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=TOC} {toc:minLevel=2} {cloak}{panel} Release Notes ============= |
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#Product:# caArray |
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#Version:# 2.4.0.2 |
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#Date:# February 2011 |
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Contents |
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-------- |
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1. Introduction |
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2. Release History |
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3. Anticipated Releases |
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4. Features and Defects Addressed in this Release |
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5. Known Issues/Defects |
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6. Bug Reports, Feature Requests and Support |
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7. Documentation and Files |
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8. NCICB Web Pages |
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9. Getting Started with the new API |
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Introduction |
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--------------------------- |
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caArray is an open-source, web and programmatically accessible array data management system. caArray guides the |
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annotation and exchange of array data using a federated model of local installations whose results are shareable |
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across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through |
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acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by |
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tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical |
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library of assay management. |
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* https://array.nci.nih.gov/ |
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Release History |
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------------------------ |
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* caArray v2.4.0.2 |
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-- February 2011 * caArray v2.4.0.1 |
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-- January 2011 * caArray v2.4.0 |
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-- September |
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2010 * caArray v2.3.1 |
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-- February 2010 * caArray v2.3.0.1 |
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-- November 2009 * caArray v2.2.1 |
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-- May 2009 * caArray v2.2.0 |
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-- January 2009 * caArray v2.1.1 |
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-- October 2008 * caArray v2.1.0 |
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-- August 2008 * caArray v2.0.2 |
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-- May 2008 * caArray v2.0.1 |
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-- April 2008 * caArray v2.0.0 |
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-- February 2008 Anticipated Releases ------------------------ |
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* caArray v2.5.0 |
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-- Q2 2011 (new features) |
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Features and Defects Addressed in this Release |
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----------------------------------------------- |
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This release represents a feature release of the caArray 2 software. |
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Highlights of caArray 2.4.0 are: |
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* Parsers for several new data types: |
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* Agilent raw TXT for aCGH, expression and miRNA assays. |
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* Agilent GEML/xml array designs |
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* Nimblegen pair Report TXT (raw and normalized) |
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* Nimblegen NDF array designs |
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* Illumina Sample Probe Profile TXT |
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* Illumina genotyping processed data matrix TXT |
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* Illumina BGX/TXT array designs |
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* Affymetrix CEL and CHP in AGCC/Calvin formats in addition to the old GCOS formats |
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* Affymetrix CNCHP copy number data (CN4 and CN5) |
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* Copy Number data in a prescribed MAGE-TAB Data Matrix format. |
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For details about the parsing of these files, please refer to the chapter "Importing Data Files" |
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in the caArray User's Guide. |
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* If there are array design files or data files already in the system that are "imported not parsed", and |
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if there are new parsers available that allow those file types to now be parsed, the system provides the |
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ability to reimport these files. |
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* If you have copy number data that is not in the caArray-prescribed Copy Number MAGE-TAB Data Matrix format, |
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we provide a conversion utility. The conversion utility is found inside the cn2magetab.jar file, and is invoked |
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from the command line. Please see the README_copy_number_conversion.txt for more details on its operation. |
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* For experiments created from 2.4.0 onwards, the experiment public identifier will be composed of the |
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string "EXP-" followed by a number. Already-existing experiment public identifiers will not be changed. |
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We gratefully acknowledge our collaborators at Yale and UPMC for their contribution of the Nimblegen parsers to the release. |
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The 2.4.0.2 release addresses the following issues with the 2.4.0 release: |
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* Fixes out-of-memory errors with the parsers. |
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* Fixes null pointer exception in the upgrade installer. |
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* Adds probe name validation to the data file parsers. |
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* Adds a security patch to Struts 2.1.x. |
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* Correctly validates Genepix GAL array designs with non-integer block header information. |
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* Fixes an error which causes copy number data to not parse. |
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* Addresses issues recently found with 2.4.0 installers. |
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Known Issues/Defects |
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------------------------ |
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See the GForge tracker for existing open defects, community requests, resolutions and feature requests. |
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The following issues are highlighted. |
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https://tracker.nci.nih.gov/browse/ARRAY |
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- The total import job size (defined as sum of uncompressed file sizes) must be less than 3GB.
- A collaborator cannot see files in the "Uploaded" state even with read-write permissions to the experiment.
- If you are still using the Legacy API and your query results in >10,000 results, your transaction
may time out. The workaround is to modify your query into multiple queries that return smaller result sets.
- The installer does not support configuring SSL support in JBoss.
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* The total import job size (defined as sum of uncompressed file sizes) must be less than 3GB. * A collaborator cannot see files in the "Uploaded" state even with read-write permissions to the experiment. * If you are still using the Legacy API and your query results in >10,000 results, your transaction may time out. The workaround is to modify your query into multiple queries that return smaller result sets. * The installer does not support configuring SSL support in JBoss. * After installing a local copy of caArray, you must go to http://<IP_address_or_host_name>:<port>/caarray |
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in order to test your installation. Even if you are running the browser on the same machine as your caArray |
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installation, you cannot go to http://localhost: |
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<port>/caarray. |
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* Image files referenced in a MAGE-TAB SDRF cannot be validated or imported. |
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* Multiple MAGE-TAB imports can result in duplicate persons in the database. |
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* Experiments with multiple array designs may cause copy number data to be Imported (not parsed). For more |
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information, please go to https://tracker.nci.nih.gov/browse/ARRAY-1811 |
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. |
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* Data import can fail if experiment is associated with multiple array designs. For more |
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information, please go to https://tracker.nci.nih.gov/browse/ARRAY-1837 |
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* In IE browser only, pane overflows "Download Selected Experiment Files" leaf in Download Data tab so buttons are obscured. |
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For more information, please go to https://tracker.nci.nih.gov/browse/ARRAY-1626 |
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- GUI installer suddenly quits when illegal characters present in password fields.
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* GUI installer suddenly quits when illegal characters present in password fields. Bug Reports, Feature Requests, And Support ------------------------------------------ |
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Send email to ncicb@pop.nci.nih.gov to request technical support. To report a bug or request a new feature, |
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please visit the Molecular Analysis Tools Knowledge Center resources at: |
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https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page |
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Existing requests and resolution may be viewed at the caArray issue tracker URL: |
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https://tracker.nci.nih.gov/browse/ARRAY |
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Documentation And Files |
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----------------------- |
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Please note: new wiki based technical guide and the installation guide can be |
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found at |
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following locations: |
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caArray 2.4.0 Installation Guide: https://wiki.nci.nih.gov/display/caArray2/caArray+2.4.0+Data+Portal+Local+Installation+Guide+Wiki+Main+Page |
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caArray 2.4.0 Technical Guide: https://wiki.nci.nih.gov/display/caArray2/caArray+2.4.0+Technical+Guide+Wiki+Main+Page |
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caArray 2.4.0 API Guide (unchanged for this release): https://wiki.nci.nih.gov/display/caArray2/caArray+2.4.0+API+Guide |
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Links to all other documentation and files can be found at: |
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https://cabig.nci.nih.gov/tools/caArray |
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NCI CBIIT Web Pages |
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--------------- |
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* The NCI Center for Bioinformatics, http://ncicb.nci.nih.gov/ |
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* NCI CBIIT Application Support, http://ncicb.nci.nih.gov/NCICB/support |
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* NCI CBIIT Download Center, http://ncicb.nci.nih.gov/download/ |
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Getting Started with the caArray API |
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------------------------------------ |
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To get started with the caArray Service API v1.0, please download the client libraries |
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(caarray-client-external-v1_0.zip). Example client code for the Java API is available |
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in java_api_client_examples_v1_0.zip. Example client code for the Grid API is available |
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in grid_api_client_examples_v1_0.zip. Both the example packages contain a README.txt that will get you started. |
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Please note that applications with no authentication requirement can use the Java API or the Grid API. |
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But applications needing authenticated access must use the Java API. We will add authentication support to the Grid API |
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in a future release. |
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If, for some reason, you do not wish to use the new Service API yet, you can continue to use the legacy API, |
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but you must upgrade to the latest version. To do this, please download the client libraries (caarray-client-legacy.zip). |
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FEEDBACK
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FEEDBACK Please post feedback on the Molecular Analysis Tools Knowledge Center forum: https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page |
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