'''caArray Road Map
The table below outlines the priority features ordered and grouped by priorities.
Development Focus |
High Priority Items: To be implemented after 2.4.0 release. |
The following are high priority features that will be incorporated in future caArray releases:
- Fix collaborator group access to unimported files
- Integrate caArray with biospecimen systems (caTissue)
- Simplify the import of large data sets
- Support Grid API access to protected data
- Enable development and distribution of plug-in parsers
|
Intermediate Priority Items |
The table below outlines the major features in scheduled and past release(s). The table below outlines the major features in up-coming release(s).
Version |
Development Focus |
Release Date |
2.4.0 |
This release represents a feature release of the caArray 2 software: Focus is around data parser.
The following data parsers will be included in caArray 2.4.0:
- Agilent:
- GEML/xml array designs (aCGH, gene expression and miRNA)
- Raw TXT data files (aCGH, gene expression and miRNA)
- Nimblegen - Community Code Contribution:
- NDF array designs
- Pair Report (raw and normalized) data files
- Illumina:
- BGX/TXT array designs
- Gene expression: Sample Probe Profile TXT files with unique Probe_Id
- Genotyping: Processed matrix TXT files with unique IlmnID values
- Affymetrix:
- AGCC/Command Console formats for CDF, CEL and CHP files.
- CNCHP files with copy number and LOH data.
- Copy number data in MAGE-TAB Data Matrix format
|
August 2010 |
2.3.1 |
This release represents a feature release of the caArray 2 software: Focus is around data export to GEO.
Highlights of caArray 2.3.1 include:
- caArray will allow the user to export an experiment into GEO SOFT format. This SOFT package can then be submitted to GEO.
- The initial release will support single-channel experiments that have Affymetrix CHP data files, and that are based on array designs (platforms) already in GEO.
- Focussing on CHP files allows us to package the native data files in the SOFT package as opposed to having to derive data tables to include in the SOFT submission.
|
February 2010 |
2.3.0 |
This release represents a feature release of the caArray 2 software: Focus is around new programmatic interface to caArray application.
Highlights of caArray 2.3.0 include:
- 15578: Redesign Grid API to support backwards compatibililty via external data model
- 18908: Keep an audit trail of permissions changes made to an experiment.
|
October 2009 |
2.2.1 |
This release represents a minor release of the caArray 2.x software: Focus is around access control and ownership of experiments
Highlights of caArray 2.2.1 include:
- 19324: Genepix data files must require an accompanying SDRF and sample names must not be mandated.
- 15443: Ability to change experiment ownership
- 19532: System administrator should be able to change collaborator group ownership.
2.2.0 |
*80 features/issues were addressed * |
- Highlights:
- 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.
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