Choose the Browse button next to the desired measurement type Open appears Note Simulated data files are used when the number of measurement points in the simulated protocol run is the same as those present in the data file When the number of measurement points is different the software generates random data 3 In Open browse to desired data file Any data file with a dat extension may be selected including prior measurement results DYNEX Technologies Inc gt Concert TRIAD Series Installing Setting Up and Using the Software 1 19 4 Choose Open to select the data file and return to Software Settings OR Choose Cancel to close Open without selecting a different data file 5 Repeat steps 2 4 for each simulated data file desired to change 6 Choose Apply to set the new default data file s 1 4 2 3 Choosing the Directory Where Exported Measurement Results are Saved Exported measurement results files regardless of format are saved in a single directory The default storage directory is C Documents and Settings All Users Application Data Multimode Detection Software data Use Directory Settings to
27. E E Gis R Aea dia a A SS 7 1 7 2 Viewing Measurement Results in the Result Viewer 7 3 7 2 1 Viewing RaW Daa cosac ameua ie oo awe aE A E E E E 7 4 7 2 2 Niewing Reduced Data 65240sus0ene0 subeense ga beewenseees 7 5 1 2 3 Viewing Mean Data ii 24440 s402459404944 R5064 0245400RR Oo 7 6 72 4 Views Graphs socere gt canoe ceo eS a 6S e55 SSeS Se SHES 7 7 7 2 4 1 Viewing Two Dimensional Graphs 7 8 7 2 4 2 Viewing Three Dimensional Graphs 7 9 7 2 5 Recalculating Data Reduction 20244408 4o0455se0eduseeu cede es 7 10 7 2 6 Exporting Measurement Results to Microsoft Excel 7 12 Teel Saving Measurement Results 0 0 0 0 cece eee eee nee 7 12 73 Viewing and Reevaluating Results from an Analysis Application 7 14 7 3 1 Viewing Results From an Analysis Protocol 04 7 14 7 3 1 1 Changing the Standard Curve Graph View 7 15 7 3 2 Reevaluating Results from an Analysis Protocol 7 17 7 4 Viewing Exported Measurement Results 0 0 0 e cee eee eee ee 7 19 7 4 1 Viewing Measurement Results in Microsoft Excel 7 19 7 4 1 1 Viewing Protocol and Measurement Information 7 20 7 4 1 2 Viewing Raw Data 22 cece eee 7 21 7 4 1 3 Viewing Reduced and Transformed Data 7 22 7 5 Signing Measurement Results nannu nannu 7 23 76 Deleting Measurement Result
28. Excitation Filter Appears only when configuring bichromatic measurements Figure 4 4 Defining absorbance measurement parameters To define absorbance method parameters 1 Enter a Method Name Figure 4 4 2 In Excitation Filter nm select the measurement filter Creating and Editing Detection Methods 4 7 3 Ifa bichromatic measurement is being defined in Reference Excitation Filter nm select the reference filter Note The filters available are those installed on the excitation filter slide loaded in the instrument and configured for absorbance techniques in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides 4 Choose Save to save the new absorbance detection method The new method appears in the Detection Method Selection List OR Choose Back to define a different Method Type refer to Section 4 2 2 Selecting the Method Type OR Choose Cancel to close the Method Editor without saving the new detection method 4 2 3 2 Defining Luminescence Method Parameters A luminescence method performs glow luminescence measurements on samples Generally luminescence measurements do not require a filter however cutoff filtration using an emission filter may be specified to eliminate photoluminescence generated by the microplate itself if desired 5 Method Editor Method Parameters Method Technique Method Parameters gt Method Name Luminescence glow Emission Filt
29. Labware without completing the optimization DYNEX Technologies Inc Creating and Editing Labware 5 19 5 6 5 Verifying Well Centers Use Verify Well Centers to verify that the x and y offsets and distances between rows and columns are correct Figure 5 11 If desired the offsets distances and lot name may be edited in Verify Well Centers 3r Optimizing Labware Weber96deep Verify Well Centers Select a detection method Verify well measurements below Click save to save optimization or back to adjust values graphically Prepare the Labware Optimize Select Center of Left Top Well E Labware Lot Measurements Column distance 0 9 Select Center of Left Bottom Well Lower left x offset 1 435 Select Center of Right Top Well Lower left y offset 1 135 Select Center of Right Bottom Well Lower right x offset 1 435 Verify Well Centers gt Lower right y offset 1 135 Row distance 0 9 Property Upper left x offset 1 435 rid Upper left y offset 1 135 g Upper right x offset 1 435 Upper right y offset 1 135 E Labware Lot Name Lot ID Name Lot 2005 03 03T 15 16 52 Column distance Information about the j Distance between columns cm 4 field bein g confi gure d Figure 5 11 Verifying well centers To verify and edit offsets distances and lot name 1 If necessary click the next to Labware Lot Measurements to display the fields in the category Note More information about the fiel
30. OR Choose Cancel to close Open without selecting an application DYNEX Technologies Inc Creating Protocols 6 45 5 If the selected application supports command line parameters in Command line parameter enter the desired parameter For example if using Net exe entering the parameters SEND Workstation1 Finished instructs the application to send the message Finished to a computer named Workstation when the protocol run completes 6 2 12 Signing a Protocol When Signet is enabled on the system protocols may be signed to prevent the configured parameters from being edited Protocols may be signed at any time after the configuration is complete Protocols may be signed by users who are assigned a role containing the Sign permission Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To sign a protocol 1 In the Protocol Selection List select the protocol to sign 2 From the toolbar choose Sign the selected protocol Sign the Selected Item appears OR From the Actions menu choose Sign the selected protocol OR Right click on the selected labware and choose Sign the selected protocol 3 In Sign the Selected Item add comments and an electronic signature by following the instructions in Section 3 4 5 Adding Electronic Signatures and Comments to Items Concert TRIAD Series Software User s Ma
31. Results 7 13 2 Choose Yes to overwrite existing results The results are overwritten and Message appears asking if parameters edited in the Result Viewer should also be saved to the protocol definition Figure 7 13 Proceed to step 4 Note When Signet is enabled on the system measurement results that have been signed may not be overwritten Refer to Section 7 5 Signing Measurement Results for more information about signing results OR Choose No to save the results with a different name Result Name appears Figure 7 12 Result Name Enter a new name for these measurement results 20050318 141152 0 Figure 7 12 Entering a new name for saved results 3 Enter a new name for the results and choose OK The results are saved to the database Message appears asking if parameters edited in the Result Viewer should also be saved to the protocol definition Figure 7 13 Do you want to save the Result Viewer parameters to the Protocol Definition Figure 7 13 Saving parameters edited in the Result Viewer to the protocol 4 Choose Yes to save the new parameters to the protocol definition Note When Signet is enabled on the system parameters changed in the Result Viewer may not be saved to protocols that have been signed OR Choose No to ignore any changes made and retain the original parameters configured in the protocol Concert TRIAD Series Software User s Manual 7 14 Viewing Measurement Results
32. Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To sign measurement results 1 In the Results Selection List select the measurement results to sign 2 From the toolbar choose Sign the selected result Sign the Selected Item appears OR From the Actions menu choose Sign the selected result OR Right click on the desired results and choose Sign the selected result 3 In Sign the Selected Item add an electronic signature by following the instructions in Section 3 4 5 Adding Electronic Signatures and Comments to Items Concert TRIAD Series Software User s Manual 7 24 Viewing Measurement Results 7 6 Deleting Measurement Results Measurement results may be deleted from the Results Selection List When the optional Signet module is installed and enabled on the system results that have been signed may not be deleted refer to Section 7 5 Signing Measurement Results Note When Signet is enabled only users assigned a role containing the Delete permission may delete measurement results refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts To delete measurement results 1 In the Results Selection List select the results to delete 2 From the toolbar choose Delete the selected result Message appears Figure 7 20 OR From the Actions menu choose Delete the select
33. Setting Up and Using the Software 1 11 1 3 5 Repairing or Removing the Concert TRIAD Series Software Installation The Concert TRIAD Series Software installation may be repaired if required components are missing or damaged Try repairing the installation if the software will not open or does not run correctly The software may also be removed uninstalled from the system Repair and removal options are accessed from the Add or Remove Programs control panel in Windows To repair or remove the software 1 Exit all open Windows programs 2 Make sure the current user account has Administrator privileges Accounts with Standard or Restricted access are not permitted to modify or remove software Contact the site system administrator for more information about account privileges 3 If repairing the installation insert the Concert TRIAD Series Software installation CD into the CD ROM drive 4 From the Start menu choose Settings gt Control Panel Control Panel appears 5 In Control Panel choose Add or Remove Programs Add or Remove Programs appears 6 In Add or Remove Programs choose Multimode Detection Software Repair and removal options for the software appear 7 To repair the installation choose Click here for support information Support Info appears Figure 1 5 Proceed to step 8 OR To remove the software choose Remove and follow the onscreen instructions until the removal process is finished Note W
34. Software Installer choose Finish The software is now ready for use DYNEX Technologies Inc Installing Setting Up and Using the Software LE 1 3 3 Installing Concert TRIAD Series Software on Windows NT When installing the software on a Windows NT system required components that must be installed before the software are selected manually from a link on a web page Figure 1 4 To install the verification plate software 1 Exit all Windows programs before running the setup program 2 Make sure the current user account has Administrator privileges Accounts with Standard or Restricted access are not permitted to run the setup program Contact the site system administrator for more information about account privileges 3 Insert the installation CD into the CD ROM drive and browse to the contents of the CD 4 In the contents of the CD open Begin here for NT systems 5 In Begin here for NT systems double click Installer htm Concert TRIAD Series Software opens in a web browser window Figure 1 4 A series of links lists all of the components that must be installed to enable the verification plate J Concert TRIAD Series Software Microsoft Internet Explorer olx File Edit View Favorites Tools Help e Q Ala a alB 4 2 4 inl Back Forward Stop Refresh Home Search Favorites History Mail Size Address fe INNT Profiles Administrator D esktop Multimode Disc Images Disklmage C CP Begin her
35. a minimum of 2 standard points Cubic Spline All standard points are connected by the best fitting curve Note Can only be used for nonlinear and nonsigmoid functions Cubic Spline Requires a minimum of 3 standard points This procedure can be used only to characterize sigmoid curves The curve is calculated according to the formula 4 Parameter Fit d A a d x b p 4 Parameter Fit a zero dose response upper asymptote d infinite dose response lower asymptote c dose level which results in a response midway between a and d b slope factor yrs Requires a minimum of 3 standard points DYNEX Technologies Inc 10 Creating Protocols 6 35 Select the Number of standards to configure Up to 12 standards may be configured in a protocol Standards configured in the labware layout are automatically added to Concentration In Extrapolation enter a percentage value to extrapolate the standard curve above and below the highest and lowest standard points in the curve if desired Extrapolation may be configured for linear regression cubic spline and four parameter fit curve fitting methods In Y Axis select the Base for the axis e Measurement the reduced data from the protocol run Transformation the value calculated using the transformation formula configured in Transformation This option is available only whe
36. and the perpendicular polarization intensity components divided by the sum of the two orthogonal fluorescence intensity components Polarization is G Factort Polarization calculated according to the formula i _ I parallel G factor x I perpendicular Threshold bt Ete ar I parallel G factor x I perpendicular vey Provides raw fluorescence intensity measurements in the parallel and the perpendicular polarization planes with respect to the plane of linearly polarized excitation light Total intensity is calculated j Total Intensity according to the formula G Factor Total Intensity I parallel G factor x 2 x I perpendicular The ratio of the difference between the parallel and perpendicular polarization intensity components divided by the sum of the fluorescence intensity parallel to the excitation plane plus the fluorescence intensity perpendicular to the excitation plane G Factort Anisotropy multiplied by two Anisotropy is calculated according to the formula Threshold _ _ I parallel G factor x perpendicular parallel G factor x 2 x I perpendicular In polarization data reduction techniques intensity defines sample raw data minus the average of blank replicate raw data The G factor factors out differences in detection efficiency between the polarization planes The default G factor is derived from fluorescein measurements performed on several instruments If a more ac
37. assigned to as many roles as desired Three preconfigured roles are installed with the module refer to Table 3 2 These roles may be assigned to user accounts as is or edited renamed or deleted as desired Note Refer to the Account Management online help for more detailed information To access online help press F1 or choose the help button in the lower right corner of the window To configure roles 1 In Account Management choose the Roles tab Figure 3 4 Account Management EA Accounts a Roles a Settings g Repositories amp Audit Permissions tA Lab Administrator Concert TRIAD Series amp Lab Technician Copy amp Protocol Developer Create Delete Edit InstrumentSettings Optimize Preconfigured Sign roles installed with ViewAuditEntry the module za Permissions Checks indicate permissions assigned to the role selected in the Roles pane Create Role Delete Role Set Description Figure 3 4 Configuring roles 2 In Roles create a new or select an existing role to edit Table 3 2 describes the default roles provided with the software 3 In Permissions select the permissions to include in the selected role Table 3 1 describes the permissions available for Concert TRIAD Series Software 4 Repeat steps 2 and 3 for each role being configured 5 When all roles are configured as desired choose the Accounts tab Concert TRIAD Series So
38. bottom luorescein Top Measurement Technique Absorbance Fluorescence Intensity Top Absorbance Absorbance Absorbance Fluorescence Intensity Bottom Absorbance Fluorescence Intensity Top Fluorescence Intensity Bottom Fluorescence Intensity Top Measurement Type Created 2 28 2005 3 3 2005 3 3 2005 3 3 2005 3 3 2005 3 4 2005 3 3 2005 3 4 2005 3 4 2005 3 4 2005 Monochromatic Monochromatic Monochromatic Monochromatic Monochromatic Monochromatic Monochromatic Monochromatic Monochromatic Monochromatic Figure 5 7 Selecting the detection method for labware optimization To select the detection method 1 To optimize labware for use in absorbance fluorescence intensity or luminescence protocols choose a detection method configured in the protocol OR To optimize labware for use in fluorescence polarization or time resolved fluorescence protocols choose a fluorescence intensity top method at a similar wavelength to the polarization or TRF measurement s configured in the protocol 2 Choose Next to Prepare Labware refer to Section 5 6 2 Preparing and Loading the Labware OR Choose Cancel to close Optimizing Labware without performing the optimization Concert TRIAD Series Software User s Manual 5 16 Creating and Editing Labware 5 6 2 Preparing and Loading the Labware Labware dimensions are optimized by reading the four corner wells of the plate Prepare Labware provides cont
39. by selecting a different data reduction method Figure 7 9 Data reduction may be recalculated for any detection method configured with data reduction in the protocol When multiple detection methods are configured in the protocol data reduction for the measurement sequence may also be edited Note The Edit tab is available only for measurement results that use data reduction or for results from protocols where a sequence of detection methods is configured Result Viewer 20050320 164521 DTX 880 View measurement results and graphs in the tabs below Raw data Reduced Data Graphs Edit Method Selection Method Properties Sequence Data Reduction scan Lassesso Scan ABS 405 or the Sequence Select a detection method Data Reduction Data Reduction is used to determine a single value per sample based on the results of a sequence of measurements over a period of time Figure 7 9 Changing data reduction parameters in the Results Viewer Viewing Measurement Results 7 11 To change parameters l 2 ie Select the Edit tab if necessary If multiple detection methods using data reduction appear in Method Selection choose the desired method or Sequence The data reduction method currently used appears in Method Properties In Method Properties click in Data Reduction and choose the configuration button Data Reduction Method appears Figure 7 10 3 Data Reduction Method M
40. change the storage directory if desired Figure 1 13 Note All measurement results are also stored in the Concert TRIAD Series Software database and may be accessed using the Result Viewer refer to Section 7 2 Viewing Measurement Results in the Result Viewer Connected Filter Slides Ex 2 Em 1 Protocols Results by Detection Methods Labware E Instruments Software Settings Print Settings Simulated Data Directory Settings Data Directory C Documents and Settings All Users Application Data Multimode Detection Softwareid A Browse for desired Figure 1 13 Choosing the directory where data is saved To choose a different storage directory 1 Choose the Directory Settings tab Directory Settings appears Figure 1 13 2 In Data Directory enter the complete path of the desired storage directory for example C documents multimode measurement results MyResults Proceed to step 4 OR Choose Browse for a directory Open appears Concert TRIAD Series Software User s Manual 1 20 Installing Setting Up and Using the Software 3 In Open browse to desired directory 4 Choose Open to select the directory and return to Output Settings OR Choose Cancel to close Open without selecting a new storage directory 5 Choose Apply to set the new storage directory DYNEX Technologies Inc Setting Up and Controlling Instruments 2 1 Overview Before defining measuremen
41. configuration is inserted or the filters on a slide change the slide must be configured in the Filter Slides tab Up to 31 excitation filter slides and 31 emission filter slides may be stored in Concert TRIAD Series Software at one time This section covers e Adding Filter Slides Section 2 3 2 1 e Configuring Filter Slides Section 2 3 2 2 e Removing Filter Slides Section 2 3 2 3 e Exporting and Importing All Filter Slide Configurations Section 2 3 2 4 e Exporting and Importing Individual Filter Slide Configurations Section 2 3 2 5 Note Refer to the TRIAD Series Multimode Detector User s Manual Section 1 3 2 Exchanging Filter Slides for information on physically installing filters and filter slides as Instrument Settings Basic Settings Filter Slides Manual Control Excitation Emission Add Slide Filter Slide Properties Slide ID 1 Slide Name 1 Remove Slide Export Slides Import Slides Export This Slide Slide ID Identification number of the selected filter slide Import Single Slide oe Figure 2 3 Instrument Settings Filter Slides DYNEX Technologies Inc Setting Up and Controlling Instruments 2 9 2 3 2 1 Adding Filter Slides When a new filter slide is used with the instrument for the first time it must be added so Concert TRIAD Series Software can identify the slide and filter configuration To add filter slides
42. configuring output settings 6 42 configuring reading direction 6 14 configuring scan measurements 6 20 configuring scan methods 6 18 configuring transformation formulas 6 32 configuring validation rules 6 40 configuring variables 6 31 copying 6 55 creating 6 3 deleting 6 56 editing 6 53 optimizing read height 6 48 overview 6 1 printing 6 57 running in simulation mode 6 51 on an instrument 6 46 selecting analysis options 6 5 selecting labware 6 8 selecting methods advanced mode adding set temperature preparation methods 6 29 configuring a shake preparation method 6 28 configuring set temperature preparation methods 6 29 DYNEX Technologies Inc selecting technique type 6 7 signing 6 45 R raw data viewing 7 4 viewing in Microsoft Excel 7 21 read height optimizing 6 48 setting before a protocol run 6 47 reduced data viewing 7 5 S scan measurements configuring 6 20 data reduction techniques A 1 sequence data reduction techniques A 1 shaking configuring a shake preparation method 6 28 manual control 2 13 signing adding electronic signatures to items 3 17 detection methods 4 13 labware 5 8 measurement results 7 23 protocols 6 45 unlocking signatures 3 19 viewing signatures 3 19 viewing unlocked signatures 3 20 simulated data files choosing default 1 18 selecting before a protocol run 6 51 simulation mode choosing default simulated data files 1 18 enabling manually 2 5 running protocols
43. dimensional graphs Figure 7 6 Two dimensional graphs may be printed a Graphic View File Well A1 Figure 7 7 Viewing a two dimensional absorbance graph To print the graph 1 From the File menu choose Print Note Depending on how Print Settings are configured Print and or Print Preview may appear before the protocol configuration prints Refer to Section 1 4 2 1 Configuring Print Settings for more information about enabling and disabling Print and Print Preview 2 If Show Printer Settings and Print Preview are not enabled in Print Settings the graph prints automatically OR If Print appears configure printing options as desired and choose OK Note Print is the dialog box that appears when Show Printer Settings is selected OR If Print Preview appears use the toolbar controls to change the magnification layout view or page s displayed if desired Refer to Section 7 7 Printing Measurement Results for more information about Print Preview DYNEX Technologies Inc Viewing Measurement Results 7 9 7 2 4 2 Viewing Three Dimensional Graphs Selecting an individual area scan graph a row column or all samples in the Graph tab displays a three dimensional graph Figure 7 8 Three dimensional graphs may be rotated horizontally or vertically and printed als Graphic View 2 _Well Al Use the vertical scroll bar to rotate the graph vertically Use the horizontal scrol
44. e Plot Change the plotting method and enable or disable 3 D shadows and data point markers e Subsets This tab contains no configurable options e Axis Change the properties of the X and Y axes e Font Change the font used for titles and labels e Color Change the color of any graph attribute except data points and lines e Style Change the colors and styles of data points and lines displayed in the graph Note Many of the options available in Customization are the same as those in the menu that appears when right clicking on the graph Export Dialog Open the Export dialog box DYNEX Technologies Inc Viewing Measurement Results 7 17 7 3 2 Reevaluating Results from an Analysis Protocol Multiple what if analyses on transformed data may be performed by editing the parameters configured for an analysis option and then reevaluating the data with the new parameters The parameters used to calculate the transformed data currently displayed in the Result Viewer are viewed in the Parameters tab Parameters are edited in the Edit tab To reevaluate measurement results 1 In the left pane choose an analysis option to edit Only analysis options configured in the protocol are listed The selected analysis option appears Figure 7 15 Note Select Data to view measurement results and edit data reduction parameters configured in the protocol Refer to Section 7 2 Viewing Measurement Results
45. from the protocol run e Concentration the value calculated using the standard curve configured in Concentration This option is available only when Concentration is configured in the protocol refer to Section 6 2 8 Configuring Concentration Concert TRIAD Series Analysis Software onl e Transformation the value calculated using the transformation formula configured in Transformation This option is available only when Transformation is configured in the protocol refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only Note Transformation is the default name for transformation formulas If a different name is entered in Transformation that name appears in Basis of Evaluation refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only 2 Choose the Number of groups to configure 3 Enter a Name for each group 4 Enter the formulas and or values used to classify samples into groups The cutoff formula or value entered represents the maximum value included the group being configured for example in Figure 6 26 Group 2 Ideal includes all samples with values between 2 3 and 2 8 Note The results calculated from the formulas or the values entered must ascend Results or values that do not ascend generate will generate an error during protocol runs 5 Choose Report Options and select the cutoff informati
46. layout refer to Section 6 2 4 Configuring Labware Layout Settings OR Choose Cancel to close Create Protocol without saving the new protocol 6 2 5 1 1 Configuring a Kinetic Method Kinetic measurements perform a specified series of measurements on each sample at specified intervals Final measurement results are calculated from raw data using a data reduction method gt TRIAD Kinetic measurements may be configured for all method types except fluorescence polarization To configure a kinetic measurement 1 In Type select Kinetic Method Properties appears Figure 6 10 2 In Method Properties enter the number of Kinetic Cycles to be performed Kinetic measurements may be set to perform 2 to 100 cycles 3 In Method Properties enter the desired Kinetic Interval in seconds The interval is the length of time between each measurement of the same well Note The minimum kinetic interval is populated automatically in Kinetic Interval and is determined by the labware type and layout settings configured in the protocol The maximum interval between measurement cycles is 65 535 seconds 4 In Method Properties choose the browse button to select and configure a Data Reduction method Data reduction calculates a single value for each sample from measurement data collected during each cycle in a protocol run Data Reduction Method appears Figure 6 11 5 Data Reduction Method Method M ax Slope Maximum slope of
47. of the standard curve Refer to Concentration Section 7 3 1 1 Changing the Standard Curve Graph View for information about customizing the graph display Parameters Displays the parameters used to calculate the Variables transformed data currently displayed in the Layout Transformation View and List View tabs Concentration Cutoff Validation Edit Edit the parameters configured for the analysis option Variables using the same configuration screen that appears in Transformation the Create Protocol wizard refer to Section 7 3 2 Concentration Reevaluating Results from an Analysis Protocol Cutoff Validation 7 3 1 1 Changing the Standard Curve Graph View The standard curve graph view may be changed by zooming in on a selected region or changing view options To zoom in on a region of the graph 1 Position the cursor at the desired starting point for the region then click and hold the mouse button down The cursor icon changes to a magnifying glass 2 Drag the mouse until the desired region is selected The selected region is highlighted in black 3 Release the mouse button The selected region is displayed To zoom out and view the graph at the original size Right click on the graph and choose Undo Zoom from the menu that appears To change view options Right click on the graph and choose a view option from the menu that appears Table 7 4 describes the view options available Concert TRIA
48. on which module is currently selected in the navigation pane For example when Protocols is selected the Protocol Selection List is displayed which provides access to configured protocols and functionality specific to the Protocols module 1 2 3 Accessing Online Help Concert TRIAD Series Software contains a detailed online help system that covers defining and editing labware detection methods and protocols performing measurements and exporting measurement results The online help is context sensitive which provides instant access to help for the active screen To access online help Press F1 at any time to display online help for the active screen Figure 1 2 OR From the Help menu choose Help to display the table of contents E Concert TRIAD Series Software Help DER mH e gt Hide Back Forward Stop Refresh Print Conteris Index Search You are here Defining Editing and Running Protocols gt Creating Setting Up and Using the Software Protocols gt Selecting the Labware Type Used in the Protocol Setting Up and Controlling Instruments g Creating and Editing Labware is z 4 Dain ura adfurraPatea Selecting the Labware Type Used in the Protocol Overview Use Labware Selection to select the type of labware used in the protocol 20 Creating Protocols Labware must be configured prior to configuring the protocol Only labware Configuring General Settings configured for the selected technique type
49. or loading filter slides Manual Control is divided into five subsections Temperature Control TRIAD only Section 2 3 3 1 Shake Control Section 2 3 3 2 Plate Control Section 2 3 3 3 Excitation and Emission Filter Slide Control Section 2 3 3 4 gt Instrument Settings Basic Settings Filter Slides Manual Control Plate Control Eject Load Check if plate is inserted Vv before each read Temperature Control Actual o Linear iei v Set Point Shake Control beis Excitation Filter Slide Control Eject Load Emission Filter Slide Control Eject Load Intensity Low Duration s 5 Shake OK Cancel Figure 2 5 Instrument Settings Manual Control 2 3 3 1 Temperature Control is used to set the microplate chamber temperature The temperature is set by heating the microplate chamber cooling the chamber is not supported Depending on the light source used to perform measurements configured in the protocol the temperature may range from 3 C 5 4 F or 4 C 7 2 F above ambient to 45 C 113 F Actual displays the current temperature of the instrument Temperature Control TRIAD only To set the temperature 1 In Set Point enter the desired temperature in Celsius 2 Choose Set Temperature control is activated for the instrument and begins to heat to the desired temperature The set temperature is maintained until it is changed or the instrument is powere
50. simulations simulated absorbance data dat al e Browse to the location where the desired data file is saved and select it Note Results from prior measurements saved in dat format may be used as simulated data files refer to Section 6 2 11 Configuring Output Settings Simulated data files are used when the number of measurement points in the simulated protocol run is the same as those present in the data file When the number of measurement points is different the software generates random data When a different simulated data file is selected in Prepare to Run Protocol the file is used for the current simulated run only After the simulated run has finished the data file defaults to the file selected in Software Settings refer to Section 1 4 2 2 Choosing Simulated Data Files Concert TRIAD Series Software User s Manual 6 52 Creating Protocols 6 Choose Run or Next to run the selected protocol OR Choose Cancel to close Run Protocol without running the protocol S DYNEX Technologies Inc Creating Protocols 6 53 6 4 Editing Protocols Parameters configured in a protocol may be edited When the optional Signet module is enabled on the system signed protocols may not be edited Note When Signet is enabled on the system only users assigned a role containing the Edit permission may edit protocol definitions Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accoun
51. the desired action e sign the item refer to Section 3 4 5 1 Signing Items e view or unlock an existing signature refer to Section 3 4 5 2 Viewing or Unlocking Signatures for an Item e view unlocked signatures refer to Section 3 4 5 3 Viewing Unlocked Signatures 3 4 5 1 Signing Items To sign an item 1 In the Sign tab Figure 3 13 enter a Comment A comment is required to complete an electronic signature 2 Select the type of signature Sign or Approved The selected type is saved in the audit trail 3 If the Password field is visible enter the password for the user account Note Passwords are required only when Signet with password checks for signing and check in is the selected support level refer to Section 3 2 2 Setting the Signet Support Level 4 Choose OK to sign the item OR Choose Cancel to close Sign the Selected Item without signing the item Setting Up and Using Signet 3 19 3 4 5 2 Viewing or Unlocking Signatures for an Item Users assigned a role with the Sign permission may view active signatures for an item in the Signatures tab Users with the Sign permission may also unlock any signature attached to an item An unlocked signature is deactivated and moved from Signatures to History signatures are never permanently removed from the system refer to Section 3 4 5 3 Viewing Unlocked Signatures Unlocking all signatures attached to an item allows the item to be edited aga
52. the right of the screen with well A1 highlighted in red Choose Next to start the optimization refer to Section 5 6 3 Performing the Optimization Read The optimization read begins automatically OR Choose Back to select a different detection method refer to Section 5 6 1 Selecting the Detection Method OR Choose Cancel to close Optimizing Labware without performing the optimization Creating and Editing Labware 5 17 5 6 3 Performing the Optimization Read Optimization in Progress displays the status of the optimization read and provides the ability to cancel the optimization in progress Figure 5 9 The optimization read requires several minutes to complete a Optimizing Labware Weber96deep Optimization in Progress Select a detection method Wells are currently being read Please wait Prepare the Labware Select Center of Left Top Well Select Center of Left Bottom Well Select Center of Right Top Well Select Center of Right Bottom Well Verify Well Centers Performing optimization scan Estimated Time 00 01 14 Elapsed Time 00 00 13 Press Stop Optimization to cancel labware Stop Optimization optimization Figure 5 9 Labware optimization in progress During the optimization read Choose Stop Optimization to cancel the optimization process and close Optimizing Labware without saving the optimization data When the optimization read is complete Choose Next to select the centers of th
53. type of labware used in the protocol ee eeeeeeseceseeeeeeeeseeesneeeeeeeaees 6 8 Figure 6 6 Configuring Layout Settings for a Basic application eee eeeeeeseeeseceeeeeeeeeenees 6 9 Figure 6 7 Configuring Layout Settings for an Analysis application ee eeeeseeeeeeeeeeeees 6 11 Figure 6 8 Selecting how wells on the plate are read 0 e eee eeeececeseeceeeeeceeeeecseeeecsteeeesteeeenaes 6 14 Figure 6 9 Configuring a detection method in Method Selection ee eee eeeeeeeeereeeneeeeeeeees 6 15 Figure 6 10 Configuring a method in basic mode eee eeeeeeeeseceeeeesceceeeceeeeteneeeaeessaeenaeenees 6 16 Figure 6 11 Selecting a data reduction method for a kinetic measurement ce eeeeeeeeeee 6 18 Figure 6 12 Configuring an area SO AUN cada dese dad ces Seded cape nectnesdeastsadedactnsiadeieanddReieieeanieeentate 6 20 Figure 6 13 Configuring a linear scan sessazsesescsensandosenasdandaediviescadeanivassvensscnsaneneedastaudoaasiecasen saad 6 21 Figure 6 14 Selecting a data reduction method for a scan method ss ssssssesssesssssessseessssee 6 22 Figure 6 15 Configuring a method in advanced M0d eo eeeeeeeeeeseceseceseeeeseesaeceeeeeeeeeaeeees 6 23 Figure 6 16 Adding a kinetic detection method 000 0 eee eeeeeseceeeceeeeeesceceaeeeeeseeeesneeesaeenseenses 6 24 Figure 6 17 Configuring Loop Properties for a kinetic measurement cceeeeeeeeereeeeeeeees 6 25 Figure 6 18 Selecting a data reduction me
54. ust eneery ta oeni 2 13 Zoo Plate Controle ssceriecsotersve r terena n caseaed 2 13 2 3 3 4 Excitation and Emission Filter Slide Control 2 13 3 Setting Up and Using Signet 3 1 OVETVIEW 2 432524 ect ee deca eh eke e os eee eee eee ee eeee ase R 3 1 3 2 Setting UP SIGH ss susa arasa k ne aaa Loe a a E E a S 3 2 3 2 1 Changing the Administrator Password 0 0000 e ee eee 3 2 322 Setting the Signet Support Level 202 424 lt sceeernbcaoverdocicexss 3 3 33 Performing System Administration Tasks 0 0 00 e eee eee eee eee 3 5 3 3 1 Administering User Accounts and Roles 0000 3 5 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts 0 00000 ee 3 7 3 3 2 Restoring the Administrator Password 0000 eee eee 3 9 3 3 3 Viewing the System Activity Audit Log 04 3 10 3 4 Performing Signet User Actions in Concert TRIAD Series Software 3 11 3 4 1 Logging On and Off the System 2 05 42s4eecne chads necededs 3 12 3 4 1 1 Logging On the System 0 0 00 eee eee 3 12 3 4 1 2 Logging Off the System 202c2s24seuadereeesa wees 3 13 3 4 1 3 Handling Disabled Accounts 0000 3 13 3 4 2 Changing the Password of the User Currently Logged Into TNS Syste e eho wetted Sue E eee eee ee eee oee ees 3 14 3 4 3 Viewing and Searching the Concert TRIAD Series Software PUIG 32 36 3 3 oe eae Ses tece ed era sede eee aye e
55. well as numerical constants and mathematical operators A response formula is often simply the value of a measured standard which is expressed as STD1 STD2 or STDS Note Refer to Appendix B Mathematical Operators and Functions for detailed information about mathematical operators supported by the software DYNEX Technologies Inc Creating Protocols 6 37 13 If configuring a linear regression curve fitting method choose the Validation tab to validate the protocol based on acceptable coefficient of correlation if desired Figure 6 24 Note The Validation tab appears only when configuring a linear regression curve fitting method ap Edit Protocol Kinetic 340 12 cycle temp 35 Concentration General Settings Choose a curve fitting method and configure response formulas and concentrations as desired Technique Type Labware Selection Layout Settings Y Axis X Axis Method Selection Curve Type LinearRegression Variables Number of standards 8 iw BE Measurement x Name Concentration Transformation Extrapolation p Type linear X Type linear Cutoff Graph Preview Graph Setup Validation port Op validation Correlation Output Settings Linear Regression Check Correlation Iv Linear Regression Min Correlation 8 50 al y Figure 6 25 Configuring standard curve validation parameters 14 Choose Linear Regression Check Correlation to enable validation 15 In Linea
56. which are shown to DYNEX Technologies reasonable satisfaction to have been nonconforming or to refund the purchase price or if not paid to a credit amount of the purchase price therefore THE FOREGOING WARRANTIES ARE EXCLUSIVE AND ARE GIVEN AND ACCEPTED IN LIEU OF ANY AND ALL OTHER WARRANTIES EXPRESS OR IMPLIED INCLUDING WITHOUT LIMITATION THE IMPLIED WARRANTY OF MECHANTABILITY AND THE IMPLIED WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE NEITHER PARTY SHALL BE LIABLE TO THE OTHER FOR ANY INCIDENTAL INDIRECT SPECIAL OR CONSEQUENTIAL DAMAGES Concert TRIAD Series Software User s Manual Safety Information All Warnings and Cautions in this document include an exclamation point a lightning bolt or a light burst symbol framed within a triangle Please pay special attention to the specific safety information associated with these symbols Technologies Inc the protection provided by the equipment may be WARNING If the equipment is used in a manner not specified by DYNEX impaired Warning and Caution Definitions The exclamation point symbol is an international symbol which serves as a reminder that all safety instructions should be read and understood before installation use maintenance and servicing is attempted When this symbol is displayed in this manual pay special attention to the specific safety information associated with the symbol WARNING A WARNING calls attention to a condition or possible situa
57. 0 e eee 5 16 5 6 3 Performing the Optimization Read 0 0 0 0 00 00 5 17 5 6 4 Selecting the Centers of the Four Corner Wells 5 18 5 6 5 Verifying Well Centers 2 4i2i ekenoxkdebes bescetaee beaded e s 5 19 5 7 Exporting and Importing Labware 0 0 cece eee 5 21 6 Creating Protocols 6 1 OVEIVIEW eer goietan EE needa eabaradanah nse enedeataboe when eae 6 1 6 2 Creating Basic and Analysis Protocols 0 00 c eee eee ene 6 3 6 2 1 Configuring General Settings 00 0 c eee ee ee eee 6 5 6 2 2 Selecting the Technique Type ci3 lt 44542 dee enes edeeabdeedee ed 6 7 6 2 3 Selecting the Labware Type Used in the Protocol 6 8 6 2 4 Configuring Labware Layout Settings 2005 6 9 6 2 4 1 Configuring the Sample Layout for Basic Applications 6 9 6 2 4 2 Configuring the Sample Layout for Analysis Applications i 544 e18 8 seaweed eeeedaeabercades 6 11 6 2 4 3 Configuring Reading Direction 6 14 6 2 5 Configuring Detection and Preparation Methods 6 15 6 2 5 1 Configuring a Method in Basic Mode 6 16 6 2 5 2 Configuring a Method in Advanced Mode 6 23 6 2 6 Configuring Variables Concert TRIAD Series Analysis SoftWare Only sacca styo aah oie Anse baw e e a eee eKA 6 31 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only 0 0 e cence eee ee
58. 005 4 id Detection Methods Absorbance Monochromatic 3 3 2005 3 3 2005 Absorbance Monochromatic 3 3 2005 3 3 2005 Fluorescence Intensity Bottom Monochromatic 3 4 2005 3 4 2005 Fluorescence Intensity Top Monochromatic 3 3 2005 3 3 2005 Fluorescence Polarization Multichromatic 3 4 2005 3 4 2005 Time Resolved Fluorescence Monochromatic 3 4 2005 3 4 2005 Labware Instruments w Be Software Settings Detection Methods _ All detection method functions are accessed from the Detection Method Selection List Available detection method functions are Figure 4 1 Accessing detection method actions e Creating Detection Methods Section 4 2 e Editing Detection Methods Section 4 3 e Copying Detection Methods Section 4 4 e Deleting Detection Methods Section 4 5 e Exporting and Importing Detection Methods Section 4 6 DYNEX Technologies Inc Creating and Editing Detection Methods 4 3 4 2 Creating Detection Methods Detection methods are created in the Method Editor which guides the creation process with a wizard type interface Creating a new detection method requires e Selecting a Method Technique Section 4 2 1 e Selecting the Method Type Section 4 2 2 Method Type is configured for absorbance detection methods only e Defining Method Parameters Section 4 2 3 e Optionally Signing a Detection Method Section 4 2 4 to prevent methods from being edited or delete
59. 04 1 637 3 217 0 11 1 438 0 033 2102 0 367 3 066 3 12 0 744 2 629 3437 3 919 1 399 3 13 2 465 0 345 1 959 3 98 2 014 14 37 3 638 1 714 2476 2 722 3 Well 1 3 1 2 3 4 5 6 1 1 016 2 693 3 545 0 306 1 864 3 2 0 218 1727 0 102 3 621 1 423 2 3 1712 3 702 3 671 0 259 3 217 2 4 3 718 3 743 1413 0 484 3 007 1 5 2 532 0 651 2 874 3 266 3 84 1 6 4 219 3 194 0 819 3 037 1 251 1 Figure 7 18 Viewing raw data excerpt To view raw data 1 In Excel access the workbook containing raw data for the desired measurement results Titles of workbooks containing raw data always contain the name of a specific detection method configured in the protocol for example ABS340 Figure 7 18 2 In the worksheet choose the Cycle tab for the desired measurement cycle Concert TRIAD Series Software User s Manual 7 22 Viewing Measurement Results 7 4 1 3 Viewing Reduced and Transformed Data Reduced and transformed data are exported to a different Excel workbook than raw data Reduced data generally appears in a sheet named Measurement transformed data appears in sheets with names corresponding to the analysis options configured in the protocol Note Transformed data appears in results for protocols with analysis options configured The optional Concert TRIAD Series Analysis Software module must be installed to configure analysis options in protocols 4 Microsoft Excel 20050316 142548_Multiwavelengh Kinetic 340 405 03 21 2005_04 04 02 51
60. 05 General Settings Technique Type Labware Selection Layout Settings Method Selection gt Output Settings YE E t Kinetic Properties appear cela TERTIT TERES when Kinetic above the desired detection method is selected Report Options Basic Advanced Method Selection Kinetic Properties Sequence Kinetic Cycles Kinetic Interval Lassesdo Data Reduction Kinetic L aB5 405 Kinetic Cycles Choose the number of measurement cycles to perform Figure 6 17 Configuring Loop Properties for a kinetic measurement If configuring a kinetic measurement configure Kinetic Properties by following the instructions in Section 6 2 5 1 1 Configuring a Kinetic Method OR If configuring a scan measurement configure Scan Properties by following the instructions in 6 2 5 1 2 Configuring a Scan Method Add and configure additional detection methods by repeating steps 2 4 if desired To add a preparation method choose Add a method to this protocol and select Add Preparation Method gt Shake or Add Preparation Method gt Set Temperature from the menu OR Right click in Method Selection and select Add Preparation Method gt Shake or Add Preparation Method gt Set Temperature from the menu gt TRIAD Set Temperature is available only when controlling this instrument Configure Method Properties for the preparation method Refer to Section 6 2 5 2 1 Configuring a Shake Prepar
61. 2005 13 53 9 ValidState Invalid 10 11 Software Multimode Detection Software 12 Version 2 0 0 4 13 14 Instrument Name Multimode Reader 15 Serial Number aooo 16 17 Labware 18 Name BCFlat 96 19 Rows 8 20 Columns 12 21 ProtectionState 0 22 WellShape Round 23 BottomShape Flat 24 Created 36 2005 10 58 25 DateEdited 3416 2005 10 58 ot Default ot Figure 7 17 Viewing protocol information in the General worksheet excerpt To view the General worksheet 1 In Excel access either workbook containing the desired results 2 Choose the General tab in the lower left corner of the window DYNEX Technologies Inc Viewing Measurement Results 7 21 7 4 1 2 Viewing Raw Data Measurement results exported to Excel display raw data in matrices corresponding to the plate layout Figure 7 18 Data from each measurement cycle or point is presented in a separate sheet within the workbook Note Results from protocols containing multiple detection methods export raw data from each detection method to a separate workbook The title of workbooks containing raw data always includes the name of the detection method E3 Microsoft Excel 20050321 135246_340 Area Scan Analysis ABS340 0_03 21 2005_02 41 22 14 xml File Edit View Insert Format Tools Data Window Help Adobe PDF am a The name of the detection method always appears in the title of a workbook containing o raw data 3 1 3 10 1 213 0 122 0 7
62. 4 Note A data reduction method must be selected in all protocols that perform reads with multiple detection methods 4 Data Reduction Method Method Peak Value Used to detect the highest value per sample within a Smoothing Points 5 sequence of measurements Figure 6 18 Selecting a data reduction method for the sequence 13 In Data Reduction Method select the desired Method If required by the selected method additional parameters such as smoothing points appear 14 Configure additional parameters for the selected data reduction method if required Note Refer to Table A 1 in Appendix A Data Reduction Techniques for details about the data reduction methods available for kinetic measurements 15 Choose OK to confirm the selection of the data reduction method DYNEX Technologies Inc Creating Protocols 6 27 16 Choose Report Options and select the method information and measurement results data included in printouts Reduced Data results calculated using the selected data reduction method Available when kinetic measurements scan measurements or multiple detection methods are configured in the sequence Method Information details about the configured method including technique type and filter s used Print in Matrix results arranged in a matrix corresponding to the plate layout Available for single point measurements only e Graph kinetic or scan graphs of results f
63. 42548 pos0316 135406 hos0316 135136 bos0316 123417 20050316 121747 20050316 121731 20050316 120833 20050316 120222 20050316 120132 20050316 120039 20050316 110359 Result Name Date Protocol name Measured 3 16 2005 3 47 PM 3 16 2005 3 44 PM 3 16 2005 3 44 PM 3 16 2005 2 26 PM 3 16 2005 2 26 PM 3 16 2005 1 54 PM 3 16 2005 1 51 PM 3 16 2005 12 34 PM 3 16 2005 12 17 PM 3 16 2005 12 17 PM 3 16 2005 12 08 PM 3 16 2005 12 02 PM 3 16 2005 12 01 PM 3 16 2005 12 00 PM 3 16 2005 11 04 AM Like Evaluated Protocol Name 3 16 2005 3 48 PM Multiwavelenght Kinetic 340 405 3 16 2005 3 44 PM Fluorescein Top Read 384 3 16 2005 3 44 PM Basic Absorbance DNA Quantitation 96 3 16 2005 3 18 PM Multiwavelengh Kinetic 340 405 3 16 2005 2 27 PM Multiwavelengh Kinetic 340 405 3 16 2005 1 54 PM Multiwavelength 340 405 3 16 2005 1 51 PM Absorbance 405 96 3 16 2005 12 34 PM New Basic 340 ABS 3 16 2005 12 18 PM Basic Absorbance Area Scan 96 3 16 2005 12 17 PM Absorbance ELISA 450 96 avelengh Kinetic 340 405 bance ELISA 405 96 o pt i ons Absorbance korien 96 Absorbance Multiwavelength 96 3 16 2005 11 04 Al Absorbance ELISA 405 96 fless Than or Equal v 3 16 2005 v Clear Like d Figure 7 1 Accessing measurement result actions Application T lt Analysis Basic Basic Analysis Analysis Basic Basic Basic Basic Basic Analysis Basic Basic Basic Basic Concert TRIAD Series Software User s Manual
64. 6 41 To configure validation rules 1 Choose the Number of formulas to configure Up to ten formulas may be configured 2 Choose the Basis of Evaluation for the first formula e Measurement the reduced data from the protocol run e Concentration the value calculated using the standard curve configured in Concentration This option is available only when Concentration is configured in the protocol refer to Section 6 2 8 Configuring Concentration Concert TRIAD Series Analysis Software only Transformation the value calculated using the transformation formula configured in Transformation This option is available only when Transformation is configured in the protocol refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only Note Transformation is the default name for transformation formulas If a different name is entered in Transformation that name appears in Basis of Evaluation refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software onl 3 Enter the first formula Formulas may contain e any controls standards or variables defined in the protocol For controls and standards use the same labels displayed in Layout Settings for example STD1 for standard 1 C2 for control 2 P5 for positive control 5 or N2 for negative control 1 a numeric constants e mathematical operators and functi
65. 6 51 software settings choosing data storage directory 1 19 choosing default simulated data files 1 18 configuring 1 16 configuring print settings 1 17 T handling disabled accounts 3 13 temperature control logging off 3 13 configuring a temperature preparation logging on 3 12 method 6 29 wee reactivating disabled message boxes 3 16 configuring in Instrument Settings 2 12 time resolved fluorescence detection methods y configuring 4 12 transformation formulas yalicanon nee f configuring in analysis protocols 6 32 configuring My ata sis BrOIscOls 0 20 variables U configuring in analysis protocols 6 31 users accessing in User Selection List 3 11 Ww changing password 3 14 well status indicators 7 4 Concert TRIAD Series Software User s Manual
66. Add Scan and then select a detection method OR To create a new detection method to be added to the protocol choose New Method Refer to Chapter 4 Creating and Editing Detection Methods for detailed information about creating detection methods df Create Protocol NewProtocol3 Method Selection eneral setings Select a method and methd Technique Type Only detection methods Labware Selection compatible with the selected Suniel i measurement type are listed _ Report Options Method Selection gt thod Selecti Basic Advanced lethod Selection 5 Cea Variables Method Selection Sequence Properties Transformation z Concentration i Eai D bass s40 Add Method Validation ABS 340 Output Settings Add Scan a N Add Preparation Method Abs450 Cutoff Abs595 x Abs260 ABS ELISA 405 ABS ELISA 450 m ABS 260 ABS 340 ABS 405 ABS 450 ABS 595 ABS 620 Abs 450 bichromatic Figure 6 16 Adding a kinetic detection method 3 If adding a kinetic detection method in Method Selection select Kinetic above the method being configured Kinetic Properties replaces Method Properties in the right pane Figure 6 17 OR If adding a scan detection method in Method Selection select Scan above the method being configured Scan Properties replaces Method Properties in the right pane DYNEX Technologies Inc Creating Protocols 6 25 5 Create Protocol MultiKinetic 340 4
67. C Software Error Troubleshooting Software Error Codes Table C 1 lists software error codes error messages and recommended solutions for resolving errors Table C 1 Software Error Codes and Solutions Error Message Recommended Solution Commanded transport motion exceeds actual physical travel limits Check plate parameters configured in Labware Information refer to Section 5 2 1 Defining Labware Information Auto calibration ramp parameter exceeds valid range Make sure the microplate carrier movement is not obstructed and run the measurement again Transport is not operational or the transport sensor is defective Make sure the transport lock has been removed from the microplate carrier Transport lost more than 2 full steps Make sure the microplate carrier movement is not obstructed Calibration positioning failed N A Offset calculated in auto calibration is out of expected range Possible causes ADC values are too low lamp is not adjusted incorrect EEPROM parameters Check filter parameters configured in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides Filter transport adjustment is out of expected range Possible causes insufficient sensor steps insufficient ramp value incorrect EEPROM parameters Contact a DYNEX Technologies Service Engineer 10 Z transport adjust error Possible causes wrong well for adjus
68. D Series Software User s Manual 7 16 Viewing Measurement Results View Option Viewing Style Table 7 4 Standard Curve Graph View Options Description Select how the graph is displayed in Color Monochrome or Monochrome with symbols Numeric Precision Select the numeric precision of graph data displayed onscreen or exported to text files Precision up to three decimal positions may be specified Plotting Method Select how the graph is plotted Line is the default method Customization Data Shadows Enable shadows that give the graph a 3 D appearance Grid Options Customize the grid display Grid lines may be displayed hidden or changed to a different style such as thick thin or dashed Include Data Select to display labels for data points on the curve Labels Mark Data Points Select to mark each data point with a small circular symbol Undo Zoom Select to display a zoomed graph at the original size Available only when the graph is zoomed Maximize Select to display a full screen version of the graph Close the maximized view by pressing the Esc key or clicking on the title bar of the maximized window Open the Customization dialog box Customization options are grouped in a Dialog series of tabs e General Enter a title for the graph change the viewing style color or monochrome set the numeric precision up to 3 decimal positions and change the grid appearance
69. DYNE X Absorbance Plate Washing 7 Ba Concert TRIAD Series Software User s Manual Automated Processing lt 7 Software Consumables DYNEX Technologies Inc 14340 Sullyfield Circle Chantilly VA 20151 1621 Phone 703 631 7800 FAX 703 803 1441 www dynextechnologies com Revision History Revision Date April 2005 Catalog No 61000025 This manual is published by DYNEX Technologies Inc Questions or comments regarding the content of this manual can be directed to the address below or to your supplier DYNEX Technologies Inc 14340 Sullyfield Circle Chantilly VA 20151 1621 USA Telephone 800 288 2354 703 631 7800 Fax 703 803 1441 Website www dynextechnologies com DYNEX Technologies reserves the right to make technical improvements to this equipment and documentation without prior notice as part of a continuous program of product development This manual supersedes all previous editions Microsoft and Windows are registered trademarks of the Microsoft Corporation IBM is a trademark of International Business Machines Corporation in the United States other countries or both Pentium is a registered trademark of Intel Corporation Adobe Acrobat and Postscript are either registered trademarks or trademarks of Adobe Systems Incorporated in the United States and or other countries All other trademarks appearing in this manual are the property of their respec
70. Editor without saving the new detection method 4 2 4 Signing a Detection Method When Signet is enabled on the system detection methods may be signed to prevent method properties from being edited or methods from being deleted Detection methods may be signed at any time after the configuration is complete Detection methods may be signed by users who are assigned a role containing the Sign permission Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To sign labware 1 In the Detection Method Selection List select the detection method to sign 2 From the toolbar choose Sign the selected method Sign the Selected Item appears OR From the Actions menu choose Sign the selected method OR Right click on the selected labware and choose Sign the selected method 3 In Sign the Selected Item add comments and an electronic signature by following the instructions in Section 3 4 5 Adding Electronic Signatures and Comments to Items Concert TRIAD Series Software User s Manual 4 14 Creating and Editing Detection Methods 4 3 Editing Detection Methods ii Parameters configured in user defined detection methods may be edited however the method technique may not be changed Default methods installed with the software and methods used in protocols may be edited but not renamed Note When Signet is enabled on the
71. Microsoft Excel Description Saves results in a format compatible with Microsoft Excel and automatically opens Excel after completing a protocol run Note Versions of Excel prior to Office 2000 are not supported by the Export to Microsoft Excel function but can open measurement results stored in tab delimited data dat files Show Result Viewer Automatically opens the measurement results in the Result Viewer after completing a protocol run refer to Section 7 2 Viewing Measurement Results in the Result Viewer Create XML and dat data files Automatically exports measurement results to a tab delimited data dat file and an XML file These files may be opened by software applications compatible with tab delimited data or XML files Note The directory where the data files are saved is configured in System Settings Refer to Section 1 4 2 3 Choosing the Directory Where Exported Measurement Results are Saved Print options Automatically prints the results after completing a protocol run Concert TRIAD Series Software User s Manual 6 44 Creating Protocols 6 2 11 1 Configuring a Program to Execute after a Protocol Run Completes Output Settings can be configured to open an external software application after completing a protocol run If the selected application supports entering commands using a command line interface a specific command for the application may also be
72. Note Refer to Section 5 2 1 1 General Labware Selection Guidelines for more information about labware technique compatibility Edit the labware Notes if desired Choose Next to select and edit labware lots and save changes made to the labware refer to Section 5 3 2 Selecting and Editing Labware Lots OR Choose Cancel to close the Labware Editor without saving changes Creating and Editing Labware 5 11 5 3 2 Selecting and Editing Labware Lots Use Labware Lots to select the active lot and or edit and save changes made in the Labware Editor Figure 5 5 Lots can be selected and edited for all labware including labware used in measurement protocols Note Labware Lots are created by optimizing labware refer to Section 5 6 Optimizing Labware a Labware Editor Weber 96deep Labware Lots Labware Information Choose the lot to use or edit B Labware Lot Info ot True Landscape Absorbance Property E Labware tot Measurements g rid Lower left x offset 1 435 Lower left y offset 1 135 Lower right x offsel 1 435 Lower right y offsel 1 135 Upper left x offset 1 435 Upper left y offset 1 135 Upper right x offsel 1 435 Upper right y offsel 1 135 B Well Measurements Column distance 0 9 Row distance 0 9 Column distance Distance between columns cm Figure 5 5 Configuring offsets and well dimensions in Labware Lots To select and edit lots 1 From the pull down men
73. R Optimization in Progress Select a detection method Reading height is currently being optimized Please wait Prepare the Labware Optimization Complete Optimizing Estimated Time 00 02 12 Figure 6 33 Read height optimization in progress 8 While the optimization is in progress choose Cancel to stop the optimization read and close the wizard if desired When the read is finished Optimization Complete appears displaying the Optimized Read Height Figure 6 34 a Read Height Optimization Wizard DER Optimization Complete Select a detection method Optimization is complete Click Save to save the optimized read height Prepare the Labware Optimize Optimization Complete gt Optimized Read Height 4 37 am Figure 6 34 Read height optimization completed 9 In Optimization Complete choose Save to save the optimized read height in the protocol The optimized read height is used for all subsequent runs of the protocol until reset by performing a new optimization or manually selecting a read height option OR Choose Cancel to close the wizard without saving and using the optimized read height in the protocol run DYNEX Technologies Inc Creating Protocols 6 51 6 3 2 Running a Protocol When Simulation Mode is Enabled Running a protocol in simulation mode allows the protocol configuration to be tested using simulated data before performing the protocol on actual samples Simulated da
74. S 1 1 1 2 Using Concert TRIAD Series Software 26 s06csebeceeseneecnvesas 1 2 1 2 1 Launching the Software wc sak eensa ossseeaeao sn heehee eeniwek eee 1 3 1 2 2 Using the Software Interface i664 25 33s p Seeds dee SGee Re eedends 1 4 1 2 2 1 About the Navigation Pane 0 2 000 e 1 4 1 2 2 2 About the Toolbar c20 v2ciassdasaakeaeadeiieeas 1 5 12 2 3 About the Selection and Configuration Pane 1 5 1 2 3 Accessing Online Help pis 2 c lt n5seeke isan ex eaeeareewcesaees 1 5 1 3 Installing Concert TRIAD Series Software 0 0 0000 000 1 6 1 3 1 Meeting System Requirements n nonnene nanne 1 6 1 3 2 Installing Concert TRIAD Series Software on Windows 2000 0E XP ve csaak ee gda eae arkaa a ed ans e A a S 1 7 1 3 3 Installing Concert TRIAD Series Software on Windows NT 1 9 1 3 4 Installing Optional Modules 20 00 cee eee eee ee 1 10 1 3 5 Repairing or Removing the Concert TRIAD Series Software Installation 3 icesserssdessededoerenerededs 1 11 1 4 Setting Up Concert TRIAD Series Software 0 000000 eee 1 12 1 4 1 Configuring Communication Settings 00 eee 1 14 1 4 2 Configuring Software Settings 0 0 eee eee eee 1 16 1 4 2 1 Configuring Print Settings 00008 1 17 1 4 2 2 Choosing Simulated Data Files 4 1 18 1 4 2 3 Choosing the Directory Where Exported Measureme
75. Settings gt Type Sample X Method Selection Output Settings Index fi Fill Delete Click this button to select all wells on the plate Figure 6 6 Configuring Layout Settings for a Basic application Concert TRIAD Series Software User s Manual 6 10 Creating Protocols 2 To import a plate layout from an existing protocol choose Import Layout and select the desired protocol from the list that appears Only protocols with compatible labware and application types are listed OR To create a new or edit an existing plate layout select the desired wells to label To select e all wells on the plate click the small button in the upper left corner of the plate layout display Figure 6 6 e all wells in a single column or row click the desired column or row header Multiple columns or rows may be selected by holding down the CTRL key while selecting each header desired e individual wells click on the desired well Multiple wells may be selected by holding down the CTRL key while clicking on each well desired e groups of wells click and drag over the desired group of wells Multiple groups may be selected by holding down the CTRL key while dragging over each desired group 3 In Index choose the initial label number for the sequence of selected wells 4 Choose Fill to label the selected wells OR Choose Delete to delete existing labels from the selected wells 5 Repeat steps 2 4
76. Shake Intensity The intensity of the shaking operation Figure 6 19 Configuring a Shake preparation method CAUTION Shake low density plates such as 6 or 48 well plates at low A N speed only Shaking low density plates at higher speeds may cause liquid in wells to spill 2 In Shake Intensity select the desired intensity of shaking Low Medium or High 3 In Shake Interval enter the length of time in seconds 0 60 to shake the microplate 4 In Shake Mode select the desired shaking pattern e Linear shakes from side to side e Orbital shakes labware in a circular pattern e Squared shakes labware in a square pattern moving at right angles DYNEX Technologies Inc Creating Protocols 6 29 6 2 5 2 2 Configuring a Set Temperature Preparation Method TRIAD only A Set Temperature preparation method sets the temperature inside the microplate chamber by heating the chamber cooling the chamber is not supported Depending on the light source used in the protocol the set temperature may range from 3 C 5 4 F or 4 C 7 2 F above ambient to 45 C 113 F A minimum of 30 minutes is required for the instrument to reach the desired temperature The actual time required depends on the relative change in temperature When a protocol with a Set Temperature preparation method is run the protocol does not pause to wait for the desired temperature to be reached To set an exact temperature befor
77. Software User s Manual 5 10 Creating and Editing Labware 5 3 1 Viewing and Editing Labware Information Use Labware Information to view and edit labware dimensions information and supported techniques Plate information for default labware included in the software installation and labware used in protocols may be viewed but not edited gt Labware Editor Weber 96deep Labware Information gt Labware Lots B Labware Info Labware Information Supported techniques ate edi 206 ivi Absorbance Weber96deep _ Luminescence B Labware Measurements LuminescenceGlow Height 1 4 LuminescenceFlash Height with lid 2 222 Bio Luminescence RET Pro perty Length 12 77 Fluorescence RET Reading height 1 06 Fluorescence Intensity Top g rid Width 8 57 v Fluorescence Intensity Bottom _ Fluorescence Polarization B Well Info Columns 12 Rows 8 Well bottom shape Flat Well shape Round Well volume 300 Time Resolved Fluorescence Plate Name Name of this labware Notes None Figure 5 4 Editing labware dimensions and well information To edit labware information 1 DYNEX Technologies Inc In the property grid edit labware dimensions and information as desired Refer to Section 5 2 1 Defining Labware Information for more information about the fields available in the property grid In Supported Techniques change the measurement techniques supported by the labware if desired
78. Table 2 1 Basic Settings Read Only Fields Field Description Instrument Name The model of the instrument Serial Number The serial number of the instrument Instrument Type A numerical code used by the software to identify the instrument type Firmware Version The version of firmware loaded for the instrument PIC FW Version The version of firmware loaded for the instrument PIC processor Features The types of measurements the instrument is capable of performing Concert TRIAD Series Software User s Manual 2 8 Setting Up and Controlling Instruments 2 3 2 Defining and Editing Filter Slides The Filter Slides tab Figure 2 3 is used to add remove and configure filter slides and the filters installed on a filter slide Slide definitions may also be imported and exported as desired Filters used to perform measurements are mounted on two types of interchangeable slides One slide is reserved for excitation filters used in absorbance and fluorescence measurements the other is used for emission filters used in fluorescence and some luminescence measurements Excitation and emission filter slides are different sizes to prevent them from being installed in the incorrect position Each slide can hold up to six filters When exchanging slides an identification code built into the slide allows Concert TRIAD Series Software to recognize the new slide and filter configuration When a slide with a new
79. a 2e dau tase ndar Limtt Good _ fundar LimitfUnder Limit Minar Lime 65 pA mti Good Goog 1 2 2 05 3 78 06 4332 der rund Linunder Lirit under nfo 3307 1657 sa 843 wm 2s ass 313 a908 1 145 jeder Lire becer it ur Lit ter Lind 579 sao sa A oza 1061 218 Good Under Lmitjunder Limit Under Lima funder Limi 7 7 T s91 s92 s9 ss 4 os 1 826 403 2531 Thternational Laboratones Figure 7 21 Previewing a measurement results printout Concert TRIAD Series Software User s Manual 7 26 Viewing Measurement Results 3 In Print Preview choose Print to print out the measurement results 4 In Print Preview choose Close to close the window Note Choosing Close without first choosing Print cancels the printout DYNEX Technologies Inc Appendix A Data Reduction Techniques A 1 Supported Data Reduction Techniques The tables in this appendix describe the data reduction techniques supported by the software e Table A 1 describes the techniques available for scan measurements and measurement sequences configured in protocols e Table A 2 describes the techniques available for kinetic measurements e Table A 3 describes techniques available for fluorescence polarization measurements performed on a TRIAD Table A 1 Scan Measurement and Sequence Data Reduction Techniques Data Reduction Description Parameters Technique Delta Difference between
80. ailable e Export to Microsoft Excel saves results in a format compatible with Microsoft Excel and automatically opens Excel Refer to Section 7 4 1 Viewing Measurement Results in Microsoft Excel for more information about viewing exported results in Excel Note Concert TRIAD Series Software automatically determines the appropriate export method based on the version of Microsoft Office installed on the host computer XML xml files are exported when Office XP is installed When Office 2000 installed the measurement results are copied into a new spreadsheet which must be saved in Excel Versions of Excel prior to Office 2000 are not supported by the Export to Microsoft Excel function but can open measurement results stored in tab delimited data dat files e Create XML and dat data files saves results in xml and tab delimited data dat files which may be opened by compatible software applications Note Refer to Section 6 2 11 Configuring Output Settings for more information about configuring export and file options To view saved measurement results 1 Open the desired software application 2 Browse to the directory where exported measurement results are stored and open the desired file Exported measurement results are stored in the data directory selected in Software Settings refer to Section 1 4 2 3 Choosing the Directory Where Exported Measurement Results are Saved 7 4 1 Viewing Measurem
81. anagement Administrator Login appears Concert TRIAD Series Software User s Manual 3 6 Setting Up and Using Signet 5 In Administrator Login enter the administrator password and choose OK Account Management appears Figure 3 3 Account Management EA accounts amp Roles BY Settings J Repositories Audit Accounts Roles Protocol Developer E Lab Technician Name Full Name 8 Anais Anais Miller PY Berkeley Berkeley Rattan Bort Donald Thomlinson Configure Detector Jane Loomis Sandra Patterson Thorsten Smeltzer Wyatt Singletary B Jane 8 Sandy 8 Thorsten 8 Wyatt Cl Account is disabled Create Account Set Description Set Password Figure 3 3 Account Management DYNEX Technologies Inc Setting Up and Using Signet 3 7 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts Concert TRIAD Series Software permissions which control access to software actions are installed with the Concert TRIAD Series Analysis Software with Signet module Permissions are not assigned directly to user accounts instead the system administrator assigns permissions to roles which are then assigned to accounts as desired Roles may be assigned multiple permissions When several software applications that support Signet are installed on the same system permissions from different applications may be assigned to the same role A permission may be
82. and Configuration Pane The navigation pane provides access to the selection lists that provide the majority of the functionality built into the software The options available in the toolbar and configuration pane are determined by the selection list currently selected in the navigation pane 1 2 2 1 About the Navigation Pane The navigation pane is the narrow pane on the left of the Concert TRIAD Series Software window Figure 1 1 Use the navigation pane to switch between selection lists e Protocols opens the Protocol Selection List and provides the ability to define run edit copy delete and print measurement protocols refer to Chapter 6 Creating Protocols e Results opens the Results Selection List and provides the ability to view saved measurement results and modify data reduction parameters in the Result Viewer When the optional Concert TRIAD Series Analysis Software module is installed measurement results may be reevaluated using parameters different from those configured in the original protocol refer to Chapter 7 Viewing Measurement Results e Labware opens the Labware Selection List and provides the ability to create edit optimize copy and delete labware types refer to Chapter 5 Creating and Editing Labware e Detection Methods opens the Detection Method Selection List and provides the ability to create edit copy and delete detection methods refer to Chapter 4 Creating and E
83. arameters TRIAD only Section 4 2 3 4 Defining Fluorescence Polarization Method Parameters TRIAD only Section 4 2 3 5 Defining Time Resolved Fluorescence Method Parameters TRIAD only Section 4 2 3 6 4 Choose Save to close the Method Editor and save the changes OR Choose Cancel to close the Method Editor without saving changes Concert TRIAD Series Software User s Manual 4 16 Creating and Editing Detection Methods 4 4 Copying Detection Methods Copies may be made of existing detection methods After a copy has been created it may be used as a template for a new detection method using the same method technique Note When Signet is enabled on the system only users assigned a role containing the Copy permission may create copies of detection methods Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To make a copy of a detection method 1 In the Detection Method Selection List select the detection method to copy 2 From the toolbar choose Make a copy of the selected method hi From the Actions menu choose Make a copy of the selected method OR Right click on the selected detection method and choose Make a copy of the selected method from the menu that appears Note The default name format for copied detection methods is Copy of OriginalName To change the name edit the detection metho
84. ation Method or Section 6 2 5 2 2 Configuring a Set Temperature Preparation Method TRIAD only for more information Add and configure additional preparation methods by repeating steps 6 and 7 if desired Concert TRIAD Series Software User s Manual 6 26 Creating Protocols 9 To change the order of detection and preparation methods executed in the A OCZ sequence in Method Selection select the method to be moved and choose Move the selected method forward or Move the selected method backward OR In Method Selection right click on the desired method and choose Move Up or Move Down Note To move a kinetic or scan method select Kinetic or Scan above the method desired to move not the method itself a 10 To delete a detection or preparation method from the protocol in Method Selection select the method to be deleted and choose Delete the selected method from this protocol OR In Method Selection right click on the desired detection or preparation method and choose Remove Method Note To delete a kinetic or scan method select Kinetic or Scan above the method desired to delete not the method itself 11 If multiple detection methods are configured in the sequence in Method Selection choose Sequence Sequence Properties replaces Method Properties in the right pane M 12 In Method Properties click in Data Reduction and choose the configuration button Data Reduction Method appears Figure 6 1
85. atures may be viewed in the History tab 3 4 5 3 Viewing Unlocked Signatures Unlocked signatures are never permanently removed from the system Users assigned arole with Sign permission may view unlocked signatures for an item in the History tab Figure 3 15 1 Choose the desired item and open Sign the Selected Item following the steps in Section 3 4 5 Adding Electronic Signatures and Comments to Items 2 Choose the History tab Figure 3 15 oF Sign the Selected Item Add a new electronic signature to the item view or unlock existing signatures or view the history of unlocked signatures Sign Signatures History Signature Signed 3 5 2005 4 3 5 2005 4 48 11 PM x Unlocked 3 27 2005 4 43 54 PM 8 Berkeley Rattan my Updated to use 405nm excitation filter Version 1 Cancel Figure 3 15 Viewing unlocked signatures 3 Click on the or to the left of a signature to expand or collapse details about the signature Details for each signature are listed on four lines e date and time the signature was created e date and time the signature was unlocked e the full name of the user signing the method e comments entered by the user e version Creating and Editing Detection Methods 4 1 Overview Concert TRIAD Series Software stores measurement configuration parameters in detection methods Stored parameters include the method technique for example absorbance filter s used and parameters spe
86. bware type 1 In the Labware Selection List select the labware type to copy 2 From the toolbar choose Make a copy of the selected labware type OR From the Actions menu choose Make a copy of the selected labware type OR Right click on the selected labware type and choose Make a copy of the selected labware type from the menu that appears Note The default name format for copied labware types is Copy of OriginalName To change the name edit the labware type refer to Section 5 3 Editing Labware DYNEX Technologies Inc Creating and Editing Labware 5 13 5 5 Deleting Labware User defined labware may be deleted from the Labware Selection List Some labware may not be deleted e labware used in protocols e default labware installed with Concert TRIAD Series Software e labware that has been signed on a system with the optional Signet enabled Note When Signet is enabled on the system only users assigned a role containing the Delete permission may delete user defined labware Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To delete labware 1 In the Labware Selection List select the labware to delete gt 2 From the toolbar choose Delete the selected labware type j From the Actions menu choose Delete the selected labware type OR Right click on the selected labware and choose Delete the sele
87. cific to the selected method such as integration time The software supports absorbance luminescence and fluorescence method techniques The method techniques available for configuration depend on the capabilities of the instrument being controlled Detection methods are created and edited using the Method Editor Configured detection methods are listed in the Detection Method Selection List and are available for use in measurement protocols refer to Chapter 6 Creating Protocols Note When Signet is enabled on the system only users assigned roles containing the Sign Copy Create Delete and Edit permissions may perform all of the actions covered in this chapter Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions Concert TRIAD Series Software User s Manual 4 2 Creating and Editing Detection Methods To view available detection methods and access the Method Editor From the navigation pane choose Detection Methods The Detection Method Selection List appears Figure 4 1 d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 BAE Fie Actions Help Detection method actions Detection Method Selection List Measurement Technique Measurement Type Created Last Edited Absorbance Monochromatic 2 28 2005 2 28 2005 Absorbance Monochromatic 3 3 2005 3 4 2005 Absorbance Monochromatic 3 3 2005 3 3 2
88. cted labware type from the menu that appears Message appears Figure 5 6 2 4re you sure you want to delete the labware Weber96deep Figure 5 6 Confirming a labware deletion 3 Choose Yes to delete the selected labware OR Choose No to cancel the deletion Concert TRIAD Series Software User s Manual 5 14 Creating and Editing Labware 5 6 DYNEX Technologies Inc Optimizing Labware Microplate dimensions may vary slightly between production lots which potentially affects measurement accuracy Concert TRIAD Series Software allows labware dimensions to be optimized by determining the centers of the four corner wells on the plate Each time a labware type is optimized a new labware lot is created with dimensions specific to that lot Note When Signet is enabled on the system only users assigned a role containing the Optimize permission may optimize labware to create new labware lots Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for details about permissions New labware lots may be created by optimizing labware for labware types that have been signed refer to Section 5 2 3 Signing Labware Labware is optimized in Optimizing Labware Figure 5 7 which guides the process with a wizard type interface Optimizing labware includes e Selecting the Detection Method Section 5 6 1 e Preparing and Loading the Labware Section 5 6 2 e Performin
89. ction 6 2 2 Selecting the Technique Type OR Choose Create a new detection method to create a new method using the technique type currently selected in the protocol Refer to Chapter 4 Creating and Editing Detection Methods for more information about creating detection methods DYNEX Technologies Inc Creating Protocols 6 17 3 Select the measurement Type e Single Point perform a single measurement on each sample Single point measurements do not require configuring Method Properties e Kinetic perform a specified series of measurements on each sample at specified intervals Kinetic Method Properties appear e Scan perform an area or linear scan on each sample Scan Method Properties appear Note Scan measurements may be configured for absorbance and fluorescence intensity measurements only 4 For kinetic or scan measurements configure Method Properties Refer to Section 6 2 5 1 1 Configuring a Kinetic Method or Section 6 2 5 1 2 Configuring a Scan Method for more information 5 Choose Report Options and select the method information and measurement results data included in printouts Reduced Data results calculated using the selected data reduction method Available for kinetic and scan measurement only Method Information details about the configured method including technique type and filter s used e Print in Matrix results appear arranged in a matrix corresp
90. ction methods configuring 4 11 data reduction techniques A 3 G graphs changing the standard curve view 7 15 viewing for an entire plate 7 7 viewing three dimensional 7 9 viewing two dimensional 7 8 H host computer removing software from 1 11 system requirements 1 6 installing software installing optional modules 1 10 meeting system requirements 1 6 on a Windows 2000 or XP system 1 7 on a Windows NT system 1 9 overview 1 6 repairing an installation 1 11 instrument connecting to 2 4 initializing 2 4 instrument selection list overview 2 1 instrument settings configuring 2 6 filter slides 2 8 manual control 2 12 emission filter slide control 2 13 excitation filter slide control 2 13 plate control 2 13 temperature control 2 12 K kinetic measurements data reduction techniques A 2 kinetic methods configuring 6 18 L labware configuring labware lots 5 7 configuring layout settings in a basic protocol 6 9 configuring layout settings in a protocol 6 11 configuring layout settings in an analysis protocol 6 11 copying 5 12 creating 5 3 defining dimensions 5 3 defining well information 5 3 deleting 5 13 editing dimensions 5 10 editing well information 5 10 exporting and importing 5 21 optimizing manually selecting well centers 5 18 overview 5 14 performing the optimization 5 17 preparing for optimization 5 16 selecting detection method 5 15 verifying well centers 5 19 overview 5 1 selecting and editing lo
91. curate G factor has been determined for the connected instrument it may be entered in the data reduction method configuration Threshold defines the minimum number of counts values measured below the threshold are noise Concert TRIAD Series Software User s Manual Appendix B Mathematical Operators and Functions B 1 Supported Mathematical Operators and Functions The tables in this appendix describe the mathematical operators and functions that may be used in formulas e Table B 1 describes the mathematical and logical operators supported e Table B 2 describes the mathematical functions supported Note In formulas where multiple parameters are configured separate parameters with a semicolon for example max S3 S5 Table B 1 Mathematical and Logical Operators Operator Description Sums two numbers Compares two expressions to determine if they are equal Divides two numbers and returns a numeric result lt gt Compares two expressions to determine if they are not equal gt Compares two expressions to determine if one is greater than the other gt Compares two expressions to determine if one is greater than or equal to the other lt Compares two expressions to determine if one is less than another lt Compares two expressions to determine if one is less than or equal to another Multiplies two numbers Performs subtraction of two expressi
92. d Methods may be signed only when Signet is enabled on the system Note When Signet is enabled on the system only users assigned a role containing the Create permission may create new detection methods To sign detection methods users must be assigned a role containing the Sign permission Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To create and define a new detection method From the toolbar choose Create a new method VY o From the Actions menu choose Create a new method OR Right click in the Detection Method Selection List and choose Create a new method from the menu The Method Editor appears Figure 4 2 Concert TRIAD Series Software User s Manual 4 4 Creating and Editing Detection Methods 4 2 1 Selecting a Method Technique In the Method Editor the type of detection method to create is selected in Method Technique Figure 4 2 Only techniques supported by the instrument currently selected in the Instrument Selection List are available for configuration refer to Chapter 2 Setting Up and Controlling Instruments a Method Editor Method Technique Method Technique gt Method Type Supported techniques Absorbance X Method Parameters Figure 4 2 Selecting a Method Technique To select a method technique 1 In Supported techniques choose the desired detection method 2 If defini
93. d refer to Section 4 3 Editing Detection Methods DYNEX Technologies Inc Creating and Editing Detection Methods 4 17 4 5 Deleting Detection Methods User defined detection methods may be deleted from the Detection Method Selection List Some detection methods may not be deleted including e methods used in protocols e default methods installed with Concert TRIAD Series Software e methods signed on systems with the optional Signet enabled Note When Signet is enabled on the system only users assigned a role containing the Delete permission may delete user defined detection methods Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To delete a detection method 1 In the Detection Method Selection List select the detection method to delete 2 From the toolbar choose Delete the selected method oR From the Actions menu choose Delete the selected method OR Right click on the selected detection method and choose Delete the selected method from the menu Message appears Figure 4 11 jJ amp re you sure you want to delete the method Polarization 485 Figure 4 11 Confirming the deletion of a detection method 3 Choose Yes to delete the selected detection method OR Choose No to cancel the deletion Concert TRIAD Series Software User s Manual 4 18 Creating and Editing Detection Methods 4 6 E
94. d Restore Note Leave Administrator Password Restore open until technical support supplies a new code The new code is based on the code displayed in the upper field which changes each time Administrator Password Restore is opened 4 In the lower field of Administrator Password Restore enter the new code provided by technical support 5 Choose OK to close Administrator Password Restore and accept the new code 6 Follow any additional instructions provided by technical support Concert TRIAD Series Software User s Manual Setting Up and Using Signet 3 3 3 Viewing the System Activity Audit Log The system administrator may view the Audit Log which displays the audit trail for all user activity in software applications that support Signet System activity is logged even when Signet is set to No Support refer to Section 3 2 2 Setting the Signet Support Level Note Administrator activity other than changing the level of support for Signet is not saved in the Audit Log Administrator activity is viewed in the Audit tab of the Account Management application User activity within Concert TRIAD Series Software may be viewed in the Audit Viewer refer to Section 3 4 3 Viewing and Searching the Concert TRIAD Series Software Audit Log To view the Audit Log 1 In the Windows Start menu choose Settings gt Control Panel Control Panel appears 2 In Control Panel double click Administrative Tool
95. d being defined is displayed below the property grid Figure 5 11 2 In Column distance verify the distance between columns and edit the dimension All offsets and well dimensions are entered in centimeters if desired 3 Verify the x and y offsets for the lower two wells and edit the dimensions if desired 4 In Row distance verify the distance between rows and edit the dimension if desired 5 Verify the x and y offsets for the upper two wells and edit the dimensions if desired 6 If necessary click the next to Labware Lot Name to display the default name assigned to the new labware lot 7 Enter a new Lot ID Name if desired Concert TRIAD Series Software User s Manual 5 20 Creating and Editing Labware 8 Choose Save to save the optimization data and create the new labware lot Note To use the optimized lot in a measurement protocol open the labware for editing and select the new Labware Lot refer to Section 5 3 2 Selecting and Editing Labware Lots OR Choose Back to redefine well centers graphically refer to Section 5 6 4 Selecting the Centers of the Four Corner Wells OR Choose Cancel to close Optimizing Labware without completing the optimization DYNEX Technologies Inc Creating and Editing Labware 5 21 5 7 Exporting and Importing Labware User defined labware can be exported to an XML file and imported later to restore that configuration or share it with a copy of C
96. d black N A Top Fluorescence Intensity black with clear N A Bottom bottom Fluorescence solid black Microplates must not be covered with a lid or Polarization plastic film during fluorescence polarization measurements Time Resolved solid white N A Fluorescence DYNEX Technologies Inc Creating and Editing Labware 5 7 5 2 2 Configuring Offsets and Well Dimensions for the Default Labware Lot Use Labware Lots to define row and column offsets and well dimensions Figure 5 3 The offsets and dimensions entered when new labware is created define the default labware lot DefaultLot After the new labware has been saved additional lots may be created by optimizing the labware to compensate for dimensional variations between different production lots refer to Section 5 6 Optimizing Labware In Labware Lots x and y offsets are defined for all four corners of the labware An x offset is the distance from the edge of the microplate to the center of wells on the first row a y offset is the distance from the edge of plate to the center of wells in the first column Well dimensions defined include well depth length and width as well as distances between rows and columns To configure offsets and well dimensions 1 If necessary click the next to Labware Lot Measurements to display the fields in the category More information about the field being defined is displayed below the property grid Figure 5 3 Note Th
97. d off Note A minimum of 30 minutes is required for the instrument to reach the desired temperature The actual time required depends on the relative change in temperature To turn off temperature control In Set Point enter 0 then choose Set OR Turn power to the instrument off and on Setting Up and Controlling Instruments 2 13 2 3 3 2 Shake Control Shake Control is used to manually shake the microplate loaded in the instrument To manually perform a shaking operation 1 In Mode select the desired shaking mode e Linear shakes from side to side e Orbital shakes in a circular pattern e Squared shakes in a square pattern moving at right angles CAUTION Shake low density plates such as 6 or 48 well plates at low UN speed only Shaking low density plates at higher speeds may cause liquid in wells to spill 2 In Intensity select the desired shaking intensity Low Medium or High 3 In Duration enter the length of time to shake in seconds 4 Choose Shake The instrument shakes the microplate according to the configured settings 2 3 3 3 Plate Control Plate Control provides options to eject or load the plate carrier It also features an option to sense that a microplate is in the plate carrier before starting a measurement To manually control the plate carrier e Choose Eject to extend the plate carrier outside the instrument e Choose Load to retract the plate carrier inside the instrument e Se
98. diting Detection Methods Instruments opens the Instrument Selection List and provides the ability to manually control instrument actions such as shaking and configure communications settings and filter slides refer to Chapter 2 Setting Up and Controlling Instruments e Software Settings configures software settings including system language print options default simulated data files and the directory where measurement results are saved refer to Section 1 4 2 Configuring Software Settings e Users appears in the navigation pane only when the optional Concert TRIAD Series Analysis Software with Signet module is installed and enabled on the system Signet is an integrated set of features that help Concert TRIAD Series Software users comply with electronic signature regulations such as 21 CFR Part 11 refer to Section 3 4 Performing Signet User Actions in Concert TRIAD Series Software Installing Setting Up and Using the Software 1 5 1 2 2 2 About the Toolbar The toolbar provides easy access to common software actions The module chosen in the navigation pane determines which actions are available on the toolbar for example Optimize Labware is only available when the Labware module is active 1 2 2 3 About the Selection and Configuration Pane The selection and configuration pane is the large pane to the right of the navigation pane Options available in this pane change depending
99. ds 22 lt 24 5624344 85 x od eRe eb Ser eos eaededs 4 14 4 4 Copying Detection Methods 0 cece cee eens 4 16 4 5 Deleting Detection Methods sae ese eed ote ee eed ese neeeeeewes 4 17 4 6 Exporting and Importing Detection Methods 00 0000 4 18 5 Creating and Editing Labware 5 1 OVErvViEW cesat aei nets Bee ee Bee ee Gkb eee ete e eet eeee sarees 5 1 32 Creating eaWalest hee eee ecuenseeenyee doe eenend eens Oe EEDE ERCE 5 3 5 2 1 Defining Labware Information 0 0 00 c eee eee eee 5 4 5 2 1 1 General Labware Selection Guidelines 5 6 5 2 2 Configuring Offsets and Well Dimensions for the Default Labw re Lot i 2 cc005badaceee cad idda ae ana E a 5 7 5 2 3 Signine LAB Wales sedha aeaa a a aa a eee ease Heads 5 8 5 3 Editing Labware s 2205 246 ner1 G4 leer ee ianei ae Gai E E AE RAAE GE EE 5 9 5 3 1 Viewing and Editing Labware Information 5 10 5 3 2 Selecting and Editing Labware Lots 0000 000 5 11 5 4 Copying Labware sis ekkadad ese ad dwn raga ehaseer ered ataeheeiens 5 12 5 5 Deleting Labware 39 6 aes darearen BY aad oo tho a ao a S a a aoe OOM 5 13 Concert TRIAD Series Software User s Manual 5 6 Optimizing Labware si cceias caged ede ndene adeeb eee eadas aa ee doles 5 14 5 6 1 Selecting the Detection Method 0 0 0 e eee eee eee 5 15 5 6 2 Preparing and Loading the Labware 000
100. e 6 32 6 2 8 Configuring Concentration Concert TRIAD Series Analysis Software Only 2ceccsesesedectea seeds eteassaeeae ne 6 33 6 2 9 Configuring Cutoff Values Concert TRIAD Series Analysis DOTOVARCOULY 5 t te Gee Se ee SEES RR AES coe SER EOE PSE REX 6 38 6 2 10 Configuring Validation Rules Concert TRIAD Series Analysis Software only 0 0 2 cece eee eee eee 6 40 6 2 11 Configuring Output Settings 320 2se lt sdecnndesdedessdeaders 6 42 6 2 11 1 Configuring a Program to Execute after a Protocol Run Completes an a dctu o aie ebb 4g ae oe ee aeR 6 44 6 2 12 Siging a Protocol 2 252 seared ded eeidnteee een NEEE ERT 6 45 6 3 Running Protwocols 2 cc accinsedadaws cdbee dies aseaeeiaes ceeauees 6 46 6 3 1 Running a Protocol on an Instrument 000005 6 46 6 3 1 1 Optimizing Read Height TRIAD only 6 48 6 3 2 Running a Protocol When Simulation Mode is Enabled 6 51 64 Editing ProtGcdls sc ben kare no hee ete ee ee EEEE Sede ERRED OERE EE 6 53 65 Copying Protocols 2sc 22222scieeedevaused ces iiereceasekeed hee eeees 6 55 6 6 Deleting Protocols s 6 ciscavias cee peed deeded egies bees seas abe es aula 6 56 6 7 Printing Protocol Configuration Information 0 0 00 e ee eee 6 57 6 8 Exporting and Importing Protocols 0 e cee eee eee nee 6 59 DYNEX Technologies Inc 7 Viewing Measurement Results 7 1 OVEDVIOW 2435552442228 bee ER Eea EATE aaa
101. e UV band using the deuterium lamp the minimum temperature is 4 C 7 2 F above ambient The maximum temperature that may be set is 45 C 113 F Note The temperature remains at the current setting until overridden by another Set Temperature preparation method by changing the temperature in Manual Control or by turning the instrument off and on DYNEX Technologies Inc Creating Protocols 6 31 6 2 6 Configuring Variables Concert TRIAD Series Analysis Software only Up to ten variables may be defined for use in formulas configured in the protocol Figure 6 21 Variables are typically used with test kits that have cutoff values or standard correction values based on lot number Note Variables appears only when selected in General Settings refer to Section 6 2 1 Configuring General Settings 5 Create Protocol Kinetic 340 Variables General Settings Enter numeric values for up to 10 variables Variables can be used in any formula defined in the protocol Technique Type Labware Selection soit egilea Number of variables 3 Se Method Selection User Defined Variables Transformation Variable Name Value Name to be used in reports Concentration Cutoff Vi Y fart Validation F Paos Output Settings put Setting po oo Figure 6 21 Configuring variables in an analysis protocol To configure variables 1 Select the Number of variables to be configured Up to ten variables may be con
102. e and the layout orientation on the plate e Vertical replicates are arranged vertically in columns e Horizontal replicates are arranged horizontally in rows Note Replicate parameters are available for configuration only when Incremental Flow is selected 9 Choose Fill to label the selected wells OR Choose Delete to delete existing labels from the selected wells 10 Repeat steps 2 9 to define additional well selections if desired 11 Choose Report Options and select which information about plate layouts appears in printed reports e CV the coefficient of variation of a replicate group Available only when replicates are configured in the layout e Print in Matrix well label identifiers appear arranged in a matrix corresponding to the plate layout e Print in List well label identifiers appear in a list e Standard Deviation the measure of dispersion from the mean value of a replicate group Available only when replicates are configured in the layout Concert TRIAD Series Software User s Manual 6 14 Creating Protocols 6 2 4 3 Configuring Reading Direction In a protocol run wells may be read row by row column by column or individually one at a time To select how wells are read 1 Choose the Reading Direction Settings tab to configure the order in which wells are read in the protocol Figure 6 8 ip Edit Protocol FloTopKinetic 12 cycle Layout Settings General Setti
103. e fields in Labware Lot Info may not be configured when creating new labware 2 Enter column and row x and y offsets for each of the four corner wells All offsets and well dimensions are entered in centimeters ap Labware Editor Weber 96deep Labware Lots Labware Information fmt SS B Labware Lot Info t True Landscape Absorbance B Labware Lot Measurements Lower left x offset 1 435 Lower left y offset 1 135 Lower right x offsel 1 435 Lower right y offsel 1 135 Upper left x offset 1 435 Upper left y offset 1 135 Upper right x offsel 1 435 Upper right y offsel 1 135 B Well Measurements Column distance 0 9 Row distance 0 9 COST Stance Information about the Distance between columns cm j i field being configured Figure 5 3 Defining offsets and well dimensions 3 If necessary click the next to Well Measurements to display the fields in the category Concert TRIAD Series Software User s Manual 5 8 Creating and Editing Labware In Column Distance enter the distance between columns In Row Distance enter the distance between rows 4 5 6 7 Enter the Well depth In Well Length enter the diameter of the well in the direction of the columns on the plate In Well Width enter the diameter of the well in the direction of the rows on the plate In Notes enter information about the labware lot or configuration if desired 10 Choose Save to sa
104. e for NT systems Installer htm e Go Links The following products are required to install Concert TRIAD Series Software under Windows NT4 0 To insure proper installation please execute the links below in the order in which they appear All links below must be installed Windows Installer Technology Microsoft Internet Explorer 6 0 please reboot after installing Microsoft NET Framework 1 1 4322 Microsoft SOL Server version 8 0 please reboot after installing Signet 3 0 Concert TRIAD Series Software H Downloading from site file C WINNT ProfilestAdministratorsDesktop Multimode Disc Images Disklmage C CPY 1E My Computer Z Figure 1 4 Installing the software on a Windows NT system Concert TRIAD Series Software User s Manual 1 10 Installing Setting Up and Using the Software 6 Click on a link to launch the installer for that component During installation keep in mind that e the components must be installed in the order listed e when an installer requires restarting the computer the computer must be restarted before installing the next component in the list Note After the system restarts browse to the contents of the installer CD and open Installer htm again to continue installing components Note If a prompt to Run or Save the installer appears before the installation wizard choose Run to start the wizard 7 Follow the steps in the component installer until the ins
105. e four corner wells refer to Section 5 6 4 Selecting the Centers of the Four Corner Wells OR Choose Cancel to close Optimizing Labware without performing the optimization Concert TRIAD Series Software User s Manual 5 18 Creating and Editing Labware 5 6 4 Selecting the Centers of the Four Corner Wells Use Select Center to precisely define the centers of the corner wells read in the optimization Figure 5 10 Select Center displays an image of the well generated by the optimization read Well centers are defined graphically by dragging cross hairs to the position visually identified as the center Select Center is performed for each corner well individually Optimizing Labware Weber96deep Select Center of Left Top Well Select a detection method Select the center of the well graphically below Click next to proceed or back to optimize the labware again Prepare the Labware Optimize Select Center of Left Bottom Well Select Center of Right Top Well Select Center of Right Bottom Well Verify Well Centers Figure 5 10 Selecting the well center To define the centers of the wells 1 Place the cursor in the well image then click and drag the cross hairs to the desired center of the well 2 Choose Next to define the center of the next well read When all four well centers are defined Verify Well Centers appears refer to Section 5 6 5 Verifying Well Centers OR Choose Cancel to close Optimizing
106. e starting a protocol run use Manual Control to set the temperature and check it at regular intervals until the desired temperature is reached refer to Section 2 3 3 1 Temperature Control TRIAD only Note Set Temperature preparation methods are useful for kinetic measurements intended to measure the effects of temperature changes on samples To configure a Set Temperature preparation method 1 In Method Selection choose the desired Set Temperature preparation method Method Properties for the selected method appear Figure 6 20 a5 Create Protocol NewProtocol3 General Settings Technique Type Labware Selection Layout Settings Method Selection gt Basic Advanced Variables Transformation Concentration Cutoff validation Output Settings Method Selection Select a method and method type Report Options Method Selection Method Properties Sequence Set Temperature Shake ABS 340 Kinetic Shake Abs405 Set Temperature Temperature in C to set chamber Figure 6 20 Configuring a Set Temperature preparation method Concert TRIAD Series Software User s Manual 6 30 Creating Protocols 2 In Set Temperature enter the desired microplate chamber temperature in degrees Celsius In protocols that perform measurements only at visible wavelengths gt 359 nm the minimum temperature that may be set is 3 C 5 4 F above ambient When the protocol performs measurements in th
107. e system signed protocols may not be deleted Note When Signet is enabled on the system only users assigned a role containing the Delete permission may delete protocols Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To delete a user defined protocol 1 In the Protocol Selection List select the protocol to delete 2 From the toolbar choose Delete the selected protocol Message appears A X Figure 6 37 OR From the Actions menu choose Delete the selected protocol OR Right click on the selected protocol and choose Delete the selected protocol from the menu 2 Are you sure you want to delete the protocol Basic Luminescence 96 Figure 6 37 Confirming the deletion of a protocol 3 Choose Yes to delete the selected protocol OR Choose No to cancel the deletion DYNEX Technologies Inc Creating Protocols 6 57 6 7 Printing Protocol Configuration Information Information about the protocol configuration and sample layout may be printed separately from measurement results To print protocol configuration information 1 In the Protocol Selection List select the protocol to print 2 From the toolbar choose Print the selected protocol OR From the Actions menu choose Print the selected protocol OR Right click on the selected protocol and choose Print the selected protocol from the menu
108. e the exported detection method will be saved DYNEX Technologies Inc Creating and Editing Detection Methods 4 19 4 Choose OK to export the detection method The exported detection method is saved using the default file name format Method__ MethodName xml In order to import the file at a later date the filename must not be changed OR Choose Cancel to stop the operation without exporting the detection method To import a detection method from an exported XML file 1 From the File menu choose Import gt Detection Method Open appears 2 In Open browse to and select the desired XML file to import 3 Choose Open The detection method is imported to the Detection Method Selection List Concert TRIAD Series Software User s Manual Creating and Editing Labware 5 1 Overview Concert TRIAD Series Software supports a wide range of labware with many common microplate formats already preconfigured and ready for use in protocols Configured labware types are listed in the Labware Selection List and are available for use in protocols New labware types may be created at any time using the Labware Editor The Labware Editor also provides the ability to edit and delete existing labware types not used in protocols make copies of labware types and optimize labware dimensions to compensate for slight dimensional variations that may exist between production lots The types of labware supported depend on the capabili
109. e the plate The filter passes only the wavelength necessary to excite samples The objective lens collects the resulting fluorescence and directs it through an emission filter to separate background light from the specific wavelengths generated by samples This signal is detected by the photo multiplier tube When performing a fluorescence intensity top method on a TRIAD excitation of samples from below the plate is stopped Gp Method Editor Fluorescence Intensity top Method Parameters Method Technique Method Parameters gt Method Name Fluorescence Intensity top Excitation Filter nm 535 SL 1 Emission Filter nm 595 SL 1 X Integration Time seconds o o01 Date created Figure 4 6 Defining fluorescence intensity top method parameters DYNEX Technologies Inc Creating and Editing Detection Methods 4 9 To define fluorescence intensity top method parameters 1 Enter a Method Name Figure 4 6 2 Select the Excitation Filter nm 3 Select the Emission Filter nm Note The filters available are those installed on the slides loaded in the instrument and configured for fluorescence techniques in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides 4 In Integration Time seconds enter the length of time in seconds the signal is collected from samples The integration time may be set within the range of 0 00005 to 3600 seconds 5 Choose Save to save the new
110. each well desired and selecting Accept Well 4 From the toolbar choose Reevaluate current measurement results to recalculate the results with outliers removed Note The Reevaluate button appears on the toolbar only when a parameter in the results such as data reduction technique has been edited Concert TRIAD Series Software User s Manual 7 6 Viewing Measurement Results 7 2 3 Viewing Mean Data The Mean Data and Mean Data List tabs display the well identifier mean reduced value well status coefficient of variation CV and standard deviation for replicate groups Mean data is also displayed for fluorescence polarization results from a TRIAD The Mean Data tab displays this information in a matrix corresponding to the plate layout Figure 7 5 the Mean Data List tab displays the same information in a list Wells may be rejected as outliers when the calculated value falls outside the expected result The results may be recalculated with outliers removed if desired ab Result Viewer 2005031 8 141152 DTX 880 View measurement results and graphs in the tabs below Raw data Reduced Data Mean Data MeanDatatist Graphs Edit m Result List M Show Status MV Show Well Identifier i C A Le ley St S4 56 276 390 327 OK OK OK 0 0 0 0 0 0 0 0 0 514 S15 516 518 S19 60 S 462 832 5 OK OK OK 989 95 181 07 133 16 76 41 21 66 66 85 593 97 387 49 615 18 383 180 31 452 55 526 S2 530 531 126
111. ecreasing Select the type of graph that best represents how the concentrations of the standards are configured in the protocol The graph preview refreshes to display the type selected In Graph Preview click on any point to view the X and Y values for that point if desired Figure 6 23 The X and Y values currently displayed may be changed Changes made in Graph Preview are reflected in Graph Setup Concert TRIAD Series Software User s Manual 6 36 Creating Protocols 11 Choose the Graph Setup tab to configure standards Figure 6 24 Edit Protocol Kinetic 340 12 cycle temp 35 Concentration General Settings Choose a curve fitting method and configure response formulas and concentrations as desired Technique Type Labware Selection X Axis Layout Settings Y axis J Method Selection Curve Type LinearRegression Base Measurement Name Concentration Number of standards 8 hai Variables Transformation Extrapolation p z A Type linear Type linear 7 Concentration gt Graph Preview Graph Setup Validation Report Options Cutoff Validation Standards Output Settings Response Formula Concentration fmt Booe it 3 we ms o te o toy we Figure 6 24 Configuring standards 12 In Standards edit each Response Formula and the corresponding Concentration as desired Response formulas may contain any controls standards or variables defined in the test as
112. ection 2 2 5 Enabling Simulation Mode This allows protocols detection methods and labware to be defined edited and tested for the selected instrument even though it is not physically connected to the host computer DYNEX Technologies Inc Setting Up and Controlling Instruments 2 3 2 2 Controlling Instrument Actions Instrument actions such as ejecting or loading the plate carrier and initializing the instrument can be performed directly from the Instrument Selection List using the buttons on the toolbar Actions that may be controlled include e Ejecting the Plate Carrier Section 2 2 1 e Loading the Plate Carrier Section 2 2 2 e Initializing the Instrument Section 2 2 3 e Connecting to the Instrument Section 2 2 4 e Enabling Simulation Mode Section 2 2 5 2 2 1 Ejecting the Plate Carrier Eject the plate carrier moves the plate carrier outside the instrument to allow access for placement or removal of a microplate To eject the plate carrier 1 In the Instrument Selection List select the desired instrument Figure 2 1 2 From the toolbar choose Eject the plate carrier OR From the Actions menu choose Eject the plate carrier OR Right click on the desired instrument and choose Eject the plate carrier from the menu that appears 2 2 2 Loading the Plate Carrier Load the plate carrier retracts the plate carrier and microplate back inside the instrument in preparation of performi
113. ed result OR Right click on the desired results and choose Delete the selected result from the menu that appears 2 j Do you want to delete this result 20050318 141152 Figure 7 20 Confirming the deletion of measurement results 3 Choose Yes to delete the selected results OR Choose No to cancel the deletion DYNEX Technologies Inc Viewing Measurement Results 7 25 7 7 alo Printing Measurement Results Measurement results may be printed from the Results Selection List or the Result Viewer Printed reports include information about the protocol and all Report Options configured in the protocol int preview Change Depending on how Print Settings are configured Print and or Print Preview may appear before the measurement results print Refer to Section 1 4 2 1 Configuring Print Settings for information about enabling and disabling Print and Print Preview To print measurement results OR 1 To print from the Results Selection List select the results to print and choose the print button on the toolbar To print from the Result Viewer choose the print button on the toolbar 2 If Print appears configure printing options as desired and choose OK OR If Print Preview appears use the toolbar controls to change the magnification layout view or page s displayed if desired Figure 7 21 layout view Detection Results layout view Laboratories Posie Monday narch
114. eight configured must not be less than that of the 4 Enter the Height of the plate A labware dimensions are entered in centimeters 5 Enter the Height with lid 6 Enter the Length of the plate 7 In Reading height enter the height from the top of the plate at which the plate is read DYNEX Technologies Inc 13 14 15 16 17 Creating and Editing Labware 5 5 Enter the Width of the plate If necessary click the next to Well Info to display the fields in the category 10 11 12 Enter the number of Columns on the plate Enter the number of Rows on the plate Click in either column of Well bottom shape then click on the down arrow and choose the shape of well bottoms Flat Cone or Round Click in either column of Well shape then click on the down arrow and choose the shape of the wells Round Square or Cone Enter the maximum Well volume in microliters In Supported Techniques select all measurement techniques compatible with the plate being defined The labware being configured will only be available for use in protocols configured with compatible measurement techniques Note Refer to Section 5 2 1 1 General Labware Selection Guidelines for more information about choosing the appropriate labware for the desired techniques In Notes enter information about the labware or configuration if desired Choose Next to define the default row and column offsets and well dimensions for t
115. elected protocol C Default Maximum Set Value Optimize Read Height Available for the TRIAD only Figure 6 30 Preparing to run a protocol on an instrument DYNEX Technologies Inc Creating Protocols 6 47 Enter a new Result Name if desired Use Eject Plate Carrier and Close Plate Carrier to load the microplate into the instrument if necessary Select the orientation that matches how the plate is positioned on the plate carrier e Landscape the long edges of the plate run parallel to the front of the instrument with well A1 located in the upper left corner Portrait the short edges of the plate run parallel to the front of the instrument with well A1 located in the upper right corner e Opposite Landscape the edges of the plate run parallel to the front of the instrument with well A1 located in the lower right corner e Opposite Portrait the short edges of the plate run parallel to the front of the instrument with well A1 located in the lower left corner Note Well A1 is identified in the plate graphic by a red highlight When preparing to run a luminescence fluorescence top fluorescence polarization or time resolved TRF protocol choose Optimize Read Height to automatically determine and set the optimal read height used in the protocol run refer to Section 6 3 1 1 Optimizing Read Height TRIAD only gt TRIAD Optimize Read Height is available fo
116. ence polarization and time resolved fluorescence TRF measurements The measurement methods available to users depend on the capabilities of the instrument being controlled Measurement results may be viewed in Concert TRIAD Series Software or easily exported to compatible applications such as Microsoft Excel Optional modules may be purchased separately to extend the functionality of the software Available modules include Concert TRIAD Series Analysis Software which provides advanced protocol configuration and evaluation capabilities and Concert TRIAD Series Analysis Software with Signet which adds support for electronic signature regulations such as 21 CFR Part 11 The simple interface divides the main window into three basic sections which provide easy access to system functionality Most operations use a wizard type interface to efficiently guide the task being performed This user s manual covers the functionality provided by Concert TRIAD Series Software and the optional Concert TRIAD Series Analysis Software and Concert TRIAD Series Analysis Software with Signet modules including e Setting Up and Controlling Instruments Chapter 2 e Setting Up and Using Signet Chapter 3 e Creating and Editing Detection Methods Chapter 4 e Creating and Editing Labware Chapter 5 e Creating Protocols Chapter 6 e Viewing Measurement Results Chapter 7 This chapter introduces users to the soft
117. ength or filter type in current detection method is not installed Check filter parameters configured in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides Filter wavelength in command is not defined in any Slide Check filter parameters configured in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides Currently inserted slide code does not match set slide code Reinsert slide Make sure the correct filter slides are installed in the instrument No filter slide detected Make sure filter slides are installed Currently inserted filter slide code is invalid Make sure the correct filter slides are installed in the instrument Currently inserted filter slide contains no valid defined filters Make sure the correct filter slides are installed in the instrument and check filter parameters configured in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides 51 Temperature setpoint exceeds 45 C 113 F Check the temperature set in Manual Control and or the protocol Set a desired temperature less than 45 C if necessary refer to Section 2 3 3 1 Temperature Control TRIAD only Currently inserted LED is not defined Contact a DYNEX Technologies Service Engineer LED causing ADC overflow Make sure the correct filter slides are installed in the instrument and check filter pa
118. ensions and information may be viewed but not edited for e default labware installed with Concert TRIAD Series Software e labware used in protocols e labware that has been signed on a system with the optional Signet enabled Note When Signet is enabled on the system only users assigned a role containing the Edit permission may edit labware definitions Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions All labware in the Labware Selection List may be optimized to create new labware lots refer to Section 5 6 Optimizing Labware Labware lots compensate for dimensional variations between production lots When multiple lots exist for a labware type the active lot may be changed Labware lot properties may be edited for all labware types except those that have been signed Labware is edited in the Labware Editor Figure 5 4 Editing includes e Viewing and Editing Labware Information Section 5 3 1 e Selecting and Editing Labware Lots Section 5 3 2 To view and edit labware dimensions and information 1 In the Labware Selection List select the labware to edit 2 From the toolbar choose Edit the selected labware type OR From the Actions menu choose Edit the selected labware type OR Right click on the selected labware and choose Edit the selected labware type from the menu that appears Concert TRIAD Series
119. ent Results in Microsoft Excel When measurement results for a protocol run are exported to Excel multiple workbooks spreadsheets are created A workbook is created for the raw data read for each detection method configured in the protocol Reduced and transformed data are included in a separate workbook Note Transformed data is available only when the optional Concert TRIAD Series Analysis Software module is installed on the system This section covers e Viewing Protocol and Measurement Information Section 7 4 1 1 e Viewing Raw Data Section 7 4 1 2 e Viewing Reduced and Transformed Data Section 7 4 1 3 Concert TRIAD Series Software User s Manual 7 20 Viewing Measurement Results 7 4 1 1 Viewing Protocol and Measurement Information Information about the system and parameters configured in the protocol is saved in the General worksheet General is included in all worksheets exported from a set of measurement results Figure 7 17 R1 Microsoft Excel 20050321 135246_340 Area Scan Analysis_ABS340 0_03 21 2005_02 41 22 14 x File Edit View Insert Format Tools Data Window Help Adobe PDF Arial Unicade MS 78 PIB Z U 2 M E34 v fe A ji B C D E fi 1 Operator Operator 2 Header 340 Area Scan Analysis 3 Identification 340 Area Scan Analysis 4 Date 3 21 2005 14 41 5 Description Description 6 Platetlame 20050321 135246 7 DateMeasured 3 21 2005 13 52 8 DateEvaluated 3 21
120. er nm OSL v Integration Time seconds 0 001 Date created Figure 4 5 Defining luminescence measurement parameters To define luminescence method parameters 1 Enter a Method Name Figure 4 5 Concert TRIAD Series Software User s Manual 4 8 Creating and Editing Detection Methods 2 In Emission Filter nm select O when no cutoff filtration is desired Most luminescence measurements do not require cutoff filtration OR In Emission Filter nm select the cutoff filter if desired Note The filters available are those installed on the emission filter slide loaded in the instrument and configured for luminescence techniques in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides 3 In Integration Time Seconds enter the length of time in seconds the signal is collected from samples The integration time may be set within the range of 0 00005 to 3600 seconds 4 Choose Save to save the new luminescence detection method The new method appears in Detection Method Selection List OR Choose Back to select a different Method Technique refer to Section 4 2 1 Selecting a Method Technique OR Choose Cancel to close the Method Editor without saving the new detection method 4 2 3 3 Defining Fluorescence Intensity Top Method Parameters In a fluorescence intensity top method the source light is focused by an objective lens and directed through an excitation filter abov
121. er to Section 6 2 9 Configuring Cutoff Values Concert TRIAD Series Analysis Software only Validation configure up to ten validation formulas to evaluate if a protocol run meets the specified conditions required to be valid refer to Section 6 2 10 Configuring Validation Rules Concert TRIAD Series Analysis Software only Note Only Analysis Options that have been selected appear in the Create Protocol navigation pane and are available for configuration in the protocol Creating Protocols 6 7 6 2 2 Selecting the Technique Type Use Technique Type to select the measurement technique performed by the protocol Figure 6 4 Only techniques supported by the instrument and for which detection methods have already been defined are available For more information about technique types refer to Chapter 4 Creating and Editing Detection Methods 6 Create Protocol Kinetic 340 Technique Type General Settings Select the desired technique type from the list below Technique Type gt Labware Selection Layout Settings Method Selection Technique Type Absorbance Variables Fluorescence Intensity To Fluorescence Intensity Bottom Fluorescence Polarization Concentration Time Resolved Fluorescence Cutoff Validation Transformation Output Settings Figure 6 4 Selecting the measurement technique for a TRIAD To select a technique type In Technique Type choose the desired technique Note If edi
122. ert TRIAD Series Software User s Manual 3 12 Setting Up and Using Signet 3 4 1 Logging On and Off the System When Signet is enabled users must log on before Concert TRIAD Series Software or other installed applications that support Signet may be accessed Only one user may be logged onto the system at time Once logged in the current user may access all applications installed on the system that support Signet This section covers e Logging On the System Section 3 4 1 1 e Logging Off the System Section 3 4 1 2 e Handling Disabled Accounts Section 3 4 1 3 3 4 1 1 Logging On the System When the software launches or is idle with no user logged on Logon appears Figure 3 8 Please enter user name and password User Name Password Figure 3 8 Logon To log on the system 1 Enter the desired account User Name and Password Note The first time a user logs on using a new account or after having the password changed by the administrator Concert TRIAD Series Software prompts for the password to be changed The new password must be different from the original and may include alphanumeric characters and spaces and be up to 250 characters in length Passwords are not case sensitive 2 Choose OK The user is logged on to Concert TRIAD Series Software and any other supported software applications installed on the system The current user s full name appears in the title bar next to inst
123. es support for closed systems only access over a network is not supported In a location where several systems are present Signet must be installed and enabled separately for each system where compliance is desired Users require separate accounts on each system they need to access Note Compliance with regulations such as 21 CFR Part 11 requires implementing site processes beyond the control of the software A single system administrator sets up the level of support provided by Signet creates and manages roles assigned to user accounts and configures Signet system parameters This chapter covers e Setting Up Signet Section 3 2 e Performing System Administration Tasks Section 3 3 e Performing Signet User Actions in Concert TRIAD Series Software Section 3 4 Concert TRIAD Series Software User s Manual 3 2 Setting Up and Using Signet 3 2 DYNEX Technologies Inc Setting Up Signet Signet allows a single system administrator account to exist on a system The administrator is responsible for setting up the system and performing ongoing system administration tasks such as configuring user accounts Setting up Signet includes e Changing the Administrator Password Section 3 2 1 e Setting the Signet Support Level Section 3 2 2 3 2 1 Changing the Administrator Password The administrator password should be changed from the default password provided with the module before enabling Signet
124. eseseessseessressersseeesssessseessressesssseenseee 7 2 Table 7 2 Well Stat s Indicators 1c c2gacccashcetseiesssasceusraactanidercyunsdaraetagectasiteeyrteioloaeceamleeies 7 4 Table 7 3 Measurement Results Tabs Displayed for Analysis Options ccceeeeceeeseeeeeees 7 15 Table 7 4 Standard Curve Graph View Options cesscesssscecececeseeeceeeeeceeeeecseneeceteeessneeessaes 7 16 Table A 1 Scan Measurement and Sequence Data Reduction Techniques cceeeeeeeeee A 1 Table A 2 Kinetic Data Reduction Techniques ssensssessesesessseeeeseeesseessresserssseesseessresseesseee A 2 Table A 3 Fluorescence Polarization Data Reduction Techniques TRIAD only A 3 Table B 1 Mathematical and Logical Operators sssesssseseseseessseesseessesssesrsseessseessresseseseeenseee B 1 Table B 2 Mathematical PUMCUIONS ciiiccascacctssscceeasssusenesasnecedsasncedadseaucces saasecandsgusdacsonscedeasbesaaesals B 2 Table C 1 Software Error Codes and Solon s siccssscsvinsstacnnsasstacesaasassesedsoatesdedncdeennssanctevaneesans C 1 Concert TRIAD Series Software User s Manual Installing Setting Up and Using the Software 1 1 Overview Concert TRIAD Series Software configures and controls all measurement protocols and actions performed by the TRIAD LT and TRIAD Multimode Detectors The software supports performing absorbance glow luminescence fluorescence intensity top and bottom fluoresc
125. ethod Peak Value Used to detect the highest value per sample within a sequence of measurements Smoothing Points p Figure 7 10 Selecting a data reduction method for the sequence In Data Reduction Method select a different Method or edit the method parameters if available If a different method was selected configure additional parameters for the selected data reduction method if required Note Refer to Appendix A Data Reduction Techniques for details about the data reduction methods available for different measurement types Choose OK to confirm the selection of the data reduction method In the Edit tab choose Report Options and select the method information and measurement results data included in printouts Method Information details about the configured method including technique type and filter s used e Graph graphs of results for all measured samples e Raw Data results from each detection method kinetic cycle or well scanned Choose Reevaluate current measurement results to recalculate the results using the new data reduction configuration Note The Reevaluate button appears on the toolbar only when a parameter in the results such as a data reduction technique has been edited Concert TRIAD Series Software User s Manual 7 12 Viewing Measurement Results 7 2 6 Exporting Measurement Results to Microsoft Excel Results displayed in the Re
126. figured Entry fields for each variable appear 2 For each variable enter the desired Value and Name to be used in reports 3 Choose Report Options and select Definition to include all variable names values and names used in reports in printouts if desired Concert TRIAD Series Software User s Manual 6 32 Creating Protocols 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only Use Transformation to configure an algebraic formula X that is applied to every well in a set of reduced data X Figure 6 22 The transformation formula must include X and may include mathematical operators but not relational or logical operators Refer to Appendix B Mathematical Operators and Functions for more information about supported mathematical operators Note For single point measurements X represents the measured value Note Transformation is available for configuration only when selected in General Settings refer to Section 6 2 1 Configuring General Settings gt Edit Protocol Kinetic 340 12 cycle temp 35 Transformation General Settings Enter a transformation formula and its name Technique Type Labware Selection Layout Settings Report Options Method Selection Transformation Variables Transformation gt Concentration Cutoff i ei ae Validation Output Settings Name of x Transformation Figure 6 22 Configuring a transformati
127. filters equipped with polarizing filters to distinguish the parallel and perpendicular polarization states The polarized signals are then detected sequentially by the photo multiplier tube Note The read direction settings configured in a protocol determine when polarization states are measured during a run refer to Section 6 2 4 3 Configuring Reading Direction When Read by well is selected both states are measured for each sample before proceeding to the next sample When Read by row or Read by column is selected the parallel states are measured for all samples in a row or column before measuring the perpendicular states of the same group of samples Sf Method Editor Method Parameters Method Technique ei Pares oo Excitation Filter nm 485 SL 1 Emission Filter nm 535 SL 1 x Integration Time seconds o 001 Date created 4 2005 Figure 4 8 Defining fluorescence polarization method parameters To define fluorescence polarization parameters 1 Enter a Method Name Figure 4 8 2 Select the Excitation Filter nm 3 Select the Emission Filter nm Note The filters available are those installed on the excitation and emission filter slides loaded in the instrument and configured for fluorescence polarization techniques in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides 4 In Integration Time seconds enter the length of time in seconds the signal is collected from
128. fluorescence intensity top detection method The new method appears in the Detection Method Selection List OR Choose Back to select a different Method Technique refer to Section 4 2 1 Selecting a Method Technique OR Choose Cancel to close the Method Editor without saving the new detection method 4 2 3 4 Defining Fluorescence Intensity Bottom Method Parameters TRIAD only In a fluorescence intensity bottom method the source light is directed through an excitation filter which passes only the wavelengths necessary to excite samples and focused by an objective lens below the plate The objective lens collects the resulting fluorescence from below the plate and directs it through an emission filter to separate background light from the specific wavelengths generated by samples This signal is detected by the photo multiplier tube When performing a fluorescence intensity bottom method on a TRIAD excitation of samples from above the plate is stopped ap Method Editor Fluorescence Intensity bottom Method Parameters Method Technique Method Parameters gt Method Name Fluorescence Intensity bottom Excitation Filter nm 535 SL 1 x Emission Filter nm 625 SL 1 X Integration Time seconds 0 001 Date created Figure 4 7 Defining fluorescence intensity bottom method parameters Concert TRIAD Series Software User s Manual 4 10 Creating and Editing Detection Methods To define fluorescence inten
129. ftware User s Manual 3 8 Setting Up and Using Signet 6 In Accounts choose a user account and select the desired role s to assign to the account Table 3 1 Concert TRIAD Series Software Permissions Permission Copy Description Allows users to make copies of protocols labware types and detection methods Create Allows users to create protocols labware types and detection methods Delete Allows users to delete protocols labware types and detection methods Edit Allows users to edit protocols labware types and detection methods Instrument Settings Optimize Allows users to configure instrument settings refer to Chapter 2 Setting Up and Controlling Instruments Allows users to optimize labware to account for slight dimensional variations that occur between production lots refer to Section 5 6 Optimizing Labware Sign Allows users to add view and unlock electronic signatures refer to Section 3 4 5 Adding Electronic Signatures and Comments to Items View Audit Entry Allows users to view the Concert TRIAD Series Software audit log in the Audit Viewer refer to Section 3 4 3 Viewing and_ Searching the Concert TRIAD Series Software Audit Log Table 3 2 Role Lab Administrator Protocol Developer Concert TRIAD Series Software Default Roles Description Contains all Concert TRIAD Series Software permissions Users ass
130. g Up and Using the Software Concert TRIAD Series Control Software Installer Concert TRIAD Series Control Software 2 0 0 9 The following products are required to install Concert TRIAD Series Control Software Windows Installer Technology version 2 0 2600 1106 is installed Microsoft Internet Explorer version 6 0 2800 1106 is installed Microsoft NET Framework version 1 1 4322 is installed Microsoft SQL Server version 8 0 761 is installed 7 Accounts and Permissions version 3 0 3 is installed rt Install Concert TRIAD Series Control Software 2 0 0 9 Figure 1 3 Starting the installation 6 Choose Update or Install for the first component indicated Components are installed one at a time and should be installed in the order listed 7 Follow the steps in the component installer until the component installation is complete Note If a component installation requires restarting the system restart before installing the next component listed After the system restarts browse to the contents of the installer CD and launch the installer again to continue installing components 8 Repeat steps 6 and 7 for each component required When all components are installed properly the Install Concert TRIAD Series Software button activates 9 Choose Install Concert TRIAD Series Software to launch the software installation wizard and follow the steps in the wizard 10 In Concert TRIAD Series
131. g the Optimization Read Section 5 6 3 e Selecting the Centers of the Four Corner Wells Section 5 6 4 e Verifying Well Centers Section 5 6 5 To optimize labware 1 In the Labware Selection List select the labware to optimize 2 From the toolbar choose Optimize the selected labware type OR From the Actions menu choose Optimize the selected labware type OR Right click on the selected labware and choose Optimize the selected labware type from the menu that appears 5 6 1 Creating and Editing Labware 5 15 Selecting the Detection Method Labware is optimized by performing measurements of the four corner wells of the microplate and then defining the well centers using images of the wells generated by the measurements To ensure the most accurate optimization is performed use Select Detection Method to select the most appropriate detection method for the optimization Figure 5 7 ap Optimizing Labware Weber96deep Select a detection method gt Prepare the Labware Optimize Select Center of Left Top Well Select Center of Left Bottom Well Select Center of Right Top Well Select Center of Right Bottom Well Verify Well Centers Select Detection Method Select a detection method to proceed The detection method should use the same technique that will be used in the target assay topS35 625 bs405 bs450 bs595 loBottom 535 595 bs260 luorescence Intensity top luorescence Intensity
132. gies Inc Creating Protocols 6 55 6 5 Copying Protocols Copies may be made of existing protocols A copy of an existing protocol may be used as a template for a new protocol using the same technique Note When Signet is enabled on the system only users assigned a role containing the Copy permission may create copies of protocols Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions Signed protocols may be copied Copies of signed protocols are unsigned and may be edited To make a copy of a protocol 1 In the Protocol Selection List select the protocol to copy 2 From the toolbar choose Make a copy of the selected protocol A copy of the selected protocol appears in the Protocol Selection List OR From the Actions menu choose Make a copy of the selected protocol OR Right click on the selected protocol and choose Make a copy of the selected protocol from the menu Note The default name format for copied protocols is Copy of OriginalName To change the name open the protocol for editing and enter the new protocol name refer to Section 6 4 Editing Protocols Concert TRIAD Series Software User s Manual 6 56 Creating Protocols 6 6 Deleting Protocols Protocols that are no longer used to perform measurements may be deleted from the Protocol Selection List When the optional Signet module is enabled on th
133. gure communications settings 1 From the navigation pane choose Instruments The Instrument Selection List appears Figure 5 Concert TRIAD Series Simulated File Actions Help Instrument Selection List Serial Measurement Techniques Multimode Reader 0000 Absorbance Luminescence Fluorescence Intensity Top Fluorescence Intensity Bottom Fluorescencq i Simulated instrument Figure 1 8 Instrument Selection List with simulated instrument selected DYNEX Technologies Inc Installing Setting Up and Using the Software 1 15 2 From the toolbar choose Instrument Settings Instrument Settings appears Figure 1 9 OR From the Actions menu choose Instrument Settings aay Se Instrument Settings Basic Settings Filter Slides Manual Control Communication Settings Instrument Port com information fields Baudrate 38400 Instrument Name TR IAD Serial Number fooos Instrument Type 123 Firmware Version Features PIC FW Version 1 0 18 06 04 Figure 1 9 Configuring communications settings 3 Select the Basic Settings tab if necessary 4 In Port select the serial communications port on the host computer that connects to the instrument 5 In Baudrate select 38400 6 Choose Apply to detect the instrument When the instrument is detected the instrument information fields are autopopulated with information about the connected inst
134. h a known maximum signal to a single well on the microplate used in the optimization The concentration of the optimization sample should be at least ten times greater than the detection limit The sample volume should be the same as that of samples measured in the protocol Note When optimizing reading height for a fluorescence protocol make sure the optimization sample is the same fluorescent substance the detection method is configured to detect 5 Load the plate into the instrument dp Read Height Optimization Wizard Prepare Labware Select a detection method Prepare the labware by pipetting liquid into a well making sure the concentration is at least ten times higher than the Prepare the Labware gt detection limit Select the well in the layout below Click Next to proceed Optimize Optimization Complete Select the well containing the optimization sample Figure 6 32 Selecting the well read in the read height optimization 6 In Prepare Labware select the well containing the optimization sample Figure 6 32 7 Choose Next to start the optimization Optimization in Progress appears Figure 6 33 The optimization may take several minutes OR Choose Back to change the detection method used in the calibration OR Choose Cancel to close the wizard without performing the optimization Concert TRIAD Series Software User s Manual 6 50 Creating Protocols ie Read Height Optimization Wizard DE
135. he file at a later date the filename must not be changed OR Choose Cancel to stop the operation without exporting labware To import labware from an exported XML file 1 From the File menu choose Import gt Labware Open appears 2 In Open browse to and select the desired XML file to import 3 Choose Open The labware is imported to the Labware Selection List DYNEX Technologies Inc Creating Protocols 6 1 Overview A protocol stores all parameters required to perform a measurement including technique type detection method s labware type and preparation methods such as shaking Multiple measurements including kinetic and scan measurements may be configured in a single protocol Protocols also specify how measurement results are viewed exported or printed when a protocol run completes The Concert TRIAD Series Analysis Software module may be purchased separately to add advanced evaluation and analysis capabilities to the software This chapter includes instructions for configuring the analysis features provided by the module Note Always verify the parameters configured in a protocol Failing to verify all configured parameters may result in incorrect measurement results Protocols are listed in the Protocol Selection List Figure 6 1 which provides access to all protocol actions e Creating Basic and Analysis Protocols Section 6 2 e Running Protocols Section 6 3 e Editing Protocols Section 6
136. he measurement method detection method configuration 142 Current measurement incomplete wrong Check the parameters configured in the command received protocol 144 Instrument is busy Wait until the amber LED on the instrument is off If instrument is still busy when the LED is off turn the instrument off and on 400 Unknown PIC error Contact a DYNEX Technologies Service Engineer 401 Communication timeout with PIC controller Contact a DYNEX Technologies Service Engineer 403 PIC timeout during a measurement or Contact a DYNEX Technologies Service initialize Engineer 410 Number of steps are zero Check the parameters configured in the protocol 411 LED transport commanded to move to a Contact a DYNEX Technologies Service position less than 0 Engineer 412 Shutter transport commanded to move to a Contact a DYNEX Technologies Service position less than 0 Engineer 413 Z transport commanded to move to a position Contact a DYNEX Technologies Service less than 0 Engineer Concert TRIAD Series Software User s Manual C 4 Appendix C Software Error Codes Error 670o 415 Table C 1 Software Error Codes and Solutions Error Message LED transport commanded to move to a position greater than maximum travel Recommended Solution Contact a DYNEX Technologies Service Engineer 416 Shutter transport commanded to move to a position greater than maximum travel
137. he Actions menu choose Simulate the current instrument OR Right click on the desired instrument and choose Simulate the current instrument from the menu that appears Concert TRIAD Series Software User s Manual 2 6 Setting Up and Controlling Instruments 2 3 Configuring Instrument Settings Communication settings and filter slides used by the instrument are configured in Instrument Settings Configuring Instrument Settings informs Concert TRIAD Series Software about the instrument such as the communication speed and port used and the configuration of filter slides and individual filters Instrument features such as microplate shaking may also be controlled manually Note When Signet is enabled on the system only users assigned a role containing the Instrument Settings permission may configure instrument settings Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To configure instrument settings 1 Select the desired instrument in Instrument Selection List 2 From the toolbar choose Instrument Settings Instrument Settings appears or From the Actions menu choose Instrument Settings OR Right click on the desired instrument and choose Instrument Settings from the menu that appears 3 Configure instrument settings on the three tabs as described in the following sections e Configuring Basic Instrument Settings Secti
138. he desired Font and Font Size for printed text 7 Choose Apply to save the new print settings Concert TRIAD Series Software User s Manual 1 18 Installing Setting Up and Using the Software 1 4 2 2 Choosing Simulated Data Files Protocols may be run in simulation mode which allows the protocol configuration to be tested using simulated data before performing the protocol on actual samples In simulation mode all features for the instrument type currently selected in the Instrument Selection List are available but measurement results are either randomly generated by the software or read from a data file Use Simulated Data to choose the default data files for simulated absorbance luminescence and fluorescence measurements Figure 1 12 Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 Software Settings Print Settings Simulated Data Directory Settings Absorbance Simulated Data File C Documents and Settings All Users Application Data Multimode Detection Software d Luminescence Simulated Data File C Documents and Settings All Users Application Data Multimode Detection Software d Fluorescence Simulated Data File C Documents and Settings All Users Application Data Muttimode Detection Softwareld NL Software Setti Software ettings Browse for desired data files Figure 1 12 Choosing the Simulated Data files To choose different simulated data files 1 Choose the Simulated
139. he labware type in Labware Lots refer to Section 5 2 2 Configuring Offsets and Well Dimensions for the Default Labware Lot OR Choose Cancel to close the Labware Editor without creating or saving new labware Concert TRIAD Series Software User s Manual 5 6 Creating and Editing Labware 5 2 1 1 General Labware Selection Guidelines When creating labware select only measurement techniques compatible with the microplate being defined Each measurement technique requires labware of a specific color and or material be used Table 5 1 provides general labware color and material guidelines for each measurement technique Along with these basic guidelines always select microplates with a surface treatment suitable for the desired application and follow any additional guidelines provided by the plate manufacturer Table 5 1 General Microplate selection guidelines Measurement Supported Additional Technique Plate Color Considerations Absorbance clear white with Clear polystyrene or film plates with transparent clear bottom or bottoms are suitable Polypropylene or PVC black with clear plates do not provide sufficient optical quality bottom Luminescence Glow solid black or solid Black plates are recommended unless the signal Type white is weak enough to require the higher sensitivity of white plates However with strong signals white plates may produce crosstalk Fluorescence Intensity soli
140. hen removing the software only files installed during the initial installation are removed The software database and files created after the installation such as exported measurement results remain Support Info Multimode Detection Software Use the Following information to get technical support For Multimode Detection Software Publisher Beckman Coulter Version 2 0 0 If this program is not working properly you may f reinstall it by clicking Repair Figure 1 5 Repairing the installation 8 In Support Options choose Repair to search for and automatically reinstall any missing or damaged files required to run the software 9 When the repair is complete choose Close Concert TRIAD Series Software User s Manual 1 12 Installing Setting Up and Using the Software 1 4 Setting Up Concert TRIAD Series Software After installing the software and physically connecting the instrument to a serial port on the host computer communications and software settings must be set up Setting up the software includes e Configuring Communication Settings Section 1 4 1 e Configuring Software Settings Section 1 4 2 To set up Concert TRIAD Series Software 1 From the Windows Start menu choose Programs gt Dynex Technologies gt Concert TRIAD Series gt Concert TRIAD Series Concert TRIAD Series Software appears Figure 1 6 Note If Concert TRIAD Series Software is not found in the Start menu
141. hen the Audit Log is open while applications that support Signet are open system activity is logged but not refreshed onscreen automatically Choose Refresh to view system activity logged since the Audit Log was opened or since the last time displayed data was refreshed DYNEX Technologies Inc Setting Up and Using Signet 3 11 3 4 Performing Signet User Actions in Concert TRIAD Series Software When Signet is enabled users are required to log in to Concert TRIAD Series Software Permissions configured in the roles assigned to accounts determines which actions in the software are available to users The User Selection List provides access to Signet actions Figure 3 7 Signet user actions include e Logging On and Off the System Section 3 4 1 e Changing the Password of the User Currently Logged Into the System Section 3 4 2 e Viewing and Searching the Concert TRIAD Series Software Audit Log Section 3 4 3 e Reactivating Disabled Message Boxes Section 3 4 4 Adding Electronic Signatures and Comments to Items Section 3 4 5 Filter Slides Ex 2 Em 1 Berkeley Rattan DER User actions Current user Name Password changed Anais Miller 3 5 2005 Berkeley Rattan 3 5 2005 Donald Thomlinson 3 5 2005 Jane Loomis 3 5 2005 Sandra Patterson 12 8 2005 Thorsten Smeltzer 2 14 2005 Wyatt Singletary 3 5 2005 Figure 3 7 Accessing user actions Conc
142. ication with the instrument or enters simulation mode when no instrument is detected The connection to the instrument may be established manually after physically connecting a different instrument to the computer or when switching from simulation mode refer to Section 2 2 5 Enabling Simulation Mode To connect to the instrument 1 In the Instrument Selection List select the desired instrument Figure 2 1 2 From the toolbar choose Connect to the instrument The button remains depressed while the instrument is connected and not in simulation mode OR From the Actions menu choose Connect to the instrument OR Right click on the desired instrument and choose Connect to the instrument from the menu that appears Setting Up and Controlling Instruments 2 5 2 2 5 Enabling Simulation Mode Concert TRIAD Series Software can operate in simulation mode whether or not an instrument is connected Simulation mode enables all features supported by the instrument currently selected in the Instrument Selection List but measurement results are generated randomly or read from a file Refer to Section 1 4 2 2 Choosing Simulated Data Files for more information about selecting simulated data files To enable simulation mode 1 In the Instrument Selection List choose the desired instrument 2 From the toolbar choose Simulate the current instrument The button remains depressed while the instrument is in simulation mode OR From t
143. ick Signet Support Options exe When prompted enter the Administration Password and choose OK Support Options appears Figure 3 2 Note Ifthe Administration Password is lost forgotten or not known follow the steps in Section 3 3 2 Restoring the Administrator Password Concert TRIAD Series Software User s Manual 3 4 Setting Up and Using Signet DYNEX Technologies Inc Support Options Concert TRIAD Series Software No support C Signet Signet with password checks for signing and check in cme Figure 3 2 Support Options Choose the Concert TRIAD Series Software tab if necessary Multiple tabs appear only when several software applications with Signet support are installed on the system Select the level of support No support User accounts are not required to access Concert TRIAD Series Software Users have access to all software operations and functionality System activity is logged in the audit trail and may be viewed in the Audit Log refer to Section 3 3 3 Viewing the System Activity Audit Log e Signet Enables the use of user accounts and permissions for Concert TRIAD Series Software Users must log in to use the software and may access only features and actions for which they have permission Actions performed in the software such as signing a labware type or protocol do not require password confirmation Note Signet without password checks may
144. igned this role may perform all software actions Contains the Concert TRIAD Series Software Copy Create and Edit permissions Users assigned this role may create and edit protocols labware and detection methods but may not sign or delete items Lab Technician No Concert TRIAD Series Software permissions are assigned Users assigned this role may run protocols and view measurement results but not create edit delete or sign items or change instrument settings DYNEX Technologies Inc Setting Up and Using Signet 3 9 3 3 2 Restoring the Administrator Password Only one administrator account exists on a system with Signet installed If the administrator password is lost or forgotten DYNEX Technologies Customer Technical Support must be contacted to restore access to the Account Management application To restore the administrator password 1 Place the Signet CD in the drive and browse to the contents of the CD 2 Double click Administrator Password Restore exe Administrator Password Restore appears Figure 3 5 Administrator Password Restore Give this to customer technical support do not close this app until you get the code back 7549 A044 7E7D 4568 A9F8 E7B3 AE 19 XXXX Type the code customer technical support gives you here ee Cancel Figure 3 5 Password Restore 3 Contact technical support and provide the code displayed in the upper field of Administrator Passwor
145. iguring Layout Settings for an Analysis application Concert TRIAD Series Software User s Manual 6 12 Creating Protocols 2 To import a plate layout from an existing protocol choose Import Layout and select the desired protocol from the list that appears Only protocols with compatible plate layouts are listed OR To create a new or edit an existing plate layout select the desired wells to label To select e all wells on the plate click the small button in the upper left corner of the plate layout display Figure 6 7 e all wells in a single column or row click the desired column or row header Multiple columns or rows may be selected by holding down the CTRL key while selecting each header desired e individual wells click on the desired well Multiple wells may be selected by holding down the CTRL key while clicking on each well desired e groups of wells click and drag over the desired group of wells Multiple groups may be selected by holding down the CTRL key while dragging over each desired group 3 Choose the Type of wells to add to the plate layout e Standard a well with a known concentration used to develop or correct a standard curve Up to twelve standards may be configured on a plate e Control a well with a known expected signal used to verify the results of the plate e Positive Control a control well in which a known amount of target reagent generates a signal to verif
146. in To view existing signatures 1 Choose the desired item and open Sign the Selected Item following the steps in Section 3 4 5 Adding Electronic Signatures and Comments to Items 2 Choose the Signatures tab Figure 3 14 a5 Sign the Selected Item Add a new electronic signature to the item view or unlock existing signatures or view the history of unlocked signatures Sign Signatures History Signature Approved 3 5 2005 3 5 2005 4 49 17 PM ER Thorsten Smeltzer rey Passed validation amp is approved Version 2 Signed 3 5 2005 3 5 2005 4 48 11 PM S amp S Berkeley Rattan Fy Updated to use 405nm excitation filter Version 1 User Thorsten Password Precise Figure 3 14 Viewing active signatures 3 Click on the or to the left of a signature to expand or collapse details about the signature Details for each signature are listed on four lines e date and time signature was entered e the full name of the user signing the item e user comments e version Concert TRIAD Series Software User s Manual 3 20 Setting Up and Using Signet DYNEX Technologies Inc 4 If the Password field is visible enter the password for the user account Note Passwords are required only when Signet with password checks for signing and check in is the selected support level refer to Section 3 2 2 Setting the Signet Support Level 5 To unlock the selected signature choose Unlock Unlocked sign
147. in the Result Viewer for more information Result Viewer 20050321 135246 DTX 880 Transformation Variables View transformed measurement results or edit the transformation formula if reevaluating the results is desired Data Transformation gt Concentration Layout View List View Parameters Edit l Cutoff p Parameters Validation X few Nae o Figure 7 15 Viewing existing transformation parameters in the Results Viewer 2 Select the Layout View or List View tab to view the current transformed data Layout View displays data in a matrix corresponding to the plate layout List View displays the same data in a list 3 Select the Parameters tab to view the parameters used to calculate the transformed data currently displayd for example Figure 7 15 shows transformation parameters Concert TRIAD Series Software User s Manual 7 18 Viewing Measurement Results 4 Select the Edit tab to edit parameters as desired Figure 7 16 Parameters in the Edit tab are identical to those in the corresponding screen in the protocol configuration Refer to the appropriate section in Chapter 6 for more information e Section 6 2 6 Configuring Variables Concert TRIAD Series Analysis Software only e Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only e Section 6 2 8 Configuring Concentration Concert TRIAD Series Analysis Software only
148. installed on another system Detection method s and labware configurations used in the protocol are also saved in the export file Protocols that use default detection methods and labware installed with Concert TRIAD Series Software may be imported and exported however default methods and labware are not imported with the protocol because these items are present on all systems and may not be edited deleted or overwritten Note When Signet is enabled signed protocols may be exported for use on another system however electronic signatures attached to the protocol are not retained which allows the protocol to be edited Importing a signed method to the system from which it was originally exported is not permitted because signed methods may not be deleted or overwritten To export a protocol 1 In the Protocol Selection List select the protocol to export 2 From the File menu choose Export gt Protocol Browse for Folder appears Figure 6 39 Browse For Folder Desktop B My Documents W This Computer a My Network Places Recycle Bin O Exported Protocols Make New Folder Figure 6 39 Choosing the folder where an exported protocol will be saved 3 In Browse for Folder browse to the folder where the exported protocol will be saved OR Choose Make New Folder to create a new folder where the exported protocol will be saved Concert TRIAD Series Software User s Manual 6 60 Crea
149. is available Labware cannot be edited 2 Selecting the Technique Type once it is used in a protocol See Creating and Editing Labware for detailed ENARE CAERE information about creating and configuring labware Configuring Labware Layout Se Configuring Detection and Prep To select labware F Configuring Output Settings z Running Protocols 1 Select the desired Type of Labware from the list Editing Protocols 2 Choose Next to configure the plate layout see Configuring Labware B Copying Protocols ji 5 ayout Settings Deleting Protocols Printing Protocol Configuration Infor OR Exporting and Importing Protocols Choose Back to change the measurement technique performed by the Viewing Measurement Results protocol see Selecting the Technique Type Software Error Codes Copyright Information OR Choose Cancel to close Labware Selection without saving the new protocol Figure 1 2 Using online help Concert TRIAD Series Software User s Manual 1 6 Installing Setting Up and Using the Software 1 3 Installing Concert TRIAD Series Software The Concert TRIAD Series Software installer provides the ability to install the software on a new system Installing the software requires e Meeting System Requirements Section 1 3 1 e Installing Concert TRIAD Series Software on Windows 2000 or XP Section 1 3 2 OR e Installing Concert TRIAD Series Software on Windows NT Secti
150. is shall be the limit of DYNEX Technologies liability Furthermore DYNEX Technologies shall not be liable for incidental or consequential damages Failure of the Customer to notify DYNEX Technologies of a claimed defect by registered mail within thirty days of the discovery thereof shall constitute a waiver of any claim for breach of warranty When a product is required by DYNEX Technologies to be installed by a DYNEX Technologies engineer or technician the period of this Warranty shall begin on the date of such installation provided however that any use of the product prior to such installation shall at the sole election of DYNEX Technologies void this Warranty When installation by DYNEX Technologies personnel is not required the period of this Warranty shall begin on the date of shipment from DYNEX Technologies The period of this Warranty shall begin as described above whether or not the product has been installed or shipped pursuant to a purchase order and any trail period shall be deducted from the Warranty period that would otherwise apply under a subsequent placed purchase order for that product Limitation of Liability Notwithstanding anything to the contrary contained herein the liability of SELLER whether by reason of breach of warranty breach of contract tort or otherwise including without limitation under any indemnification provision contained herein shall be limited to replacement of goods returned to DYNEX Technologies
151. istering User Accounts and Roles Signet system administration tasks are performed in the Account Management application included as part of the Signet installation The system administrator sets up and configures user accounts passwords and roles and configures system settings such as automatic password expiration and system logout time A single system administrator password is used on a system System administration tasks may be performed only on the computer where Account Management is installed access to Account Management over a network is not supported Note If the administrator requires access to Concert TRIAD Series Software a separate user account must be created Note Regulations such as 21 CFR Part 11 contain additional requirements for account management beyond the control of this software This section covers accessing Account Management and configuring roles that are assigned to user accounts refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts Refer to the Account Management online help for detailed information about Signet system administration tasks To open Account Management 1 Log off and close all software applications using Signet 2 In the Windows Start menu choose Settings gt Control Panel Control Panel appears 3 In Control Panel double click Administrative Tools Administrative Tools appears 4 In Administrative Tools double click Account M
152. ith the Sign permission Signing an item adds a user s comments and electronic signature to the audit trail and prevents the item from being edited or deleted An item may be signed multiple times by multiple users Users assigned a role with the Sign permission may also view existing signatures for signed items and unlock any signature attached to an item An unlocked signature is deactivated and moved from Signatures to History signatures are never permanently removed from the system When all signatures for an item are unlocked the item is no longer signed and may be edited again To sign an item or view or unlock an existing electronic signature 1 From the desired Selection List select the item to sign 2 From the toolbar choose Sign the selected lt item gt Sign the Selected Item appears Figure 3 13 OR From the Actions menu choose Sign the selected lt item gt OR Right click on the selected item and choose Sign the selected lt item gt from the menu a Sign the Selected Item Add a new electronic signature to the item view or unlock existing signatures or view the history of unlocked signatures Sign Signatures History Comment Updated to use 405nm excitation Filter Sign Type Signed X User Berkeley Password eea Unlock Cancel Figure 3 13 Signing an item Concert TRIAD Series Software User s Manual 3 18 Setting Up and Using Signet DYNEX Technologies Inc 3 Choose
153. ithout changing the password DYNEX Technologies Inc Setting Up and Using Signet 3 15 3 4 3 Viewing and Searching the Concert TRIAD Series Software Audit Log Users assigned a role with the View Audit Entry permission may view or search the audit log of user activity within Concert TRIAD Series Software Refer to Table 3 1 for more information about the permissions available to users The Concert TRIAD Series Software audit log lists actions performed within the software only To view a log of systemwide Signet activity use the system Audit Log refer to Section 3 3 3 Viewing the System Activity Audit Log To view records in the log or search for specific records 1 In the navigation pane choose Users to access the User Selection List if necessary 2 From the toolbar choose View the audit log for this software Audit Viewer appears Figure 3 11 OR From the Actions menu choose View the audit log for this software OR Right click in the User Selection List and choose View the audit log for this software from the menu a Audit Viewer Description 3 4 2005 5 01 PM Signing Method with Index 16 and Version 1 3 4 2005 4 09 PM Saving Detection Method Polarization 3 4 2005 4 09 PM Creating Detection Method Polarization 3 4 2005 4 06 PM Saving Detection Method Fluorescence TRF 3 4 2005 4 06 PM Creating Detection Method Fluorescence TRF 3 4 2005 4 00 PM Saving Detection Method Fluorescei
154. l bar to Puls rotate the graph horizontally Figure 7 8 Viewing a three dimensional area scan graph To rotate the graph e Use the vertical scroll bar to rotate the graph vertically e Use the horizontal scroll bar to rotate the graph horizontally e Double click on the graph to start and stop a continuous animated horizontal rotation of the graph To print the graph 1 From the File menu choose Print Note Depending on how Print Settings are configured Print and or Print Preview may appear before the protocol configuration prints Refer to Section 1 4 2 1 Configuring Print Settings for more information about enabling and disabling Print and Print Preview Concert TRIAD Series Software User s Manual 7 10 Viewing Measurement Results DYNEX Technologies Inc 2 If Show Printer Settings and Print Preview are not enabled in Print Settings the graph prints automatically OR If Print appears configure printing options as desired and choose OK Note Print is the dialog box that appears when Show Printer Settings is selected OR If Print Preview appears use the toolbar controls to change the magnification layout view or page s displayed if desired Refer to Section 7 7 Printing Measurement Results for more information about Print Preview 7 2 5 Recalculating Data Reduction The Edit tab allows reduced data to be recalculated by editing the parameters of the current data reduction method or
155. le 7 1 describes the search options available Results matching the search parameters appear in the Results Selection List Table 7 1 Measurement Results Search Options Search Option Description Result Name Enter a partial or complete Result Name Searching for result names may also be limited to specific date s configured in Date Date Select the desired range option Less Than or Equal Equal Greater Than or Equal or Between then choose the desired date s Protocol Name Enter a partial or complete Protocol Name Searching for protocol names may also be limited to specific date s configured in Date Go Perform the search Matching results appear in the Results Selection List Clear Clear search results and display all measurement results in the Results Selection List DYNEX Technologies Inc 7 2 Viewing Measurement Results 7 3 Viewing Measurement Results in the Result Viewer Measurement results accessed from the Results Selection List are viewed in the Result Viewer Figure 7 2 Results are displayed in a series of tabs The tabs displayed depend on the measurement type s configured in the protocol for example reduced data is not displayed when data reduction is not configured Results may also be printed saved or exported to a Microsoft Excel spreadsheet using the Result Viewer actions Results calculated using data reduction may be reevaluated by editing data reduction
156. lect Check if plate is inserted before each read to sense if a microplate is in the plate carrier before starting each measurement 2 3 3 4 Excitation and Emission Filter Slide Control Excitation Filter Slide Control and Emission Filter Slide Control are used to manually eject or load the excitation or emission filter slides To manually eject or load the excitation or emission filter slide e Choose Eject from the desired filter slide control section to unload the filter slide from the filter compartment and partially open the compartment door Note To remove the filter slide it is still necessary to grasp it by the tab and pull it until it is free of the geared track Store the removed filter slide in a protected dust free area preferably in the original packaging e Choose Load from the desired filter slide control section to retract the filter slide into position Concert TRIAD Series Software User s Manual Setting Up and Using Signet 3 1 Overview To assist users in complying with electronic signature regulations such as 21 CFR Part 11 the optional Concert TRIAD Series Analysis Software with Signet module may be purchased separately When Signet is enabled for Concert TRIAD Series Software users must have a valid user account and password on the system to access the software Each user is assigned roles that contain specific permissions which determine the software actions the user may perform Signet provid
157. lter Properties Wavelength 485 R Technique s Fluorescence Remove Slide Name 485 i Bandwidth 20 Export Slides Properties of Installed Yes selected filter Import Slides j ie A ak Name Name of the selected filter Import Single Slide SEE omes Figure 2 4 Configuring filter properties Concert TRIAD Series Software User s Manual 2 10 Setting Up and Controlling Instruments DYNEX Technologies Inc 10 11 12 In Wavelength enter the wavelength of the filter Click in the Technique s field and then click the down arrow to display a list of the available detection techniques Select all techniques for which the filter applies The filter can be used only for measurements of the selected technique type s When techniques are selected the read only Installed field displays Yes When No is displayed no techniques are selected and the filter may not be used in any techniques gt TRIAD Select Polarization only for filter positions where a polarization filter is installed In Name enter a name for the selected filter Filter names default to the wavelength entered but may be renamed as desired In Bandwidth enter the bandwidth in nanometers of the selected filter Repeat steps 6 to 11 to configure additional filters on the slide 2 3 2 3 Removing Filter Slides If a filter slide is no longer used with an instrument it can be removed from Concert TRIAD Serie
158. mber is out of valid range 0 15 Contact a DYNEX Technologies Service Engineer 441 LED not initialized Contact a DY NEX Technologies Service Engineer 442 The LED is not powered Contact a DYNEX Technologies Service Engineer 443 The LED has exceeded maximum allowed power consumption Contact a DYNEX Technologies Service Engineer 444 LED power is low Contact a DY NEX Technologies Service Engineer 445 LED power overflow Contact a DY NEX Technologies Service Engineer DYNEX Technologies Inc Appendix C Software Error Codes C 5 Table C 1 Software Error Codes and Solutions Error Error Message Recommended Solution Code 446 No LED installed Contact a DYNEX Technologies Service Engineer 450 No temperature installed Check instrument configuration 451 Temperature setpoint exceeds maximum valid Decrease the temperature setting refer to setpoint Section 2 3 3 1 Temperature Control TRIAD only 452 Temperature sensor is not responding Check the current temperature setting refer to Section 2 3 3 1 Temperature Control TRIAD only 453 Temperature sensor not found Decrease the temperature setting refer to Section 2 3 3 1 Temperature Control TRIAD only Concert TRIAD Series Software User s Manual index A absorbance detection methods configuring 4 6 selecting type 4 5 Account
159. n Top 3 4 2005 4 00 PM Creating Detection Method Fluorescein Top 3 4 2005 3 58 PM Deleting Method Polarization 485 3 4 2005 3 55 PM Saving Detection Method Fluorescence Intensity bottom 3 4 2005 3 55 PM Creating Detection Method Fluorescence Intensity bottom 3 4 2005 3 53 PM Saving Detection Method Fluorescence Intensity top 3 4 2005 3 53 PM Creating Detection Method Fluorescence Intensity top 3 4 2005 3 31 PM Saving Detection Method Abs260 3 4 2005 3 31 PM Deleting Method Abs260 3 4 2005 3 31 PM Editing Detection Method Abs260 3 4 2005 2 13 PM Deleting Labware Copy of WeberS6deep 3 4 2005 2 13 PM Editing Labware WeberS6deepMax 3 4 2005 2 12 PM Copying Labware from WeberS6deep to Copy of WeberS6deep 3 4 2005 11 14 AM Imorting Labware weberS6deep 3 4 2005 9 49 4M Optimizing Labware Weber96clear Lot Lot 2005 03 04T09 49 49 3 4 2005 9 49 4M Signing Labware with Index 9 and Version 1 3 4 2005 9 49 4M Deleting Labware Copy of WeberS6deep 3 4 2005 9 49 4M Editing Labware Weber96clear of gt m Search criteria Close Export Date from l 32 5 2004 x to 3 5 2005 z Figure 3 11 Viewing records in the Audit Viewer Concert TRIAD Series Software User s Manual 3 16 Setting Up and Using Signet DYNEX Technologies Inc 3 In Audit Viewer perform the action desired Table 3 3 describes the actions available Table 3 3 Audit Log Actions Action Description Close Close the Audit Viewer
160. n Transformation is configured in the protocol refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only Note Transformation is the default name for transformation formulas If a different name is entered in Transformation that name appears in Base refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only In Y Axis select the Type of scale for the Y Axis linear or logarithmic Note Type is not available when configuring a four parameter fit curve In X Axis enter a Name for the axis if desired In X Axis select the Type of scale for the X Axis linear or logarithmic Note Type is not available when configuring a four parameter fit curve Choose Report Options and select the concentration information and data included in printouts e Definition curve type parameters and statistics such as intercept and slope e Graph the standard curve Print in Matrix the transformed result calculated for each sample appears in a measurement results matrix corresponding to the plate layout Print in List the transformed result calculated for each sample appears in a list of measurement results e Print Status status indicating whether or not the well was read successfully In Graph Preview select the type of graph Standard Curve Values Increasing or Standard Curve Values D
161. n an account is automatically disabled Administrator Notification appears Figure 3 9 The administrator password must be entered before Concert TRIAD Series Software may be accessed by users Administrator Notification Account Berkeley Berkeley Rattan was disabled because of too many failed login attempts Please enter the administrative password to dismiss this dialog Figure 3 9 Administrator Notification Concert TRIAD Series Software User s Manual 3 14 Setting Up and Using Signet 3 4 2 Changing the Password of the User Currently Logged Into the System The user currently logged into the system may change their password To change the password 1 In the navigation pane choose Users to access the User Selection List if necessary 2 From the toolbar choose Change password of user currently logged in mA Change Password appears Figure 3 10 OR From the Actions menu choose Change password of user currently logged in OR Right click in the User Selection List and choose Change password of user currently logged in from the menu Change Password Please enter the new password Stok Please enter the new password again for confirmation iaa cm Figure 3 10 Changing the user password 3 In the upper field enter the new password desired 4 In the lower field re enter the new password to confirm 5 Choose OK to change the password OR Choose Cancel to close Change Password w
162. nce parameters 1 Enter a Method Name Figure 4 9 2 Select the Excitation Filter nm 3 Select the Emission Filter nm Note The filters available are those installed on the excitation and emission filter slides loaded in the instrument and configured for time resolved fluorescence techniques in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides DYNEX Technologies Inc Creating and Editing Detection Methods 4 13 4 In LED on Time seconds enter the length of time in seconds that the LED light source remains turned on 5 In Number of Pulses enter the number of excitation measurement cycles performed in the measurement The number of pulses sets the exposure received by samples during measurements 6 In Delay Before Measure Seconds enter the interval in seconds between switching off the light source and performing the measurement The delay may be set within the range of 0 000001 to 0 0075 of a second 7 In Integration Time seconds enter the length of time in seconds each sample is measured The integration time may be set within the range of 0 00005 to 0 0075 of a second 8 Choose Save to save the new time resolved fluorescence detection method The new method appears in the Detection Method Selection List OR Choose Back to select a different Method Technique refer to Section 4 2 1 Selecting a Method Technique OR Choose Cancel to close the Method
163. ng a measurement To load the plate carrier 1 In the Instrument Selection List select the desired instrument Figure 2 1 2 From the toolbar choose Load the plate carrier OR From the Actions menu choose Load the plate carrier OR Right click on the desired instrument and choose Load the plate carrier from the menu that appears Concert TRIAD Series Software User s Manual 2 4 Setting Up and Controlling Instruments DYNEX Technologies Inc 2 2 3 Initializing the Instrument Initializing the instrument moves the optics and microplate transports to home positions The instrument is initialized automatically each time it turned on If necessary the instrument may be initialized manually for example after an emergency stop has been performed refer to the TRIAD Series Multimode Detector User s Manual Section 1 3 1 1 Performing an Emergency Stop Note When a hardware error occurs turning the instrument off and on is the recommended initialization method To manually initialize the instrument 1 In the Instrument Selection List select the desired instrument Figure 2 1 2 From the toolbar choose Initialize the instrument OR From the Actions menu choose Initialize the instrument OR Right click on the desired instrument and choose Initialize the instrument from the menu that appears 2 2 4 Connecting to the Instrument When started Concert TRIAD Series Software automatically establishes commun
164. ng an absorbance method choose Next to select the Method Type refer to Section 4 2 2 Selecting the Method Type OR If defining a luminescence or fluorescence method choose Next to define Method Parameters refer to Section 4 2 3 Defining Method Parameters OR Choose Cancel to close the Method Editor without defining a new detection method DYNEX Technologies Inc Creating and Editing Detection Methods 4 5 4 2 2 Selecting the Method Type When defining an absorbance detection method use Method Type to select whether a monochromatic or bichromatic method will be defined Figure 4 3 Monochromatic methods perform a single wavelength measurement Bichromatic methods perform a second measurement at a reference wavelength which is subtracted from the first to calculate the final result Note Method Type appears only when defining absorbance methods a Method Editor Method Type Method Technique Method Type gt Method Type Monochromatic v Method Parameters Figure 4 3 Selecting an absorbance Method Type To select a method type 1 In Method Type choose the desired method Monochromatic or Bichromatic 2 Choose Next to define Method Parameters refer to Section 4 2 3 Defining Method Parameters OR Choose Back to select a different Method Technique refer to Section 4 2 1 Selecting a Method Technique OR Choose Cancel to close the Method Editor without defining a new detection method
165. ng communications settings eee eeee ese este ceeeceeeeeeaeeceaeeeseeseeeeeaeeeaeens 1 15 Figure 1 10 Configuring Software Settings ces eeecceesseecssececeeceeeseeeesaeceesaeeeenaeceeaeceeaeeeeas 1 16 Figure 1 11 Configuring Print Settings ssori irupen riis aas 1 17 Figure 1 12 Choosing the Simulated Data files eee eeeeeeeneeceeeeeeeeeaeeceaeeeseeeeeeeeaeeenaeens 1 18 Figure 1 13 Choosing the directory where data is saved 0 eeeesseesseceeeesececeaeeeteeseeeesneeenaeens 1 19 Figure 2 1 Instrument Selection List recccsscesnaycacessnecsacedvarzeaconanansievtecechonnseabapredaceeaeaneeveeceaanegie 2 2 Figure 2 2 Instrument Settings Basic Settings sesssssesssessessseresstessressresseeeseeessseessresseesses 2 7 Figure 2 3 Instrument Settings Filter Slides c ssicscecccissscenctivceecresecesieeeseenuicaiasegscnse 2 8 Figure 2 4 Configuring filter properties ceesccessceceenceceseeeceeeeeceeneececeeceeeeeceeeeeseeesseeeenaees 2 9 Figure 2 5 Instrument Settings Manual Control 00 cece eeeceeeeeesseceeeeeeeeeeaeeceaeceeeeseeesaeenes 2 12 Fig r 3 1 Accou t IVigMa BORIC sssini iiini n a i 3 2 Fig re 3 2 Support OPtiONS sacar eh tec catcti te deedeacseezeseeed cee tiied ceeded cede gh ceneebiadSeuua kik ssia iiaii 3 4 Figure 3 3 Account Management srasni a ernie E AEE A E aS 3 6 Figure 3 4 Configuring roles ss ssnssessseseseeessseesseessesrseeessretsstessesseeesseesstesstesseeeseeessseessees
166. ngs A Layout Selection Settings Reading Direction Settings Technique Type Labware Selection Select the reading drection of the plate below To read a plate row by row select Read by row To read a plate a column by column select Read by column To read well by well select Read by well The well by well reading Layout Settings gt method reads an entire well before moving on to the next well which can be useful for scan and fast kinetic Method Selection measurements Variables Transformation Concentration Read by row pa Read by Column alidation Read E arcaiumn Available for all measurement techniques except absorbance Output Settings Read by well Figure 6 8 Selecting how wells on the plate are read 2 Select the desired reading direction e Read by row reads plates row by row e Read by column reads plates column by column Available for all measurement techniques except absorbance e Read by well reads each well individually before reading the next well which is useful for kinetic and scan measurements DYNEX Technologies Inc Creating Protocols 6 15 6 2 5 Configuring Detection and Preparation Methods Use Method Selection to select and configure detection and preparation methods Figure 6 9 Two configuration modes are available e Basic Select to configure protocols requiring a single detection method only Single point kinetic and scan measurement types are supp
167. not provide adequate support to comply with 21 CFR Part 11 or other regulations Each site must evaluate the level of support required for a given system Signet with password checks for signing and check in Enables the use of user accounts and permissions and electronic signatures for Concert TRIAD Series Software Users must log in to use the software and may access only features and operations for which they have permission Support for 21 CFR Part 11 or other regulations is provided by requiring password checks for operations such as signing a detection method Note When other applications that support Signet are installed on the system each must be configured with the same support level as Concert TRIAD Series Software Note Regulations such as 21 CFR Part 11 contain additional requirements for account management beyond the control of this software Choose OK to activate the support level chosen and close Support Options OR Choose Cancel to close Support Options without changing the support level Setting Up and Using Signet 3 5 3 3 Performing System Administration Tasks On a system with Signet enabled a single administrator account provides the ability to perform Signet system administration tasks including e Administering User Accounts and Roles Section 3 3 1 e Restoring the Administrator Password Section 3 3 2 e Viewing the System Activity Audit Log Section 3 3 3 3 3 1 Admin
168. nt Results are Saved 04 1 19 Concert TRIAD Series Software User s Manual viii 2 Setting Up and Controlling Instruments 2 1 OVErViEW lt isa enag die one te eve eh eer eee eee ee E ye eR 2 1 2 2 Controlling Instrument Actions 0 0 00 c eee eee ene 2 3 22 1 Ejecting the Plate Carrier i224 4duc45 24665058 84S oie eee 24K ee 2 3 222 Loading the Plate Carrilet osese so desde ye ted ed ee eevee abe eee 2 3 2 2 3 Initializing the Instrument 44 3 44 44 400424 9404 94 480 eanad reales 2 4 2 2 4 Connecting to the Instrument 0 0 cee eee eee 2 4 2 2 Enabling Simulation Mode 006 006 00ecn eee eneecnneees 2 5 2 3 Configuring Instrument Settings nunnu ununa enea 2 6 2al Configuring Basic Instrument Settings 000 2 7 2 3 2 Defining and Editing Filter Slides 000 2 8 2 3 2 1 Adding Filter Slides 2222 lt ie bacevaieedias conve 2 9 2 3 2 2 Configuring Filter Slides 00 2 9 2 3 2 3 Removing Filter Sldes 3 4 6 c5s lt s bee nnana 2 10 2 3 2 4 Exporting and Importing All Filter Slide Configurations senasa god eaSeecadd caSees 2 11 2 3 2 5 Exporting and Importing Individual Filter Slide Configurations 4 5 4s0s0esee00ee e008 2 11 2 3 3 Manually Controlling the Instrument nnna nananana 2 12 2 3 3 1 Temperature Control TRIAD only 2 12 23 93 22 Spake CONG ssessserrocent
169. nual 6 46 Creating Protocols 6 3 Running Protocols Saved protocols may be accessed and run at any time either on an instrument or in simulation mode The run options available are different for each mode For more information refer to e Running a Protocol on an Instrument Section 6 3 1 e Running a Protocol When Simulation Mode is Enabled Section 6 3 2 6 3 1 Running a Protocol on an Instrument Running a protocol on an instrument performs measurements on samples and outputs results data following the parameters configured in the protocol To run a protocol on an instrument 1 In the Protocol Selection List select the protocol to run 2 From the toolbar choose Run the selected protocol Prepare to Run appears Figure 6 30 Note When running an Analysis protocol with variables configured Variables appears as the first screen in Run Protocol Change the values of the variables if desired and choose Next to continue Prepare to Run appears OR From the Actions menu choose Run the selected protocol OR Right click on the selected protocol and choose Run the selected protocol from the menu 5 Run Protocol Basic TRF Europium 96 Prepare to Run Prepare to Run Click Run to run the protocol Run Protocol Result Name 20050313 173940 Select Plate Orientation Eject Plate Carrier Sb Landscape Optimized Portrait Close Plate Carrier K Opposite Landscape Opposite Portrait Run the s
170. of points measured in Method Properties click in Scan Points and choose the configuration button Scan Selection Editor appears Figure 6 12 Scan Selection Editor Select the scan resolution and measurement points to read The type of linear scan that may be configured is determined by which reading direction is configured in Layout Settings When ntal linear scan may be configured When Read by cg Resolution mm b may be configured When Read by well is selected oi d Resolution mm Selected Scan Points Points x 14 Points Y 14 boundary Measurement points Click and drag until the desired number of points is selected OK Cancel Figure 6 12 Configuring an area scan 3 In Resolution mm use the up and down arrows to choose the proximity of measurement points Choosing a smaller value increases the number of measurement points available choosing a larger value decreases the number of points available Available resolutions are determined by the type of labware DYNEX Technologies Inc Creating Protocols 6 21 selected for use in the protocol Refer to Sections 6 2 3 Selecting the Labware Type Used in the Protocol and 6 2 4 Configuring Labware Layout Settings for more information 4 To configure an area scan click anywhere inside the well boundary except the center row and drag until the desired number of measurement points is selected Figure 6 12 OR
171. on General Settings Choose a curve fitting method and configure response Formulas and concentrations as desired Technique Type Labware Selection Layout Settings Y Axis m X Axis Method Selection Curve Type LinearRegression zl Variables DEn oN Eain E fe xi Base Transformation Name Concentration i m linear flo jarithmic z Transformation Extrapolation p gt Type Type g Cutoff Graph Preview Graph Setup Validation port Op validation Standard Curve Preview Output Settings Standard Curve Values Increasing X Click on a point to view the X and Y values for that point Trarsformation e N U Ao OA SY Ow Y istp3 Displayed X and Y values may be edited Figure 6 23 Configuring concentration parameters To configure a standard curve and standards 1 Select a Curve Type Point to Point Linear Regression Cubic Spline or Four Parameter Fit Refer to Table 6 1 more information about curve fitting methods Concert TRIAD Series Software User s Manual 6 34 Creating Protocols Table 6 1 Curve Fitting Methods Method Description Example Linear Regression Construction of a straight line using the least squares method with the highest possible Linear regression approximation to all standard points Requires a minimum of 2 standard points Point to Point A Direct connection of all standard points Point to Point Requires
172. on Variables Data Concentration Layout View ist View Parameters Edit View transformed measurement results or edit the transformation formula if reevaluating the results is desired Cutoff Result List Validation M show Status Iv show Well Identifier a a S Gia e 1 52 53 54 144 20 482 61 348 14 994 Navigation 482 61 348 149 S12 513 Si4 36 554 77 616 17 444 OK OK OK S22 523 524 0 1 47 52 724 OK OK OK 532 533 534 22 736 22 148 5 88 OK OK OK 54 544 53 704 7 938 OK OK 552 Figure 7 14 Viewing existing transformation parameters in the Results Viewer DYNEX Technologies Inc Viewing Measurement Results Toate 2 Choose the tab desired to view Table 7 3 describes each tab and lists which analysis options display the tab Table 7 3 Measurement Results Tabs Displayed for Analysis Options Tab Description Appears In Layout View Displays transformed results and measurement status Transformation for the selected analysis option in a matrix Concentration corresponding to the plate layout Cutoff Note Results may be rejected as outliers in any Layout View tab To reject a result right click on the desired sample and choose Reject Well Results may be reevaluated with outliers removed List View Displays transformed results and measurement status Transformation for the selected analysis option in a list Concentration Cutoff Standard Curve Displays a graph
173. on 1 3 3 Note The installation procedure varies depending on the operating system in use on the target system Follow the instructions in the appropriate section to install the software e Installing Optional Modules Section 1 3 4 1 3 1 Meeting System Requirements To install and use the software successfully the host computer must meet the minimum system requirements listed in Table 1 1 Where relevant Table 1 1 also lists recommended specifications Table 1 1 Host Computer System Requirements Component Minimum Requirements CPU Pentium II 300 Mhz RAM 128 MB minimum 256 MB recommended Hard Drive 300 MB free space CD ROM Drive 4X Monitor 800x600 resolution Keyboard 101 key Mouse IBM compatible Serial Port 1 free serial port Operating Systems Windows NT 4 Service Pack 6a Windows 2000 Service Pack 1 Windows XP Service Pack 1 DYNEX Technologies Inc Installing Setting Up and Using the Software 1 7 Table 1 1 Host Computer System Requirements Component Minimum Requirements Operating System Language English U S Database Microsoft SQL Server 8 0 Personal Edition included on the installation CD Note The storage limit for SQL Server Personal Edition is 2GB Contact DYNEX Technologies Sales or Customer Technical Support if more storage is required Web Browser Internet Explorer 6 0 or later included on the installation CD
174. on 2 3 1 e Defining and Editing Filter Slides Section 2 3 2 e Manually Controlling the Instrument Section 2 3 3 DYNEX Technologies Inc Setting Up and Controlling Instruments 2 7 2 3 1 Configuring Basic Instrument Settings The Basic Settings tab Figure 2 2 contains information about the connection from the instrument to the operating computer as well as identifying information about the instrument The Port and Baudrate must be configured correctly to enable Concert TRIAD Series Software to communicate with the instrument ap Instrument Settings Basic Settings Filter Slides Manual Control Communication Settings 9 Instrument Port com information fields Baudrate 38400 Instrument Name fT RIAD Serial Number 0004 Instrument Type 123 Firmware Version V1 0 01 13 2005 Features PIC Fw Version V1 0 18 06 04 Cancel Apply Figure 2 2 Instrument Settings Basic Settings To configure basic instrument settings 1 In Instrument Settings choose the Basic Settings tab if necessary 2 In Port select the serial communications port on the host computer that connects to the instrument 3 In Baudrate select 38400 4 Choose Apply to detect the instrument When the instrument is detected the instrument information fields are autopopulated with information about the connected instrument Refer to Table 2 1 for more information about each field
175. on and data included in printouts Definition the basis for measurement group names and cutoff values and or formulas configured e Print in Matrix the cutoff group classification for each sample appears in a measurement results matrix corresponding to the plate layout e Print in List the cutoff group classification for each sample appears in a list of measurement results e Print Status status indicating whether or not the well was read successfully Concert TRIAD Series Software User s Manual 6 40 Creating Protocols 6 2 10 Configuring Validation Rules Concert TRIAD Series Analysis Software only Use Validation to configure up to ten validation rules Figure 6 27 Protocol runs that do not meet the conditions specified in the rules are invalidated Note Validation is available for configuration only when selected in General Settings refer to Section 6 2 1 Configuring General Settings a Create Protocol Kinetic 340 Validation General Settings Configure up to 10 validation rules Technique Type Labware Selection Layout Settings Number of formulas 2 Se Report Options Method Selection pj Validation Rules Basis of Evaluation Rule Variables Transformation Concentration Measurement pi gt 1 andp2 gt 2 Cutoff si Concentration v stdi gt 4 Output Settings Figure 6 27 Configuring validation rules DYNEX Technologies Inc Creating Protocols
176. on formula To configure a transformation formula 1 In X enter the desired transformation formula Refer to Appendix B Mathematical Operators and Functions for detailed information about mathematical operators supported by the software 2 In Name of X enter a new name for the transformation formula if desired The name appears in printed reports and in protocol configuration screens where a basis for evaluation must be selected DYNEX Technologies Inc Creating Protocols 6 33 3 Choose Report Options and select the transformation information included in printouts e Definition the transformation formula and name are listed Print in Matrix the transformed result calculated for each sample appears in a measurement results matrix corresponding to the plate layout e Print in List the transformed result calculated for each sample appears in a list of measurement results e Print Status status indicating whether or not the well was read successfully 6 2 8 Configuring Concentration Concert TRIAD Series Analysis Software only Use Concentration to choose a curve fitting method preview the standard curve and configure concentration and response formulas for standards Figure 6 23 Note Concentration is available for configuration only when selected in General Settings refer to Section 6 2 1 Configuring General Settings up Edit Protocol Kinetic 340 8 cycle Concentrati
177. oncert TRIAD Series Software installed on another system Default labware installed with Concert TRIAD Series Software is present on all systems and may not be edited deleted or overwritten For this reason importing default labware from an XML export file is not permitted Note When Signet is enabled signed labware may be exported for use on another system however electronic signatures are not retained which allows labware to be edited when imported to another system Because signed labware may not be deleted or overwritten importing signed labware into the system from which it was originally exported is not permitted To export labware 1 In the Labware Selection List select the labware to export 2 From the File menu choose Export gt Labware Browse for Folder appears Figure 5 12 Browse For Folder Desktop B My Documents 4 This Computer a My Network Places Recycle Bin Exported Protocols Figure 5 12 Choosing the folder where exported labware will be saved 3 In Browse for Folder browse to the folder where the exported labware will be saved OR Choose Make New Folder to create a new folder where the exported labware will be saved Concert TRIAD Series Software User s Manual 5 22 Creating and Editing Labware 4 Choose OK to export the labware The exported labware is saved using the default file name format Labware__LabwareName xml In order to import t
178. onding to the plate layout Available for single point measurements only e Graph kinetic or scan graphs of results for all measured samples Available for kinetic and scan measurements only e Raw Data results from each kinetic cycle or scan point Available for kinetic and scan measurements only e Print Status status indicating whether or not the well was read successfully 6 Select Shake before read to shake the microplate before the performing measurements in a protocol run In kinetic measurements the plate is shaken for the specified intensity and interval before each measurement cycle Shake Info appears Figure 6 10 CAUTION Shake low density plates such as 6 or 48 well plates at low AN speed only Shaking low density plates at higher speeds may cause liquid in wells to spill 7 In Shake Info select the desired Shake Intensity Low Medium or High 8 Enter the desired Shake Interval in seconds 1 60 9 Select the desired Shake Mode e Linear shakes from side to side e Orbital shakes labware in a circular pattern e Squared shakes labware in a square pattern moving at right angles Concert TRIAD Series Software User s Manual 6 18 Creating Protocols 10 When the detection method is configured as desired choose Next to configure how measurement results are saved and or printed refer to Section 6 2 11 Configuring Output Settings OR Choose Back to configure the plate
179. onfigured in advanced mode To select and configure a method in advanced mode 1 In Method Selection choose the Advanced tab to toggle from basic mode if necessary Advanced mode configuration parameters appear Figure 6 15 Note Refer to Section 6 2 5 1 Configuring a Method in Basic Mode to configure a protocol requiring only a single detection method a Create Protocol NewProtocol3 Method Properties General Settings Method Selection View and edit properties for the Technique Type Add remove and rearrange sequence selected measurement Labware Selection methods in the sequence type or selected method Layout Settings Method Selection gt Variables Method Selection Method Properties Transformation A Sequence ExcitationFilber Concentration q Cutoff Validation Output Settings ExcitationFilter Excitation Filter nm Figure 6 15 Configuring a method in advanced mode Concert TRIAD Series Software User s Manual 6 24 Creating Protocols 2 To add an existing detection method choose Add a method to this protocol L select a measurement type Add Method single point Add Kinetic or Add Scan and then select a detection method Figure 6 16 Only detection methods compatible with the selected measurement and technique types are listed in the menu OR Right click in Method Selection select a measurement type Add Method single point Add Kinetic or
180. ons Unary negation operator indicating the negative value of a numeric expression Concert TRIAD Series Software User s Manual B 2 Appendix B Mathematical Operators and Functions Table B 1 Mathematical and Logical Operators Operator Description AND Logical AND operator Performs a logical conjunction on two expressions NOT Logical NOT operator Performs logical negation on an expression OR Logical OR operator Performs logical disjunction on two expressions Table B 2 Mathematical Functions Function Description abs number Returns the absolute value of a number acos number Returns the arccosine of a number asin number Returns the arcsine of a number atan number Returns the arctangent of a number cos number Returns the cosine of a number exp number Returns e the base of natural logarithms raised to a power log number Returns the natural logarithm of a number max num1 num2 Returns the greater of two supplied numeric expressions min num1 num2 Returns the lesser of two supplied numeric expressions pow base exponent Returns the value of a base expression taken to a specified power sin number Returns the sine of a number sqrt number Returns the square root of a number tan number Returns the tangent of a number DYNEX Technologies Inc C 1 Codes Appendix
181. ons and logical operators Refer to Appendix B Mathematical Operators and Functions for a complete list of supported operators and functions Table 6 2 Example test validation formulas Application Validation Formula The results from a protocol run are valid only if the mean absorption value of the P2 lt 0 8 positive control well s P2 is less than or 7 equal to 0 8 OD The results from a protocol run are valid only if both controls are within the linear 0 1 lt C1 AND C1 lt 3 0 AND 0 1 lt C2 AND C2 lt 3 0 range of the instrument 4 Repeat steps 2 and 3 for any additional formulas 5 Choose Report Options and select Definition to include the validation configuration and state pass fail for all rules in printouts Concert TRIAD Series Software User s Manual 6 42 Creating Protocols 6 2 11 Configuring Output Settings Use Output Settings to specify which measurement result export view and print actions are performed automatically when a protocol run completes Figure 6 28 An external software application such as a notification utility may also be configured to execute when a run completes Create Protocol Kinetic 340 Output Settings General Settings Select data output and printer options Technique Type Labware Selection Layout Settings Bx Export to Microsoft Excel M Perform after completing measurement s Method Selection M Perform after completing measurement s
182. or all measured samples Available for kinetic and scan measurements only e Raw Data results from each kinetic cycle or scan point Available when kinetic measurements scan measurements or multiple detection methods are configured in the sequence e Print Status status indicating whether or not the well was read successfully Concert TRIAD Series Software User s Manual 6 28 Creating Protocols 6 2 5 2 1 Configuring a Shake Preparation Method A Shake preparation method may be placed in the desired location in the sequence or attached to a kinetic measurement when interval shaking between each measurement cycle is desired To configure a Shake preparation method 1 In Method Selection choose the desired Shake preparation method Method Properties for the selected method appear Figure 6 19 a Create Protocol NewProtocol3 Method Selection General Settings Select a method and A Shake preparation method eek ona placed in the sequence between Lab Selecti e PATRE other methods is performed Layout Settings E Basc Advanced once during a protocol run Variables Method Selection Method Properties Transformation Cornceniration fae Shake Intensity Medium Shake lt q 44 J4 Shake Interval 5 Cutoff ABS 340 Shake Mode Linear Validation Kinetic Output Settings Abs405 A shake preparation method attached to a kinetic method is performed before each kinetic measurement cycle L
183. or performing other system administration tasks The administrator password is changed in the Account Management application To access Account Management and change the administrator password 1 Install the Concert TRIAD Series Analysis Software with Signet module if necessary refer to Section 1 3 4 Installing Optional Modules 2 When the module installation is complete from the Start menu choose Settings gt Control Panel Control Panel appears 3 In Control Panel choose Administrative Tools 4 In Administrative Tools choose Account Management Administrator Login appears 5 In Administrator Login enter password the default administrator password Account Management appears Figure 3 1 s Account Management EA Accounts di Roles Gv Settings E Repositories Audit General Options Automatica Choose Settings to access fle F minute s d Admin Password options H Failed attempts to log into that account C User passwords must be changed every F 0 gt day s Password alidation Users cannot reuse the last i password s C Users cannot reuse any passwords in the last f 0 day s ee Choose or press F1 C The Admin password must be changed every F 0 2 day s to access online help Set Admin Password Project Actess Choose Set Admin Password to change the password Figure 3 1 Account Management Setting Up and Using Signet 3 3
184. orted Microplate shaking may be configured if desired refer to Section 6 2 5 1 Configuring a Method in Basic Mode Advanced Select to configure protocols requiring multiple detection methods such as a multiwavelength absorbance measurement Detection methods and preparation methods such as microplate shaking are arranged as desired in a linear execution sequence refer to Section 6 2 5 2 Configuring a Method in Advanced Mode up Edit Protocol FloTopKinetic 12 cycle Method Selection General Settings Select a method and method type Technique Type Labware Selection Layout Settings Basi Method Selection gt a Advanced Variables Method Selection Method Properties i inetic Cycles Transformation Fl top535 625 Ki i yi Concentration 9 Kinetic Interval Type Data Reduction Cutoff validation C Single Point Output Settings Kinetic Kinetic Cycles Choose the number of measurement cycles to perform C Scan IV Shake before read sbeke Info Shake Intensity Medium Shake Interval 5 Shake Mode Linear Shake Intensity The intensity of the shaking operation Figure 6 9 Configuring a detection method in Method Selection Concert TRIAD Series Software User s Manual 6 16 Creating Protocols 6 2 5 1 Configuring a Method in Basic Mode Configuring a method in basic mode includes selecting a detection method and configuring properties for a kinetic or
185. parameters or selecting a different method gt Result Viewer 2005031 Ctos asain oon Result Viewer actions View measurement results and graphs in the tabs below Raw data Reduced Data Graphs Edit ABS 450 Figure 7 2 Viewing results of an area scan measurement This section covers Result Viewer functionality provided in the Data screen which is displayed for basic and analysis applications including Viewing Raw Data Section 7 2 1 Viewing Reduced Data Section 7 2 2 Viewing Mean Data Section 7 2 3 Viewing Graphs Section 7 2 4 Recalculating Data Reduction Section 7 2 5 Exporting Measurement Results to Microsoft Excel Section 7 2 6 Saving Measurement Results Section 7 2 7 Note When the optional Concert TRIAD Series Analysis Software module is installed the Result Viewer also displays transformed measurement results for analysis options configured in the protocol refer to Section 7 3 Viewing and Reevaluating Results from an Analysis Application Concert TRIAD Series Software User s Manual 7 4 Viewing Measurement Results 7 2 1 Viewing Raw Data The Raw Data tab displays all data measured during the protocol run Figure 7 3 Depending on the measurement type s configured in the protocol the left pane lists all detection methods measurement cycles or wells in a tree view Selecting a method cycle or well displays measured values and sta
186. r Regression Min Correlation enter the minimum correlation percentage value for the test to be valid Concert TRIAD Series Software User s Manual 6 38 Creating Protocols 6 2 9 Configuring Cutoff Values Concert TRIAD Series Analysis Software only Use Cutoff to configure qualitative evaluations that classify measured samples into groups according to defined cutoff formulas or values Figure 6 26 Up to ten groups may be configured Note Cutoff is available for configuration only when selected in General Settings refer to Section 6 2 1 Configuring General Settings Sp Edit Protocol Kinetic 340 12 cycle temp 35 General Settings Cutoff configures qualitative evaluations that classify measured samples according to defined cutoff values Up to ten Technique Type groups of samples may be classified using cutoff formulas Groups are separated by the cutoff Formulas Labware Selection Sapt STATS Basis of Evaluation Measurement Meeieilers Method Selection Number of groups 3 Variables eden Transformation Groups and Cutoff Formulas Name Concentration Cutoff gt Group 3 High Max Value Cutoff Formulas Values Validation B60 Output Settings Group 2 deal B20 0 Group 1 flow Figure 6 26 Configuring cutoff values DYNEX Technologies Inc Creating Protocols 6 39 To configure cutoff groups and formulas 1 Choose the Basis of Evaluation e Measurement the reduced data
187. r this instrument only OR Select the read height manually e Default uses the read height defined in Labware Information for the labware type used in the protocol refer to Section 5 2 1 Defining Labware Information Maximum sets the read height at 11 mm the maximum height supported by the instrument e Set Value manually sets the reading height using the adjacent configuration field Setting the reading height manually is useful when the height determined by a prior optimization for the same labware type is known Choose Run to start the protocol run OR Choose Cancel to close Run Protocol without running the protocol Concert TRIAD Series Software User s Manual 6 48 Creating Protocols 6 3 1 1 Optimizing Read Height TRIAD only The TRIAD features an objective lens that may be moved up and down to optimize the read height used in luminescence fluorescence intensity top fluorescence polarization and time resolved fluorescence protocols Read height is the distance between the top surface of the microplate being read and the lower surface of the objective lens Optimizing read height matches the focus of the optics with the sample volume This maximizes the raw signal which yields the highest precision and maximum sensitivity Read height is optimized using the Read Height Optimization Wizard Figure 6 31 A single sample with a known maximum signal is placed on the same type of microplate
188. rameters configured in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides DYNEX Technologies Inc Appendix C Software Error Codes C 3 Table C 1 Software Error Codes and Solutions Error Error Message Recommended Solution Code 62 LED energy too low Make sure the correct filter slides are installed in the instrument and check filter parameters configured in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides 63 No LED for selected filter installed Contact a DYNEX Technologies Service Engineer 64 ADC gain cannot be maintained Contact a DYNEX Technologies Service Engineer 65 LED gain setting failed Contact a DYNEX Technologies Service Engineer 66 ADC gain fluctuated during measurement Run the measurement again correction of PMT counts is not possible Try measurement again 67 Reference ADC too high for valid Make sure the filter compartment and luminescence measurement microplate chamber doors are closed 68 PMT dark counts exceed valid range for Make sure the filter compartment and measurement Check threshold or ensure that microplate chamber doors are closed flaps are closed 69 Reference ADC LED too low retry Run the measurement again measurement 140 Command canceled Aborted by user N A 141 Measurement time exceeds limit for current Use a shorter measurement time in t
189. re 7 19 Viewing reduced data excerpt iiscacsvsscvsecesndantsdcensasanatienssederescedeadeos Mgaedsansteeaseneeces 7 22 Figure 7 20 Confirming the deletion of measurement results ee eeeceeeeeeceesteeeetteeeenseeeenee 7 24 Figure 7 21 Previewing a measurement results printout 0 sees eeeecseeceeeeeseeeeseecsaeenseesees 7 25 Concert TRIAD Series Software User s Manual xvii List of Tables Table 1 1 Host Computer System Requirements c csssssecssssccscesssessectesnescesnenceesecenssaccoens 1 6 Table 2 1 Basic Settings Read Only Fields wisccnezsacsusvesetcedsnndswoasdants doresusdedwanenlasdaasudvedsasdsdlenscnuins 2 7 Table 3 1 Concert TRIAD Series Software Permissions s ssssesssssesesssesseesseseseesseressseessrese 3 8 Table 3 2 Concert TRIAD Series Software Default Roles eee eecceceeeceseseeeeeeeeeeeteeeenaeeens 3 8 Table 3 3 Audit Log Actions ccs aeicseasceaeRescoeesenstaiecninnietannenonea anna ances 3 16 Table 5 1 General Microplate selection guidelines ceecceceseeeceseeeceececeeeeeceeeeecseeeeseteeeenaeees 5 6 Tabl e 6 1 Cutve Fit une Methods sccasasss cnsarsaustsasnsnavensenvsndnegee eens enp EE EE EEEE EE EEEE Et 6 34 Table 6 2 Example test validation formulas ssssessnneeesseesseseseeeseeesseesseesseesseersseeesseesseesseesset 6 41 Table 6 3 Output OPOS caecis n a er rE EEE EEY 6 43 Table 7 1 Measurement Results Search Options sssssssses
190. rkeley Rattan logged off Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in Application Multimode Detection Software was set to use accounts Application Biomek Software was set to use accounts Application Multimode Detection Software was set to not require password re entry for check in and signatures Application Multimode Detection Software was set to not use accounts Application Biomek Software was set to not require password re entry for check in and signatures Application Biomek Software was set to not use accounts Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in i Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in j Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off 3 2 2005 1 42 56 PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in 3 2 2005 1 42 41 PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off 3 2 2005 10 18 24 4M Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in t Figure 3 6 Signet Audit Log 4 Choose Export to export the entire audit log to a text file if desired The exported file may be opened read and printed in any application that supports text files Note W
191. rols to load and eject labware from the instrument and to choose the orientation of the plate on the microplate carrier Figure 5 8 a Optimizing Labware Weber96deep Select a detection method Prepare Labware Insert the labware in landscape orientation into the reader The highlighted wells will be scanned to optimize Prepare the Labware gt the labware Click Next to proceed Optimize Select Center of Left Top Well EA Eject Plate Carrier S Select Plate Orientation Landscape Select Center of Left Bottom Well C Portrait Select Center of Right Top Well Select Center of Right Bottom Well Verify Well Centers C Opposite Landscape Opposite Portrait Y Close Plate Carrier Plate orientation Well A1 is highlighted in red Figure 5 8 Preparing the labware for optimization To prepare labware for optimization DYNEX Technologies Inc Choose Eject Plate Carrier to move the microplate carrier outside the instrument Fill the corner wells of the plate with identical samples To ensure accuracy samples must be appropriate for the selected detection method Sample concentration and volume must be identical in each well Place the microplate to be optimized on the plate carrier Choose Close Plate Carrier to load the microplate into the instrument In Select Plate Orientation choose the orientation of the plate on the microplate carrier The selected orientation is displayed graphically to
192. ruary 28 2005 2 06 PM None DetauttLot Manday February 28 2005 3 06 PM Monday February 28 2005 4 06 PM None Weaswement Method T Shake Type Shake Intonstty Shake Duration Measurement Method 2 Excitation Fiter nm Emession Filter arn Integration Time seconds UnitName Measurement Technique Date Creates Date Edited Shake Linear Medium 5 Fhuorescnin Top 1 08 485801 535811 1 RFU Fuuorescance intensity Top Thursday May 08 2004 12 00 AM Thursday May 08 2004 12 00 AM Matrx Legend Poston Atocation Theernatonsi Laborsiories Change page s displayed Multimode Detector Protocol International Laboratories ie Sunday March 13 2005 vrntOulUser Berkeley Rattan Definition Fluorescein Top Read 96 Matrix Legond Poston Atocation Tneernauonal Laborsiories Figure 6 38 Previewing a protocol configuration and sample layout printout 4 In Print Preview choose Print to print out the measurement results 5 In Print Preview choose Close to close the window Note Choosing Close without first choosing Print cancels the printout DYNEX Technologies Inc Creating Protocols 6 59 6 8 Exporting and Importing Protocols A protocol can be exported to an XML file which may be imported at a later time to restore the configuration saved in the file or shared with a copy of Concert TRIAD Series Software
193. rument Refer to Table 2 1 for more information about each field 7 Choose OK to close Instrument Settings Concert TRIAD Series Software User s Manual 1 16 Installing Setting Up and Using the Software 1 4 2 Configuring Software Settings Concert TRIAD Series Software can be customized using the options available in Software Settings Figure 1 10 Use the tabs in Software Settings to configure printout options default simulated data files and the directory where measurement results are stored To configure Software Settings 1 From the navigation pane choose Software Settings Software Settings appears Figure 1 10 d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 Software Settings Protocols Print Settings Simulated Data Directory Settings a Print Header Line 1 International Laboratories Line 2 Line 3 Fluorescence Intensity Top Reading r Footer Software Settings Footer International Laboratories Comment Cee at Print Options Software gt V Pri i i E S e tti n g s Print Preview Font Arial I Show printer settings Font Size 8 Figure 1 10 Configuring Software Settings 2 Configure the settings in the desired tab s e Configuring Print Settings Section 1 4 2 1 e Choosing Simulated Data Files Section 1 4 2 2 e Choosing the Directory Where Exported Measurement Results are Saved Section 1 4 2 3 DYNEX Technologie
194. rument status Figure 3 7 DYNEX Technologies Inc Setting Up and Using Signet 3 13 3 4 1 2 Logging Off the System The current user must log off the system before another user may log on Logging off automatically logs the user off all installed applications that support Signet To log off the system and close the software From the File menu choose Log out and exit Note Choosing Exit or closing Concert TRIAD Series Software does not automatically log a user out of the system The current user will remain logged on until the software is reopened and the account is logged off or until the login times out automatically Refer to the Account Management online help for more information about setting automatic logon time outs To log off the system and leave the software open for the next user 1 In the navigation pane choose Users to access the User Selection List if necessary 2 From the toolbar choose Log out current user The user is logged out of Concert TRIAD Series Software and any other supported software applications installed on the system OR From the Actions menu choose Log out current user OR Right click in the User Selection List and choose Log out current user from the menu 3 4 1 3 Handling Disabled Accounts The administrator may manually disable user accounts in Account Management or configure accounts to be automatically disabled after a number of logon attempts for the account fail Whe
195. s Administrative Tools appears 3 In Administrative Tools double click Audit Log The Audit Log appears Figure 3 6 GS Audit Log 3 5 2005 2 52 20 PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off j Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in Application Multimode Detection Software was set to use accounts Application Biomek Software was set to use accounts Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in Application Multimode Detection Software was set to not use accounts Application Biomek Software was set to mot use accounts ki Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off 3 4 2005 1 39 14 PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in 3 4 2005 1 39 03 PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off 3 4 2005 12 18 14 PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in Elie 12 me ea PM Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged off Berkeley Berkeley Rattan Account Berkeley Berkeley Rattan logged in Berkeley Berkeley Rattan Account Berkeley Be
196. s Inc Installing Setting Up and Using the Software 1 17 1 4 2 1 Configuring Print Settings Measurement results and protocol configurations may be printed Printing parameters such as headers and footers are configured in the Print Settings tab Figure 1 11 d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 Software Settings Print Settings Simulated Data Directory Settings Print Header Line 1 International Laboratories Line 2 Line 3 Fluorescence Intensity Top Reading Footer No a Software Settings Footer International Laboratories Comment Po r Print Options Instruments Print Preview Font Arial X N Show printer settings Font Size 8 v Figure 1 11 Configuring Print Settings To configure print settings 1 Choose the Print Settings tab Print Settings appears Figure 1 11 2 In Print Header enter text for each header Line as desired Header lines may be left blank 3 In Footer enter text for the Footer and Comment as desired The comment appears on printed pages below the footer The footer and comment may be left blank 4 In Print Options select Print Preview to preview the page layout onscreen each time a protocol configuration or measurement results are printed 5 In Print Options choose Show printer settings to display printing options each time a protocol or measurement results are printed 6 In Print Options select t
197. s amp Permissions administering user account 3 5 changing administrator password 3 2 changing current user s password 3 14 configuring roles 3 7 default roles 3 8 handling disabled user accounts 3 13 logging off 3 13 logging on 3 12 overview 3 1 permissions 3 8 setting support level 3 3 setting up 3 2 signing items 3 17 system administration restoring the administrator password 3 9 unlocking signatures 3 19 viewing detection software audit log 3 15 viewing signatures 3 19 viewing the audit log 3 10 viewing unlocked signatures 3 20 analysis protocols configuring concentration 6 33 configuring cutoff values 6 38 configuring plate layout 6 11 configuring transformation formulas 6 32 configuring validation rules 6 40 configuring variables 6 31 curve fitting methods 6 34 reevaluating results 7 17 Cc communication settings configuring 1 14 concentration configuring in analysis protocols 6 33 viewing the standard curve graph 7 15 Concert TRIAD Series Software accessing online help 1 5 configuring communication settings 1 14 configuring software settings 1 16 error codes C 1 installing 1 6 launching 1 3 overview 1 1 setting up 1 12 system requirements 1 6 using the software interface 1 4 viewing audit log 3 15 copying detection methods 4 16 labware 5 12 protocols 6 55 creating detection methods 4 3 labware 5 3 protocols 6 3 Concert TRIAD Series Software User s Manual curve fitting methods 6 34 cutoff
198. s 2 5 00544956 46944444 40044s454eo05e4404 7 24 7 1 Printing Measurement Results nonn nnnau nuaa 7 25 A Appendix A Data Reduction Techniques A l Supported Data Reduction Techniques 0 00 annan A 1 B Appendix B Mathematical Operators and Functions B 1 Supported Mathematical Operators and Functions nesse aenean anea B 1 C Appendix C Software Error Codes C 1 Troubleshooting Software Error Codes 0 00 ce cece eee eee C 1 Concert TRIAD Series Software User s Manual List of Figures Figure 1 1 Concert TRIAD Series Software main window eecceeseesseceseeeeeeenaeeeteeeseeennees 1 3 Fig re 1 2 Using online MU py seseccssesuessteeat teuncnnncdasnte dane dedudata gel eenia aa 1 5 Figure 1 3 Starting the installation so sscces pts needs vasancessoceacednaeeivednns teaddnsoedessunqaesseediedncdaceitveniaeentees 1 8 Figure 1 4 Installing the software on a Windows NT system cceeceeeseeseeceeeeeeeeeneeenteeees 1 9 Figure 1 5 Repairing the installation casscicansocescundeasieaseniactendeneceancoiaexaaseardeotateaam is eiastenieaesenncne 1 11 Figure 1 6 Concert TRIAD Series Software main screen ee eeeeeseeeseeeeeeeneeeeseeeeeeeeaeeeaeens 1 12 Figure 1 7 Warning Instrument is not Connected 0 0 eee eeeeeeeseecseeceeeeeececaeeeseeeseeeeaeeesaeens 1 13 Figure 1 8 Instrument Selection List with simulated instrument selected eeeeeeeeteees 1 14 Figure 1 9 Configuri
199. s 4 4 Figure 4 3 Selecting an absorbance Method Type s esssssessessssrsesssrersessrrsrresersrrsrerrensessrerreeseese 4 5 Figure 4 4 Defining absorbance measurement parameters eseseseesresreesesreestrrereererserererreeseese 4 6 Figure 4 5 Defining luminescence measurement parameters 0 0 eeeeeeeseceeeeeeesnaeceseeeeeeeeaees 4 7 Figure 4 6 Defining fluorescence intensity top method parameters ccccceeseeeeeseeeesneeeeeees 4 8 Figure 4 7 Defining fluorescence intensity bottom method parameters eee eeeeeeereeereees 4 9 Figure 4 8 Defining fluorescence polarization method parametefS ceccceeeeeeseseeeeeteeeeees 4 11 Figure 4 9 Defining time resolved fluorescence method parameterS cescceeeseeeeeeeeeeteees 4 12 Figure 4 10 Editing a fluorescence intensity top Method 00 0 0 eee eseeesseceeeeeeeeeeseeenaeeneeeees 4 14 Figure 4 11 Confirming the deletion of a detection method ceeeeeeesseceeeeeeeeeeeeesaeeneenees 4 17 Figure 4 12 Choosing the folder where an exported detection method will be saved 4 18 Figure 5 1 Accessing lab ware actions sicecsiosescsusdseiasiagssaddaceastetjoussdiangendedsasentesdagrecessdedenesnneeaeede 5 2 Figure 5 2 Defining plate dimensions and information sesssssesseesresesrresressrsereseeserrreseesereeresee 5 4 Figure 5 3 Defining offsets and well dimensions essesssessessssrsssessessesstssresressresresrensersesreeseeee 5 7 Figure 5 4 Edi
200. s Software To remove a filter slide 1 Select the type of filter slide to remove Excitation or Emission The list of filter slides displays all slides of the selected type Select the desired filter slide to remove from the list Filter Slide Properties displays information about the selected slide Choose Remove Slide The selected filter slide is removed from the list Setting Up and Controlling Instruments 2 11 2 3 2 4 Exporting and Importing All Filter Slide Configurations Information for all excitation and emission filter slides configured for the instrument can be exported to an XML file and imported at a later time to restore that configuration or share the filter slide configuration with another instrument Importing the filter slide configuration from an XML file replaces the current configuration for all filter slides with the configuration from the file Note If necessary the default filter slide configuration may be restored by importing the file for the type of instrument in use located in Documents and Settings All Users Application Data Multimode Detection Software Filters To export all filter slides 1 Choose Export Slides Save As appears 2 In Save As select the desired directory and enter a file name 3 Choose Save Slide information is saved as an xml file with the specified path and file name To import all filter slides from a previously exported file 1 Choose Import Slides Open appears
201. samples The integration time may be set within the range of 0 00005 to 3600 seconds Concert TRIAD Series Software User s Manual 4 12 Creating and Editing Detection Methods 5 Choose Save to save the new fluorescence polarization detection method The new method appears in the Detection Method Selection List OR Choose Back to select a different Method Technique refer to Section 4 2 1 Selecting a Method Technique OR Choose Cancel to close the Method Editor without saving the new detection method 4 2 3 6 Defining Time Resolved Fluorescence Method Parameters TRIAD only In a time resolved fluorescence measurement the excitation light source is turned off and the measurement is performed from above the plate after a specified delay Several of these excitation measurement cycles may be performed on each sample When multiple excitation measurement cycles are performed the results from all cycles are used to calculate a single measurement result for each sample Gp Method Editor Fluorescence TRF Method Parameters Method Technique Method Parameters gt Method Name Fluorescence TRF Excitation Filter nm azosi o SY Emission Filter nm ess o LED on Time seconds boon s Number of pulses C Delay Before Measure seconds ooo Integration Time seconds o oo Date created 3 4 2005 Figure 4 9 Defining time resolved fluorescence method parameters To define time resolved fluoresce
202. scan measurement and shaking if desired To select and configure a method in basic mode 1 In Method Selection choose the Basic tab to toggle from advanced mode if necessary Basic mode configuration parameters appear Figure 6 10 Refer to Section 6 2 5 2 Configuring a Method in Advanced Mode to configure a method with multiple detection and or preparation methods S5 Edit Protocol FloTopKinetic 12 cycle Method Selection Method Properties Appears when configuring kinetic General Settings Select a method and method type Technique Type or scan measurements only Labware Selection Layout Settings ae Report Options asic Method Selection gt Advanced Variables Method Selection Method Properties Transformation Fi top535 625 Kinetic Cycles Concentration Kinetic Interval Cutoff Type Data Reduction Single Point Validation Output Settings Kinetic Kinetic Cycles Choose the number of measurement cycles to perform C Scan Shake Info Shake Intensity Medium S ha ke l nfo Shake Interval 5 Appears when Shake Mode Linear gt i a befo ie read Shake Intensity is selected only The intensity of the shaking operation IV Shake before read Figure 6 10 Configuring a method in basic mode 2 In Method Selection select the detection method for use in the protocol Only detection methods of the technique selected for the protocol are available refer to Se
203. seseresre 6 46 Figure 6 31 Selecting the detection method used in the read height optimization 6 48 Figure 6 32 Selecting the well read in the read height optimization eee eeeeeeesseeeeeeeees 6 49 Figure 6 33 Read height optimization in Progress eceeeeeseceseceeeeeeeeeeaeceeeeseneesaeecsaeesseeees 6 50 Figure 6 34 Read height optimization completed eeceesseseeeeeesceceseceeeeeseeeeaeesnaeesaeeees 6 50 Figure 6 35 Preparing to run a protocol in simulation MOC ee eee eseceeeceeeeeeeeceaeeneeeees 6 51 Figure 6 36 Editing an absorbance protocol sscsscecissvoeccscutesdcesesoieancgnvodecdeastaaclssxetceeeeeeaseeteceees 6 53 Figure 6 37 Confirming the deletion of a protocol sssesseseesssssesssresserssessseersseesssresseesseessee 6 56 Figure 6 38 Previewing a protocol configuration and sample layout printout eee 6 58 Figure 6 39 Choosing the folder where an exported protocol will be saved eeeeeeees 6 59 Figure 7 1 Accessing measurement result actionS e seeseseesessrsesesreestesrrsrtsstrserressresrrsreeseeseese 7 1 Figure 7 2 Viewing results of an area scan measurement eessseeseeseeeriesesressreerrrrreserererreeseese 7 3 Figure 7 3 Viewing raw data for an area scan measurement eseseeesresreseesresrrsriresersreereeseese 7 4 Figure 7 4 Viewing reduced data for a measurement performed in a multiwavelength protocol ES eee ee me er a eo etree ee Br ee 7 5 Figure 7
204. sesset 3 7 Figure 3 5 Password Rest tS risiini e a E etre ae ee 3 9 Fig re 3 6 Signet Audit LO gassins snanta singes aiana Sa ES EE eT RES 3 10 Figure 3 7 Accessing user actions s cic csesasiesccssnacssansesiadesansdecdastanedasansecdseanaded saansdadasanseadevanesendess 3 11 Fig r 3 8 LOZO neon en neem cee ee nee nee eae ia ae ea ataa eiai aaie nee ere a RES 3 12 Figure 3 9 Administrator Notification seseesseeseeeseserssessesressrssresressessrseresrenstssrenrenseeeresreeseeee 3 13 Figure 3 10 Changing the user password gaicesssaccsssgectenssttacles deeds eee ees 3 14 Figure 3 11 Viewing records in the Audit Viewer eesssesseereesessessereresresresstssresrerseeereseresesee 3 15 Figure 3 12 Activating disabled messages 0 eecceesseesseceseeeseeeeseceseeeseeeeneecsaeeaeenseeesaeeesaeens 3 16 Pip tine 3 13 Signing an MEM sssaaa ninasi aes iair E E naeia EEE ENEEK werent 3 17 Concert TRIAD Series Software User s Manual Xiv Figure 3 14 Viewing active signatures sci utce ccedaeesbesdbcleenestaceecdvstaeez eel ieeceeeatid cad ea bbenewnadgeendaed 3 19 Figure 3 15 Viewing unlocked signatures azcsccacesscesscesasieeccsdaseubaracdeunactapureseveeqensscausenedscpauactoeds 3 20 Figure 4 1 Accessing detection method actions cccssccscssscecsscceensscesnccssnsseesnsecseaserssessees 4 2 Figure 4 2 Selecting a Method ee Mini Qie is ccaveadecvaverdecgeseuasucdasseicesaaddnnasiceascvoraeeausbautenexsinddeees
205. sity bottom method parameters 1 2 3 DYNEX Technologies Inc Enter a Method Name Figure 4 7 Select the Excitation Filter nm Select the Emission Filter nm Note The filters available are those installed on the slides loaded in the instrument and configured for fluorescence techniques in Instrument Settings refer to Section 2 3 2 Defining and Editing Filter Slides In Integration Time seconds enter the length of time in seconds the signal is collected from samples The integration time may be set within the range of 0 00005 to 3600 seconds Choose Save to save the new fluorescence intensity bottom detection method The new method appears in the Detection Method Selection List OR Choose Back to select a different Method Technique refer to Section 4 2 1 Selecting a Method Technique OR Choose Cancel to close the Method Editor without saving the new detection method Creating and Editing Detection Methods 4 11 4 2 3 5 Defining Fluorescence Polarization Method Parameters TRIAD only A fluorescence polarization method measures two orthogonal perpendicular polarization states by performing two sequential fluorescence intensity measurements from above the plate Light is directed through an excitation filter which passes only the wavelength necessary for excitation and a polarizing filter The fluorescence resulting from the excitation of the sample is passed through two emission
206. sult Viewer may be exported to Microsoft Excel Exported results are saved in the directory selected in Directory Settings refer to Section 1 4 2 3 Choosing the Directory Where Exported Measurement Results are Saved To export results to Excel 1 From the toolbar choose Export the current measurement results to Excel Excel opens automatically 2 In Excel note that exported results appear in multiple workbooks A workbook may contain general information and raw data for a single detection method or general information and reduced data Note Refer to Section 7 4 1 Viewing Measurement Results in Microsoft Excel for information about viewing exported results in Excel 7 2 7 Saving Measurement Results The measurement results currently being viewed may be saved to the database from within the Result Viewer which allows results that have been reevaluated by editing data reduction or analysis parameters to be saved with a different name Optionally parameters edited in the Result Viewer may be saved in the original protocol definition To save measurement results 1 From the toolbar choose Save the current measurement results to the database Question appears asking if the existing results should be overwritten Figure 7 11 Question 2 J Overwrite existing measurement results e O e Figure 7 11 Choosing to overwrite existing measurement results DYNEX Technologies Inc Viewing Measurement
207. sults 7 5 7 2 2 Viewing Reduced Data The Reduced Data tab is displayed when the detection method s configured in the protocol use data reduction to calculate a single value from multiple measurement cycles or points Figure 7 4 Wells may also be rejected as outliers when the calculated value falls outside of the expected result Reduced data for the plate may be recalculated with outliers removed if desired Result Viewer 20050320 164521 DTX 880 St 52 A 1 284 0 78 OK OK 514 365 0 117 OK Select a data reduction technique to view results in the right pane 537 338 OK OK 526 1 299 OK 550 0 843 OK 562 2 129 OK 574 575 0 179 2 962 OK 586 Figure 7 4 Viewing reduced data for a measurement performed in a multiwavelength protocol To view reduced data reject outliers and recalculate reduced data 1 Select the Reduced Data tab if necessary 2 If multiple detection methods with data reduction techniques are configured in the protocol choose the desired data reduction technique from the left pane Reduced data for selected method appears in the right pane 3 To reject a well as an outlier right click on the desired well and select Reject Well A red X appears over the well and the Reevaluate current measurement results button appears on the toolbar Note Multiple wells may be rejected as outliers Rejected wells may be included in the measurement results again by right clicking on
208. system only users assigned a role containing the Delete permission may delete user defined detection methods Signed methods may not be deleted Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To edit a detection method 1 In the Detection Method Selection List select the detection method to edit 2 From the toolbar choose Edit the selected method OR From the Actions menu choose Edit the selected method OR Right click on the selected detection method and choose Edit the selected method from the menu The Method Editor appears Figure 4 10 a Method Editor Fluorescein Top Method Parameters Method Parameters gt DYNEX Technologies Inc Method Name Fluorescein Top Excitation Filter nm ass Emission Filter nm sssi o Integration Time seconds oor s Date created Figure 4 10 Editing a fluorescence intensity top method Creating and Editing Detection Methods 4 15 3 Edit the method parameters as desired For more information about the parameters for a specific detection method refer to the section that covers defining the desired detection method Defining Absorbance Method Parameters Section 4 2 3 1 Defining Luminescence Method Parameters Section 4 2 3 2 Defining Fluorescence Intensity Top Method Parameters Section 4 2 3 3 Defining Fluorescence Intensity Bottom Method P
209. t protocols detection methods and labware or running protocols on an instrument using Concert TRIAD Series Software the instrument must be set up and configured All configured instruments are listed in the Instrument Selection List The Instrument Selection List allows quick access to common instrument actions such as loading and ejecting the plate carrier and to configure instrument settings Use the Instrument Selection List for e Controlling Instrument Actions Section 2 2 e Configuring Instrument Settings Section 2 3 Concert TRIAD Series Software User s Manual 2 2 Setting Up and Controlling Instruments To configure and manually control instruments From the navigation pane choose Instruments The Instrument Selection List appears Figure 2 1 d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 File Actions Help Instrument actions lt _ Instrument Selection List Serial Measurement Techniques 0102 Absorbance Luminescence Fluorescence Intensity Top Fluorescence Intensity Bottom Fluorescencd Detection Methods Labware Software Settings Figure 2 1 Instrument Selection List All instruments that have been connected to the host computer and configured in the software are displayed in the Instrument Selection List When an instrument not currently connected to the computer is selected the software automatically enters simulation mode refer to S
210. t with permission to access the software Refer to Section 1 3 2 Installing Concert TRIAD Series Software on Windows 2000 or XP for more information about installing the software for a single or multiple user accounts a Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 Berkeley Rattan DER File Actions Help Toolbar S Protocols Application Type Created Last Edited Last Executed Area Scan 01 2 28 2005 5 56 PM 2 28 2005 6 00 PM 2 28 2005 5 56 PM Results Abs 340 Basic 2 28 2005 5 56 PM 2 28 2005 5 57 PM 2 28 2005 5 56 PM Abs 340 12 cycle kinetic Basic 2 28 2005 5 56 PM 2 28 2005 5 58 PM 2 28 2005 5 56 PM Detection Methods Lymi 4 cvcle kinetic Rasic 2 28 2005 5 56 PM 2 28 2005 5 59 PM 2 28 2005 5 56 PM Links to S Labware Selection Lists Instruments Software Settings Selection and Users configuration pane Navigation pane Figure 1 1 Concert TRIAD Series Software main window Concert TRIAD Series Software User s Manual Installing Setting Up and Using the Software DYNEX Technologies Inc 1 2 2 Using the Software Interface Concert TRIAD Series Software uses a simple interface that is divided into three basic sections e navigation pane refer to Section 1 2 2 1 About the Navigation Pane e toolbar refer to Section 1 2 2 2 About the Toolbar e selection and configuration pane refer to Section 1 2 2 3 About the Selection
211. ta is either generated randomly or read from a data file Simulation mode is automatically enabled when the host computer is not connected to an instrument When an instrument is connected simulation mode may be enabled manually in Instruments refer to Section 2 2 5 Enabling Simulation Mode To run a protocol in simulation mode 1 In the Protocol Selection List select the protocol to run 2 From the toolbar choose Run the selected protocol Prepare to Run appears Figure 6 35 Note When running an Analysis protocol with variables configured Variables appears as the first screen in Run Protocol Change the values of the variables if desired and choose Next to continue Prepare to Run appears OR From the Actions menu choose Run the selected protocol OR Right click on the selected protocol and choose Run the selected protocol from the menu Figure 6 35 Preparing to run a protocol in simulation mode 3 Enter anew Result Name if desired 4 Select Check to generate random data to run the protocol using random data generated by the software if desired 5 In Use this data simulation file for this read e Leave the directory path of the simulated data path as configured to use the data file selected in Software Settings refer to Section 1 4 2 2 Choosing Simulated Data Files e Enter the directory path of the desired data file The complete directory path must be entered for example c detection software
212. tallation is complete 8 Repeat steps 6 and 7 until all components and Concert TRIAD Series Software are installed The software is now ready for use 1 3 4 Installing Optional Modules Optional modules that extend the functionality of Concert TRIAD Series Software may be purchased separately and installed on the system Optional modules use an installation system that is nearly identical to the Concert TRIAD Series Software installer To install an optional module 1 Exit all Windows programs 2 Make sure the user currently logged into Windows has Administrator privileges Accounts with Standard or Restricted access are not permitted to install the software Contact the site system administrator for more information about account privileges 3 Insert the module installation CD into the CD ROM drive and browse to the contents of the CD 4 If installing the module on a Windows XP or 2000 system open Begin here for XP or W2K systems The module installer appears OR If installing the module on a Windows NT system open Begin here for NT systems A list of components that must be installed appears in a web browser window 5 If installing on a Windows XP or 2000 system Install or Update each required component listed as such then install the module OR If installing on a Windows NT system install the required components in the order listed then install the module DYNEX Technologies Inc Installing
213. the curve as measurement value minute The line with the highest slope is calculated The accuracy p of this calculation depends on the number of measurement Smoothing Points cycles selected Cancel Figure 6 11 Selecting a data reduction method for a kinetic measurement 5 In Data Reduction Method select the desired Method If required by the selected method additional parameters such as smoothing points appear DYNEX Technologies Inc Creating Protocols 6 19 6 Configure additional parameters for the selected data reduction method if required Note Refer to Table A 2 in Appendix A Data Reduction Techniques for details about the data reduction methods available for kinetic measurements 7 Choose OK to confirm the selection of the data reduction method Concert TRIAD Series Software User s Manual 6 20 Creating Protocols 6 2 5 1 2 Configuring a Scan Method Area and linear scan measurements may be configured for absorbance and fluorescence intensity methods Area scans read a number of measurement points arranged in a grid pattern across each well Linear scans read a number of points in a linear axis crossing the center of each well Note Scan measurements may be configured in protocols configured to use plates with 96 or fewer wells only To configure an area or linear scan 1 In Type select Scan Method Properties appears Ea 2 To configure the type of scan measurement and the number
214. the first and last points N A measured in a well Mean Determines the mean value per sample from the N A points measured Peak Value Used to detect the highest measured value per Smoothing sample Points Concert TRIAD Series Software User s Manual Data Reduction Technique Appendix A Data Reduction Techniques Table A 2 Kinetic Data Reduction Techniques Description Parameters Determines the average slope of the reaction curve by calculating Average Slope the average of all linear regressions calculated over each group of Smoothing 9 p Smoothing Points in the kinetic reading sequence A decreasing Points slope shows a decline Difference between the first and last kinetic measurements in a Delta N A protocol run Difference between the first measurement and the center point of the maximum slope Delta Max Slope Smoothing Note The center point of the maximum slope is calculated by Points determining the center point between the smoothing points of the regression line with the maximum slope Delta Time Time elapsed from one preselected measurement value to another Lower Limit Absolute Upper Limit Time difference in seconds between the first measurement and the occurrence of the center point of the maximum slope Delta Time Max Smoothing Slope Note The center point of the maximum slope is calculated by Points determining the center point between
215. the list DYNEX Technologies Inc Creating Protocols 6 9 6 2 4 Configuring Labware Layout Settings Use Layout Settings to configure how wells on the plate are read Figure 6 6 Settings are configured in two tabs e Layout Selection Settings configures which wells are read in the measurement Refer to Section 6 2 4 1 Configuring the Sample Layout for Basic Applications or Section 6 2 4 2 Configuring the Sample Layout for Analysis Applications depending on the type of application being configured e Reading Direction Settings configures the order of how wells are read row by row column by column or well by well refer to Section 6 2 4 3 Configuring Reading Direction 6 2 4 1 Configuring the Sample Layout for Basic Applications In Basic applications use Layout Selection Settings to configure the location of sample wells on the plate Note Basic applications support sample wells only The optional Concert TRIAD Series Analysis Software module supports configuring other well types such as blanks controls and standards To configure labware layout settings 1 In Layout Settings choose the Layout Selection Settings tab to view the layout of the selected labware Figure 6 6 Gp Create Protocol Abs 340 Kinetic 6 cycle Layout Settings General Settings r Layout Selection Settings Reading Direction Settings Technique Type Labware Selection Import Layout Report Options Layout
216. the smoothing points of the regression line with the maximum slope Delta Time Time elapsed in seconds from the first measurement to reaching a i i In Decrease Relative set increase decrease amount from the first measurement value Determines the maximum declining rate of the reaction curve by a eh calculating a linear regression over each group of Smoothing i ope Points in the kinetic reading sequence 8 seq Determines the maximum inclining rate of the reaction curve by Smoothing Max Inclining calculating a linear regression over each group of Smoothing Points Slope Fe ae Points in the kinetic reading sequence Maximum slope of the curve in measurement value min The line with the highest slope is calculated along with maximum reaction speed Smoothing Max Slope Points Note The accuracy of this calculation depends on the number of measurement cycles selected Mean Determines the mean value per sample within a sequence of N A measurements Smoothing Time Peak Used to detect the time elapsed until the peak value is reached Points Peak Value Used to detect the highest value per sample within a sequence of Smoothing measurements Points DYNEX Technologies Inc Appendix A Data Reduction Techniques A 3 Table A 3 Fluorescence Polarization Data Reduction Techniques TRIAD only Data Reduction Description Parameters Technique Ratio of the difference between the parallel
217. thod for the sequence eee eeeeeseeeeeeereeeneeeeeeeeees 6 26 Figure 6 19 Configuring a Shake preparation method 0 eecceeeseecesceceeeeeceeeeecseeeecnteeeeeaeees 6 28 Figure 6 20 Configuring a Set Temperature preparation method eeeeeeeseeeeseeeeeeeeeeeeees 6 29 DYNEX Technologies Inc Figure 6 21 Configuring variables in an analysis protocol eseeseeseceseceseeeeeeeeseeesaeeneenees 6 31 Figure 6 22 Configuring a transformation formula eee eseeeseceseeeeeeeeneeeseeesneeeneecnaeeneeeeees 6 32 Figure 6 23 Configuring concentration parameters ee eeeeeseceeeeeeeseeceaeceseesseeesseecsaeeneeees 6 33 Figure 6 24 Configuring standards rs ces cca tees Weadicniseu vtbeesiieedceuaeoia eccsbesaceueremheesss uateedestuieeneees 6 36 Figure 6 25 Configuring standard curve validation parameters cceesceeeeeeeeeeseeseseeeeeeeees 6 37 Figure 6 26 Configuring cutoff values cciccccotcaccecsecescececessccdivaseuscensaceeecebshiesceedacensedeuercedanneudeedane 6 38 Figure 6 27 Configuring validation rules sseeseeeeesseesessessreereeseresesresstssersrestesseestesreesreseeseeesee 6 40 Figure 6 28 Configuring output settings eseeseesreeseesessrssrerresserererresstrstrsrenstestsreestesseseresresse 6 42 Figure 6 29 Configuring an external software application in Output Settings eee 6 44 Figure 6 30 Preparing to run a protocol on an instrument eeseseesseseesesesreesresrieeresres
218. ties of the instrument gt TRIAD LT supports 96 well and 384 well microplates gt TRIAD supports 6 to 384 well microplates Note When Signet is enabled on the system only users assigned roles containing the Sign Copy Create Delete Optimize and Edit permissions may perform all of the actions covered in this chapter Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions Labware actions are accessed from the Labware Selection List Figure 5 1 Labware actions include e Creating Labware Section 5 2 e Editing Labware Section 5 3 e Copying Labware Section 5 4 e Deleting Labware Section 5 5 e Optimizing Labware Section 5 6 e Exporting and Importing Labware Section 5 7 Concert TRIAD Series Software User s Manual 5 2 Creating and Editing Labware To define and edit labware From the navigation pane choose Labware The Labware Selection List appears Figure 5 1 S Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 File Actions Help Labware actions Labware Selection List Number of Wells Created Last Edited Last Optimization 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM 2 28 2005 3 06 PM
219. ting Protocols 4 Choose OK to export the protocol The exported protocol is saved using the default file name format Protocol_ Protoco Name xml In order to import the file at a later date the filename must not be changed OR Choose Cancel to stop the operation without exporting the protocol To import a protocol from an exported XML file 1 From the File menu choose Import gt Protocol Open appears 2 In Open browse to and select the desired XML file to import 3 Choose Open The protocol as well as detection method s and labware used in the protocol are imported Any default detection method s or labware used in the protocol are not imported because default methods and labware may not be edited deleted or overwritten Instead the imported protocol uses the same default methods and labware stored in the software DYNEX Technologies Inc Viewing Measurement Results 7 1 Overview Measurement results from each protocol run are stored in the Concert TRIAD Series Software database and are accessed from the Results Selection List Figure 7 1 which also provides access to result actions and the ability to search for specific results based on names and or dates d Concert TRIAD Series Connected Filter Slides Ex 2 Em 1 File Actions Help Result actions Results Selection List Result Name DA 20050316 154720 ty Results 20080316 154436 20050316 154402 20050316 142548b 20050316 1
220. ting an existing protocol selecting a different technique type deletes any detection methods previously configured in Method Selection New detection methods must be configured before the protocol may be used to perform measurements refer to Section 6 2 5 Configuring Detection and Preparation Methods Concert TRIAD Series Software User s Manual 6 8 Creating Protocols 6 2 3 Selecting the Labware Type Used in the Protocol Use Labware Selection to select the type of labware used in the protocol Figure 6 5 Labware must be configured prior to configuring the protocol Only labware configured for the selected technique type is available Labware cannot be edited once it is used in a protocol Refer to Chapter 5 Creating and Editing Labware for detailed information about creating and configuring labware d Create Protocol Kinetic 340 Labware Selection General Settings Select the desired labware type from the list below Technique Type Layout Settings Method Selection Type of Labware Number of Wells Variables Transformation Concentration Cutoff Validation Output Settings Costar Cone 96 Round Costar Flat 384 Square Greiner 24 Greiner 384 Cone PP Greiner 384 Flat pp Greiner 384 Thermal Cycler Greiner 96 Cone PP Greiner 96 Cone PS Greiner 96 Flat Greiner 96 Round PP Figure 6 5 Selecting the type of labware used in the protocol To select labware Select the desired Type of Labware from
221. ting labware dimensions and well information sesseeseeseseeesesrresreerrsrresrsrresre 5 10 Figure 5 5 Configuring offsets and well dimensions in Labware Lots eesceeseeeteeeeeeeees 5 11 Figure 5 6 Confirming a labware deletion eeseessecsseceeeeesseecsceceseesseeesneesaeesneseneesnaeenes 5 13 Figure 5 7 Selecting the detection method for labware optimization ce eeeseeeeeseeeeeeeeees 5 15 Figure 5 8 Preparing the labware for OptimiZatiOn ee eee eeseceeeeeeceaeceseeeseeesaeessaeenseesees 5 16 Figure 5 9 Labware optimization in PRO STeSS scjcips sodas cgadasa cascaseaastenscdasasereacecuseaeesinegenouaays 5 17 Figure 5 10 Selecting the well center ps ccete re ccckcscttieh tasted teid nie taececata tie eat dedeaal ed Sande decat 5 18 Figure 5 11 Verifying well centers i csccacoccsccecatcems tic teendei teers ieee aucrssent piacsteedecedeeedaleaa ple beedate 5 19 Figure 5 12 Choosing the folder where exported labware will be saved s es 5 21 Figure 6 1 Protocol Selection M180 occecusectinenscs es sontcrnsotcentesaaeiainsenscated teen qveceteesanmegrecauetsers 6 2 Figure 6 2 Selecting the application type ssccainsutecsgsntatenesetgucsiivsgtcnasdnaceyetedeteseseuneeaaseaesaeevaleeeece 6 4 Figure 6 3 Defining a protocol name and entering notes about the protocol seessseeceseeeseee 6 5 Figure 6 4 Selecting the measurement technique for a TRIAD 0 00 eee eeeeeeeeeereeeneeeeeeeeeeees 6 7 Figure 6 5 Selecting the
222. tion Date last run Monday March 07 2005 Concentration Cutoff Validation Notes Analysis Options Analysis Options IV variables Available only when an IZ Transformation Analysis application type I Concentration is being configured cutoff IM validation Figure 6 3 Defining a protocol name and entering notes about the protocol To configure the general settings for a new protocol 1 In Protocol name enter a unique name for the protocol 2 In Notes enter a description for the protocol if desired Concert TRIAD Series Software User s Manual 6 6 Creating Protocols DYNEX Technologies Inc 3 If configuring an Analysis application select the desired Analysis Options to be configured in the protocol Variables define up to ten numeric values that may be used in any formula configured in the protocol refer to Section 6 2 6 Configuring Variables Concert TRIAD Series Analysis Software only Transformation configure an algebraic formula to transform measurement data refer to Section 6 2 7 Configuring a Transformation Formula Concert TRIAD Series Analysis Software only Concentration choose a curve fitting method and configure response formulas refer to Section 6 2 8 Configuring Concentration Concert TRIAD Series Analysis Software only Cutoff configure cutoff formulas to classify measured samples according to defined cutoff values ref
223. tion that could cause injury to the operator CAUTION A CAUTION calls attention to a condition or possible situation that could damage or destroy the product or the operator s work Concert TRIAD Series Software User s Manual Warnings and Cautions Found in this Manual Please read and observe all cautions and instructions Remember the most important key to safety is to use Concert TRIAD Series Software with care The WARNINGs and CAUTIONSs found within this document are listed below WARNING If the equipment is used in a manner not specified by DYNEX AN Technologies Inc the protection provided by the equipment may be impaired speed only Shaking low density plates at higher speeds may cause f CAUTION Shake low density plates such as 6 or 48 well plates at low liquid in wells to spill actual plate Doing so may cause the TRIAD optics transport to collide f CAUTION The plate height configured must not be less than that of the with the plate during a Read Height Optimization DYNEX Technologies Inc vii Table of Contents Safety Information ssassannnnnnnnnnnnnnnnnnnnnnnnnnn V Table of Contents 4 cc00c cece sad en anes ds bb ee eee ae ee wee vii EIS Of PIQUIES 26 4 noche Sicha esi ede ee ee Ree Re eee Cease oe xiii List of T bl S crar bas traesan a a ee eee ae ee xvii 1 Installing Setting Up and Using the Software 1 1 OVERVIEW sd 6225 beso edge Eaa Ep bees E E Geb oe thee Eaa a a O aa
224. tive owners 2005 Beckman Coulter Inc All rights reserved DYNEX Technologies Inc Warranty and Special Provisions Limited Warranty DYNEX Technologies products are fully guaranteed for one year against defects in parts materials and workmanship Defective parts and materials will be replaced or at the discretion of DYNEX Technologies repaired at no charge for a period of one year and labor required for such replacement or repair will be provided at no charge for a period of one year provided that the products are utilized and maintained in accordance with the instructions in the applicable operating and servicing manual and provided further that the products have not as determined solely by DYNEX Technologies been subject to misuse or abuse by the Customer or other parties unrelated to DYNEX Technologies DYNEX Technologies makes no warranty expressed or implied as to the fitness of any product for any particular purposes other than those purposes described in the applicable operating and servicing manual nor does DYNEX Technologies make any other warranty whether expressed or implied including merchantability other than those appearing on the face hereof Where DYNEX Technologies guarantees any product whether under this Warranty or as a matter of law and there is a breach of such guarantee the Customer s only and exclusive remedy shall be the replacement or repair of defective parts and materials as described above Th
225. tment low fluorescein concentration Measurement attempted with no labware loaded In the Read Height Optimization Wizard confirm that the correct well is selected for the optimization read refer to Section 6 3 1 1 Optimizing Read Height TRIAD only Load a plate into the instrument Concert TRIAD Series Software User s Manual 05 Appendix C Software Error Codes Error 670o 11 Table C 1 Software Error Codes and Solutions Error Message The current labware definition is invalid Recommended Solution Check plate parameters configured in Labware Information refer to Section 5 2 1 Defining Labware Information 12 Detection method parameters are invalid Check the configuration of detection method parameters 13 The current labware format is not supported Make sure the plate type has been defined refer to Section 5 2 Creating Labware Currently loaded labware is not in the correct orientation Load the plate into the instrument with the orientation configured in the protocol Linear scan range exceeds well diameter Reduce the number of measurement points in the scan configuration refer to Section 6 2 5 1 Configuring a Method in Basic Mode Bright measurement below limit Check Platedefinition Check plate parameters configured in Labware Information refer to Section 5 2 1 Defining Labware Information Filter wavel
226. to define additional well selections if desired 6 Choose Report Options and select plate layout options for printouts e Print in Matrix well label identifiers appear arranged in a matrix corresponding to the plate layout e Print in List well label identifiers appear in a list DYNEX Technologies Inc Creating Protocols 6 11 6 2 4 2 Configuring the Sample Layout for Analysis Applications In Analysis applications use Layout Selection Settings to configure well types and locations replicates and the layout of well identifiers on the plate Note Analysis applications may be configured only when the optional Concert TRIAD Series Analysis Software module is installed on the system To configure labware layout settings 1 In Layout Settings choose the Layout Selection Settings tab to view the layout of the selected labware Figure 6 7 5 Create Protocol Kinetic 12 cycle Layout Settings General Settings e n Layout Selection Settings Reading Direction Settings Technique Type Labware Selection Import Layout Report Options Layout Settings gt Filling r Flow Replicates Type Sample X Method Selection Vertical C Constant Number 1 j variables Index ft Horizontal Incremental C vertical Horizontal Transformation Concentration Cutoff validation Delete View Identifiers Output Settings saa oin GOSOOOOO on the plate Figure 6 7 Conf
227. ts for more information about roles and permissions To edit a protocol 1 In the Protocol Selection List select the protocol to edit 2 From the toolbar choose Edit the selected protocol Edit Protocol appears Figure 6 36 OR From the Actions menu choose Edit the selected protocol OR Right click on the selected protocol and choose Edit the selected protocol from the menu OR Double click on the selected protocol Edit Protocol Basic Absorbance Multiwavelength 96 General Settings Please enter a name and notes for this protocol Technique Type Labware Selection Layout Settings Protocol name Basic Absorbance Multiwavelength 96 Method Selection Date created Wednesday April 07 2004 Output Settings Date edited Sunday March 13 2005 Date last run Wednesday April 07 2004 Notes Multiple wavelength absorbance measurement at 260nm 340mm 405nm 450nm 595nm and 620nm with Ssec shake in between each read Auto export data to Excel Figure 6 36 Editing an absorbance protocol Concert TRIAD Series Software User s Manual 6 54 Creating Protocols 3 Edit the parameters in each Edit Protocol screen as desired Note Refer to Section 6 2 Creating Basic and Analysis Protocols for detailed information about configuring protocol parameters 4 Choose Save to close Edit Protocol and save the changes OR Choose Cancel to close Edit Protocol without saving changes DYNEX Technolo
228. ts 5 11 selecting in protocols 6 8 selection guidelines 5 6 signing 5 8 logging off 3 13 logging on 3 12 logical operators B 1 luminescence detection methods configuring 4 7 M mathematical functions B 2 mathematical operators B 1 measurement results choosing storage directory 1 19 exporting to Microsoft Excel 7 12 from a basic protocol 7 3 printing 7 25 recalculating reduced data 7 10 reevaluating 7 17 saving 7 12 searching for 7 2 signing 7 23 viewing exported results 7 19 viewing graphs 7 7 viewing raw data 7 4 viewing reduced data 7 5 viewing results in Excel 7 19 well status indicators 7 4 measurement techniques selecting in protocols 6 7 message boxes reactivating disabled 3 16 microplate carrier ejecting 2 3 loading 2 3 O online help accessing 1 5 optimizing labware 5 14 optimizing read height 6 48 P preparation methods configuring in protocols 6 15 configuring shake 6 28 Concert TRIAD Series Software User s Manual printing configuring settings 1 17 measurement results 7 25 protocols 6 57 protocols configuring an external program to run 6 44 configuring concentration 6 33 configuring cutoff values 6 38 configuring detection methods 6 15 configuring general settings 6 5 configuring labware for analysis layouts 6 11 configuring labware for basic layouts 6 9 configuring labware layout 6 11 configuring methods in advanced mode 6 23 configuring methods in basic mode 6 16
229. tus in the right panel A result may be rejected as an outlier when the value falls outside of the expected result Note Results for single point measurements are displayed in Raw Data To view raw data 1 Select the Raw Data tab if necessary ap Result Viewer 2005031 6 121747 DTX 880 Detection methods Raw data for each cycles and wells cycle or well s in the tal Figure 7 3 Viewing raw data for an area scan measurement 2 From the tree view in the left pane select the detection method measurement cycle or well desired to view Results and status appear in the right pane Table 7 2 describes the status indicators that may be displayed Table 7 2 Well Status Indicators Status Description OK The sample was measured successfully Error The sample was not measured because an instrument error occurred Overflow No result is available because the value exceeds the indication limit Underflow No result is available because reduced data could not be calculated Extrapolated The result fell within the extrapolation percentage set for a standard curve Not Evaluated The measurement result was not evaluated Rejected The sample was rejected as an outlier by a user Samples may be rejected in any tab displaying a matrix view of measurement results Unused The sample was not selected for measurement in the protocol DYNEX Technologies Inc Viewing Measurement Re
230. u choose the lot to use or edit The default lot created when the labware was defined and all lots configured using Optimizing Labware are available refer to Section 5 6 Optimizing Labware 2 Click in Current labware lot and choose True if necessary True must be selected in order to save changes made to the labware lot 3 In the property grid edit lot dimensions and information as desired Refer to Section 5 2 2 Configuring Offsets and Well Dimensions for the Default Labware Lot for more information about the fields available in the property grid 4 Edit the lot Notes if desired 5 Choose Save to save changes made in the Labware Editor OR Choose Back to view or edit Plate Information refer to Section 5 3 1 Viewing and Editing Labware Information OR Choose Cancel to close the Labware Editor without saving changes Concert TRIAD Series Software User s Manual 5 12 Creating and Editing Labware 5 4 Copying Labware Labware can be copied and then used as a template for a new labware type by editing the dimensions and parameters in the Labware Editor refer to Section 5 3 Editing Labware Note When Signet is enabled on the system only users assigned a role containing the Copy permission may create copies of labware definitions Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To make a copy of a la
231. used in the protocol The sample is measured using the same or very similar detection method used in the protocol The optimized read height is saved in the protocol and is used for all subsequent runs of the protocol until reset by performing a new optimization or manually selecting a read height option To optimize read height 1 In Run Protocol select Optimize Read Height The Read Height Optimization Wizard appears Figure 6 31 up Read Height Optimization Wizard Select Detection Method See eA Sciect a detection method to use for the optimization Click Next to proceed Prepare the Labware Optimize Name Measurement technique Measurement type Created Last Edited Fluorescein Top FluorescenceIntensityTop Monochromatic 1 28 2004 1 28 2004 PicoGreen FluorescencelntensityTop Monochromatic 4 1 2004 4 9 2004 Rhodamin Top FluorescenceIntensityTop Monochromatic 1 28 2004 1 28 2004 Optimization Complete Figure 6 31 Selecting the detection method used in the read height optimization 2 In Select Detection Method select the detection method used in the optimization Only detection methods configured in the protocol are available for selection 3 Choose Next to select the well measured to perform the optimization Prepare Labware appears Figure 6 32 OR Choose Cancel to close the wizard without performing the optimization DYNEX Technologies Inc Creating Protocols 6 49 4 Pipette liquid wit
232. values configuring in analysis protocols 6 38 D data reduction recalculating in Result Viewer 7 10 techniques for fluorescence polarization measurements A 3 techniques for kinetic measurements A 2 techniques for measurement sequences A 1 techniques for scan measurements A 1 viewing reduced data 7 5 viewing reduced data in Microsoft Excel 7 22 deleting detection methods 4 17 labware 5 13 protocols 6 56 detection methods configuring absorbance 4 6 configuring fluorescence intensity bottom 4 9 configuring fluorescence intensity top 4 8 configuring fluorescence polarization 4 11 configuring in protocols 6 15 configuring luminescence 4 7 configuring time resolved fluorescence 4 12 copying 4 16 creating 4 3 deleting 4 17 editing 4 14 exporting and importing 4 18 overview 4 1 selecting absorbance type 4 5 selecting for labware optimization 5 15 selecting technique 4 4 signing 4 13 E editing detection methods 4 14 labware 5 9 labware dimensions 5 10 labware lots 5 11 DYNEX Technologies Inc protocols 6 53 well information 5 10 error codes C 1 exporting and importing detection methods 4 18 labware 5 21 F filter slides adding 2 9 configuring 2 9 exporting and importing all configurations 2 11 exporting and importing individual 2 11 overview 2 8 removing 2 10 fluorescence intensity bottom detection methods configuring 4 9 fluorescence intensity top detection methods configuring 4 8 fluorescence polarization dete
233. ve the new labware and close the Labware Editor OR Choose Back to edit Plate Information refer to Section 5 2 1 Defining Labware Information OR Choose Cancel to close the Labware Editor without creating new labware 5 2 3 Signing Labware When Signet is enabled on the system labware may be signed to prevent labware properties from being edited Signed labware may not be optimized to create new labware lots unless all signatures attached to the labware are unlocked which changes the labware status to unsigned Labware may be signed by users who are assigned a role containing the Sign permission Refer to Section 3 3 1 1 Configuring Roles for Concert TRIAD Series Software User Accounts for more information about roles and permissions To sign labware DYNEX Technologies Inc In the Labware Selection List select the labware type to sign From the toolbar choose Sign the selected labware type Sign the Selected Item appears OR From the Actions menu choose Sign the selected labware type OR Right click on the selected labware and choose Sign the selected labware type In Sign the Selected Item add an electronic signature by following the instructions in Section 3 4 5 Adding Electronic Signatures and Comments to Items Creating and Editing Labware 5 9 5 3 Editing Labware Dimensions and information for user defined labware not used in measurement protocols may be edited Dim
234. ware and provides instructions for e Using Concert TRIAD Series Software Section 1 2 e Installing Concert TRIAD Series Software Section 1 3 e Setting Up Concert TRIAD Series Software Section 1 4 Concert TRIAD Series Software User s Manual 1 2 Installing Setting Up and Using the Software 1 2 Using Concert TRIAD Series Software Concert TRIAD Series Software uses a simple interface that divides the main window into three basic sections navigation pane toolbar and selection and configuration pane Figure 1 1 The interface includes easy access to the selection lists that provide system functionality and a comprehensive context sensitive online help system This section covers e Launching the Software Section 1 2 1 e Using the Software Interface Section 1 2 2 e Accessing Online Help Section 1 2 3 DYNEX Technologies Inc Installing Setting Up and Using the Software LES 1 2 1 Launching the Software To launch Concert TRIAD Series Software From the Windows Start menu choose Programs gt Dynex Technologies gt Concert TRIAD Series gt Concert TRIAD Series Concert TRIAD Series Software appears Figure 1 1 Note If Concert TRIAD Series Software is not found in the Start menu the software may have been installed for a single user account on the system instead of all accounts Check with the site system administrator or login to the user accoun
235. ware names dimensions well parameters and supported measurement techniques Figure 5 2 Gp Labware Editor Weber96deep Labware Information Labware Information gt Labware Lots E Labware Info Supported techniques d 1 lt lv Absorbance Weber96deep _ Luminescence iE Labware Measurements _ LuminescenceGlow Height 1 4 L LuminescenceFlash Height with lid 2 222 Bio Luminescence RET Pro perty Ea 12 77 Fluorescence RET grid Reading height 1 06 V Fluorescence Intensity Top Width 8 57 IV Fluorescence Intensity Bottom B Well Info L Fluorescence Polarization Time Resolved Fluorescence Columns 12 Rows 8 Well bottom shape Flat Well shape Round Well volume 300 I N etenam Information about the Name of this labware field being configured Notes None Figure 5 2 Defining plate dimensions and information To define Labware Information 1 If necessary click the next to Labware Info to display the fields in the category 2 Enter the Plate Name A name must be entered to proceed to the second configuration screen Labware Lots 3 If necessary click the next to Labware Measurements to display the fields in the category Note More information about the field being defined is displayed below the property grid Figure 5 2 actual plate Doing so may cause the TRIAD optics transport to collide with the plate during a Read Height Optimization f CAUTION The plate h
236. xml File Edit View Insert Format Tools Data Window Help Adobe PDF ea nanl fo 4 ResultData always appears in the 7 d title of a workbook containing reduced or transformed data Arial Unicode MS 8 BZU Ii il E 1 1 633 0 411 2 491 0 299 2 2 431 0 098 1 678 0 278 3 1 091 0 635 2 626 0 927 4 0 536 3 413 0 618 2 873 5 0 844 3 025 3 699 0 55 6 4 663 1 5 0 875 2 326 T 3 447 4 632 2 909 0 339 8 2 664 0 209 1 651 3 374 ColorCode AnaylsisStatus OK Overflow Error Underflow Figure 7 19 Viewing reduced data excerpt To view reduced or transformed data 1 In Excel access the workbook containing reduced or transformed data for the desired measurement results Workbooks containing reduced or transformed data always contain ResultData in the title 2 In the worksheet choose the desired tab to view DYNEX Technologies Inc Viewing Measurement Results 7 23 7 5 Signing Measurement Results On systems with the optional Signet module installed and enabled measurement results may be signed to prevent them from being deleted or overwritten Signed results from protocols configured with data reduction and or analysis options may be reevaluated however reevaluated results must be saved using a different name Reevaluated results are not signed by default Results may be signed at any time by users who are assigned a role containing the Sign permission Refer to
237. xporting and Importing Detection Methods A user defined detection method can be exported to an XML file and imported later to restore that configuration or share it with a copy of Concert TRIAD Series Software installed on another system Default detection methods installed with Concert TRIAD Series Software are present on all systems and may not be deleted or overwritten For this reason importing default detection methods from an XML export file is not permitted Note When Signet is enabled signed detection methods may be exported for use on another system however electronic signatures are not retained which allows the protocol to be edited when imported to another system Importing a signed method to the system from which it was originally exported is not permitted because signed methods may not be deleted or overwritten To export a detection method 1 In the Detection Method Selection List select the detection method to export 2 From the File menu choose Export gt Detection Method Browse for Folder appears Figure 4 12 Browse For Folder Desktop B My Documents 9 This Computer 3 My Network Places Recycle Bin Exported Protocols Make New Folder Figure 4 12 Choosing the folder where an exported detection method will be saved 3 In Browse for Folder browse to the folder where the exported detection method will be saved OR Choose Make New Folder to create a new folder wher
238. y 3 15 3 4 4 Reactivating Disabled Message Boxes 000000 3 16 DYNEX Technologies Inc 3 4 5 Adding Electronic Signatures and Comments to Items 3 17 3 4 5 1 Signing ems 45 4569 heb es kae eee lees Foe Seas es 3 18 3 4 5 2 Viewing or Unlocking Signatures for an Item 3 19 3 4 5 3 Viewing Unlocked Signatures 0 4 3 20 4 Creating and Editing Detection Methods 4 1 OVETVIEW 2c Suh ie touel dudceees e aa a erase hae hear e hp aeete als 4 1 4 2 Creating Detection Methods 2 5c cccssncebbe bene enaeoeanaeebewannees 4 3 4 2 1 Selecting a Method Technique 2 04 lt i2cee ses4ese eueeeeawes 4 4 42 2 Selecting the Method Type lt lt s646 os400e504ene4 Jee eewe lt siws 4 5 4 2 3 Defining Method Parameters 4 402446 sedan kee eee ea beens ee os 4 6 4 2 3 1 Defining Absorbance Method Parameters 4 6 4 2 3 2 Defining Luminescence Method Parameters 4 7 4 2 3 3 Defining Fluorescence Intensity Top Method Parameters 22202Fisaced eer beoduasitbabacadad 4 8 4 2 3 4 Defining Fluorescence Intensity Bottom Method Parameters TRIAD only 220000 4 9 4 2 3 5 Defining Fluorescence Polarization Method Parameters TRIAD only 2005 4 11 4 2 3 6 Defining Time Resolved Fluorescence Method Parameters TRIAD only 2004 4 12 4 2 4 Signing a Detection Method 0 0 cee eee eee eee nee 4 13 4 3 Editing Detection Metho
239. y positive results measured in sample wells e Negative Control a control well lacking the target reagent that generates little to no signal verifies negative results measured in sample wells e Sample a well containing a sample to measure e Blank a well filled with reagents but no reacting sample Blank wells are used to measure background noise When blanks are configured background correction is automatically applied to measurement results e Empty a well that is left empty 4 If configuring Blank wells select the type of Blank Validity desired Plate Row or Column The mean value of all blank wells in the selected validity option is subtracted from sample wells to provide background correction Note Blank Validity replaces Filling Flow and Replicate options in Layout Settings when configuring Blank wells 5 In Index choose the initial label number for the sequence of selected wells DYNEX Technologies Inc Creating Protocols 6 13 6 In Filling choose the desired direction for labeling the selected wells e Vertical labels wells column by column e Horizontal labels wells row by row 7 In Flow choose how the index is applied to wells in the selection e Constant all well identifiers in the selection are assigned the current index number Incremental increases each well identifier in the selection by one 8 In Replicates select the number of replicates for each sampl
240. ypes available in the pull down menu depend on which optional modules have been installed on the system This chapter covers configuring e Basic default application type Basic protocols may be quickly configured to perform a complex sequence of measurements in a protocol run but do not provide the ability to transform and analyze measurement data based on parameters configured in the protocol e Analysis available only when the optional Concert TRIAD Series Analysis Software module is installed Analysis applications allow measurement data to be transformed and analyzed using formulas variables and parameters configured in the protocol 3 Choose Next to configure the protocol Create Protocol appears displaying General Settings refer to Section 6 2 1 Configuring General Settings DYNEX Technologies Inc Creating Protocols 6 5 6 2 1 Configuring General Settings Use General Settings to define the protocol name and enter any related notes about the protocol Figure 6 3 When the optional Concert TRIAD Series Analysis Software module is installed Analysis Options to include in the protocol are available for selection a Create Protocol Kinetic 340 General Settings Please enter a name and notes for this protocol Technique Type Labware Selection Layout Settings Protocol name Kinetic 340 Method Selection Date created Monday March 07 2005 Variables Date edited Monday March 07 2005 Transforma

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