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* Version Number and Release Date: 2.4.1 October 2011
* Primary audience: Microarray data producers and application developers
* caBIG® Tool Bundle: (LSD, CTMS, DSIC) 
* Grid Enabled? Yes
* Compatibility Level: Silver Compatibility (5/28/2009)
* Installation Level: Intermediate - technical assistance may be required, download may require supporting infrastructure or software
* System Requirements: Refer to the [#System Requirements] section.
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{tip:title=Are you new to caArray?}For those who are new to caArray, we have prepared a [short guide|https://wiki.nci.nih.gov/pages/viewpage.action?pageId=56796714] to help you find necessary information fast.{tip}

h2. Tool Overview

{multiexcerpt:name=caArray} !caarray.jpg|width=100px,alt="caArray logo"! 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.{multiexcerpt}

h2. Installation and Downloads

h3. Downloads

* [Download, Install or Upgrade caArray|http://ncicb.nci.nih.gov/download/downloadcaarray.jsp]
* [NCI caArray|https://array.nci.nih.gov/caarray/home.action] public server is free to the whole community.
A public [caArray|https://array.nci.nih.gov/caarray/home.action] hosted by NCI is free to community. A free account will be issued upon registration.
* [Download Sample Data|caArray2:caArray Demo Testing Data]

h3. System Requirements

While caArray is a web-based application, it does have a dependent software stack, which includes: MySQL 5.0.27 database; JBoss 4.0.4 (hosts the caArray grid service) and JBoss 4.0.5 (hosts the caArray application); JEMS installer 1.0.2 GA (supports EJB 3.0 specification)

|| Dependent Software || Version || URL ||
| J2SE Development Kit | 5.0 Update 10 (J2SE 5.0) | [J2SE 5.0|http://java.sun.com/products/archive/j2se/5.0_10/] |
| Apache Ant | 1.7.0 | [apache-ant-1.7.0-bin.zip|https://gforge.nci.nih.gov/svnroot/lsd/trunk/tools/apache-ant-1.7.0-bin.zip] |
| MySQL | 5.0.27 | [mysql 5.0.27|http://downloads.mysql.com/archives.php?p=mysql-5.0&v=5.0.27] |
| JBoss for UPT | 4.04 | -- |
| JBOSS for Grid Service | 4.04 | -- |
| JBOSS for caArray application | 4.05 | -- |

h2. Forum and Support for caArray

* [End User Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=6]
* [Developer Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=8]
* [caArray Developers Listserv|http://list.nih.gov/archives/caarray_developers-l.html] (archived, not in use)
* [caArray Users Listserv|http://list.nih.gov/archives/caarray_users-l.html] (archived, not in use)
* [Report a Defect or Request a Feature at caArray Jira Tracker|https://tracker.nci.nih.gov/browse/ARRAY]
* [Mini-how to Submit Bug reports or Feature Requests in JIRA|https://wiki.nci.nih.gov/x/fpKNAg] A tutorial on how to use JIRA for caArray.
* [Application Support|mailto:ncicb@pop.nci.nih.gov]

h2. What's New

caArray 2.4.1 was officially released on 10/3/2011 and is available on the [NCI CBIIT production server|https://array.nci.nih.gov/caarray/home.action].

[An important notice on Using UPT to create groups for caArray|https://wiki.nci.nih.gov/display/caArray2/Important+Notice+on+Using+UPT+to+Create+Groups+for+caArray]

Eighty (80) citations were added to the [caArray2:caArray Citations].

For more news, visit [caArray2:What's new for caArray].

h2. Presentations, Demos and Other Materials

* [caArray2:caArray Demos]
* [caArray overview presented at the AACR 2011 Annual Meeting|caArray2:caArray^CaArray_Overview_AACR_2011_v2.ppt]
* [Newly Made caArray Demonstration (applicable up to caArray 2.3.x)|http://cabigtrainingdocs.nci.nih.gov/caArrayDemo2009/caArray-Demo-2009.html] (Make sure your speakers are on to play audio.)
* [Previous caArray Demonstration -- 20-minute Audio over Slides and Screencast (applicable up to caArray 2.0.x)|http://cabigtrainingdocs.nci.nih.gov/caArrayDemo/caArray_demo_v2.html] (Make sure your speakers are on to play audio.)
* [Instructor-led training on caArray|http://ncicbtraining.nci.nih.gov/TPOnline/TPOnline.dll/Public%20Course/COURSENO=COUR2006011114141308840025]
* [caArray2:caArray Roadmap]
* [caArray Brochures|https://cabig.nci.nih.gov/tool_brochures/caARRAY_toolsheet_31208v1_Final.pdf]

h2. Documentation and Training

h3. caArray Documentation

* [An important notice on Using UPT to create groups for caArray|https://wiki.nci.nih.gov/display/caArray2/Important+Notice+on+Using+UPT+to+Create+Groups+for+caArray]
* [caArray 2.4.x User Guide|https://wiki.nci.nih.gov/display/caArray2doc/caArray+2.4.x+User%27s+Guide]
* [caArray Tool Summary Page|https://cabig.nci.nih.gov/tools/caArray] (On caBIG® Community Website)
* [caArray Project site|http://caarray.nci.nih.gov/]
* [caArray 2.4.x Installation Guide|caArray2doc:caArray 2.4.x Data Portal Local Installation Guide]
* [UPT 4.2.1 User/Programmer/Installation Guide|https://gforge.nci.nih.gov/frs/download.php/7770/caCORE_CSM_v421_ProgrammersGuide.pdf]
* [caArray 2.4.x Technical Guide|caArray2doc:caArray 2.4.x Technical Guide]
* [caArray 2.4.x API Guide|caArray2doc:caArray 2.4.x API Guide]
* [Multi-Server caArray Installation|caArray2:caArray^CaArray_Multi_Server_Install.pdf]
* [NCI UPT FAQ|https://wiki.nci.nih.gov/x/ygGy]
* [caGrid Service Deployment Guide|http://cagrid.org/display/knowledgebase/Grid+Service+Deployment+Guide] | * [Download Sample Data|caArray2:caArray Demo Testing Data] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
* [GlaxoSmithKline Cancer Cell Line Genomic Profiling Data|https://cabig.nci.nih.gov/caArray_GSKdata/]
* [UPT 3.2.2 Installation Guide|https://gforge.nci.nih.gov/frs/download.php/7022/upt_3_2_2_lsd_1_1_0_installation_guide.pdf]
* [caArray Archived Site (GForge)|http://gforge.nci.nih.gov/frs/?group_id=305] |

h2. caArray Knowledge Base

Find the answers to the most frequently asked questions; understand how caArray works.
* [caArray FAQ and In-depth Articles|caArray2:caArray FAQ and In-depth Articles]
* [caArray2:caArray Tutorials]

If you still don't know if caArray is for you, explore the [caArray2:caArray Case Studies]. Case studies show examples of how caArray could be used in different scenarios.

For a list of articles that discuss caArray, visit [caArray2:caArray Citations].

h2. Open-source development

* [caArray Open Development Code Base (svn)|https://ncisvn.nci.nih.gov/WebSVN/listing.php?repname=caarray2]
* [caArray gForge Open Application Download|https://gforge.nci.nih.gov/frs/?group_id=305]

h2. Integration with other tools

h3. Integration with geWorkbench

geWorkbench can query for data in an instance of caArray via a Java API. Several operations are supported. You can:

# Query for experiments, for example by platform or by species.
# Select from which hybridizations in an experiment you wish to download data.
# Download derived (summarized, probeset-level) data that has been parsed into the database. An example is the values loaded from Affymetrix CHP files (created through GCOS/MAS5). geWorkbench does not currently support retrieving or analyzing Affy CEL files directly.

The current release of geWorkbench, version 2.1.0, connects with caArray 2.3.0, 2.3.1, and 2.4.0.2
For more information, visit the [geWorkbench project page|http://www.geworkbench.org].

The software can be [downloaded|https://gforge.nci.nih.gov/frs/?group_id=78].

h3. Integration with caIntegrator

caIntegrator can extract the genomic data from caArray hosted on either a private server or the [NCI site|https://caintegrator2.nci.nih.gov/caintegrator2/login.action]. You can:

# Extract the genomic data into caIntegrator.
# Integrate the genomic data with the clinical data and imaging data in caIntegrator.
# Perform genomic data analysis with the built-in GenePattern Tool within caIntegrator.

The current release of caIntegrator, version 1.2.0, can work with caArray 2.3.0, 2.3.1, and 2.4.0.2 .

You may use the publicly accessible [NCI site|https://caintegrator2.nci.nih.gov/caintegrator2/login.action]. To install a local copy, [download a copy of software|https://gforge.nci.nih.gov/frs/?group_id=507].

h3. Integration with GenePattern

GenePattern has a module that can retrieve data from caArray using its Java API. The caArray2.3.0 Importer lets you retrieve raw data files from caArray by experiment name or id. You can specify the extension of the data file that you want to download. The default is .CEL.

You can process CEL files using the GenePattern module ExpressionFileCreator. Once you have used ExpressionFileCreator, the data can be further analyzed using many different GenePattern analysis modules.

The caArray 2.3.0 Importer module is compatible with caArray v2.3.x. You may [download the caArray2.3.0Importer|https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/trunk/genepattern/cabig_ey2_2008/caArrayImporter/caArray2.3.0Importer/caArray2.3.0Importer.zip?root=genepattern&view=log].

The caArray 2.1.0 Importer module is compatible with caArray v2.1.x and v2.2.0. You may [download the caArray2.1.0Importer|https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/trunk/genepattern/cabig_ey2_2008/caArrayImporter/caArray2.1.0Importer/caArray2.1.0Importer.zip?root=genepattern&view=log].

The GenePattern team has recently devleoped caArray2ImportViewer, a visualizer to import data from caArray into GenePattern. It is compatible with caArray 2.4.0.x. Please see the [documentation|https://ncisvn.nci.nih.gov/svn/icr_portal/genepattern/trunk/genepattern/cabig_2011/CaArray2ImportViewer/doc/CaArray2ImportViewer.pdf] to learn more.

You may also [download GenePattern|http://www.genepattern.org|http://www.genepattern.org].

Once you've fetched your microarray data from caArray from any of the above versions of the caArrayImporter, you can use that data in any GenePattern module or pipeline that accepts gene expression data. To view compatible modules from within GenePattern you can click the context arrow next to the imported file (the result file of your caArrayImporter job in Recent Jobs) to see which modules can accept this dataset.