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caArray is an open source microarray data management system that allows users to submit, annotate and download microarray data. caArray was developed using the caBIG compatibility guidelines, as well as the Microarray Gene Expression Data (MGED) society standards for microarray data. Compatibility with these standards and guidelines will facilitate data sharing and integration of diverse data types including clinical, imaging, tissue and functional genomics data. A number of analytical tools that connect to caArray are already available, including geWorkbench and GenePattern that both provide a variety of data analysis, visualization and annotation functions for microarray and other data types. |
Download
caArray source code is available at the NCICB download site: http://ncicb.nci.nih.gov/download for local installation.
Feedback & Feature Requests
caArray users are encouraged to sign up for a GForge account and join the caArray project to submit feedback and feature requests.
Go to https://gforge.nci.nih.gov and click on 'New Account' in the upper right hand corner. A Quick Start guide is available at https://gforge.nci.nih.gov/docman/view.php/47/495/GForge_Quick%20Start_and_User_Guide.pdf
We encourage users to visit Gforge to get up-to-the-minute access to the state of caArray and its related projects. Not only does GForge provide access to all the application assets, it is also the place where one can report bugs or request new features, and as importantly, keep up-to-date with their ongoing status. Visit caArray Portal and API for more.
Technical Documentation
The caArray Portal distribution contains the caArray database
installation instructions, the caArray database dump file, the caArray
DDL Schema file, the caArray local installation instructions, the
caArray Portal source code, and the caArray Java documents.
| caArray Release Notes |
caarray_release_notes.pdf |
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| caArray Local Installation Instructions |
caArray_1_6_Installation_Guide.pdf |
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| caArray Update Utility Instructions |
caArray_1_6_Update_Utility.pdf |
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| caArray User's Guide |
caArray_1_6_Users_Guide.pdf |
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| caArray Technical Guide |
caArray_1_6_Technical_Guide.pdf |
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| caArray Portal API Documentation |
caarray-javadoc.1.6.zip |
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| caArray Data Migration Guide |
caArray_1.3.1_DataMigrationGuide.pdf |
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caAMEL is a web-based application that validates MAGE-ML documents and loads the data contained within valid MAGE-ML documents into a caArray repository.
The caArray MAGE-OM API objects access data in the caArray
database via remote method invocations issued to a dedicated
MAGE server. There are two primary types of objects
defined in the API:
- MAGE-OM-compliant objects
- Custom MAGE-OM Impl (implementation) objects.
The MAGE-compliant objects are implemented as Java interfaces,
which the custom MAGE-OM Impl objects implement as concrete
Java classes. The caArray MAGE-OM API is a set of Java objects that adhere to the
object model defined by OMG's Gene Expression v1.1.
The MGED Society web site is an excellent source for
supplemental material on the MAGE object model.
The caArray MAGE-OM Grid Service API is a caGrid Data Service
that exposes the functionality of MAGE-OM API over the grid. The Grid Service
provides access to data in the caArray database via a web service call issued
to a dedicated Grid Service server at NCI or any other site with an accessible
caArray MAGE-OM Grid Service installation. For more information about caGrid,
see http://www.cagrid.org.
The caGrid 1.0 User and Programmer Guides are excellent sources for additional material,
see http://gforge.nci.nih.gov/frs/?group_id=25
Below are some utilities that are available to assist both users and developers of caArray.
| Name |
Description |
URL |
| UCSF Spot To Genepix Utility v1.6 |
This is a perl script utility that converts a UCSF Spot clone list file or a UCSF Spot CGH results file to GenePix .gal files and .gpr files |
spot2genepix.pl |
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