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GEMTools Installation and Administration Guide

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1. Click Browse to open a window that will allow you to set a new location for the database This location should have sufficient disk space and good I O performance This location is the directory for the GEM Tools Server software Database Devices and GEMTools Client software distribution The directory will be accessible as a Windows Network Shared Directory after installation For the highest levels of performance the GEMTools data directory should reside on a SCSI disk device ideally a RAID Redundant Array of Inexpensive Disks device with 3 or more disks la IncyteGenomics Software Installation 15 Figure 2 6 GEMTools GEMtools Database Configuration Ea Database Configuration Window GEMtools Setup will create database devices in the directory shown below The recommended initial database sizes may be modified as desired r GEMtools Data Storage Location ENGEMTools m GEMtools Databases A Production Database Size MB 2s Sequence Database Size MB 2s te ee 8 Click Next 9 For new installations specify the size of the Production and Sequence databases Recommended sizes appear automatically 10 Click Next to open the Database Login Information window Figure 2 7 GEMTools GEMtools Database Configuration Database Login Information PJ Database Login Information i for the GE iuei Window In order for the GEMtools Server Setup to continue it needs account informatio
2. 68 GEMTools Installation and Administration Guide la IncyteGenomics Databases and Database Devices GEMTools requires that database devices and databases be created during installation e Devices are operating system files used to store databases transaction logs and their backups e Databases are storage space for data and schema design that is allocated on a device One device can store many databases and a database can be stored across more than one device Note GEM Tools database creation scripts are available for advanced users See Database and Device Creation on page 57 for more information See the Microsoft SQL Server reference manual for information about manually creating databases You can also use the Utilities window in the GEMTools client software to create GEMTools databases Devices and Databases in SQL Server 2000 and SQL Server 7 0 When you install GEMTools with SQL Server 7 0 the databases and devices are built simultaneously The databases and devices will expand automatically as required Devices and Databases in SQL Server 6 5 When you install SQL Server 6 5 these devices are created e The MASTER database device e The MSDBDATA and MSDBLOG database devices 4 IncyteGenomics Microsoft SQL Server Reference 69 e The MSDBDATA device is used by the msdb scheduling database and the MSDBLOG device is used by its transaction log e Three dump devices DISKDUMP DISKETTEDU
3. Creating a New Sort Order To create a new sort order 1 Click New 2 Enter a name for the sort order in the text box and click OK 3 Select the desired criteria from the Available Fields section of the window 4 Click Add to move the criteria to the Selected Fields section of the window 5 Specify the ascending descending order by clicking on the drop down menus to the right of the Order column entries If you do not specify the default order is used 4 IncyteGenomics Utilities 47 Piguie d 18 Order DropDown Menu _ Field Description Order E Differential Expression ASC DES Probel Name 6 Click Apply Deleting a Sort Order To delete a sort order 1 Select a sort order from the Sort Order menu 2 Click Delete 3 Click Yes Note Sort orders assigned by Incyte are read only and cannot be deleted Object Types Use the Object Types window to create new object types and delete and modify existing object types 48 GEMTools Installation and Administration Guide la IncyteGenomics Figure 3 19 Object Types Window Object GEM x New Type GEM Type Object Type Information gt GeneAlbum 2 0 Object Type Name GeneAlbum 2 0 Object Type Notes Creating New Types To create a new object type 1 Click New Type 2 Enter the new object type in the text box 3 Click OK Modifying an Object Name To modify t
4. Joint Venture diaDexus LLC 3303 Octavius Drive Santa Clara CA 95054 Tel 1 408 496 6600 Fax 1 408 496 5777 Customer Support If you have any questions or would like more information about our training programs contact our customer support at Incyte Technical Support 4678 World Parkway Circle St Louis Missouri 63134 Tel 1 800 430 0030 toll free in the U S Fax 1 888 919 3324 toll free in the U S E mail service stl incyte com viii GEMTools Installation and Administration Guide fa IncyteGenomics Requirements System Configuration The Incyte GEMTools software is a powerful set of integrated tools for managing and analyzing gene expression information GEM Tools software provides a complete enterprise solution based on relational database technology and the Microsoft Windows operating system The GEMTools software uses ODBC compliant client server technology and is designed to integrate with Microsoft SQL Server 2000 SQL Server 7 0 and Microsoft SQL Server 6 5 Note The GEMTools database can also be integrated with extended bioinformatics systems using Oracle database technology The GEM Tools software can be deployed on systems ranging from a stand alone laptop installation to a worldwide network of thousands of GEM Tools workstations In a multi user client server installation the GEMTools shared database and housekeeping software reside on a central server running Windows 2000 or Window
5. S Fa IncyteGenomics The GEMTools Registration window opens Figure 2 3 GEMTools Registration Window GEMTools Registration xi To complete the installation of GEMTools Server you must enter a valid registration key To obtain a registration key please provide the identification numbers listed below to your Incyte Microarray Systems customer representative Phone 1 800 430 0030 E mail gemsupport incyte com Server Identification Number SGT 57231902 5 Client Identification Number SGT 76208351 Enter your GEMT cols Product Registration Key below Registration Key 4e a lt Back Next gt Cancel 4 Enter your Server Product Registration Key To obtain a server registration key for new installations call our Customer Service see Customer Support on page 23 If you have previously installed GEMTools on your computer your current registration key remains valid Provide the customer service representative with the product identification numbers displayed in the GEMTools Registration window The representative will provide you with a registration key needed to install GEMTools on your workstation It is important that you write down this registration key for future reference 5 Enter the license key provided to you by your Incyte customer service representative or the temporary license key you received via e mail after downloading the GEMTools evaluation software from the web si
6. removing 32 removing privileges 34 Utilities window 25 to 50 Administrator tab 36 to 50 Change Password window 26 Companies tab 29 to 30 Databases tab 27 to 28 Preferences tab 35 zo 36 Privileges tab 33 to 34 Users tab 31 to 32 Ww web browser changing default 35 Web Links 61 to 63 Web links creating 44 deleting 44 Web Links window 39 4 Fa IncyteGenomics S
7. 1 Click Delete 2 Click Yes at the Prompt or click No to exit without deleting To change your default database 1 Click the Users tab of the Utilities window 2 Select a new database from the Default Database drop down list 28 GEMTools Installation and Administration Guide la IncyteGenomics Companies Use the Companies tab to view company information create new company profiles and delete existing company profiles When you select a company name you can only view the associated company information or delete the company profile You cannot change the company name associated with the current user profile Figure 3 3 Utilities Window Utilities mMm E Companies Tab Curent Database Pemor tration User Name Change Password Privileges Company Name Poo Delete New Edit r Company Information Address Phone Contact Name Contact Phone Customer Representative Customer Rep Phone M Defining a New Company To define a new company profile 1 Click New in the Companies window to open the New Company window 4e IncyteGenomics Utilities 29 Y Figure 3 4 New Company Window r Company Information Company Name Address Company Phone FC Contact Name Contact Phone Customer Representative Po Customer Rep Phone Notes 2 Enter the requested information in the fields in this window Note At least o
8. 9 Synchronize Window File name a Location mo El Browse button To synchronize your database 1 Click the browse button denoted by the ellipsis to search for and select the lt file gt cab file created by the Transfer Utility Your local CD ROM drive is selected by default 2 Click Start to import the differential update file into your database Before the update takes place GEMTools verifies the integrity of the data import file GEMTools also performs a security check to ensure the import file can only be imported into an authorized destination database If an error occurs please report it to our customer service department The transfer utility inserts rows into the current database and outputs a lt file gt log file containing the outcome of each record insertion The synchronization feature automatically updates the statistics of all GEMTools table indexes and truncates database logs Note Backup the database before a synchronization The log is truncated prior to synchronization 4 IncyteGenomics Utilities 37 Round Trip Confirmation The log file is named lt file gt log and resides in the Transfer subdirectory This file contains information about each record imported into the database The log file must be returned to the microarray facility after import for processing Ifan import fails for a particular record an ODBC or SQL error message is recorded in the log file Insertion
9. Company 29 Users 31 Choosing a Default Database 31 Adding New Users 31 Editing User Profiles 32 Removing Users 32 Privileges 33 Adding Privileges 33 Removing Privileges 34 Preferences 35 Web Browser 35 Default Adjustment Parameters 36 Administrator 36 Synchronize Databases 37 Internet Download 38 Import Sequences 40 Transfer 41 Web Links 43 Clone Source 45 Sort Builder 46 Object Types 48 4 GEMTools Server Reference 51 GEMTools Shared Directory 51 GEMTools Client Distribution Software 52 Objects 52 Configuration Objects 52 Customer Databases 53 Access Privileges 54 Access Privileges for GEM Microarrays Direct Customers 55 Users 56 Companies 57 iv GEMTools Installation and Administration Guide 4 IncyteGenomics GEMTools Server Installation 57 SQL Server Temporary Database 57 Database and Device Creation 57 GEMTools SQL Server Login 58 Configuring SQL Server for Optimal Performance 59 GEMTools Client Distribution Configuration File 60 External Application Interface 61 LifeSeq to GEMTools Gateway 63 Using the LifeSeq to GEMTools Gateway 65 5 Microsoft SQL Server Reference 67 Installing Microsoft SQL Server 67 Starting SQL Server 67 Administering SQL Server 68 Databases and Database Devices 69 Devices and Databases in SQL Server 2000 and SQL Server 7 0 69 Devices and Databases in SQL Server 6 5 69 Backing up Databases 70 Resizing a Database 71 Restoring a Database 71 Transaction Log 72 Truncating the Transactio
10. NT GEMTools server automatically configures the SQL Server Service to start automatically On Windows 95 and Windows 98 you can specify this option during SQL Server installation After installation you can change the autostart option by using SQL Enterprise Manager Refer to the Microsoft SQL Server documentation for more information Administering SQL Server Use the SQL Server Enterprise Manager to administer SQL Server 2000 SQL Server 7 0 and SQL Server 6 5 The first time you start SQL Enterprise Manager the Register Server window appears You must provide the name of one or more SQL Servers that you will be managing using SQL Enterprise Manager Each time you enter a new server name you must complete the login information After you enter a server name select either Use Standard Security or Use Trusted Connection This choice determines the type of security that will be used for the connection when SQL Enterprise Manager connects If you selected Use Standard Security in the Login ID box type the login ID of a valid administrative account such as sa for that server and in the Password box type the password for that login ID If you selected Use Trusted Connection the login ID and password are unnecessary Once you have registered a server it appears in the Server Manager window each time you start SQL Enterprise Manager You can immediately begin to perform tasks for that server using SQL Enterprise Manager
11. Reference 71 Full database and transaction log backups remain the basis of a proper backup strategy Refer to the Microsoft SQL Server documentation for more information on restoring a database Important After you restore GEMTools database you MUST change the database owner to be GEMTools This can be done using the sp_changedbowner stored procedure Transaction Log A database transaction log records all committed changes made to the database since the last full backup Transactions logs can be useful for data recovery The system administrator SA is responsible for maintaining the transaction log which requires the following steps 1 Placing the transaction log onto a separate database device from its database This is recommended for all user databases 2 Monitoring the transaction log with the sp_spaceused and sp_helpdb system procedures or the DBCC SQLPERF LOGSPACE statement 3 Backing up the transaction log 4 Keeping the transaction log at a reasonable size when the log is in a separate database device by regularly using the DUMP TRANSACTION statement or backup utility Note Databases may be set to use the option Truncate Log on Checkpoint to automatically truncate log information periodically For robust server operation this setting is typically not recommended Please consult the SQL Administration guide for advantages and disadvantages to this approach 72 GEMTools Installatio
12. ZooSeq Rat Incyte Clone ID URL http lt LIFESEQ SERVER gt Search Pattern cgi bin ZooSeq5 GeneQueryResults QueryMethod Clone ID amp Data s Search Fields Clone ID Description Links to Incyte s ZooSeq Rat Database LifeSeq Public Incyte Clone ID URL http www incyte com Search Pattern ilifeseq cid Data s amp QueryMethod Clone ID Search Fields Clone ID Description Links to Incyte s LifeSeq Public Database Prior registration is required to view the contents of this publicly accessible database 4 70 IncyteGenomics GEMTools Server Reference 61 SeqServer Sequence Information 5 Sequence ID URL http lt LIFESEQ SERVER gt Search Pattern cgi bin SeqServer SeqServer source LS amp module mretrieve amp qid s Search Fields 5 sequence ID Description Links to Incyte s SeqServer using the 5 Incyte Sequence ID SeqServer Sequence Information 3 Sequence ID URL http lt LIFESEQ SERVER gt Search Pattern cgi bin SeqServer SeqServer source LS amp module mretrieve amp qid s Search Fields 3 sequence ID Description Links to Incyte s SeqServer using the 3 Incyte Sequence ID LENS Clone Information ClonelD URL http www cbil upenn edu LENS lens Search Pattern id value s amp id_type image id amp page id_query amp method queryResults Search Fields Clone ID Description Links to the LENS Linking ESTs and their associated Name Space database using
13. and information Microsoft SQL Server 7 0 creates and optimizes this database automatically On SQL Server 6 5 a temporary database TEMPDB is created on the master device By default this database is only 2 MB which is insufficient for proper GEMTools operation For SQL Server 6 5 a temporary database of at least 300 MB is recommended for the GEMTools Server The GEMTools Server Setup can automatically expand your temporary database at install time Alternately an advanced system administrator may choose to expand their temporary database manually prior to GEM Tools Server installation for maximum control Database and Device Creation The GEMTools Server automatically creates all databases and devices needed for its operation at installation time The setup program also creates the complete database schemas The following schemas 4e IncyteGenomics GEMTools Server Reference 57 Wf databases and associated devices are created during GEM Tools Server Setup 1 GEMConfig Database and Server Configuration Users Security Config SQL 2 GEMAnnotation Annotation Dictionary Database Annotation SQL 3 GEMProduction Database for Production Related Information Production SQL 4 GEMSequence Sequence Related information for Gene Clones Sequence SQL 5 CustomerDatabase created using the GEMTools Client Interface CustomerTemplate SQL The build and drop scripts for the database
14. the I M A G E Clone ID NCBI GenBank Entrez 3 gi Number URL http www ncbi nlm nih gov Search Pattern entrez query fcgi cmd Retrieve amp db Nucleotide amp list_uids s Search Fields 3 gi Number Description Links to National Center for Biotechnology Information NCBI s Entrez retrieval system by the 3 gi Number NCBI GenBank Entrez Accession Number URL http www ncbi nlm nih gov Search Pattern entrez query fcgi cmd Search amp db Nucleotide amp term s Search Fields Accession Number Description Links to National Center for Biotechnology Information NCBI s Entrez retrieval system by the Accession Number 62 GEMTools Installation and Administration Guide la IncyteGenomics NCBI GenBank Entrez 5 gi Number URL http www ncbi nlm nih gov Search Pattern entrez query fcgi cmd Retrieve amp db Nucleotides amp list_uids s Search Fields 5 gi Number Description Links to National Center for Biotechnology Information NCBI s Entrez retrieval system by the 5 gi Number LifeSeq Gold Incyte ClonelD URL http lt LIFESEQ SERVER gt Search Pattern cgi bin LifeSeqGold GeneQueryResults QueryMethod Clone ID amp Data s Search Fields Incyte Clone ID Description Links to Incyte s LifeSeq Gold database by the Clone ID Prior database subscription is required LifeSeq to GEMTools Gateway Description The LifeSeq to GEMTools gateway provides a communication mechanism betw
15. Creating New Links To create a new link 1 Click New 2 Enter a name for the link in the Link Name text box Deleting Links To delete an existing link 1 Click Delete 2 Click OK Ifa link requires arguments for CGI scripts you can specify the arguments in the Search Pattern text box The search pattern acts as a template with one or more argument holders s which will be substituted by the values of the columns at run time In the example below the search template for Entrez takes one variable argument that is filled by the gene s identification number 4 F IncyteGenomics 44 GEMTools Installation and Administration Guide A 1 Example Gene Name GeneX Identification Number AB00005 Search template htbin post Entrez query form 4 amp db n amp term s amp dispmax 20 At execution time htbin post Entrez query form 4 amp db n amp term AB00005 amp dispmax 20 The number of selected columns should match the number of times s is contained in the search pattern and the order of the columns top down should correspond to their substituted location in the search pattern The columns can be ordered using the up and down arrow keys Clone Source Use the Clone Source window to identify where a clone was obtained Figure 3 16 Clone Source Clone Sources x Window New Delete Source Name Image Consortium P Image Consortium __ Incyte M Ld Incy
16. GEMTools 2 5 Installation and Administration Guide fa IncyteGenomics GEMTools 2 5 Installation and Administration Guide Document Date 10 January 2001 2001 Incyte Genomics Inc All Rights Reserved This guide and its contents are the confidential property of Incyte Genomics Inc Nothing herein is to be dis closed in any way without the prior express written permission of Incyte Genomics Inc Incyte the Incyte logo and LifeSeq are registered trademarks and LifeExpress ZooSeq GEMTools and GEM are trademarks of Incyte Genomics Inc All other products or services mentioned in this manual are the trademarks or service marks of their respective companies or organizations Contents About Incyte Genomics Inc vii Customer Support viii 1 Requirements 1 System Configuration 1 Database Requirements 1 Client Software Requirements 2 Recommended Hardware 2 2 Software Installation 7 Introduction 7 Installation Overview 8 Preparing the Operating System 8 Installing Microsoft SQL Server 10 Installing GEMTools Server 12 Installing GEMTools Client 19 Upgrading GEMTools Client 20 Upgrading GEMTools Client 20 Configuring the GEMTools Server 20 Uninstalling GEMTools Client 22 Uninstalling GEMTools Server 22 Customer Support 23 3 Utilities 25 Changing Your Password 26 Databases 27 Changing Your Database 27 Creating a New Database 28 Deleting Databases 28 fa IncyteGenomics Contents iii Companies 29 Defining a New
17. In Control Panels select Add New hardware 2 Select Add Troubleshoot Device 3 Select Add New Device 4 Choose Network Adaptors category 5 Under Manufacturers select Microsoft and under Network Adaptor select Microsoft Loopback Adaptor Windows ME 95 or 98 1 Check the GEMTools system requirements to ensure GEMTools will work properly with your system Refer to Requirements on page 1 for more information 2 Enable file sharing see the next page File sharing must be enabled to use GEMTools on Windows 95 and Windows 98 amp To enable file sharing 1 From the Start Menu select Settings gt Control Panel 2 Double click the Network icon to open the Network window 3 Click File and Print Sharing to open the File and Print Sharing window la IncyteGenomics Software Installation 9 Figure 2 1 File and Print File and Print Sharing mE Sharing Window IV want to be able to give others access to my files IV want to be able to allow others to print to my printer s Cancel 4 Select the checkbox to give others access to your files and click OK Note You may be asked to provide your Windows 95 or Windows 98 Installation CD to complete the enabling of file sharing Installing Microsoft Internet Explorer In order to use the GEMTools Internet Download feature Internet Explorer 4 0 or newer must be installed on the GEMTools machine that will be performing the Internet download Int
18. MPA and DISKETTEDUMPB When you install GEMTools with SQL Server 6 5 the databases and devices required for operation are created Advanced users can control the size of the devices and databases as described in Resizing a Database on page 71 Backing up Databases You should back up a database after you create it and then maintain a regular backup schedule to ensure smooth recovery in case of database or media failure SQL Enterprise Manager allows you to set and maintain a schedule of automatic backups Scheduling can be accomplished at the same time you define a backup You can also back up manually at any time If a transaction log is on a separate device from its database you can back up the transaction log separately You should back up a transaction log more frequently than its database You should maintain regular backups of the master database the msdb scheduling database all user databases and if the server is configured as a replication distributor the distribution database Note Database backup software utilities such as VERITAS Backup Exec make the process of backing up data much easier To back up a database or a transaction log using Enterprise Manager e See the SOL Server Administration Guide 70 GEMTools Installation and Administration Guide la IncyteGenomics Resizing a Database When any database is filled to capacity the database and device should be expanded On SQL Serve
19. New Data Source to SQL Server Data Source Wizard How should SQL Server verify the authenticity of the login ID With Windows NT authentication using the network login ID m With SOL Server authentication using a login ID and password entered by the user To change the network library used to communicate with SOL Server click Client Configuration Connect to SQL Server to obtain default settings for the additional configuration options Weteiiey B J lt Back Next gt Cancel Help ODBC supports Windows NT and standard SQL server authentication GEMTools requires SQL server authentication to operate properly 4e IncyteGenomics ODBC Reference 79 Y 10 Check the option for standard SQL Server authentication when manually configuring a data source 11 Uncheck the box next to Connect to SQL Server to obtain default settings GEM Tools does not require the additional configuration options offered by this setting 12 Click Client Configuration to open the Add Network Library Configuration window Figure 6 5 Add Network Library Configuration Window g Server alias i m Network libraries m Connection parameters Named Pipes Computer name l C Multiprotocol Port number fi 433 C NWLink IPX SPX C AppleTalk C Banyan VINES DEGret C Other This window allows you to select the SQL Server Net Library DLL that the SQL Server driver uses t
20. SSQLServer must also have Full access Full Control If you have Windows NT User groups at your site you may want to change the permissions to the directory to read only for certain user groups 4 IncyteGenomics GEMTools Server Reference 51 Ny Table 4 1 Description of Configuration Objects GEMTools Client Distribution Software A copy of the Setup exe program for installing GEMTools Client software is installed in the Setup directory on the GEMTools Server when the GEM Tools Server software is installed The Setup exe program can be used to install GEM Tools Client on the server computer and on workstation computers connected to the server through a network Refer to Installing GEM Tools Client on page 19 for more information The Client Distribution Software is updated automatically when the GEMTools Server is installed or upgraded Clients are automatically informed of updates after GEMTools Server has been upgraded Refer to GEMTools Client Distribution Configuration File on page 60 for more information Objects GEMTools supports three object types e Configuration objects used internally by GEM Tools software e Databases Privileges Configuration Objects Configuration object entries contain information regarding standard GEM Tools databases and server location Object Name Description GEMToolsServer Network name of GEMTools Server GEMToolsData Physical location of GEMT
21. Server Windows NT Server 4 0 Windows NT Workstation 4 0 Windows ME Windows 98 or Windows 95 Installation Overview While the details of installation will vary depending upon which operating system you are using the same general steps will be used in every installation 1 Prepare operating system 2 Install Microsoft SOL Server 3 Install GEMTools Server 4 Install GEMTools Client 5 Configure GEMTools Server Preparing the Operating System You may need to install additional service packs or other software to operate Microsoft SQL Server In addition you will need to enable file sharing for use with Windows 95 98 Windows 2000 or Windows NT 1 Check the GEMTools system requirements to ensure GEMTools will work properly with your system Refer to Requirements on page 1 for more information 2 Log on as the local administrator or domain administrator 3 Install Latest Operating System Service Pack if required e Service Pack 1 or newer for Windows 2000 e Service Pack 6 or newer for Windows NT 8 GEMTools Installation and Administration Guide la IncyteGenomics 4 Verify your Network Interface Card NIC is operating properly and connected to the network Standalone Installation Without a Network Connection For a standalone installation without a Network Card or if the computer is disconnected from the network you can simulate network connectivity using the Microsoft Loopback Adaptor 1
22. allow you to upgrade the software Upgrading GEMTools Client The GEMTools installation software automatically checks to see if an earlier version of GEMTools is installed If it detects an earlier version of GEMtools the installation software will allow you to upgrade the software Configuring the GEMTools Server All administration of the GEMTools Server is performed using the GEM Tools client software The GEMTools Server administrator can create new databases create user accounts and assign access privileges for each GEMTools user When you first run GEMTools you must configure the GEMTools Server by 1 Creating a customer database 2 Creating a company 3 Creating users and assigning privileges to them 4 Loading GEM data into the database 20 GEMTools Installation and Administration Guide fa IncyteGenomics amp To configure the GEMTools Server 1 Run GEMTools by selecting the GEMTools shortcut icon through the Start Menu on the Windows taskbar This icon is located in Start Programs Incyte GEM Tools GEM Tools 2 Log on using the GEMTools administrator account The default username and password for the administration account is UserName GEMTools Password gemtools Note GEMTools passwords are case sensitive Important For security reasons you should change the administrator password after installation is complete see step 6 This is the GEM Tools administrator account 3 Cre
23. ate your customer database You will need to enter the Utilities window and create a new database Contact your customer representative for the database ID that uniquely identifies your database among all the databases that Incyte maintains and supports Refer to Creating a New Database on page 28 for more information 4 Create a company After the database is created you will need to add your company information to the database Select the Companies tab in the Utilities Window Create a new company and enter your company information Refer to Defining a New Company on page 29 for more information 5 Create users Select the Users tab from the Utilities window to create new users Assign appropriate privileges to users as needed Refer to Adding New Users on page 31 and to Editing User Profiles on page 32 for more information 4e IncyteGenomics Software Installation 21 a 6 Change the GEMTools password to secure your GEMTools server Click Change Password at the top of the Utilities window Refer to Changing Your Password on page 26 for more information 7 Use the Synchronize utility to load data from a CAB file into the GEMTools database Refer to Synchronize Databases on page 37 for more information Uninstalling GEMTools Client To uninstall the GEM Tools Client software 1 From the Start menu select Control Panels 2 Double click the Add Remove Programs icon 3 Selec
24. d web access account Figure 3 11 Download from Internet Window p Available files CustomerID S1 Files available 0 creases size Select All Change Password File transfer owed Emos Description Files Current file Progress 4 IncyteGenomics Utilities 39 3 Select the file or files you wish to transfer from the list and click Download Note You can use Select All to select all files The progress of the download will be displayed on the Progress bar Each customer datafile will be automatically removed from the Web Server upon electronic confirmation that the data transfer has been completed successfully Refer to the Incyte Microarray Data Delivery Access Agreement for more information about using the Internet download feature Import Sequences You can import FASTA formatted sequence information files into the GEMTools database using data files provided by Incyte Sequence information is also available via web links to Incyte s LifeSeq software See Web Links on page 43 To import sequences into GEMTools 1 Click on Import Sequences in the Administrator tab of the Utilities window 2 Click the browse button denoted by the ellipsis to search for and select the lt file gt seq file 3 Click Import 40 GEMTools Installation and Administration Guide la IncyteGenomics Figure 3 12 Import Sequences Window Impo
25. e Incyte Clone ID are entered under Element Search Criteria la IncyteGenomics GEMTools Server Reference 65 5 Microsoft SQL Server Reference Installing Microsoft SQL Server You must have domain administrator account privileges to install Microsoft SQL Server 7 0 or 6 5 Installing Microsoft SQL Server for use with GEMTools 2 5 software requires approximately 450 MB for a complete installation e Approximately 100 MB of disk space for Microsoft SQL Server files e Approximately 50 MB of free space for a master database e Approximately 300 MB for the temporary database GEMTools databases will also be installed and will grow depending upon GEM usage You should also plan to have extra space for the database log device The log device should be approximately 25 of the estimated GEM Tools database size and preferably reside on dedicated hard drive s You must manually confirm that enough disk space is available Starting SQL Server Because Microsoft SQL Server is integrated with the Windows NT Service Control Manager it can be started and stopped as a service either locally or remotely It can be manually started stopped paused and continued using SQL Enterprise Manager SQL Service Manager the Services application in the Control Panel or the NET START command lA IncyteGenomics Microsoft SQL Server Reference 67 YY SQL Server can be started automatically as a service when Windows starts On Windows
26. e information fa IncyteGenomics Uf Requirements 3 Table 1 2 Database Size Estimates Table 1 3 Recommended GEMTools Client Workstation Configuration GEM microarrays Database growth year MB Recommended hard year disk capacity GB 20 500 2 100 700 4 500 3 500 7 1 000 7 000 14 5 000 35 000 70 10 000 70 000 140 Component Description Workstation IBM compatible workstation CPU Intel Pentium II or higher 300 MHz or faster Motherboard Intel compatible motherboard Multiprocessor Yes Support Memory Installed 128 MB Hard Drive Controller Ultra Fast SCSI or EIDE Hard Drive 4 GB Ultra Fast SCSI Video Adapter PCI Video Adapter with 4 MB Video RAM SVGA Display 1280 x 1024 65 K colors minimum Monitor PCI Network Adapter Fast Ethernet 100BaseT or 10BaseT CD ROM Drive 8x or faster CD ROM SCSI recommended Floppy Drive 1 44 MB Modem US Robotics 56 kbps or faster Keyboard and Mouse PS 2 Keyboard and Mouse Operating System Microsoft Windows 95 NT ME or 2000 4 GEMTools Installation and Administration Guide 4 IncyteGenomics Component Description Web Browser Microsoft Internet Explorer 4 01 or Newer Database Software Microsoft SQL Server 7 0 with Service Pack 2 or Microsoft SQL Server 2000 GEMTools 2 5 requires Microsoft SQL Server If you do not currently own a copy of Microsof
27. eGenomics Component Description Memory Installed 128 MB Hard Drive Controller Ultra Fast SCSI or EIDE System Hard Drive 9 GB Ultra Fast SCSI or EIDE GEMTools Hard Drive Ultra Wide SCSI for enhanced performance Controller GEMTools Hard Drive Ultra Wide SCSI see Database Size Estimates Configuration Table 1 2 to estimate the hard drive capacity required for the GEM Tools database RAID controller recommended Video Adapter PCI Video Adapter with at 4 MB Video RAM SVGA Display 1280 x 1024 65 K colors minimum Monitor PCI Network Adapter Fast Ethernet 100BaseT or 10BaseT CD ROM Drive 8x or faster CD ROM SCSI drive SCSI recommended Floppy Drive 1 44 MB Modem US Robotics 56 kbps or faster Keyboard and Mouse PS 2 Keyboard and Mouse Color Printer Tektronix 450 Phaser Printer for high quality printing Operating System Microsoft Windows 95 98 ME NT or 2000 with an adequate number of connection licenses Web Browser Microsoft Internet Explorer 4 01 or Newer Database Software Microsoft SQL Server 7 0 with Service Pack 2 or Microsoft SQL Server 2000 with an adequate number of connection licenses GEMTools 2 5 requires Microsoft SQL Server If you do not currently own a copy of Microsoft SQL Server 7 or SQL Server 2000 a 120 day evaluation of the product is available from Microsoft Please visit www microsoft com sql for mor
28. een LifeSeq and GEMTools making it possible to view LifeSeq query output in GEMTools The LifeSeq to GEM Tools Gateway takes advantage of the external application hook in LifeSeq called User Defined Links which allows the output of any query to be relayed to another web application GEMTools Server includes a Perl script that generates a web page based on the User Defined Links output that calls GEMTools via COM Automation Requirements The LifeSeq to GEM Tools gateway requires that you access LifeSeq using Internet Explorer 3 x or newer on a Windows 95 Windows 98 or Windows NT workstation that already has the GEMTools client software installed 4e IncyteGenomics GEMTools Server Reference 63 Wf Installation To install the LifeSeq to GEMTools gateway you must edit the LifeSeq Configuration File to include GEMTools as an external user application and install the gateway scripts 1 Edit your LifeSeq Configuration 2 Locate the cgi bin directory of your LifeSeq server In the cgi bin directory you need to edit the LifeSeq conf file to configure LifeSeq s User Defined Links feature 3 At the end of the LifeSeq conf file add this line UserApplicationl URL http lt LIFESEQ SERVER gt cgi bin GEMTools cgi amp NAME GEMTools Note Replace the text lt LIFESEQ_SERVER gt with your LifeSeq Server s domain name If there are additional User Applications defined change UserApplication1 to UserApplication2
29. ernet Explorer adds essential components to the Windows operating system required for data decryption and web server communication Note If you are a domestic customer we recommend installation of the 128 bit security version of Internet Explorer Internet Explorer is available for free on the Web at www microsoft com windows ie download Follow the on screen instructions to download and install Internet Explorer Installing Microsoft SQL Server Installing Microsoft SQL Server for use with GEM Tools requires approximately 450 MB of hard drive space for a complete installation Refer to Installing Microsoft SQL Server on page 67 for more information 4 Fa IncyteGenomics 10 GEMTools Installation and Administration Guide S To install Microsoft SQL Server 1 Install Microsoft SQL Server using the Installation Wizard SQL Server 2000 Use the server edition with Microsoft Windows 2000 or Windows NT Use the personal edition with Microsoft Windows 2000 Professional NT Workstation Windows ME 95 or 98 e SQL Server 7 0 Select the edition of SQL Server 7 0 you wish to install Use the standard edition with Microsoft Windows 2000 or Windows NT Use the desktop edition with Microsoft Windows 2000 Professional NT Workstation Windows ME 95 or 98 e SQL Server 6 5 Upgrade SQL Server 6 5 to Service Pack 5a if it is not already upgraded Service Pack 5a is available online from Microso
30. errors should not occur since transferred records are marked in the Incyte microarray database to prevent automatic retransfer GEM plate probe and plate group objects can only be created at the microarray facility to prevent record primary key conflicts Internet Download The Download button provides access to the Incyte Microarray Data Delivery system which allows secure shipment of GEM microarray data via the Internet This web based system is designed to eliminate the need for CD based data delivery and allows a customer to download new data as soon as it is available The Incyte Microarray Data Delivery system implements web based data distribution with automatic encryption decryption as well as other security measures To download data from the Incyte web server 1 Click Download in the Administrator tab of the Utilities window The Connect to Web Server window opens 38 GEMTools Installation and Administration Guide la IncyteGenomics Figure 3 10 Connect to Web Server Window Connect to Web Server x leena POOE Password Please enter your password It must be at least 6 characters and should contain a combination of letters and other symbols i Cancel 2 Enter your password and click OK The Download from Internet window opens when you have access to the secure web server at the microarray facility Note Please contact Incyte customer service to receive your password an
31. es Companies Users Ni Privileges il Preferences Hi Administrator Delete New p Database Information gt Database ID fe o Name Demonstration Created By gemtool DateCreated t C S Vesino Location _____ _ Current Database Current Database Databases P Demonstration Close Changing Your Database To change your current database 1 Click on a database name in the Databases list 2 Click Apply The Databases list displays only the databases to which you have access If other windows are open when you switch databases these windows close to resynchronize the data Confirmation message windows give you the opportunity to save any changes you have made to these windows before they are closed fa IncyteGenomics Utilities 27 Ga Creating a New Database To create a new database 1 Click New The Create Customer Database window opens 2 Specify parameters such as database name database ID database size logfile size and administrator password Note You must contact the Incyte Microarray Division for the Incyte database ID Databases you create in this way appear as a selectable item in the Default Database drop down list as described in the Users section The next time you log in to GEMTools this database is automatically selected for you Deleting Databases To delete the current database
32. ft at http support microsoft com support downloads 2 For Windows ME 98 95 Configure the SQL Server Auto start option To configure the auto start option From the Start menu select Programs gt Microsoft SQL 7 0 Service Manager to open the SQL Service Manager window la IncyteGenomics Software Installation 11 Figure 2 2 SQL Server Service Manager window fo SQL Server Service Manager PSE Serer MKTGOTS z Services MSSOLServer fu gt Start Continue case m Stop Auto start service when OS starts MMKTG019 MSSOLServer Stopped Select the auto start service option and close the window Note The GEMTools Server installation will automatically set the auto start option when using Windows 2000 and Windows NT Refer to Starting SQL Server on page 67 for more information Restart the computer if prompted Installing GEMTools Server Run setup exe from the server directory on the GEMTools CD ROM or run GEMTools25x exe if GEMTools was downloaded from the Internet The Welcome window of the installation wizard opens Note You can obtain the latest version of GEM Tools server and release notes on the web at http microarray incyte com gemtools update asp Click Next to continue the installation The Software License Agreement opens Review the Software License Agreement and click Yes to continue the installation 12 GEMTools Installation and Administration Guide SS
33. g Query Time e Log ODBC driver statistics to the log file Adding an ODBC Data Source To create anew ODBC data source 1 From the Start menu select Control Panel 2 Double click the ODBC icon to open the ODBC Data Source Administration window 3 Click the System DSN tab 76 GEMTools Installation and Administration Guide la IncyteGenomics Figure 6 1 ODBC Data Source ODBC Data Source Administrator 121 x Administrator Window User DSN System DSN Fite DSN Drivers Tracing Connection Pooling About System Data Sources Add Remove Configure di the indicated data provider A System data source is visible to all users on this machine including NT services An ODBC System data source stores information about how to connect to This window provides access to utilities that can be used to create a Data Source or to change the configuration of a previously created data source 4 Click Add The Add Data Source window appears Note You can also change the configuration of a previously created data source by selecting the data source in the System Data Sources list and clicking Configure la IncyteGenomics ODBC Reference 77 Figure 6 2 Create New Data Create New Data Source Source Window Select a driver for which you want to set up a data source Microsoft Access Driver mdb 3 50 3428 00 Microsoft dBase Driver dbf 3 50 3428 00 Microsoft Excel Dr
34. he name of an object type 1 Select the object name from the Type list 2 Make changes in the Object Type Name text box 3 Click Apply Deleting an Object To delete an object 1 Select the object from the Type list 2 Click Delete Type 4 IncyteGenomics Utilities 49 3 Click Yes Note Object types assigned by Incyte are read only and cannot be deleted 50 GEMTools Installation and Administration Guide la IncyteGenomics 4 GEMTools Server Reference This chapter contains supplemental information useful when installing and administering GEM Tools GEMTools Shared Directory The GEMTools Server Setup automatically creates a Windows shared directory on the GEMTools server The name of this shared directory is GEMTools and can be found in the Windows Network Neighborhood The GEMTools shared directory primarily contains the Client Distribution and Element Images It may also be used for the storage of import and export files By default the shared directory is created with access for Everyone All users of GEMTools must have Read access to the GEMTools shared directory and Read permission to all directories in the GEMTools Server tree If you decide to change the permissions to the shared directory make certain that any users performing GEM Tools administration especially database creation and Synchronization have Full access In addition the User Account for the SQL Server Service M
35. igure 3 7 Utilities Windows TA a Preferences Tab Curent Database Demonstration User Name Change Password Databases if Companies ii Users iT Privileges y Administrator r Default Adjustment Parameters Web Browser Siar fabackaoand Meme a Preferred Browser MS Internet Explorer Element Area Minimum 40 Web Browser GEMTools supports Microsoft Internet Explorer and Netscape Navigator When GEMTools is installed your site administrator selects the default web browser for new client installations An administrator will need to install the browser if it is not already installed on the client workstation M Ld IncyteGenomics Utilities 35 1 Default Adjustment Parameters Use the Default Adjustment Parameters option to specify the default element filtering values used to adjust unbalanced GEM microarrays Typically GEM microarrays are balanced with these default parameters prior to data shipment Administrator The Administrator tab contains useful tools that should only be used by the GEM Tools database administrator Figure 3 8 Utilities Window Utilities Administrator Tab 36 GEMTools Installation and Administration Guide A IncyteGenomics Synchronize Databases Use the synchronization feature to import a differential update file into your database Our microarray facility ships new data to you in electronic format on a regular basis Figure 3
36. iver xls 3 50 3428 00 Micro Microsoft FoxPro Driver dbf 3 50 3428 00 Micro Microsoft ODBC for Oracle 2 573 3711 00 Micro Microsoft Text Driver txt csv 3 50 3428 00 Micro i 3 70 06 23 Micro 5 From the list of installed drivers select SQL Server and then choose Finish Screen 1 of the Data Source Wizard appears Figure 6 3 Screen 1 of the Create a New Data Source to SQL Server Data Source Wizard This wizard will help you create an ODBC data source that you can use to connect to SOL Server What name do you want to use to refer to the data source Name ftest How do you want to describe the data source Description Which SQL Server do you want to connect to Server local x coc Hee 78 GEMTools Installation and Administration Guide A IncyteGenomics This wizard allows you to set the parameters for the data source As you complete the settings in each screen click Next to go to the next step in the installation 6 Enter a name for the data source Note The GEMTools data source is created automatically upon installation 7 Enter a description of the data in the data source 8 Enter the name of a SQL Server on your network You can select a server from the list or enter the server name 9 Click Next to go to Screen 2 of the Data Source Wizard This screen allows you to set the authentication method and other parameters Figure 6 4 Screen 2 of the Create a
37. me test Data Source Description Log Long Running Queries No Log Driver Statistics No Use Integrated Security Yes Use Regional Settings No Prepared Statements Option Drop temporary procedures on disconnect Use Failover Server No Use ANSI Quoted Identifiers Yes Use ANSI Null Paddings and Wamings Yes ie OK Cancel This window allows you to test the parameter settings and set the settings for the data source Note If you attempt to test the data source a correct GEMTools installation will generate a failed result because no default login was specified in the previous configuration step 16 Click OK to return to the Setup window 17 Click OK in the Setup window to to close the window and set the new parameters Deleting a Data Source You are not required to delete any data source if you uninstall GEMTools However if you would like to delete a data source you can use the Data Sources window 4 82 GEMTools Installation and Administration Guide GO IncyteGenomics Ye S To use the Data Sources window 1 Select the data source you want to delete from the Data Sources list 2 Choose the Delete button and then choose the Yes button to confirm the deletion fa IncyteGenomics ODBC Reference 83 Glossary Accession Number Reference to the primary key identifier in the Public Domain GenBank database Annotation A functional description of a clone which ma
38. n Log 73 6 ODBC Reference 75 Configuring Open Database Connectivity ODBC 75 ODBC Data Source Parameters 75 Adding an ODBC Data Source 76 Deleting a Data Source 82 Glossary 85 Index 87 fa IncyteGenomics Contents 7 About Incyte Genomics Inc Incyte Genomics Inc is a leading provider of an integrated platform of genomic technologies designed to aid the understanding of the molecular basis of disease Incyte develops and markets genomic databases genomic data management software microarray based gene expression services and related reagents For more information visit www incyte com Palo Alto and Fremont California Incyte Genomics Inc 3160 Porter Drive Palo Alto California 94304 Main 1 650 855 0555 Sales amp Support 1 800 430 0030 toll free in the U S 1 314 427 3222 for international calls E mail help incyte com Fax 1 650 855 0762 6519 Dumbarton Circle Fremont California 94555 Tel 1 510 739 2100 Fax 1 510 739 2200 St Louis Missouri 4678 World Parkway Circle St Louis Missouri 63134 Tel 1 314 427 3222 Toll Free Tel 1 800 430 0030 Fax 1 314 427 3324 lA IncyteGenomics About Incyte Genomics Inc vii Cambridge United Kingdom Incyte Genomics Ltd 100 Hills Road Botanic House Cambridge CB2 1FF United Kingdom Tel 44 1223 454900 Fax 44 1223 454999 214 Cambridge Science Park Milton Road Cambridge CB2 1FF United Kingdom Tel 44 1223 424 877 Fax 44 1223 424 855
39. n and Administration Guide la IncyteGenomics A transaction log can be backed up separately from the database if it is stored on a separate database device If it is then it is important to back up the transaction log frequently A transaction log dump like a database dump can take place while the database is active Typically transaction logs are backed up more often than databases A transaction log might be backed up once a day and a database might be backed up once a week Backing up a transaction log takes less time and uses less storage space than backing up a database Do not back up a transaction log unless the database has already been backed up at least once Refer to the Microsoft SQL Server documentation for more information about maintaining a transaction log Truncating the Transaction Log Truncating a transaction log removes the inactive portion of the log If the transaction log becomes full GEMTools will fail Hence it is important to monitor transaction log usage and truncate it as necessary You usually truncate a transaction log after you have backed up an entire database SQL Server 2000 and SQL Server 7 0 automatically expands database transaction logs GEM Tools will automatically truncate transaction logs each time data is imported However if you are running low on disk space or are running SQL Server 6 5 you may need to manually truncate the transaction logs Refer to the Microsoft SQL Ser
40. n general you should have no need to edit this file but the contents are provided for your reference The file format and contents are listed below Startup AppName GEMTools Client 2 5 0 FreeDiskSpace 2290 Security SiteLicense XXXXXXXXX Auto DATAServer Server_Name NetLibrary TCPIP Version 2 5 0 Build Build_ Number Internet TransferServer transfer incyte com 60 GEMTools Installation and Administration Guide fa IncyteGenomics External Application Interface GEMTools Web Links GEMTools Web Links allows GEMTools to interface with external Web based applications including Incyte s LifeSeq products Gene Information available in GEMTools can be used to access online databases and other web reference sources on your company s intranet or on the Internet Default Web Links are pre configured in GEMTools for select web sites These links can be edited using the Web Link editor accessed through the Administrator Tab on the Utilities Window Refer to Web Links on page 43 for more information The default set of GEMTools Web Links is listed below LifeSeq Gene By Gene Incyte Clone ID URL http www incyte com gxg Search Pattern idsearchbase jsp PartnerId GemTools amp querytype cloneid amp id Search Fields Incyte Clone ID Description Links to Incyte s LifeSeq Gene by Gene Database Prior registration is required to view the contents of this publicly accessible database
41. n to access your Database server Please enter the ODBC Datasource name and administrator login information for the local Database Server Server Connection Information Data Source Name lLocalServer Administrator Usemame sa Administrator Password e _coreat_ 2 IncyteGenomics 16 GEMTools Installation and Administration Guide A 11 Enter the data source GEMTools and SQL administrator login SA for your local SQL Server machine and click Next The ODBC Client Network Protocol window opens Figure 2 8 ODBC Client ODBC Client Network Protocol Network Protocol Window Please select the default ODBC network protocol to be used by GEMTools Client The selected network pre must be installed on this server Network Library TCPAP recommended Named Pipes 12 Select a default ODBC Client Network Library and click Next Tip TCP IP is recommended and usually will provide the highest level of performance Note On SQL Server 6 5 you must enable this protocol in the SQL Server Setup utility M Ld IncyteGenomics Software Installation 17 SS Figure 2 9 GEMTools Web GEMtools Web Browsing Default Settings x Browsing Default Settings Window EMtools supports the web browsers listed below Please GI select the browser in use at your company Mier Select Default Browser re C Netscape Navigator If your company subscribes to Incyte LifeSeq ser
42. ne company must be created before creating users Company profiles that have been created in this window appear in the Company drop down list in the Create New User window as described in the Users section When multiple companies exist users can only see other users who belong to their company 4 Fa IncyteGenomics 30 GEMTools Installation and Administration Guide S Users Use the Users tab to view user information create new user profiles edit or delete existing user profiles and define a default database for a user Figure 3 5 Utilities Window Utilities See Users Tab User Name Change Password if Privileges Preferences j Administrator Current Database Demonstration Databases Companies f Default Database Demonstration fd Login Name Delete New Edit Users User Information a Name o FistNamef ooa Middle Name 2 Company fine l neee Phone Oo o y O Email Notes Address LO O y O L z Choosing a Default Database The default database is the database that is automatically selected when a user logs in You may select any database that a user has the privilege to access from the Default Database drop down list Adding New Users To add a new user 1 Click New to open the Create New User window fa IncyteGenomics Utilities 31 Ga 2 Specify logon name password personal inf
43. nfiguration objects 52 creating databases 28 customer support vili 23 D data integrity for database 37 datasource 17 see ODBC data source database backing up 37 70 changing the current 27 M IncyteGenomics x changing the default 28 customer 53 deleting 28 restoring 71 to 72 selecting a default 31 structure 53 synchronizing 37 database devices 69 default adjustment parameters 36 defining company 29 deleting databases 28 ODBC data source 82 users 32 devices database 69 E editing user profiles 32 element definition of 85 element data sorting creating custom sortorder 46 Enterprise Manager 68 Entrez 44 F file sharing 9 G GEM Microarrays Direct 85 GEM Microarrays Direct Customers Access Privileges for 55 GEMTools Client software installation 19 requirements hardware 4 operating software 2 GEMTools Server software installation see software installation GEMTools Web Links see Web Links H hard disk capacity 4 hardware recommendations for client workstation 4 for server configuration 2 to 4 import sequences 40 Incyte Genomics locations of vii installation see software installation installing GEMTools server 12 installing Internet Explorer 10 Internet download 38 K key see registration key L LifeSeq Server gateway 6310 65 description 63 installation 64 Index 87 requirements 63 using 65 location 19 M Microsoft SQL Server 67 to 73 10 to 12 67
44. o communicate with the network software A default SQL Server installation supports TCP IP sockets and named pipes TCP IP may improve performance and provide improved network connectivity over a wide area network 13 Click Next to open Screen 3 of the Data Source Wizard 4 Fa IncyteGenomics 80 GEMTools Installation and Administration Guide S Figure 6 6 Screen 3 of the Create a New Data Source to SQL Server Data Source Wizard I Attach database filename ee o ooo d Create temporary stored procedures for prepared SQL statements and drop the stored procedures Only when you disconnect c When you disconnect and as appropriate while you are connected IV Use ANSI quoted identifiers M Use ANSI nulls paddings and wamings r Use the failover SQL Server if the primary SQL Server is not available lt Back Cancel Hep Uncheck the box next to Create temporary stored procedures for prepared SQL statements and drop the stored procedures and Screen 4 of the Wizard should be left at their default settings 14 Click Next on Screen 3 to open Screen 4 15 Click Finish on Screen 4 to open the ODBC Microsoft SQL Server Setup window M Ld IncyteGenomics ODBC Reference 81 SS Figure 6 7 ODBC Microsoft SQL Server Setup Window Anew ODBC data source will be created with the following configuration Microsoft SQL Server ODBC Driver Version 03 70 0623 Data Source Na
45. ools shared directory GEMConfig GEMConfg database GEMProduction GEMProduction database 52 GEMTools Installation and Administration Guide la IncyteGenomics Object Name Description GEM Annotation GEM Annotation database GEMSequence Gene Sequence tracking database Customer Databases All customer databases possess the same database schema In addition each database has the following directory structure Figure 4 1 Database Structure rin Sy Eee Analysis Build Export Fab GEMData 4 Scan Transfer Table 4 2 Database Directory Stucture Subdirectory Usage Analysis Element Image files lt GEMBarcode gt par Element Well statistics lt GEMBarcode gt wst and Grid files lt GEMBarcode gt grd Build SQL database creation scripts and database device deletion scripts Export Reports and Analysis Export files Fab Fabrication Request files lt PlateGroupBarcode gt plt and GEM Geometry Element Well Mapping files lt PlateGroupBarcode gt pix GEMData Database and log file devices 4e IncyteGenomics GEMTools Server Reference 53 Wf Subdirectory Usage Scan GEM images of Cy3 lt GEMBarcode gt 1 and Cy5 lt GEMBarcode gt 2 channels Transfer Database Synchronization files differential updates Access Privileges Privileges are required for users to have access to various features of the GEMTools user inte
46. or UserApplication3 respectively LifeSeq currently supports up to three user defined applications 4 Copy the Gateway scripts Copy the GEM Tools Gateway Perl scripts available on your GEMTools server installation to the CGI executable directory on your LifeSeq web server The two Perl Scripts are located in the GGEMTOOLS_SERVER GEMTools gateway directory e GEMTools cgi e Cgi lib pl Copy these files to the cgi bin directory of your LifeSeq server using FTP or another file copying method 64 GEMTools Installation and Administration Guide la IncyteGenomics Using the LifeSeq to GEMTools Gateway Note Using the gateway you can automatically select only those clones that are available in the GEMTools database and annotated with an Incyte Clone ID To use the LifeSeq to GEM Tools Gateway use Internet Explorer to navigate to the LifeSeq web page 1 Select the Clones of Interest in LifeSeg and select External Applications 2 Open the web browser and navigate to the LifeSeq application 3 Select Clone Information and enter the Clone IDs of your desired Incyte clones 4 Click on External Apps and select the clones you wish to view in GEMTools 5 Invoke the LifeSeq to GEM Tools Gateway 6 Click GEMTools If it is not already running the GEMTools client is launched now and you are prompted to log in The GEMTools Analysis window opens Any genes in the GEM Tools database that correspond to th
47. ormation and privileges for the new user Editing User Profiles To edit a user profile 1 Select a name from the Users list on the Utilities window This populates the text boxes in the neighboring User Information section 2 Click Edit You may edit the logon name password personal information and privileges for the user 3 Click OK Removing Users To delete a user 1 Select a name from the Users list This populates the text boxes in the neighboring User Information section 2 Click Delete to remove this user from the database 3 Click Yes in the dialog box to complete deletion 32 GEMTools Installation and Administration Guide la IncyteGenomics Privileges Use the Privileges tab to add and remove a user s access privileges Privileges can restrict access to selected databases or to certain program functions Refer to Access Privileges on page 54 for more information about user privileges Figure 3 6 Utilities Window gt Utilities Bes Privileges Tab Curent Database Demonstration User Name J Change Password es Preferences Administrator Available Privileges All Users m P Demonstration m Assign Genes J Create Company __ Create Database ry Create Genes Create User f Sime Granted Privileges Close Adding Privileges To add privileges 1 Select users from the All User
48. ple groups Ctrl click on the desired items 2 Click OK SS S Fa IncyteGenomics 42 GEMTools Installation and Administration Guide The Find GEM Groups window works in the same manner as the Find Gene Groups window To transfer microarray data to a new database 1 Click Transfer to open the Data Transfer window 2 Locate the objects you wish to transfer using the Object Type drop down list and the Find button 3 Remove unwanted objects using the Remove All and Remove buttons 4 Select a destination database from the Destination Database box 5 Click Transfer to transfer the data to the destination database or click Close to close the window without transferring data Web Links Use the Web Links window accessed from the Web Links button on the Utilities window to manage custom links to external databases or database search engines that are accessible via the World Wide Web Note Only a person with GEMTools Administrator privileges may create new web links 4e IncyteGenomics Utilities 43 Da Figure 3 15 Utilities Web Links amp Web Links LEC Window Web Link iLifeSeq PD Incyte Clone ID X MER New LikName ilifeSeqPD incyte Cnel CELAR ce URL Ripvfowwineytecom SSS Search Pattem Jiifeseq cid Data stQueyMethod ClonevD Notes Links to Incyte s iLifeSeq PD Database Prior registration is requ Selected Columns External ID 3
49. r 7 0 databases grow in size automatically On SQL Server 6 5 you can use Enterprise Manager to increase the size of a database device and then expand the database onto the newly expanded device Alternately you can use the DISK RESIZE and ALTER DATABASE statements to increase the size of a database using Transact SQL The following example increases the Customer database to 200 MB The database size for the device is specified in 2K pages Therefore multiply the number of megabytes 512 to compute the proper size DISK RESIZE NAME customer_dev1 SIZE 102400 Then use the ALTER DATABASE statement to expand the database into the expanded device The size here is specified in megabytes ALTER DATABASE customer ON customer_devl 200 Refer to the SQL Server documentation for more information about resizing a database Restoring a Database With SQL Server 2000 SQL Server 7 0 and 6 5 you can back up and restore databases and individual tables In SQL Enterprise Manager a table restore can only be performed from a table backup or from a full database backup Restoring a table is useful in a disaster recovery situation where restoring the entire database may be a poor solution For example suppose one table is corrupt and has no foreign keys and no columns that are based on other tables Restoring only this table would correct your database with the least amount of work 4 IncyteGenomics Microsoft SQL Server
50. r Cy3 or Cy5 or non labeled probes GEM Direct View GEM microarray status and find GEM microarrays on the status bar View Probe status Perform batch analysis of GEM microarrays Calibrate scanner PMTs Users At installation time GEMTools creates a SQL Server user account named GEMTools to manage GEMTools database creation and deletion The GEMTools client software uses this account internally whenever making transactions against GEM Tools databases In addition GEMTools maintains a separate user list Each user possesses a profile containing the following information e Login name e Password e First name e Middle name e Last name e Default database e Phone number e E mail address e Company Each user can be assigned a particular set of access privileges 56 GEMTools Installation and Administration Guide la IncyteGenomics Companies Users other than the GEMTools user must belong to a single company GEMTools maintains a company profile containing the following information address contact name contact phone customer representative name customer representative phone number and notes Refer to Companies on page 29 for more information GEMtTools Server Installation This section provides information for use by advanced administrators to manually configure the GEMTools installation SQL Server Temporary Database SQL Server requires a temporary database for storage of temporary tables
51. rect functionality You must be granted the specific privilege e g Create Probes to use specific functionality Note Upon installation the GEM Tools user possesses a complete set of privileges for a particular site Access to privileges and databases can be restricted on a user by user basis Refer to Privileges on page 33 for more information Access Privileges for GEM Microarrays Direct Customers The following table lists the access privileges available for GEM Microarrays Direct customers Refer to the GEMTools Direct Manual for more information about GEM Microarrays Direct functionality for GEM Microarrays Direct Table 4 4 Definition of GEMTools Access Privileges for GEM Microarrays Direct Customers Manufacturing Privilege Name Access Assign probes to GEM microarrays for hybridizations Requires Read Write privileges Image Analysis Scan and analyze GEM microarrays Track and enter image related issues Print Labels Print labels for probes or plates in a range defined by the user Edit Processing Process probe production and track the development through the following states e Arrival tissue e Total RNA e Poly A RNA e Sample Recovery e Probe Track issues related to Probe Processing fa IncyteGenomics GEMTools Server Reference 55 Privilege Name Access View Processing View Probe Processing dialog box Create Probes Create new labeled probes fo
52. required disk space 67 requirements 1 to 2 11 to 12 67 installation starting N network library 80 0 Object Type window 48 52 to 55 configuration 52 objects customer databases 53 to 54 ODBC data source 1 75 adding 76 to 82 deleting 82 75 to 76 authentication 79 parameters changing 77 description 79 drivers 78 network library 17 80 server 79 testing 82 operating system MS SQL Server requirements P password changing 26 plate types creating new 48 privileges 54 54 to 55 access 1 for GEMTools users 33 33 to 34 R registration key client 19 server 13 removing user privileges 34 S schema 57 58 scripts 58 security 37 server selecting for ODBC 79 server registration key see registration key Site License key 14 software installation 7 to 22 configuring GEMTools Server 20 to 22 changing password 22 creating company 21 creating customer database 21 creating users 21 loading database 22 installing GEMTools Client 19 installing GEMTools server 12 to 19 MS SQL Server overview 8 10 to 12 preparing operating system 8 o 10 Sort Builder window 46 Synchronize utility 22 Synchronize window 37 T transaction log 72 to 73 backup 70 truncating 73 88 GEMTools Installation and Administration Guide Transfer 41 U uninstalling GEMTools Client 22 uninstalling GEMTools Server 22 users adding new 31 adding privileges 33 editing profiles 32 profiles of 56
53. rface Users may have any combination of access privileges Table 4 3 Definition of GEMTools Access Privileges Privilege Name Access Write Access Modify any available information Create User Create edit and delete users Create Database Create and delete databases Create Company Create and edit companies View Processing View plate and or probe processing information Transfer Use data transfer utilities a Import at Client site b Export at Incyte microarray site c GEMStore at Incyte microarray site Create Genes Create edit and remove genes from the database Assign Genes Make gene well associations on plates Import Genes Import genes from gene import file Edit Gene Hierarchy Edit gene hierarchies Edit Project Hierarchy Edit project hierarchies Site Configuration Edit web links and custom sorts Edit Classifications Edit Clone Sources and object types Edit Sequences Add edit and remove clone sequence information Generate PMD Create data files for import into LifeExpress RNA SNP Admin Enter any number of arraying tips in the Arrayer Parameters dialog box 54 GEMTools Installation and Administration Guide la IncyteGenomics Privilege Name Access Element Validation Edit all fields in the Element Adjustments dialog box MicroArrays Direct Access GEM Microarrays Di
54. rt Sequences Transfer The Transfer button allows you to transfer GEM microarray data from one database to another This feature can be particularly useful when controlling the access of different users to particular sets of data Clicking on the Transfer button opens the Data Transfer window which allows you to select data to be transferred and destination databases for that data Figure 3 13 Data Transfer Data Transfer Window AA Ld IncyteGenomics Utilities 41 The Object Type drop down list and the Find button allow you to select from the following types of data Table 3 1 Types of Data You Can Transfer from One Database to Another GEM Multiple GEM Selection window described in GEMTools Analysis User Manual For this object type Clicking Find opens this window Probe Multiple Probe Selection window described in GEMTools Analysis User Manual Plate Multiple Plate Selection window described in GEMTools Analysis User Manual Gene Group Find Gene Groups window GEM Group Find GEM Groups window The Find Gene Groups window displays a list of the available gene groups Figure 3 14 Find Gene Groups Window Select one or more Gene Groups and click OK to add them to the list Gene Groups TWH Cancel To select desired Gene Groups for transfer 1 Select the desired Gene Group from the Gene Groups list Note To select multi
55. s NT GEM Tools client software is installed on networked computers and are able to access the GEMTools data through the network In a standalone system the GEMTools server and client components are installed on the same computer Database Requirements The GEMTools 2 5 server requires database server software to operate Standard installations use Microsoft SQL Server 2000 Microsoft SQL Server 7 0 or Microsoft SQL Server 6 5 lA IncyteGenomics Requirements 1 Microsoft SQL Server 2000 and Microsoft SQL Server 7 0 can be installed on e Windows 2000 Server and Advanced Server e Windows 2000 Professional e Windows NT 4 0 Server e Windows NT 4 0 Workstation e Windows 95 98 and ME SQL Server Personal Desktop Edition only Microsoft SQL Server 6 5 can be installed on e Windows NT Server 4 0 Client Software Requirements The GEMTools analysis software client can be run on e Windows 2000 Professional Server and Advanced Server e Windows NT 4 0 Server and Workstation e Windows 95 98 and ME Recommended Hardware Before you install GEMTools review the recommended components shown in Table 1 1 Table 1 1 Recommended inti GEMTools Database Server Component Description Configuration Server IBM or compatible server CPU Intel Pentium II or higher 300 MHz or higher Motherboard Intel compatible motherboard Multiprocessor Yes Support 2 GEMTools Installation and Administration Guide 4 Incyt
56. s and devices are available on the GEMTools server SERVER_NAME GEMTools Config Build The database schema scripts in parenthesis above are stored on the GEMTools server in the SERVER_NAME GEMTools Config directory GEMTools SQL Server Login The GEMTools Server Setup creates a single SQL Server login called GEMTools This standard authentication login is used by the GEMTools client software to access the GEMTools databases In addition the GEM Tools login is the owner dbo of all GEMTools databases See the GEM Tools Security architecture section for more information The GEMTools SQL Server Login is different from the GEMTools Administrator User Account used to log into the GEMTools client 58 GEMTools Installation and Administration Guide la IncyteGenomics software Only use the GEM Tools client software Utilities Window to change the GEMTools administrator password Caution Do not use SQL Enterprise Manager to change the GEMTools SQL user password This could make all clients unable to access the GEMTools server Contact Incyte Customer Service if the GEMTools password is accidentally changed Refer to Customer Support on page viii for more information Restoring Database Ownership If you transfer or restore a GEMTools related database from a backup GEMTools user ownership must be restored To restore database ownership 1 Using SQL Enterprise Manager open the SQL Query Window 2 Switch to the databa
57. s list To add privileges to multiple users at once select multiple users from the list fa IncyteGenomics Utilities 33 Ga e To select more than one contiguous item click on the first item in the list and Shift click on the last item in the list This action selects all items between the first and last items clicked e To select more than one noncontiguous item Ctrl click each item Select one or more items in the Available Privileges list Note Refer to the GEMTools Server reference for description of available GEMTools privileges see the section Access Privileges on page 54 Click Add to grant those privileges to the selected user Click Apply Note To cancel a privilege modification operation before any changes have been made click Cancel Removing Privileges amp To remove privileges 1 2 Select a user from the All Users list Select on one or more items in the Granted Privileges list Click Remove to remove those privileges from the selected user Click Apply To cancel a privilege modification operation before any changes have been made click Cancel Note You cannot remove privileges from multiple users by selecting more than one user from the All Users list 34 GEMTools Installation and Administration Guide la IncyteGenomics Preferences Use the Preferences option to define a web browser and adjust the default parameters for unbalanced GEM microarrays F
58. se that needs its ownership updated using the Combo Box 3 Execute the stored procedure sp_changedbowner using the following syntax sp_changedbowner GEMTools true Configuring SQL Server for Optimal Performance Microsoft SQL Server 2000 and SQL Server 7 0 are self optimizing However setting up a maintenance schedule using enterprise manager will keep your database running most efficiently See the SQL Server Administration guide for more information GEMTools Server will automatically configure your SQL Server 6 5 installation for optimal performance GEMTools Server Setup follows Microsoft s recommendations for a properly tuned server The Setup program detects information about your server such as system memory and sets the configuration parameters appropriately 4 IncyteGenomics GEMTools Server Reference 59 If you are an advanced administrator you may choose to configure these parameters manually using SQL Enterprise Manager If you reconfigure your server hardware by adding memory for example you should run the GEMTools server setup and select Automatic optimization to reconfigure SQL Server 6 5 GEMTools Client Distribution Configuration File The Client Distribution Setup Software contains an information file that is referenced during Client Setup This file is found in SSERVER_NAME GEMTools Setup and is configured during the Server Setup process The configuration file is named SETUPINI I
59. t GEMTools 2 5 Client from the software list 4 Click Add Remove 5 Click OK Uninstalling GEMTools Server Warning Uninstalling GEMTools Server completely will remove all GEM data and experiment information 1 Remove the GEMTools Databases using SQL Enterprise Manager The following databases must be removed e Customer database e Demonstration e GEMConfig e GEMProduction e GEMAnnotation 22 GEMTools Installation and Administration Guide la IncyteGenomics e GEMSequence Refer to the SQL Server documentation for information on using Enterprise manager 2 Uninstall GEMTools Server using Add Remove Programs as described in the procedure for uninstalling the client software above 3 Remove the GEMTools Server Directory usually C GEMTools Customer Support Incyte offers training and support to its licensed users and user organizations Additionally GEM Tools administration training is available to your Information Technology staff It is useful to have a phone line connected to your workstation modem for application support If you have any questions or would like information about our training programs you may contact customer support at 4678 World Parkway Circle St Louis Missouri 63134 Tel 1 800 430 0030 toll free in the U S Fax 1 888 919 3324 toll free in the U S E mail service stl incyte com The latest updates and information about the GEMTools software is available on Incyte s web si
60. t SQL Server 7 or SQL Server 2000 a 120 day evaluation of the product is available from Microsoft Please visit www microsoft com sql for more information fa IncyteGenomics Requirements 5 2 Software Installation Introduction This chapter provides information on installing and configuring the software necessary to use GEMTools software It describes the necessary prerequisites provides step by step instructions and includes configuration information The following items are required to use GEMTools e Microsoft Windows 2000 NT ME 98 95 e Microsoft SQL Server 2000 SQL Server 7 0 SQL Server 6 5 e Microsoft Internet Explorer 4 0 or higher for electronic download of data e GEMTools Server in electronic or CD format e Data files for GEM data in electronic or CD format Depending upon the type of system you are using you may install the SQL Server and the GEMTools Server software and databases on any of the following e Server computer running Windows NT Server 4 0 e Workstation computer running Windows NT Workstation 4 0 e Desktop computer running Windows 2000 Server or Advanced Server e Workstation computer running Windows 2000 Professional or Windows NT Workstation 4 0 e Desktop computer running Windows ME Millennium Edition Windows 98 or Windows 95 4 IncyteGenomics Software Installation 7 You may install the GEMTools client software on a computer running Windows 2000 Server or Advanced
61. te Note GEM Tools evaluation licenses will expire after 30 calendar days 4e IncyteGenomics Software Installation 13 Y You can obtain a server registration key for new or upgraded installations by calling customer support at 1 800 430 0030 or sending an e mail with your request to gemsupport incyte com Figure 2 4 Site License Site License Registration Ei Registration Window If you have obtained a site license from Incyte Microarray lou may enter it here Enter your GEMTools Site License Key below If you do not have a Site License click Next ke Site License Key 7 Ui lt e Carci 6 Enter your Site License key if you purchased a site license This key allows unlimited GEMTools client installations If you do not have a site license leave this entry blank If you obtain a site license key GEMTools client registration is not required 7 Click Next to go to the GEMTools Server Setup window This window allows you to create a directory for the GEMTools server share and client software 14 GEMTools Installation and Administration Guide 4 IncyteGenomics Figure 2 5 GEMTools Server GEMTools Server Server Setup Lx Server Setup Window GEMTools server has not been detected on this machine The GEMTools server share and client software will be installed in the destination directory listed below Destination Folder CAGEMTools Browse Cancel
62. te Visit www incyte com for the latest information la IncyteGenomics Software Installation 23 3 Utilities Use the Utilities window to perform various administrative tasks Six tabs give you access to all the maintenance units e Databases e Companies e Users e Privileges e Preferences e Administrator The specific administrative tasks you have access to depend on the access privileges that you have been granted e To open the Utilities window click Utilities on the GEMTools software main screen 4 IncyteGenomics Utilities 25 Changing Your Password The Logon Information window displays the name of the current database and user e To open the Change Password window click Change Password on the Utilities window Figure 3 1 Change Password Change Password x Window Logon Information Logon Name New Password Re enter Password To change your password 1 Type in your new password in the New Password text box 2 Type in your new password again in the Re enter Password text box for verification 3 Click OK 4 26 GEMTools Installation and Administration Guide GO IncyteGenomics Ye S Databases The Databases tab allows you to change the current database view database information create new databases and delete existing databases Figure 3 2 Utilities Window gt Utilities See Databases Tab User Name Databas
63. teGenomics Utilities 45 1 Creating a New Source To create a new clone source 1 Click Clone Sources on the Utilities window 2 Click New 3 Enter the source name in the text box 4 Click OK Modifying a Source Name To modify the name of a clone source 1 Select the source from the Clone Sources list 2 Make changes in the Source Name text box 3 Click Apply Deleting a Source Name To delete a clone source 1 Select the source from the Clone Sources list 2 Click Delete 3 Click Yes Note Clone sources assigned by Incyte are read only and cannot be deleted Sort Builder Use the Sort Builder window accessed from the Sort Builder button on the Utilities window to build a customized order for sorting that can be used in the Element Display window 46 GEMTools Installation and Administration Guide la IncyteGenomics Figure 3 177 Soe Builder Wintow Sort Order Share with Public M ait Fields Selected Fields eis Peserption _ Field Description Order P Differential Expression gt Abs Differential Expression ASC DESC __ Gene Name i ASC DESC __ Probel Name __ Probe2 Name Abs Differential E xpi __ Element Location on GEM m P1 Signal to Background __ P2 Signal to Background __ P1 Element Area __ P2 Element Area __ bs Differential Expression Close Apply
64. to complete the Server installation 17 You will be prompted to install the GEMTools Client software Choose Yes to install the Client Installing GEMTools Client You will need to install the GEMTools client software before you can finish creating databases and loading data in the GEMTools server software Note The GEMTools client setup software is installed during the installation of the GEMTools server software 1 Run the setup exe program from the Setup directory on the GEMTools Server This directory is located at lt SERVER gt GEM Tools Setup where lt SERVER3 gt is the name of your Server If your company does not have a site license setup will require a product registration key Call customer service for your registration key The registration key is unique to each system Provide the customer service representative with the product identification numbers displayed in the GEMTools Registration window The representative will provide you with a registration key needed to install GEMTools on your workstation It is important that you write down this registration key for future reference 2 Follow the on screen instructions to complete the installation 4 IncyteGenomics Software Installation 19 Upgrading GEMTools Client The GEMTools installation software automatically checks to see if an earlier version of GEMTools is installed If it detects an earlier version of GEMtools the installation software will
65. ver documentation for more information on truncating a transaction log 4e IncyteGenomics Microsoft SQL Server Reference 73 Da 6 ODBC Reference Configuring Open Database Connectivity ODBC The information presented in this chapter is provided for reference only to aid in troubleshoooting and for developing customized or test configurations GEMTools client software installs the latest ODBC drivers at installation time and automatically configures the GEMTools data source ODBC Data Source Parameters A variety of parameters control the operation of the ODBC Data Sources The parameters shown in Table 6 1 need to be set for the SQL Server ODBC data sources used with GEMTools Table 6 1 ODBC Data Source Parameter Description Parameters Data Source Name Unique identifier for the data source Description An optional description of the data source Server Name of server for the data source Authentication Method used to identify the user using a login account Client Configuration Network library used to communicate with SQL Server The remaining options should be set to the default values e Default database e Temporary stored procedures lA IncyteGenomics ODBC Reference 75 e ANSI quoted identifiers e ANSI nulls paddings and warnings e Use of Failover SQL Server e Language of SQL Server System Messages e Perform Translation for character data e Use Regional settings e Lon
66. vices please enter the name of your LifeSeq server below 2a LifeSeq Server i e server mycompany com F Z eck Coreei 13 SQL Server 6 5 only Server configuration Optional Temporary Database Configuration The GEM Tools Server Setup will give statistics on your Temporary Database and allow you to configure it if desired Refer to SQL Server Temporary Database on page 57 for more information Optional SQL Server Optimization GEMTools can optionally configure the memory settings and other parameters of your SQL Server See Configuring SQL Server for Optimal Performance on page 59 for more information Note Microsoft SQL Server 2000 and Microsoft SQL Server 7 0 are self optimizing 14 Specify the default web browser to be used by GEMTools clients at your site GEMTools supports the Internet Explorer and Netscape Navigator web browsers 15 Enter the LifeSeq server installation if Incyte LifeSeq is installed at your site and then click Next 4 F IncyteGenomics A 18 GEMTools Installation and Administration Guide 1 If you have an Incyte LifeSeq server at your site enter the full path name to the server for example lifeseq company com This entry is used to configure your default LifeSeq web links Your site may require additional changes to these links Links can be edited using the GEMTools client see the GEM Tools Analysis Manual for more information 16 Click Next
67. y include identifying attributes such as locus name keywords and Medline references Clone ID The clone identification number Clone Source Name The vendor of the clone e g Incyte IMAGE Consortium Data fields Fields in a file that the data import utilities can place in a database Delimiter A character used to separate items of data in a delimited text file The delimiter designates where one item ends e g a field in a record and where the next begins The delimiters used in GEMTools import files are the tab character and the comma Devices Fields in a file that the data import utilities can place in a database Field An item of data in a file GEM Microarrays Direct A program in which the customer hybridizes and analyzes GEM microarrays at their own facilities ODBC Open Database Connectivity An interface providing a common language for applications to access a database on a network RAID Redundant Array of Inexpensive Disks Schema A description of a database defining the fields and the relationships between fields in the database lA IncyteGenomics Glossary 85 Index A adding user privileges 33 users 31 administrator privileges 43 authentication 79 B backup see database 0 CGI scripts 44 Change Password window 26 changing password 26 client configuration 79 client registration key see registration key Clone Source window 45 company defining new 29 profile 57 co

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