GEM TOOLS 2.5.2

GEMTools ™

Microarray Analysis Suite

Version 2.5.2 (build 312)

August 2002

Corporate Internet: http://www.incyte.com

Incyte Genomics brings you GEMTools™ Software version 2.5.2 build 312.

Important: Incyte is no longer accepting any orders for bioreagent services, microarray services, LifeArray chips, or GEMTools software. This software update is provided as an unsupported maintenance release to address issues reported by existing microarray customers.

This software distribution can be used to install a new GEMTools server or upgrade an existing GEMTools server. The software updated is provided via web download. Run the self-extracting GEMTools252.exe program to install or upgrade. For additional installation instructions, please refer to the GEMTools 2.5 Installation and Administration Guide.

The information below provides a list of new features, enhancements, and technical issues that have been resolved in the GEMTools 2.5.2 software release. For more detailed information about GEMTools features, refer to the GEMTools 2.5 Analysis Manual and GEMTools 2.5 Direct Manual.

GEMTools 2.5.2 Build 312 Release Notes

Release Information

Installation

FIXED: Enterprise server and site license keys did not work correctly for new GEMTools server installations.
UPDATED: Additional support for Server Site License keys to facilitate enterprise server installation.

General

UPDATED: Version updated to 2.5.2 to correctly reflect inclusion of Navigator feature.
FIXED: Navigator caused GEMTools to crash on some Windows 95/98 installations because of an XML parser dependency.
FIXED: Low level “QueryResults” bug introduced in Build 303 that caused duplicate or incorrect entries when adding and removing rows from all GEMTools grids.
UPDATED: Updated Installshield installer for improved platform support and more reliable installation and removal. UPDATED: Code review of class library variable initialization.
FIXED: Bug that caused ODBC error when attempting to login with a user name that contained a single quote.

Genes

UPDATED: Combo-box browsing enabled on Genes window.
UPDATED: Message-box that appeared when clicking Gene Hierarchy removed.
UPDATED: Gene Group copy feature performance increased.

Probes

Enhanced: Ability to create multiple Probes at once using “New Probe” feature.
Enhanced: Processing Window displays a column to indicate “required” attributes.

Plates

Enhanced: New Plates interface streamlined.

Visualization

FIXED: Bug that caused intermitted “Failed to initialize Graphics Server” and “fatal error” message
UPDATED: Upgraded Graphics Server module to version 5.8 for more reliable generation of graphs.
UPDATED: Graphics Server Icon no longer appears in the icon tray.

Image Analysis

FIXED: Bug that caused an “GEMProduction:Automation Error” to appear after completing analysis. Code has been added to create a GEM Production record if it does not already exist in the database.
FIXED: Bug that allowed the user to inadvertently delete grids during analysis.
FIXED: Bug that caused QC report generation failure on page 4 due to intermittent Graphics Server failures.
FIXED: Bug that caused client to hang on “printing” the quality report PDF at page 5 of 5 due to an incorrectly initialized font structure that caused lockup with program attempted to render the font on Windows 95/98.

Utilities

FIXED: Bug that caused crash when creating Probe types under some circumstances.
FIXED: Bug in Laboratory/Processing that caused “Required” and “Visible” check-boxes to be ignored.
UPDATED: Support for additional barcode label types and duplex printing – including circles for tube tops.

Known Issues/Limitation

Highlighting of <Controls> on graph requires at least one gene group to have been created.

GEMTools 2.5.1 Build 303 Release Notes

Incyte Genomics brings you GEMTools™ Software version 2.5.1 Build 303. This build is an unsupported maintenance and feature release.

The information below provides a list of feature enhancements and technical issues that have been resolved in the GEMTools 2.5.1 build 303 release.

Release Information

Installation

NEW: Enterprise server and site license keys enable plate creation, batch processing, and array fabrication

User Interface

NEW: Navigation interface with hierarchical selection, toolbar and tabular data views.
NEW: Sorting and Searching functionality in tabular data views
NEW: Toolbar button to invoke the Navigator interface

Probes Module

FIXED: Bug that did not allow probes to be created without a fluorescent label selected

GEM Module

FIXED: A bug that prevented the viewing of data after image analysis.
NEW: Create GEMs feature enabled with Enterprise license

Plates Module

NEW: Plate creation enabled with Enterprise license
NEW: Plate group array batch creation enabled with Enterprise license

Image Analysis

FIXED: A bug that prevented the image analysis date from being recorded correctly
FIXED: A bug that prevented image analysis from displaying images on computers with multiple monitors
ENHANCED: Image Analysis now consumes fewer GDI resources

Data Visualization

ENHANCED: View Plates window now supports 384 well plates.

Utilities

NEW: Ability to create GEM Types and Plate Types with Enterprise license
ENHANCED: Pressing the first letter of a database or user name will scroll directly to the item

Known Issues/Limitation

Plate Group (Batch) module will incorrectly allow a batch that includes both 96 and 384 well plates.
Printed Report for Plate View does not support 384 well plates
No online help for Navigator interface
Limited online help for Plate Creation, Plate Groups, GEM Creation, and Fabrication functionality

GEMTools 2.5.1 Build 302 Release Notes

Incyte Genomics is pleased to bring you GEMTools™ Software version 2.5.1.

The information below provides a list of feature enhancements and technical issues that have been resolved in the GEMTools 2.5.1 release. For more detailed information about GEMTools features refer to the GEMTools 2.5 User Manual.

New Features Overview

LifeArray™ Server Features

GEMTools Desktop Edition
Allows organizations that do not have an enterprise database server to install a standalone version of the GEMTools server. The GEMTools Desktop edition installs its own local database engine that can support up to 5 concurrent users and 2 gigabytes of microarray data. The system can be seamlessly upgraded to Microsoft SQL Server 2000 at any time.

LifeArray™ Analysis Features

Menus: A menu system for main GEMTools functions has been added to improve navigation.
Microarray Design: From the utilities panel, administrators can view and update the details of each microarray chip design. Use this feature to browse gene lists and update plate annotations of custom arrays.
Control Identification: A dynamic <Controls> gene group is available on the Element Location window, Query Analysis screen, and Graph window.
Sample Database: An updated sample set of microarray data is included with the release.
Full featured Oracle Support (requires GEMTools Oracle Server License)

LifeArray™ Technology Features (requires LifeArray Technology License)

Barcode Data Entry: A Laboratory Scan Mode preference enables the lab manager to disable browsing of GEMs and Probes, forcing laboratory technicians to use a barcode scanner when processing arrays and probes.
Array Layout Export: Users can now export information from the Plate Group window to the Axon Gene Pix Array Format (GAL).
Barcode Printing: User can select from various label stock sizes. Intermec and Unimark printers are supported.
Image Analysis Module: Enhanced support for 16-bit grayscale TIFFs from all scanner manufacturers. Support for scans at various micron resolutions. Ability to rotate scans 90 degrees to accommodate horizontal slide scanning formats.
Improved Quality Assurance Report Layout and PDF Generation.
Updated Laboratory Management Attributes, Data-Types and Editing features.
Full-featured Oracle Support (requires GEMTools Oracle Server License)

Release Information

Installation

NEW: Desktop Edition that includes the Microsoft SQL Server 2000 Database Engine (MSDE)
ENHANCED: Installer has been upgraded to be Windows 2000 compliant.
FIXED: A bug in the installation code that did not show the license registration dialog when users upgraded their GEMTools.

User Interface

NEW: All top level windows (including GEMs, Plates, Probes, and Processing Windows) now support two modes of operation - Laboratory Mode and Browse Mode.
NEW: Menu items for main GEMTools functions have been added to improve navigation.
NEW: Menu items for window management and organization
NEW: About Box shows GEMTools license, server, and version information.
FIXED: Bug that did not allow military time entries when using Oracle.
FIXED: A bug that inserted multiple and incorrect rows into grids when only a single data element was present.
FIXED: A bug that caused a GEMTools error when the user clicked the [X] close button in the plates dialog.

Image Analysis

NEW: The Image Analysis module can now read all 16-bit gray scale TIFF (Tag[ged] Image File Format ) scan files including Macintosh TIFF scan files. Save Cy3 and Cy5 image files as Barcode_1.TIF and Barcode_2.TIF respectively.
NEW: Gridding support for 5 and 10 micron scan resolutions. Resolution detected automatically for Axon scanner images. Resolution can be set manually on Info panel for other scanner types.
NEW: Planar Detrending feature to correct for hybridization surface variations. Select using Array Info button.
NEW: By pressing the new “Rotate” button on the Inspect control bar, User may rotate images 90 degrees to accommodate layout of some scanners.
ENHANCED: Manual Gridding can be selectively enabled using the Array Info button.
ENHANCED: Auto Analysis. List of GEMs barcodes trended may contain the tab-delimited argument DD to detrend arrays.
ENHANCED: Data Values for Ratio Controls are stored in the GEM Statistics database.
ENHANCED: Auto-gridding now grids all types of arrays independently of the number of sub arrays or the number of elements in a sub arrays.
ENHANCED: The number of auto-gridding warnings and errors has been decreased and error messages clarified.
ENHANCED: Users can now reduce or enlarge the images in Inspect by pressing the <shift> '+' keys or the '-' key as well as using the respective keys on the numeric keypad.
FIXED: A bug that would not generate images on PDF (Portable Document Format) files correctly.
FIXED: A bug that did not record the laser power, laser temperature, laser wavelength, and scanner serial number of Axon scans under some circumstances
FIXED: A bug that caused Image Analysis to fail for some Arrays whose layout differed from the Arrays' design template.
FIXED: A bug that did not change an Array’s state to Scanned after the Array had been scanned.

Utilities

NEW: Databases, Users, and Privileges can be selected by pressing the First Letter of the desired entry.
NEW: Combo box added to the Preferences tab that allows the user to select t label stock size.
NEW: The serial port for the Barcode Printer can now be set in the Preferences tab in GEMTools.
NEW: Barcode Selection Preferences - Browse Mode (Default) / Laboratory Mode.
NEW: Users are now able to view and print their unique barcode from the User Tab.
ENHANCED: The Scanner button is disabled appropriately.
ENHANCED: The Synchronize, Transfer, Import Sequences, and Transfer button is disabled appropriately
FIXED: A bug that caused the database ID to be cached when database was editing

Data Export

NEW: Export options allow user to optionally include array catalog, use element display sort order, and replace rejected differential expression values with ‘?’. Selecting all three option-checkboxes will produce output identical to previous versions of GEMTools.

Data Visualization

NEW: Check box in the Element Location |Display Options Group which displays or hides control elements and recalculates the Chi Square value depending on whether control elements are or are not present.
FIXED: A bug in Graph that did not properly refresh highlighted gene groups.
FIXED: A bug in Graph that did not allow the user to select some Functional Hierarchy Gene Groups
FIXED: A bug in Graph that intermittently would not allow the user to lasso elements.

GEM Module

NEW: Users can now export array information from the Plate Group window to the Axon Gene Pix Array Format (GAL).
ENHANCED: The Delete button in the GEMs window is now disabled for most users.

GEM Design Module

NEW: GEM Design module accessible from Admin Tab of the Utilities Panel.
NEW: A new button has been added that either updates all the Batches with selected annotation information or updates the non-annotated Plates related to the selected batches using a specific GEM Design.
ENHANCED: The GEM Design Dialog works with ORACLE instances

Probes Module

FIXED: A bug that did not update information in the Probe dialog when the user accessed Probes through the GEMs window.
FIXED: A bug that caused a GEMTools exception when creating Probes on Microsoft SQL Server 6.5.

Laboratory Management Module

NEW: Data-type “COMPUTE” to allow mathematical computation of attributes within a process step
NEW: Life Array Direct customers may now edit processing states and attributes for Arrays.
ENHANCED: Improved arrow key navigation and response throughout the laboratory processing module.
FIXED: A bug that did not correctly move the blue marker icon that shows the current tab in Probe Processing.
FIXED: Current object's barcode not displayed correctly when entering the processing window in Laboratory mode.
FIXED: A bug that caused GEMTools to crash on some Windows 98 platforms in the processing window.
FIXED: A bug did not save state and group information properly.
FIXED: A bug that did not update received state of Probes correctly

Project Management

NEW: Barcodes are displayed for each node of the hierarchy
NEW: Cut and Paste functionality allows user to move hierarchy nodes
ENHANCED: Trailing Zeros (.0.0.0) have been removed from project hierarchy nodes.

Quality Control Reports Module

NEW: Control plate images are now shown on the same page where control parameters are shown.
NEW: Array statistics and sub array statistics are shown in tabular form on the page following the new Control plate images.
NEW: A new Raw Yeast Balance Coefficient has been added. For non de-trended GEMS this coefficient is the same as Yeast Balance Coefficient. For de-trended GEMs this coefficient is the yeast balance coefficient calculated with non de-trended data.
ENHANCED: The Array statistics page for de-trended GEMs contains values (excluding carryover) calculated using non de-trended data. However, control values are calculated using de-trended data.
ENHANCED: Control elements are no longer visible by default in the Location Map.

Satellites

ENHANCED: The length of the satellite name text field has been changed to accepted up to 32 characters.
ENHANCED: Users can no longer make deletions from the Satellite window.
FIXED: Bug that prevented Life Array Direct customers from creating satellites.
Fixed: A bug that inserted an extra row in Satellites grid.

Technical Enhancements

NEW: Sorting capability added to the underlying query storage system.
NEW: Support for Oracle has been added in Image Analysis.
ENHANCED: Improved error handling in Database Import module.
ENHANCED: Added a new database field to keep track of Satellite information.
ENHANCED: Improved the code to create new Objects in the Utilities window.
ENHANCED: Improved the code to query the database to find objects.
FIXED: A bug that would store the contents of the temporary table after user logout.

GEMTools 2.5.0 Release Notes

Incyte Genomics is pleased to bring you GEMTools™ Software version 2.5.

The information below provides a list of feature enhancements and technical issues that have been resolved in the GEMTools 2.5 release. For more detailed information about GEMTools features refer to the GEMTools 2.5 User Manual.

GEM Module

NEW: Expression Location Map.
NEW: Quality Assurance Report viewer.
NEW: Microarray Type and Version displayed in GEM, GEM Group, GEM Series, and GEM Find windows.
NEW: Hybridization and Imaging modules enabled with LifeArray License.

Data Visualization

FIXED: A bug that caused a GEMTools error when a GEM Series was selected for display from the Query Analyzer and then Intensity selected in the Data Visualization menu selection.
FIXED: Users can now export JPEG and PNG images of their graphs.

Gene Module

FIXED: A bug that incorrectly updated the Gene Source after applying changes.

Utilities

NEW: Users now have the ability to rename Database Identifiers using the Edit button.
ENHANCED: GEMTools displays the user's Client identifier as the default when creating a new database.
ENHANCED: Users can now only create Databases with Database Identifiers that are valid base 36 numbers greater than '03'.
FIXED: A bug that did not allow users to delete newly created object types.

Analysis

ENHANCED: Users can now search for probe amplification type in the Analysis window.

Data Visualization

NEW: The user can now highlight control elements in various colors.
NEW: The user can now highlight genes that are in a project hierarchy, in various colors.
ENHANCED: The apply button in the Graph Options window now stays disabled after being clicked until another change is made.

Image Analysis

NEW: Image Analysis Module activated with LifeArray license.
NEW: Incyte Report Writer integrated PDF Quality Assurance Report generation.
ENHANCED: The default naming convention for scanned images is now: GEMBarcode_1.tif and GEMBarcode_2.tif.

Installation

NEW: The GEMTools installer now optionally installs Adobe Acrobat Reader after the GEMTools installation has been completed.
NEW: Incyte Genomics splash screen.
ENHANCED: For users with Microsoft SQL 7.0 or greater, installation is significantly faster.
EHHANCED: Updated Sample Data Database
NOTE: Users of Microsoft SQL 6.5 need to load sample database file manually as outlined in the GEMTools manual.

Probe Module

NEW: Create Probes enabled with LifeArray license
ENHANCED: Amplification Type added to the Probe and New Probe windows.
FIXED: A bug that did not allow users to add new Annotations in certain situations.

Utilities

NEW: A new tab called Laboratory contains the Auto Analyze, Processing, and Scanner buttons.
ENHANCED: Updated Data Import module with support for GEM Designs and QC Reports
NEW: Data Export module generates GEMTools CAB files for delivery to Incyte or colleagues.

Group Management

FIXED: A bug that brought up an extra message box when the user attempted to add items already present in the group

Project Management

NEW: The Projects window now allows users to share projects.
NEW: Barcoding of Experiments and Tree Nodes.
NEW: Ability to cut and paste tree nodes in the hierarchy.
NEW: Ability to import list of microarrays from a file
NEW: Experiment Properties window (accessed by right clicking on a terminal node in the project tree) allows user to track and manage experiments and experimental design documents.

Web Integration

NEW: Incyte Gene by Gene web-link referral system.
UPDATED: Replaced the LENS web-link with the UniGene web link, for use with Mouse, UGV, and UGV2 chips

User Interface

ENHANCED: Added a Cancel button to the Hierarchy Find dialog.
ENHANCED: Clone Source displayed in the Hierarchy Find dialog.
ENHANCED: Updated controls installed to improved the functionality of Grids and Combo Boxes.
FIXED: A bug that would prevent users from shortening the existing Gene Name, Gene Group Name, Probe Name, Probe Group Name, Gem Name, Gem Group Name, Plate Name, Plate Group Name, Satellite Name, or Query Name.

Technical Enhancements

ENHANCED: Database schema updated to version 2.7.0.
NEW: Schema diagrams included on GEMTools CD in PDF format

GEMTools 2.4.2a Build 344 Release Notes

Incyte Genomics is pleased to bring you GEMTools™ Software version 2.4.2a build 344.

The information below provides a list of feature enhancements and technical issues that have been resolved in the GEMTools 2.4.2a build 344 maintenance release. For more detailed information about GEMTools features refer to the GEMTools 2.4 User Manual.

Gene Management

NEW: Gene Search – Search results can now be sorted by Clone ID.
FIXED: Gene Import Wizard – An error message is now given when an invalid file format is used.

Installation

ENHANCED: Improved ODBC configuration support.

Data Import/Export

FIXED: Corrected output of the HierarchyYN field required for LifeExpress 3.0 PMD files.
FIXED: Inability to import CAB file on new GEMTools 2.4.2a installation.

User Interface

ENHANCED: Gene Groups – Text on button used to set default web link changed from "Web Link..." to "Set Web Link..."

Web Integration

NEW: Updated web links for Incyte Gene by Gene, LifeSeq Public, and NCBI Entrez.

Technical Enhancements

ENHANCED: Database schema updated to version 2.6.1.
FIXED: Added support for additional ODBC 3.0 data types.

GEMTools 2.4.2a Build 326 Release Notes

Incyte Genomics is pleased to bring you GEMTools™ Software version 2.4.2a.

The information below provides a list of feature enhancements and technical issues that have been resolved in the GEMTools 2.4.2a maintenance release. For more detailed information about GEMTools features refer to the GEMTools 2.4 User Manual.

General

ENHANCED: Overall performance of the GEMTools client has been greatly improved.
ENHANCED: Updated Online Help. Press "F1" in any dialog for latest context sensitive help.
ENHANCED: Updated Web Links, including latest Incyte iLifeSeq and NCBI GenBank Entrez.

User Interface

NEW: Logout Button – Closes all open windows and logs off the current user.

Internet Download

FIXED: Inability to change expired password in certain cases.

Data Analysis

ENHANCED: Element Display – Improved performance of Dynamic Gene, Probe, and GEM Groups. Scrolling performance and creation of the groups is significantly faster for large groups.
ENHANCED: Element Display – Users may now select sets of elements for validation / invalidation directly from the element display.
FIXED: Element Display – Error when user attempted to print the Element Display report if there was no information to report.

Data Management

FIXED: Probe – A bug that allowed users to modify a read only Probe Group by double clicking on available probes.
ENHANCED: Gene Import – Ability to import E-Values and Match Types for Genes.

PMD Support

NEW: PMD driver compatible with LifeExpress version 3.0.

Query Builder

FIXED: Query Builder – User reported analysis window, export, and printing incorrectly included additional Genes not specified in query in some situations.
FIXED: Query Builder – A bug that did not show private GEM Groups to the GEMTools super user.
ENHANCED: Query methods have been optimized so that many classes of queries are up to two times faster.

Graph

ENHANCED: Timeseries Graph – Now can display 200 Genes instead of 40 Genes.
ENHANCED: Performance of selecting large sets of elements for view on element display significantly improved.

Utilities

NEW: Admin – Transfer feature allows user to generate CAB files for exchange with colleagues.
FIXED: Utilities – Removed incorrect error message displayed when adding or deleting users.

Find

FIXED: Find GEMs Dialog – A bug that did not show private GEM Groups to the GEMTools super user.
FIXED: GEM Groups – A bug that did not save GEMs added to GEM Groups by using the GEM Find Dialog.

Gene Management

NEW: Gene – E Values (3’ and 5’) and Match Type (3’ and 5’) added to the Genes window.
NEW: Detailed library information provided with all Incyte Gene Annotations.

GEM Management

FIXED: GEM Groups – Fixed a bug that did not save GEMs added to a new GEM Group.
FIXED: GEM Groups – Fixed a bug that did not allow users to view Public GEM groups.
FIXED: GEM Groups – Fixed a bug that allowed users that only had read access to create new GEM Groups.
FIXED: GEM Series – Fixed a bug that did not correctly save GEM Series information. This affected Element Display, Graph, and Cluster Export.
FIXED: GEM Groups – A bug that always selected the last GEM Group used, even when switching between public and private views.
NEW: Elements – Element Invalidation – Allows the user to manually mark or unmark questionable elements as invalid, and selectively removed them from the accepted elements list.

Probe Management

ENHANCED: Probe – Probe names support up to 80 characters.

Project Management

NEW: Full Cut and Paste functionality for project nodes.
NEW: Right-Click ability to add GEMs to a project from a file containing GEM barcodes.
ENHANCED – Membership – User configurable project privileges include "Read", "Write", "Change" and "Admin".

Technical Enhancements

ENHANCED: Bugs fixed and error handling improved in the database transfer module.
ENHANCED: ODBC connection pooling enabled for all database connections.
ENHANCED: Client machine name logged to SQL Server for all GEMTools connections.
NEW: The GEMTools build number is recorded in the version resource of each GEMTools library.
FIXED: P2 Calibrated Signal was not correctly rounded to the nearest integer in certain cases.
FIXED: A bug that failed to launch external applications from GEMTools on Windows 2000.
NEW: GEMTools can now import CAB files with enhanced GEM Design information.

GEMTools 2.4.2 Release Notes

We are pleased to bring you GEMTools™ Software version 2.4.2.

The information below provides a list of feature enhancements and technical issues that have been resolved in the GEMTools 2.4.2 maintenance release. For more detailed information about GEMTools 2.4.2 features refer to the GEMTools 2.4 User Manual.

General

NEW: 30-day GEMTools trial installation.
NEW: Updated Gene Functional Hierarchy Data File.
ENHANCED: Updated online-help files. Press "F1" for context sensitive help.

User Interface

NEW: Incyte Genomics branding.
FIXED: GEMTools was not appearing as a taskbar icon during logon.
FIXED: "Help" window did not always close upon the exit of GEMTools.

Database Synchronization

NEW: Cancel feature available during database Synchronization.
NEW: Shipment Barcodes published for Probes and Plates.
NEW: User Modifiable Gene Fields for Incyte Published Clones. Reference ID and Notes will not be overwritten when Incyte publishes Gene annotations.
ENHANCED: Improved reliability of database synchronization.
ENHANCED: Differential Update Data Loaded in Referential Integrity order.
ENHANCED: Additional log file messages in database synchronization log.
FIXED: Errors reported under certain conditions when synchronizing CAB files.

Internet Download

FIXED: Resolved issue where Internet password could not be reset after 30-day automatic password expiration.

Data Analysis

NEW: Element Display – Right Click on Element Image to Copy to the clipboard, or save as "GIF" image.
NEW: Plate Report – Right Click on Element Image to Copy to the clipboard, or save as "GIF" image.
NEW: Quick View – Right Click on Element Image to Copy to the clipboard, or save as "GIF" image.
ENHANCED: Wait Dialog no longer produces additional task bar icon.

Data Management

NEW: Analysis Export text file now exports Gene Reference ID and Gene Notes.
NEW: "Right-Click" Import from File feature on Project Hierarchy. A file list of GEM or Probe barcodes can be used to populate the Project hierarchy.
NEW: "Change" Project Privilege, in addition to Admin, Read, and Write, that allows users to add and edit project hierarchies but not delete.
NEW: Gene Import Wizard - User can import Reference IDs and Notes for Incyte published Clones.
ENHANCED: Updated GEM Series Cluster export to prevent time-outs and data locking.
ENHANCED: Delete order for GEMs, Plates, and Probes performed in referential integrity order.

LifeArray PMD Support

NEW: PMD driver compatible with LifeArray version 2.1.
NEW: If Incyte Clone ID not specified, Clone ID field will be exported.
NEW: Reference ID field exported to LifeArray Internal ID.
FIXED: Resolved issue that failed to populate the transcript field when both 5’ and 3’ sequence present.
FIXED: Removing multiple GEMs from PMD selection window caused an error message to appear.

Query Builder

ENHANCED: GEM Annotation category has been added to the search criteria.
ENHANCED: User can search by GEM Name or Description.
ENHANCED: Reference ID has been added as a selection under Gene Annotation.
ENHANCED: Ship Date is now a selection under the Probe category.
ENHANCED: Gene Name has been moved under the Gene Annotation category.
ENHANCED: Reference ID has been added as a selection under Gene Annotation.
FIXED: Project Search window was not invoked when the find Hierarchy button was pressed.

Graph

FIXED: Selecting genes with selection box incorrectly genes not filtered by Gene Group.
FIXED: Gene Highlighting and selections are maintained when switching between graph display types.
FIXED: Graphing locked up during large database synchronization.

Utilities

ENHANCED: Web Link Editor – Addition of Gene Reference ID.
FIXED: Database Selection - Tab would not always change databases when the dialog was not in the foreground.

Find

ENHANCED: Genes – Addition of Gene Reference ID.
ENHANCED: GEMs – In the Find the following new fields have been added to the date fields that are searchable: Analyze Date, Fabrication Date, Hybridization Date, Scan Date.
NEW: GEMs – In the Find GEM dialog name and Reference ID have been added as a searchable fields.
ENHANCED – Gene Find – Reference ID has been added as a searchable field.
FIXED: GEMs – In the Find GEM dialog change the GEM search criteria from "Notes" to "Description".
ENHANCED – Plate/Probe - Updated Find windows to use asynchronous queries.

Technical Enhancements

NEW – Improved support for Oracle based servers.

Gene Management

NEW: Creating new genes requires CloneID and Clone Source information.
ENHANCED: Data Source and Reference ID have been added as fields in the Gene window.
ENHANCED: Gene Group interface been enhanced so that duplicate gene selections do not prevent the user from adding genes that do not currently exist in the group.
ENHANCED: Increased Gene Group Multiple selection to allow the user to select up to 2,000 genes at a time.
ENHANCED - Gene Data Source and Gene Reference ID have been added as user editable fields.
FIXED: Resolved data entry which would double apostrophes in the names of new Gene Groups.

GEM Management

NEW: Addition of GEM "Name" field for GEM identification.
ENHANCED: Improved performance of GEM Series Experiment interface.
ENHANCED: Ability to create GEM Series groups from different GEM versions.
ENHANCED: GEM Series Experiments maintain time interval settings when copying experiments or editing experiment content.
FIXED: Pressing "Apply" no longer locks the shortcut window icons in the left panel.

Installation

FIXED: User reported uninstalling GEMTools corrupted ODBC settings.
FIXED: GEMTools server setup incorrectly reported success when all databases were not updated successfully.
FIXED: Trailing spaces on installation key would cause key to not be accepted.
FIXED: When installing GEMTools Server in an alternate directory an empty directory was created on the primary partition.