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Release Name: 2.4.1

Notes:
Release Notes
=============

Product: caArray
Version: 2.4.1
Date: September 2011

Contents
--------

1. Introduction
2. Release History
3. Anticipated Releases
4. Features and Defects Addressed in this Release
5. Known Issues/Defects
6. Bug Reports, Feature Requests and Support
7. Documentation and Files
8. NCICB Web Pages
9. Getting Started with the new API

Introduction
---------------------------

caArray is an open-source, web and programmatically accessible array data management system. caArray guides the
annotation and exchange of array data using a federated model of local installations whose results are shareable
across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through
acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by
tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical
library of assay management.

https://array.nci.nih.gov/

Release History
------------------------

caArray v2.4.1 – September 2011
caArray v2.4.0.2 – February 2011
caArray v2.4.0.1 – January 2011
caArray v2.4.0 – September 2010
caArray v2.3.1 – February 2010
caArray v2.3.0.1 – November 2009
caArray v2.2.1 – May 2009
caArray v2.2.0 – January 2009
caArray v2.1.1 – October 2008
caArray v2.1.0 – August 2008
caArray v2.0.2 – May 2008
caArray v2.0.1 – April 2008
caArray v2.0.0 – February 2008

Anticipated Releases
------------------------

caArray v2.5.0 – Q1 2012 (new features)

Features and Defects Addressed in this Release
-----------------------------------------------

This release represents a feature release of the caArray 2 software. Highlights of caArray 2.4.1 are:

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.
For details about this feature, please refer to the chapter "Submitting Data" in the caArray User's Guide.

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)".

Known Issues/Defects
------------------------

See the Jira tracker for existing open defects, community requests, resolutions and feature requests. https://tracker.nci.nih.gov/browse/ARRAY

The following issues are highlighted.

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
in order to test your installation. Even if you are running the browser on the same machine as your caArray
installation, you cannot go to http://localhost:<port>/caarray.

Image files referenced in a MAGE-TAB SDRF cannot be validated or imported.

Multiple MAGE-TAB imports can result in duplicate persons in the database.

Experiments with multiple array designs may cause copy number data to be Imported (not parsed). For more
information, please go to https://tracker.nci.nih.gov/browse/ARRAY-1811.

Data import can fail if experiment is associated with multiple array designs (https://tracker.nci.nih.gov/browse/ARRAY-1837).

GUI installer suddenly quits when illegal characters present in password fields.

For Agilent GEML Array Design files for miRNA, accessions are not created. See https://tracker.nci.nih.gov/browse/ARRAY-2041

Bug Reports, Feature Requests, And Support
------------------------------------------

Send email to ncicb@pop.nci.nih.gov to request technical support. To report a bug or request a new feature,
please visit the Molecular Analysis Tools Knowledge Center resources at:

https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page

Existing requests and resolution may be viewed at the caArray issue tracker URL:

https://tracker.nci.nih.gov/browse/ARRAY

Documentation And Files
-----------------------
Wiki-based guides are available at the following locations:

caArray 2.4.0 User's Guide
caArray 2.4.0 Installation Guide
caArray 2.4.0 Technical Guide
caArray 2.4.0 API Guide (unchanged for this release)

Links to all other documentation and files can be found at:

https://cabig.nci.nih.gov/tools/caArray

NCI CBIIT Web Pages
---------------

The NCI Center for Bioinformatics, http://ncicb.nci.nih.gov/
NCI CBIIT Application Support, http://ncicb.nci.nih.gov/NCICB/support
NCI CBIIT Download Center, http://ncicb.nci.nih.gov/download/

Getting Started with the caArray API
------------------------------------

To get started with the caArray Service API v1.0, please download the client libraries
(caarray-client-external-v1_0.zip). Example client code for the Java API is available
in java_api_client_examples_v1_0.zip. Example client code for the Grid API is available
in grid_api_client_examples_v1_0.zip. Both the example packages contain a README.txt that will get you started.

Please note that applications with no authentication requirement can use the Java API or the Grid API.
But applications needing authenticated access must use the Java API. We will add authentication support to the Grid API
in a future release.

If, for some reason, you do not wish to use the new Service API yet, you can continue to use the legacy API,
but you must upgrade to the latest version. To do this, please download the client libraries (caarray-client-legacy.zip).

FEEDBACK

Please post feedback on the Molecular Analysis Tools Knowledge Center forum: https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page