ABI PRISM ® 7900HT - Applied Biosystems
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1. In the Pre Installation Summary screen click Install In the Install Complete screen click Done Eject the SDS Plate Utility Software CD from the drive Upon installation the SDS Plate Utility software creates a default AIF EDS watch folder entitled Applied Biosystems Put AIF and EDS files here If the software is unable to create the folder or it is subsequently deleted the software prompts you to specify the AIF EDS watch folder upon launch of the SDS Plate Utility software The computer needs the following minimum hardware e Intel Pentium III processor or equivalent 500 MHz e 256 MB RAM CD Drive SDS Plate Utility User Guide Software Software The computer needs to have the following software e Microsoft Windows NT Service Pack 6 or Windows 2000 Service Pack 2 The SDS Plate Utility software works with the following software but does not require them for installation or operation SDS v2 1 does not work with v2 0 x e Automation Controller Note Applied Biosystems recommends installing the SDS Plate Utility software onto the computer attached to an ABI PRISM 7900HT Sequence Detection System In this configuration the software can work with the SDS Automation Controller and Detector List Builder software for the instrument SDS Plate Utility User Guide 2 3 Chapter 2 Installation 2 4 SDS Plate Utility User Guide Creating SDS Plate Documents The SDS Plate Utility v2 12. ABI PRISM 7900HT Sequence Detection System SDS Plate Utility Software User Guide Version 2 1 Applied Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses For Research Use Only Not for use in diagnostic procedures Notice APPLERA CORPORATION MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE Applera Corporation shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing performance or use of this material Notice to Purchaser License Disclaimer Purchase of this software product alone does not imply any license under any process instrument or other apparatus system composition reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation either expressly or by estoppel Copyright Information Copyright 2003 Applied Biosystems All rights reserved This document or parts thereof may not be reproduced in any form without the written permission of the publisher Printed in the United States of America Information in this document is subject to change without notice Applied Biosystems assumes no responsibility for any errors that may appear in
3. 1 container setup files 3 5 continuous argument 5 1 continuous parameter 5 3 D Database Options dialog 3 3 Database Setup command 3 3 databases 3 3 Detector Import List Glossary 2 detector information text file 4 1 detector list 4 1 Detector List Builder software 4 1 SDS Plate Utility User Guide Detector List txt 4 1 Detector Manager 4 1 E Electronic Data Sheet files 4 3 Glossary 2 Enterprise configuration 2 1 G Genomic Assays CD 3 2 H hardware 2 2 input parameter 5 2 Install Complete screen 2 2 installation 2 1 L log files 1 3 login parameter 5 1 5 2 M Microsoft DOS shell 5 1 Microsoft Excel application 1 1 N New Document dialog box 3 4 Non Enterprise configuration 2 1 noqueue parameter 5 2 Index 1 O template parameter 5 3 Options dialog 3 3 Output Folder Glossary 2 V output parameter 5 2 verbose parameter 5 3 Vial ID 3 5 P Parameters 5 2 Pre Installation Summary screen 2 2 Problem Files Glossary 3 Problem Files folder 3 3 Processed Files Glossary 3 Processed Files folder 3 3 Q queue parameter 5 2 R Reaction Container Glossary 3 Run Log window 1 3 S Scientist level 3 1 5 2 scripting language 5 1 SDS Database Glossary 3 SDS Plate Document Glossary 3 SDS plate documents 3 2 SDS Plate Utility 1 1 SDS Plate Utility dialog box 2 2 SDS Plate Utility Log Files folder 1 3 SDS Template Glossary 3 SDS Template Document 3 4 SDS templates
4. all the chemicals needed to be run on the 7900HT instrument and has a unique identifier usually in the form of a one dimensional barcode Before a reaction container real time or endpoint assay is run on a 7900HT instrument an SDS Plate Document file or database entry that contains the unique identifier of the physical reaction container must be created SDS Database The database refers to the database part of the SDS 2 1 Enterprise Option package SDS Plate Document The SDS Plate Document contains information needed to run a reaction container on the 7900HT instrument The SDS Plate Utility creates an SDS Plate Document for each Container Setup file that is successfully processed SDS Template The SDS Template document is generated by the SDS application To be used by the SDS Plate Utility an SDS Template must at a minimum contain thermocycle run conditions SDS Plate Utility User Guide Glossary 3 Glossary 4 SDS Plate Utility User Guide Index Numerics 7900HT instrument 1 1 A ABI PRISM 6700 sample prep instrument 4 2 AIF Watch Folder Glossary 1 Assay ID 3 5 Assay Information Files 4 2 Glossary 1 assay parameter 5 3 Assays on Demand products 1 1 Automation Controller software 3 3 C Choose Install Folder screen 2 2 command line interface 5 1 Command Prompt window 5 1 comments 1 4 Container Setup File format 3 6 Container Setup File Watch Folder Glossary 2 Container Setup Files 3 5 Glossary
5. eh et A Tae anne Hardware i052 2 a a A 2k Software muii ceo haw a a mw cece we ada Creating SDS Plate Documents Database Setup fis cu tats ras Ped SDS Template Files iss otis a oda eRe dibs SN He ee eS Creating an SDS Template 0 000 oo Creating Container Setup Files 000 00 cece Container Setup Files 000 00 cee eee Container Setup File Specification oooocoocconcooooo Detector List File for SDS Software Assay Information Files 0 0000 c eee eee es Electronic Data Sheet Files 0 00 c eee eee eee SDS Plate Utility User Guide Chapter 5 Using the Command Line Glossary Index SDS Plate Utility User Guide Introduction The SDS Plate Utility Software is designed for users who perform high throughput analyses and need to generate SDS Plate Documents automatically It is designed for use with the ABI PRISM 7900HT instrument and Assays on Demand products The SDS Plate Utility v2 1 software performs two related functions e Creates SDS Plate Documents for Gene Expression and Genotyping reaction containers e Generates a detector information text file using the Detector List Builder software based on assay information files from the Assays on Demand product CD You can set up the SDS Plate Utility software to run manually or automatically The SDS Plate Documents generated by the SDS Plate Utility are compatible with the SDS v2 1 Application n
6. the noqueue option Enterprise The SDS Plate Utility automatically adds created SDS Plate Documents to the SDS Enterprise Database defined during the installation Install Note Before installing in Non Enterprise mode with Automation install SDS v2 1 with Automation Note Before installing in Enterprise mode install and start the SDS Enterprise database on the server To install the software 1 Close any open applications 2 Insert the SDS Plate Utility Software CD into the CD drive and close the drive door SDS Plate Utility User Guide 2 1 Chapter 2 Installation Hardware 7 8 9 If autoplay is enabled the Introduction screen of the SDS Plate Utility installer appears momentarily If the installer does not open automatically in Windows Explorer open the CD directory SDS Plate Utility 2 1 and double click Setup exe In the Introduction screen of the SDS Plate Utility dialog box click Next Select Enterprise Mode or Non Enterprise Mode If you select Enterprise Mode setup the database connection In the Choose Install Folder screen select a destination directory for the installation To install on the D drive recommended click Next Note If you are installing in Non Enterprise mode on the same machine where the SDS v2 1 software is located you must use the directory recommended by the installer To install on another directory click Choose select a directory click OK then click Next
7. this document This document is believed to be complete and accurate at the time of publication In no event shall Applied Biosystems be liable for incidental special multiple or consequential damages in connection with or arising from the use of this document Software and firmware programs are protected by copyright It is unlawful to duplicate these programs in any manner other than for the user s personal use Specifically it is unlawful to use or duplicate these programs other than for use with the purchaser s computer Trademarks Applied Biosystems is a registered trademark and AB Design Applera and Assays on Demand are trademarks of Applera Corporation or its subsidiaries in the US and or certain other countries Microsoft and Windows NT are registered trademarks of Microsoft Corporation TaqMan is a registered trademark of Roche Molecular Systems Inc All other trademarks are the sole property of their respective owners 4343738 Rev A 4 2003 Contents Chapter 1 Chapter 2 Chapter 3 Chapter 4 Introduction Creating SDS Plate Documents 0 0 e ee eee Generating Detector List Files oooooooommoooo LOG FileS yed 02 a ee iG EA OR as Technical Support 00 0000 eee Send Comments o Further Documentation 0 0 0000 ccc eee Installation Non EnterpriSe vs s su nce eee sc eee ee ee eee es Enterpris uva AN ea A Ae ee ieee tae ia a WS tAM ss ees Stee a ete ee teed ee
8. 3 4 Select a New Watch Folder dialog box 3 2 Select an AIF EDS folder dialog box 3 2 Setup exe 2 2 software 2 3 T Technical Support 1 3 Index 2 SDS Plate Utility User Guide Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches into 150 countries on six continents For sales office locations and technical support please call our local office or refer to our web site at www appliedbiosystems com www appliedbiosystems com Applied Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 4 2003 Part Number 4343738 Rev A an Applera business
9. ainer Container Setup Files contain e Reaction container ID barcode e Plate format 384 96 well e Detector information for RQ plates optional Detector Name Reporter Quencher Description Comment e Marker information for AD plates optional e Well content information Sample Detector and Marker can reference assays defined in AIF or EDS files by either the Assay ID or Vial ID A Vial ID is a reference to a 2 D barcode on a Matrix tube shipped from Applied Biosystems A Vial ID reference found in a Container Setup File is resolved to its corresponding Assay ID by the SDS Plate Utility and then processed the same as a reference to an Assay ID No Vial ID references are passed through to the SDS Plate Document Vial ID values are 10 digits long The SDS Plate Utility will add leading zeros to any Vial ID field that is encountered that is less than 10 digits in length Note For AIF files before version 2 1 3 the Vial ID field was located in EDS files SDS Plate Utility User Guide 3 5 Chapter 3 Creating SDS Plate Documents Container Setup File Specification The Container Setup File is a tab delimited text file Container setup files cannot contain empty lines Each line terminates with a carriage return character Unicode 0x000D You can create container setup file templates in third party applications such as a database LIMS program or spreadsheet program such as Microsoft Excel Note Container Setup Fi
10. ch folders to be continuously monitored If the continuous command is not used the software looks in the folder processes the files and then stops If the input command specifies a single Container Setup File the continuous command is ignored verbose V Enables a verbose output SDS Plate Utility User Guide 5 3 Chapter 5 Using the Command Line 5 4 SDS Plate Utility User Guide Glossary AIF Watch Folder This is the folder on the computer s hard disk where the user must copy AIF and EDS files shipped on CD with each assay order The default location for this folder is D Applied Biosystems Put AIF and EDS Files Here If that location does not exist then the default will be a folder called Put AIF and EDS Files Here on the drive where the application is installed The AIF Watch folder is checked every 5 seconds by the application if running in GUI mode or in DOS Command Line mode with the continuous option to see if any new AIF and or EDS files have been copied to the folder If so then information is extracted from the new files and the Detector Import List file is updated Assay Information File AIF The Assay Information File is an ASCII text file that will be shipped on CD along with each Assay order The file contains specific information describing defining each of the Assays The information in this file will also be used by the SDS Plate Utility to help create the SDS p
11. chnical support and sales facilities SDS Plate Utility User Guide 1 3 Chapter 1 Introduction Send Comments Applied Biosystems welcomes your comments and suggestions for improving its manuals You can e mail your comments to techpubs appliedbiosystems com Further Documentation The following references contain useful information about the Applied Biosystems software and instrument Container Setup File Format PDF file on installation directory ABI PRISM 7900HT Sequence Detection System Chemistry Guide ABI PRISM 7900HT Sequence Detection System Installation Guide ABI PRISM 7900HT Sequence Detection System Service Manual ABI PRISM 7900HT Sequence Detection System Site Preparation and Safety Guide SDS v2 1 User Guide and online help SDS Plate Utility online help Automation Controller online help Assays on Demand SNP Genotyping Products Protocol SDS Plate Utility User Guide Installation The SDS Plate Utility v2 1 can be installed in one of two configurations Enterprise and Non Enterprise In both configurations the Detector List Builder software is installed Non Enterprise If you install on the same machine as the Automation Controller the SDS Plate Utility automatically adds created SDS Plate Documents to the SDS Automation Controller Queue However you can prevent adding SDS Plate Documents to the SDS Automation Controller Queue by running the SDS Plate Utility in DOS Command Line mode and using
12. elect an AIF EDS folder dialog box appears select a folder from the Applied Biosystems or other directory for example Applied Biosystems Put AIF and EDS files here Click Select Folder to use that folder To designate a watch folder a Inthe SDS Plate Utility main window click the Add a New Watch Folder button b In the Select a New Watch Folder dialog box select a folder from the Applied Biosystems or other directory for example Applied Biosystems Put Container Setup Files here c Click Select Folder to use that folder Add the container setup files containing the barcodes sample IDs and assay IDs to the selected Watch folder The system then creates the SDS Plate Documents SDS Plate Utility User Guide Database Setup 5 In Enterprise mode the system places the SDS Plate Documents in the SDS database In Non Enterprise mode the system places the SDS Plate Documents in the Applied Biosystems SDS Documents folder In Non Enterprise mode if the Automation Controller software is present on the computer the system also places the reaction containers on the Automation Controller plate queue for the 7900HT instrument The system places processed container setup files in the Processed Files folder for example Applied Biosystems Put Container Setup Files here Processed Files Note If the SDS Plate Utility is run from the DOS Command Line and the input command line argument refer
13. enerate an SDS template file file extension sdt To create an SDS template l 2 3 Launch the SDS software Select File gt New In the New Document dialog box add container information If performing quantitative PCR add thermal cycling parameters and data collection options Note Do not enter sample information You can edit detector and marker information but be aware that the specific detector and marker information will be used in all subsequent SDS Plate Documents created from that template Click OK Select File gt Save As to save the plate document as a template file In the Save As dialog box select Files of Type gt SDS Template Document sdt Navigate to the Project watch folder for example Applied Biosystems Put Container Setup Files here Click Save SDS Plate Utility User Guide Creating Container Setup Files Creating Container Setup Files You can use a database LIMS software or spreadsheet application to generate container setup files Applied Biosystems recommends creating container setup files automatically using a database or LIMS software The format of container setup files is given in Container Setup File Format Specification Example container setup files are located in the Applied Biosystems SDS Plate Utility Example Files folder Container Setup Files A Container Setup File extension txt is a description of what is ona physical reaction cont
14. er s AIF and EDS files and provide a list of those detectors in a format that can be imported into the SDS application the Detector Import List file Electronic Data Sheet file Prior to Assay Information Files AIF version 2 1 3 an Electronic Data Sheet EDS file contained the Vial IDs AIF files version 2 1 3 and higher contain the Vial ID field Starting with AIF v2 1 3 EDS are no longer needed by the SDS Plate Utility Output Folder For Non Enterprise mode this is the folder on the computer s hard disk where the SDS Plate Utility will write new SDS Plate Documents The default location of this folder is D Applied Biosystems SDS Documents Glossary 2 SDS Plate Utility User Guide Problem Files These are folders on the computer s hard disk where the SDS Plate Utility will write container setup files that were processed with errors Each Container Setup File Watch folder will have a Problem Files folder The default location of this folder is D Applied Biosystems Put Container Setup Files here Problem Files Processed Files These are folders on the computer s hard disk where the SDS Plate Utility will write setup files that were processed without error Each Container Setup File Watch folder will have a Processed Files folder The default location of this folder is DAApplied Biosystems Put Container Setup Files here Processed Files Reaction Container The reaction container typically a plate contains
15. er the command with no parameters SDSPlateUtil bat To launch the software with parameters at the command prompt enter SDSPlateUtil bat lt arguments gt An example is SDSPlateUtil bat i D InputFolder o D OutputFolder t D TemplateFile sdt c 5 1 Chapter 5 Using the Command Line Parameters can appear in any order in the command line however the parameters and their values must not be separated The maximum number of parameters and values allowed is nine 9 For example the above command has seven 7 Note You must have user access level of Scientist or above to run the SDS Plate Utility from the command line when using the login option The available command line arguments are in the following table Argument Definition login lt value gt lt value gt Only available if Enterprise option was installed lt value gt has the form username password This option disables output to Automation Controller queue queue Adds created SDS Plate Documents to the Automation Controller queue the default The queue command is ignored if login was used noqueue nq Does not add created SDS Plate Documents to the Automation Controller queue input lt value gt i lt value gt required Specifies the path of the project watch folder or the name of a single container setup file To specify multiple watch folders separate the added directo
16. es are located in the default Put AIF and EDS Files Here folder or a user specified AIF watch folder If running in SDS Enterprise mode you must log into the SDS database before the AIF Watch folder files can be processed Electronic Data Sheet Files Prior to Assay Information Files AIF version 2 1 3 an Electronic Data Sheet EDS file contained the Vial IDs AIF files version 2 1 3 and higher contain the Vial ID field Starting with AIF v2 1 3 EDS are no longer needed by the SDS Plate Utility SDS Plate Utility User Guide 4 3 Chapter 4 Detector List File for SDS Software 4 4 SDS Plate Utility User Guide Using the Command Line The SDS Plate Utility Software can be run from the command line of a Microsoft DOS shell Command Prompt window Use the command line interface to drive the application using a scripting language To run the software in Enterprise mode the login parameter must be specified so that you can log in to the database Note You must shutdown the application via the GUI if the continuous argument is used with the SDSPlateUtil bat command at the command line prompt To run the software from a command line 1 SDS Plate Utility User Guide On the desktop click Start gt Programs gt Accessories gt Command Prompt At the command prompt C gt enter cd D Program Files Applied Biosystems SDS 2 1 Press Enter To launch the software using the GUI at the command prompt ent
17. ilder to extract SDS Detector information from all your AIF and EDS files SDS Plate Utility User Guide Log Files and import the Detector List into the SDS application Detector Manager You can then select the list of available Assays on Demand detectors in the SDS application and use the SDS application GUI to design SDS Plate Documents Log Files An ASCII text file is generated every time the application is launched The log file names have the format SDSPlateUtil log yyyy mm dd hh mm ss txt For example SDSPlateUtil log 2003 01 18 10 09 45 txt The log files are in the application installation directory in the SDS Plate Utility Log Files folder The application displays a Run Log window You can close this window without affecting output to the Run Log file Technical Support To contact Applied Biosystems Technical Support in North America by telephone call 1 800 899 5858 To access the Applied Biosystems Web site go to http www appliedbiosystems com At the Applied Biosystems Web site you can e Search through frequently asked questions FAQ Submit a question directly to Technical Support e Order Applied Biosystems user documents MSDS certificates of analysis and other related documents Download PDF documents e Obtain information about customer training Download software updates and patches In addition the Applied Biosystems Web site provides telephone and fax numbers for te
18. late document Assay Information File Versions 2 1 4 and above contains the Vial ID 2D barcode field for the specific assay tubes Container Setup File This is a user generated ASCII text file that contains the description of the contents of a specific unique Plate ID reaction container including well sample information and well assay information Support for both 96 and 384 well containers as well as 384 well 7900HT Micro Fluidic Card SDS Plate Utility User Guide Glossary 1 Container Setup File Watch Folder This is a folder on the computer s hard disk where the user must place their Container Setup Files Each Setup File Watch Folder must contain an SDS Template Document To create SDS Plate Documents the utility will combine each Container Setup File with the SDS Template that is in the same folder as the Setup Files There can be multiple Setup File Watch Folders One reason that a user may wish to have multiple Setup File Watch Folders would be that they have multiple thermocycle protocols In this case they would have multiple SDS Template documents that reflect those protocols Each SDS Template must be contained in a unique Setup File Watch Folder Container Setup Files would be added to the appropriate folder depending on which thermocycle parameters were desired for the specific reaction container Detector Import List The SDS Plate Utility provides a mechanism to extract SDS Detector information from all of the us
19. le version 4 and higher documents cannot be imported directly into SDS version 2 0 or 2 1 software The Container Setup File format is described in the PDF document Container Setup File Format available in the SDS Plate Utility directory 3 6 SDS Plate Utility User Guide Detector List File for SDS Software Using one or more assay information files from the Assays on Demand product CD the SDS Plate Utility software can generate a list of detectors for the Assays on Demand reagents using the Detector List Builder software You later import the detector information text file called Detector List txt using the Detector Manager of the SDS software for use with the ABI PRISM 7900HT Sequence Detection System To create a detector information text file 1 Insert the Assays on Demand CD into the CD drive of the computer 2 Copy the assay information files AIF and electronic data sheets EDS files on the CD into the AIF EDS watch folder such as Applied Biosystems Put AIF and EDS files here Do not edit AIF or EDS files Do not remove files after they have been transferred to the watch folder 3 Repeat steps 1 and 2 for each Assays on Demand CD that you have received 4 From the desktop double click the Detector List Builder icon or select Start gt Programs gt Applied Biosystems gt Detector List Builder Note To use the detector list file open the SDS Software open the Detector Manager and impo
20. n SDS Plate Utility User Guide Electronic Data Sheet Files A Vial ID is a reference to a 2 D barcode on a Matrix tube shipped from Applied Biosystems No Vial ID references are passed through to the SDS Plate Document Vial ID values are 10 digits long The SDS Plate Utility will add leading zeros to any Vial ID field that is encountered that is less than 10 digits in length Note For AIF files before version 2 1 3 the Vial ID field was located in EDS files The following are the data fields that define an SDS Detector e Detector Name e Reporter Quencher e Description Comment An AIF helps the SDS Plate Utility generate SDS plate documents since it supplies information about the detectors and markers The SDS Plate Utility software creates detector and marker information The assay ID number and 2D bar code located on the bottom of each Assays on Demand reagent vial vial ID maps to the corresponding detector and marker information for the assay The SDS plate document matches the detectors and markers to the assay ID numbers or 2D bar codes contained in the Well Definition List section of a container setup file In order for an SDS Template Document to be combined with a Container Setup File the plate size of the two files must be identical For example an SDS Template Document that defines a 384 well reaction container cannot be combined with a Container Setup File that defines a 96 well reaction container AIF fil
21. ot with SDS v2 0 x applications Creating SDS Plate Documents The SDS Plate Utility creates SDS Plate Documents for Gene Expression and Genotyping using the following files e Container Setup Files which contain plate information SDS Template Documents which contain thermal cycling information e optional Assay Information Files which contain detector and marker information Note It is recommended that user provided Container Setup Files be generated with an automated LIMS or other software mechanism To generate the tab delimited text file in Container Setup File format you can also use a spreadsheet program such as Microsoft Excel To create single SDS Plate Documents it is recommended that you use the graphical user interface in the 7900HT software SDS Plate Utility User Guide 1 1 Chapter 1 Introduction Enterprise Mode If the application is running in Enterprise mode a temporary SDS Plate Document is written to the hard disk The temporary SDS Plate Document is then added to the SDS Enterprise Database and the temporary file is deleted from the hard disk If the SDS Plate Utility and the Automation Controller software are connected to the same SDS Enterprise database 7900HT instruments running Automation Controller software in SDS Enterprise mode will query the SDS database for SDS Plate Documents when a reaction container is presented to the 7900HT instrument Assuming the SDS Plate Utility has previousl
22. p Files added to that Watch folder to produce SDS Plate Documents For example a customer who has three different thermocycle protocols would need three SDS Template Documents and three Container Setup File Watch Folders Each Watch Folder would contain one of the SDS Template Documents SDS Plate Utility User Guide 3 1 Chapter 3 Creating SDS Plate Documents Before creating SDS plate documents 1 If you are using Genomic Assays Assays on Demand reagents copy the assay information files AIF and electronic data sheets from the Genomic Assays CD to the Put AIF and EDS files here folder The files contain the detector information required for the SDS plate documents to be made Note Do not edit AIF or EDS files Never remove AIF or EDS files from the Put AIF and EDS files here folder Place a single SDS template file with extension sdt and containing the assay method thermal cycling parameters and data collection options into the Container Setup File Watch folder you intend to use Each SDS Template has its own Watch Folder To create SDS plate documents 1 4 Open the SDS Plate Utility software by double clicking the SDS Plate Utility icon or selecting Start gt Programs gt Applied Biosystems gt SDS Plate Utility If you are running in Enterprise mode you must log in at the SDS Plate Utility Log In dialog If you are running in Enterprise mode you can also use Database Setup If the S
23. rt the Detector List txt file to display the detector and marker information in the Detector Manager window SDS Plate Utility User Guide 4 1 Chapter 4 Detector List File for SDS Software Assay Information Files 4 2 An Assay Information File AIF is an ASCII text file shipped with an Assays on Demand product There is an AIF for each Matrix TrakPlate container of assays supplied An AIF is used by the SDS Plate Utility and the Detector List Builder to generate a detector list file The detector information file can be imported into the Detector Manager of the SDS software The following data fields are extracted from AIF files by the SDS Plate Utility The following fields are available in all AIF file formats e Assay ID e Vial ID e Gene Symbol e Gene Name e Context Sequence The following fields are extracted in file versions up to and including AIF 2 1 4 e Reporter 1 e Reporter 2 this field does not appear in AIF 2 1 4 files for GeX assays Quencher The following fields are extracted from AIF files version 3 0 0 and later e Reporter 1 Dye e Reporter 1 Quencher e Reporter 2 Dye e Reporter 2 Quencher The SDS Plate Utility can process container setup files that contain no external Assay ID or Vial ID references such as files made by the ABI PRISM 6700 sample prep instrument For this case no AIF file or AIF watch folder is needed The SDS Plate Utility asks you to confirm this situatio
24. ry paths by semicolons for example SDSPlateUtil input D InputFolder E InputFolder output lt value gt o lt value gt Specifies the path of the output folder for created SDS Plate Documents for example SDSPlateUtil output D OutputFolder If output is not used the default folder is D Applied Biosystems SDS Documents 5 2 SDS Plate Utility User Guide Argument Definition t lt value gt template lt value gt Specifies the name of the SDS Template sdt file for example SDSPlateUtil template D TemplateFile sdt If the template parameter is not specified the system uses the SDS template file in the same directory as the container setup file If the input command value is a single Container Setup File the template argument must be used If the input command value is one or more Container Setup Plate Watch folders the SDS Template File defined by the template command is used instead of any SDS Template Files located in the Container Setup File Watch folders assay lt value gt a lt value gt Specifies the path of the AIF file watch folder for example SDSPlateUtil assay D AlFFolder Note Otherwise the default AIF file watch folder is used D Applied Biosystems Put AIF and EDS files here continuous C Can be added after an input command specifying a folder not a file to allow the specified wat
25. s to a single file the Container Setup File is left in its original location If the SDS Plate Utility software cannot make an SDS plate document it moves the container setup file to the Problem Files folder for example Applied Biosystems Put Container Setup Files here Problem Files and notes the action failed in the Command Prompt window Database Setup The Database Options dialog allows you to change databases To change databases 1 In the SDS Plate Utility Log In dialog click Database Setup The Options dialog displays the current connection Host Name Port Number e Service Name 2 Click New to make a new connection 3 Enter the new Host Name Port Number and Service Name In the Options dialog you can change the connection to a different SDS Enterprise Database SDS Plate Utility User Guide 3 3 Chapter 3 Creating SDS Plate Documents SDS Template Files The SDS Template Document extension sdt contains thermocycle information used to run the plate on the 7900HT instrument Thermal Cycling Conditions e Data Collection Parameters In order for an SDS Template Document to be combined with an Container Setup File the plate size of the two files must be identical For example an SDS Template Document that defines a 384 well reaction container cannot be combined with an Container Setup File that defines a 96 well reaction container Creating an SDS Template Use the SDS software to g
26. software creates SDS Plate Documents for the ABI PRISM 7900HT Sequence Detection System using container setup files reaction container information SDS template files thermocycle information and optional assay information files Assays on Demand reagent information In Non Enterprise mode the SDS Plate Utility writes the new SDS Plate Documents to the local hard disk default output folder is Applied Biosystems SDS Documents The software also adds the SDS Plate Documents to the Automation Controller plate queue if the SDS Automation Accessories software is available In Enterprise mode new SDS Plate Documents are added to the SDS Enterprise database Note You must have user access level of Scientist or above to run the SDS Plate Utility in Enterprise mode just as in the SDS application users must have Scientist or higher privileges in order to save SDS Plate Documents to the SDS database You must designate at least one Container Setup File Watch folder A Container Setup File Watch Folder is a folder on the local hard disk that as the name implies is watched by the SDS Plate Utility for Container Setup Files When Container Setup Files are added to the Watch Folder the SDS Plate Utility attempts to build an SDS Plate Document from each Container Setup File Each Watch Folder must contain one and only one SDS Template Document Thermocycle information from the SDS Template Document is combined with the Container Setu
27. y saved an SDS Plate Document for the reaction container the Automation Controller software will extract the appropriate SDS Plate Document from the SDS database Non Enterprise Mode If the application is running in Non Enterprise mode the output SDS Plate Documents are added to a designated folder on the hard disk If the SDS Plate Utility v2 1 AND the SDS v2 1 Application have been installed with the Non Enterprise option AND with Automation Accessories options the software moves the SDS Plate Document to the Automation Controller plate queue Generating Detector List Files The SDS Plate Utility generates the Detector List File which is a list of all SDS Detector information contained in Assay Information Files AIF AIF are supplied by Applied Biosystems on the Assays on Demand product CD and copied to the hard disk by the user A new Detector List File is generated each time the SDS Plate Utility is launched Alternatively it can be generated by launching the application from the Detector List Builder Windows shortcut Once built you can import the Detector List File into the Detector Manager of the SDS software for use with the ABI PRISM 7900HT Sequence Detection System Note The SDS Plate Utility does not provide a GUI to define reaction containers For customers that do not generate plate specific Container Setup Files with an automated software mechanism e g a LIMS system it is recommended to use the Detector List Bu
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