What's new on caArray

From Molecular WIKI

• caArray 2.2.0 was released on 1/21/2009. Approximately 80 features/issues were addressed in this release ([release note]. Highlights of this release are:
  • Sample search:
    • The user can now search for biomaterials (Samples and Sources) in the system.
    • The keyword search can be applied to one of a list of standard or predefined categories, or to arbitrary categories previously imported into the system via Characteristic[] columns in a MAGE-TAB SDRF document.
  • Export experiment annotations in MAGE-TAB format:
    • The user can generate and download a MAGE-TAB file set describing the annotations of an experiment.
    • The generated MAGE-TAB includes the relationship between biomaterials, hybridizations and data files, and also characteristics of the biomaterials.
    • The generated MAGE-TAB does not contain information about experimental factors, protocols, publications or people.
  • Bulk-update of experiment annotations using MAGE-TAB import:
    • When a MAGE-TAB file set is being imported, the System recognizes references to existing biomaterials and hybridizations by name.
    • Biomaterial linkages can be modified in an additive way via MAGE-TAB import. Existing linkages and biomaterials cannot be deleted via MAGE-TAB import.
    • Biomaterial characteristics can be modified or new characteristics added via MAGE-TAB import.
  • Support for GEO and ScanArray data:
    • Data files can be designated as GEO SOFT or GEO GSM and then imported (without parsing) and associated with samples.
    • ScanArray CSV data files can be imported (without parsing) and associated with samples.
  • Enhanced usability of permissions management workflow:
    • While setting sample-selective access for an experiment, the user can do a keyword search for Samples against a set of categories, select the Samples of interest, and grant access to the selected Samples as a whole.

• caArray 2.1.1 was released on 10/24/2008 as part of the Life Science Distribution (LSD) 1.1 release. It is available at NCICB (caArray 2.1.1 release note) and for local installation. Please download at https://gforge.nci.nih.gov/frs/?group_id=305. The following installer and installation guides are available:
  • For a new caArray2 installation, please use caarray_distribution_2_1_1.zip
  • To upgrade from any previous version of caArray 2.x, please use caarray_upgrade_2_1_1.zip
  • Instructions for both are in the caArray 2.1.1 Installation Guide, caarray_2_1_1_installation_guide.pdf

• A self-paced demo on installing caArray has recently been made available. Please take a look at this site.

• caArray 2.1.0 is just released on 8/13/2008. Please check it out at https://array.nci.nih.gov.
  • Improved efficiency of programmatic Grid API
    • Grid Transfer makes for fast download of file contents.
    • Grid retrieval of parsed array data is more efficient now.
  • Flexible association of data files to biomaterials
    • System can auto-generate individual biomaterial chains; OR
    • System can auto-generate a single biomaterial chain; OR
    • User can associate data files to a specific biomaterial/hybridization.
  • New Sample-centric view
    • A well-known URL to navigate directly to a Sample details page.
    • Unique Sample External ID that is defined by the user.
  • More than 40 items addressed from the Gforge trackers.
  • Rembrandt gene expression data is now hosted on caArray.
  • More TCGA data are now available.
  • The User Guide for 2.1.0 will contain detailed documentation about creating MAGE-TABfiles for bulk import into caArray.

Please also check out a short presentation about the new caArray, given at the caArray User Community Meeting.