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Highlights of caArray 2.5.0 released in July, 2012

  • User enhancements
    • Improved large data support
      • Large datasets can now be imported together – it is no longer necessary to split large imports into smaller subsets.
      • Large datasets can be uploaded easily via multiple file selection, drag and drop. (not supported in Internet Explorer)
    • Audit logging of sample and data additions and deletions
    • Ability to restrict access to samples based on sample characteristics
    • Support for automatic refresh of experiments from caIntegrator by providing information about sample and data changes.
    • Ability to configure single sign-on between caArray and caIntegrator.
  • Technical enhancements
    • Improved file storage: Uploaded files are now stored on the file system instead of in the database.
    • A plugin architecture allowing the user community to develop and deploy parsers for new data types easily.
    • Major technology upgrades: Jboss 5.1, Java 6, caGrid v1.5, Struts 2.3.1.5, and NCI build-and-deploy infrastructure (NCI Nexus repository, AntHill Pro 3, BDALite).

For more information refer to the Release Notes.

Highlights of caArray 2.4.1 released on 10/3/2011

  • The 2.4.1 release (caArray 2.4.1 Release Note) addresses the following issues:
    • Visibility into the queue of import and validation jobs, and where your job is in relation to other jobs in the system. Ability to cancel a queued job.
    • Search for experiments by publication author or PubMed ID.
    • Organisms are now restricted to terms from the NCBI Taxonomy.
    • Bug fix to allow proper import of Agilent array design files where the chromosome name is not in a strictly numeric or X/Y format.
    • The installer no longer depends on an internet connection.
    • Fix to bug where experiments with multiple array designs may cause copy number data to get imported as "Imported (Not Parsed)".

Highlights of caArray 2.4.0.2 released on 2/17/2011

  • The 2.4.0.2 release (caArray 2.4.0.2 Release Note) addresses the following issues with the 2.4.0 release:
    • Fixes an error which causes copy number data to not parse.
    • Addresses issues recently found with 2.4.0 installers.

Highlights of caArray 2.4.0.1 released on 1/6/2011

  • The 2.4.0.1 release addresses the following issues with the 2.4.0 release:
    • Fixes occasional out-of-memory errors with the parsers.
    • Addresses null pointer exception in the upgrade installer.
    • Adds probe name validation to the data file parsers.
    • Adds a security patch to Struts 2.1.x.
    • Correctly validates Genepix GAL array designs with non-integer block header information.

Highlights of caArray 2.4.0 released on 9/21/2010

  • This release represents a feature release of the caArray 2 software. Highlights of caArray 2.4.0 are:
    • Agilent raw TXT for aCGH, expression and miRNA assays
    • Agilent GEML/XML array designs
  • Nimblegen pair Report TXT (raw and normalized)
  • Nimblegen NDF array designs
    • Illumina Sample Probe Profile TXT
    • Illumina genotyping processed data matrix TXT
    • Illumina BGX/TXT array designs
    • Affymetrix CEL and CHP in AGCC/Calvin formats in addition to the GCOS formats
    • Affymetrix CNCHP copy number data (CN4 and CN5)
    • Copy Number data in a prescribed MAGE-TAB Data Matrix format.
      • If you have copy number data that is not in the caArray-prescribed Copy Number MAGE-TAB Data Matrix format, we provide a conversion utility. The conversion utility is found inside the cn2magetab.jar file, and is invoked from the command line. Please see the README_copy_number_conversion.txt for more details on its operation.

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