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Release Notes New Features in Factura

1. and Estonia Warszawa Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Russia Moskva 7 095 935 8888 7 095 564 8787 South East Europe Zagreb Croatia 385 1 34 91 927 385 1 34 91 840 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 1206 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d IJssel 31 0 180 331400 31 0 180 331409 United Kingdom Warrington Cheshire 44 0 1925 825650 44 0 1925 282502 Release Notes New Features in Factura Software v 2 2 Page 13 of 16 To Reach Technical Support Through the Internet Page 14 of 16 Telephone Fax Region Dial Dial All other countries not 44 0 1925 282481 44 0 1925 282509 listed Warrington UK Japan Japan Hacchobori 81 3 5566 6230 81 3 5566 6507 Chuo ku Tokyo Latin America 305 670 4350 Del A Obregon Mexico 305 670 4349 We strongly encourage you to visit our Web site for answers to frequently asked questions and for more information about our products You can also order technical documents or an index of available documents and have them faxed or e mailed to you through our site The Applied Biosystems Web site address is http Awww appliedbiosystems com techsupp To submit technical questions from North America or
2. You should edit your cshrc file or your profile file to set the these environment variables as follows Note These examples are given for a C shell If you are using a different shell e g a Bourne or Korn see your network administrator for assistance Page 6 of 16 Release Notes New Features in Factura Software v 2 2 BIOLIMS_CONF Specify the path name to the database connection file using the Variable BIOLIMS_CONMF environment variable This example points to a database connection file biolims conf in the user s own Factura directory setenv BIOLIMS CONF factura biolims conf If you move or rename the database connection file remember to edit your cshrc or profile file to point to the correct file name and location Note If the BIOLIMS_COMF environment variable is not set the existence of a file named biolims conf in the current directory is assumed The Database Connection File The database connection file is a four line text file of the form database account user name database account password database name server name For example the following file would permit a user named sfdb with password george to connect to the BioLIMS database sfdb on the server ID called Oracle sfdb georgel sfdb Oracle Note For Oracle the database name and the user name must be the same An example connection file named biolims conf is provided in the factura directory ORACLE_HOME You need to set the ORACLE_HOME
3. 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 then press 32 1 650 638 5981 PCR and Sequence Detection 1 800 762 4001 then press 1 for PCR 2 for the 7700 or 5700 6 for the 6700 or dial 1 800 831 6844 then press 5 1 240 453 4613 Release Notes New Features in Factura Software v 2 2 Page 11 of 16 Product or Telephone Fax Product Area Dial Dial Voyager MALDI TOF 1 800 899 5858 1 508 383 7855 Biospectrometry and then press 13 Mariner ESI TOF Mass Spectrometry Workstations Biochromatography 1 800 899 5858 1 508 383 7855 BioCAD Workstations then press 14 and Poros Perfusion Chromatography Products Expedite Nucleic acid 1 800 899 5858 1 508 383 7855 Synthesis Systems then press 15 Peptide Synthesis 1 800 899 5858 1 508 383 7855 Pioneer and 9050 Plus then press 15 Peptide Synthesizers PNA Custom and 1 800 899 5858 1 508 383 7855 Synthesis then press 15 FMAT 8100 HTS System 1 800 899 5858 1 508 383 7855 and Cytofluor 4000 then press 16 Fluorescence Plate Reader Chemiluminescence 1 800 542 2369 1 781 275 8581 Tropix U S only or 1 781 271 0045 Applied Biosystems MDS 1 800 952 4716 1 650 638 6223 Sciex Outside North America Telephone Fax Region Dial Dial Africa and the Middle East Africa English Speaking 27 11 478 0411 2
4. The Factura v 2 2 Application is included on the DNA Sequencing Analysis installation CD ROM For information on how to install Factura v 2 2 refer to Chapter 2 of the ABI PRism DNA Sequencing Analysis Software User s Manual P N 4306158 Note Be sure to check the Factura 2 2 box in the Sequencing Analysis Installer window Approximately 18 5MB of disk space is required to install Factura Vv 2 2 Sequencing Analysis Installer SS Custom Install w O ABI Prism 310 only O ABI Prism 37 only O Both 310 and 378 amp Factura 2 2 Disk space available 874 080K Approximate disk space needed 18 656K EL a aaas The folder Sequencing Analysis 3 3 will be created on J the disk Hard_Disk Install Location _Hard_Disk v Page 3 of 16 Using Factura v 2 2 Software with BioLIMS v 2 0 Database Introduction Set Up for Database Connection Page 4 of 16 Using Factura v 2 2 Software with a BioLIMS v 2 0 Database is similar to using Factura v 2 1 Software with a BioLIMS v 1 0 Database Use of Factura v 2 1 with a BioLIMS 1 0 Database is described in Appendix B of the ABI PRISM Factura Feature Identification Software User s Manual P N 904946 Differences between using Factura v 2 1 with BioLIMS v 1 0 and Factura v 2 2 with BioLIMS v 2 0 are noted below Factura v 2 2 works with the BioLIMS v 2 0 Database Your BioLIMS database may run on either an Oracle or a Sybase server B
5. 7 11 478 0349 and West Asia Fairlands South Africa South Africa 27 11 478 0411 27 11 478 0349 Johannesburg Middle Eastern Countries 39 0 39 8389 481 39 0 39 8389 493 and North Africa Monza Italia Page 12 of 16 Release Notes New Features in Factura Software v 2 2 Telephone Fax Region Dial Dial Eastern Asia China Oceania Australia Scoresby 61 3 9730 8600 61 3 9730 8799 Victoria China Beijing 86 10 64106608 86 10 64106617 Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 82 2 593 6470 6471 822593 6472 Malaysia Petaling Jaya 60 3 758 8268 60 3 754 9043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 2358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 66 2 319 9788 Europe Austria Wien 43 0 1 867 35 75 0 43 0 1 867 35 75 11 Belgium 32 0 2 712 5555 32 0 2 712 5516 Czech Republic and Slovakia Praha 420 2 61 222 164 420 2 61 222 168 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0 9 251 24 243 France Paris 33 0 1 69 59 85 85 33 0 1 69 59 85 00 Germany Weiterstadt 49 0 6150 101 0 49 0 6150 101 101 Hungary Budapest 36 0 1 270 8398 36 0 1 270 8288 Italy Milano 39 0 39 83891 39 0 39 838 9492 Norway Oslo 47 23 12 06 05 47 23 12 05 75 Poland Lithuania Latvia 48 22 866 40 10 48 22 866 40 20
6. Europe Step Action 1 Access the Applied Biosystems Technical Support Web site 2 Under the Troubleshooting heading click Support Request Forms then select the relevant support region for the product area of interest 3 Enter the requested information and your question in the displayed form then click Ask Us RIGHT NOW blue button with yellow text 4 Enter the required information in the next form if you have not already done so then click Ask Us RIGHT NOW You will receive an e mail reply to your question from one of our technical experts within 24 to 48 hours Release Notes New Features in Factura Software v 2 2 To Obtain Documents on Page 15 of 16 Demand our Web site Free 24 hour access to Applied Biosystems technical documents including MSDSs is available by fax or e mail or by download from To order documents Then by index a Access the Applied Biosystems Technical Support number Web site at http Awww appliedbiosystems com techsupp Click the Index link for the document type you want then find the document you want and record the index number Use the index number when requesting documents following the procedures below by phone for From the U S or Canada call 1 800 487 6809 or fax delivery from outside the U S and Canada call 1 858 712 0317 Follow the voice instructions to order the documents you want Note There is a limit of f
7. Release Notes New Features in Factura Software v 2 2 1998 updated 03 2001 SUBJECT ABI PRISM Factura Feature Identification Software V 2 2 Summary of New Features The new features in Factura v 2 2 Software Factura installation now part of the Sequencing Analysis v 3 3 software installation see page 3 Support for the BioLIMS Genetic Information Management System version 2 0 Macintosh client support for the BioLIMS v 2 0 Database on an Oracle Database Server see page 4 The Collections Browser was Sequence Chooser see page 5 UNIX client support for the BioLIMS v 2 0 Database on an Oracle Database Server see page 6 gt Applied KS Biosystems In These Release These release notes supplement the ABI Prism Factura Feature Notes Identification Software User s Manual P N 904946 New information and instructions not documented in the user s manual are contained in these pages Topics in this document Topic See Page Installing Factura Software 3 Using Factura v 2 2 Software with BioLIMS v 2 0 Database 4 Using Factura for UNIX v 2 2 with BioLIMS v 2 0 Database 6 Known Problems 9 Technical Support 10 Page 2 of 16 Release Notes New Features in Factura Software v 2 2 Installing Factura Software To Install Factura v 2 2 Software The Sequencing Analysis Installer Window Release Notes New Features in Factura Software v 2 2
8. as been added For more information about this window refer to Chapter 3 of the ABI PRISM DNA Sequencing Analysis Software v 3 3 User s Manual P N 4306158 or to Appendix B of the AB Prism Factura Feature Identification Software User s Manual P N 904946 Release Notes New Features in Factura Software v 2 2 Page 5 of 16 Using Factura for UNIX v 2 2 with BioLIMS v 2 0 Database Introduction Installation Factura for UNIX is packaged with the BioLIMS Server CD ROM It should have been copied into a factura directory in the database user account when the BioLIMS database was installed Factura for UNIX with a BioLIMS Database on a Sybase SQL Server If you are using Factura for UNIX v 2 2 Software with a BioLIMS v 2 0 Database running on a Sybase server follow the instructions Using the BioLIMS database found in Appendix B of the ABI Prism Factura Feature Identification Software User s Manual P N 904946 Factura for UNIX with a BioLIMS Database on an Oracle Database Server If you are using Factura for UNIX v 2 2 Software with a BioLIMS v 2 0 Database running on an Oracle server set the environment variables for Oracle Server connection as described below The Oracle There are five environment variables that you need to set in order to Environment use Factura for UNIX to process sequences from the BioLIMS Variables database BIOLIMS_CONF ORACLE_HOME LD_LIBRARY_PATH ORACLE_SID TNS_ADMIN 5 gt gt gt
9. emark and Sybase SQL Server is a trademark of Sybase Inc All other trademarks are the sole property of their respective owners P N 4304076B
10. environment variable to point to Variable the directory that contains the Oracle software For example setenv ORACLE HOME export home oracle v7 Release Notes New Features in Factura Software v 2 2 Page 7 of 16 LD_LIBRARY_ You need to include the directory of the Oracle Server shared library PATH Variable files in the library path list At installation these files are placed in the ORACLE_HOME lib directory For example setenv LD LIBRARY PATH SORACLE HOME 1lib LD LIBRARY PATH ORACLE_SID You need to set the ORACLE_SID environment variable to the value Variable of the system identifier sid of the database You should obtain this information from your database administrator For example setenv ORACLE SID oracle TNS_ADMIN You need to set the TNS_ADMIN environment variable to the path of Variable the tnsnames ora file for the Oracle Server For example setenv TNS ADMIN SORACLE HOME network admin Page 8 of 16 Release Notes New Features in Factura Software v 2 2 Known Problems Save a Copy As The Save a Copy As command used to save copies of the Factura Command Missing Log window is not available in the Factura v 2 2 program File Formats for Page A 13 of the ABI Prism Factura Feature Identification Software Factura for UNIX User s Manual P N 904946 incorrectly states that Factura for UNIX supports INHERIT files Factura for UNIX supports sample files text files and Pearson files as input formats Fac
11. ioLIMS v 1 0 worked with a Sybase SQL Server only Information about setting up the connection between the client applications e g Factura v 2 2 Sequencing Analysis v 3 3 and the database is given in Chapter 3 of the AB PRism DNA Sequencing Analysis Software v 3 3 User s Manual P N 4306158 Release Notes New Features in Factura Software v 2 2 Collection Browser The window that was called the Sequence Chooser in Factura v 2 1 is called the Collection Browser window in Factura v 2 2 Collection Browser HE Select criteria Dd Select sequences to process Collection Creator contains y Collection Name contains y Collection Type is Creation Date ani Modification Date ani Sequence Frag Name contains bad Sample Creator contains v Sample Name contains bd Instrument Name contains v Instrumentation is Start Collect Date ani Y End Collect Date ani beaa Gel File Path contains v Sequence Status Bases Length Name Modified Sample Name Type b amp 3826Test Jul 01 1998 12 10 11 PM project b amp david Jul 06 1998 04 30 15 PM project b amp jeff Jul 20 1998 04 26 55 PM project b amp L28_sequences Jul 22 1998 09 33 35 AM run oe 98 collections found Process Cancer Process Cancel Functionally this window is the same although one new search criterion Instrument Name h
12. is available at the Product Hours Chemiluminescence 8 30 a m to 5 30 p m Eastern Time Framingham support 8 00 a m to 6 00 p m Eastern Time All Other Products 5 30 a m to 5 00 p m Pacific Time Page 10 of 16 Release Notes New Features in Factura Software v 2 2 To Contact Technical Support by Telephone or Fax In North America To contact Applied Biosystems Technical Support use the telephone or fax numbers given below To open a service call for other support needs or in case of an emergency dial 1 800 831 6844 and press 1 Product or Product Area Telephone Dial Fax Dial ABI Prism 3700 DNA Analyzer 1 800 831 6844 then press 8 1 650 638 5981 DNA Synthesis 1 800 831 6844 then press 21 1 650 638 5981 Fluorescent DNA Sequencing 1 800 831 6844 then press 22 1 650 638 5981 Fluorescent Fragment Analysis includes GeneScan applications 1 800 831 6844 then press 23 1 650 638 5981 Integrated Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6844 then press 24 1 650 638 5981 ABI PRISM 3100 Genetic Analyzer 1 800 831 6844 then press 26 1 650 638 5981 Biolnformatics includes BioLIMS BioMerge and SQL GT applications 1 800 831 6844 then press 25 1 505 982 7690 Peptide Synthesis 433 and 43X Systems 1 800 831 6844 then press 31
13. ive documents per request through the a Access the Applied Biosystems Technical Support Internet for fax Web site at or e mail http Awww appliedbiosystems com techsupp delivery Under Resource Libraries click the type of document you want Enter or select the requested information in the displayed form then click Search In the displayed search results select a check box for the method of delivery for each document that matches your criteria then click Deliver Selected Documents Now or click the PDF icon for the document to download it immediately Fill in the information form if you have not previously done so then click Deliver Selected Documents Now to submit your order Note There is a limit of five documents per request for fax delivery but no limit on the number of documents you can order for e mail delivery Release Notes New Features in Factura Software v 2 2 L Copyright 2001 Applied Biosystems For Research Use Only Not for use in diagnostic procedures ABI PRISM the ABI PRISM design Applied Biosystems BioLIMS and GeneScan are registered trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries ABI and Factura are trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries Macintosh is a registered trademark of Apple Computer Inc Oracle is a registered trademark of Oracle Corporation Sybase is a registered trad
14. tura on the Macintosh does support INHERIT files Release Notes New Features in Factura Software v 2 2 Page 9 of 16 Technical Support Contacting You can contact Applied Biosystems for technical support by Technical Support telephone or fax by e mail or through the Internet You can order Applied Biosystems user documents MSDSs certificates of analysis and other related documents 24 hours a day In addition you can download documents in PDF format from the Applied Biosystems Web site please see the section To Obtain Documents on Demand following the telephone information below To Contact Contact technical support by e mail for help in the following product Technical Support areas by E Mail Product Area E mail address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing Peptide and DNA Synthesis corelab appliedbiosystems com Biochromatography PerSeptive DNA PNA and Peptide Synthesis systems CytoFluor FMAT Voyager and Mariner Mass Spectrometers tsupport appliedbiosystems com LC MS Applied Biosystems MDS Sciex apisupport sciex com or api3 support sciex com Chemiluminescence Tropix tropix appliedbiosystems com Hours for Telephone following times Technical Support In the United States and Canada technical support

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