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Tool Overview

Installation and Downloads

Downloads

• Download, Install or Upgrade caArrayNCI caArray public server is free to the whole community.
  A public caArray hosted by NCI is free to community. A free account will be issued upon registration.
• Download Sample Data

System Requirements

While caArray is a web-based application, it does have a dependent software stack, which includes: MySQL 5.0.27 database; JBoss 5.1. (hosts the caArray grid service and the caArray application); and JEMS installer 1.0.2 GA (supports EJB 3.0 specification)

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GitHub Repositories

• caArray Github Repository

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• caArray docs GitHub Repository

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Support for caArray

You can contact the NCI CBIIT Application Support if you have any questions or concerns.

• End User Forum
• Developer Forum
• caArray Developers Listserv (archived, not in use)
• caArray Users Listserv (archived, not in use)
• Report a Defect or Request a Feature at caArray Jira Tracker
• Mini-how to Submit Bug reports or Feature Requests in JIRA A tutorial on how to use JIRA for caArray.
• Application Support

What's New

caArray 2.5 was released in July, 2012 and is available on the NCI CBIIT production server.

For details and more news, visit What's new for caArray.

Presentations, Demos and Other Materials

• caArray Demos
• caArray overview presented at the AACR 2011 Annual Meeting
• Newly Made caArray Demonstration (applicable up to caArray 2.3.x) (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) (Make sure your speakers are on to play audio.)
• Instructor-led training on caArray
• caArray Roadmap
• caArray Brochures

Documentation and Training

• caArray2 Documentation
• An important notice on Using UPT to create groups for caArray
• caArray Project site
• NCI UPT FAQ

• caGrid Service Deployment Guide

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• GlaxoSmithKline Cancer Cell Line Genomic Profiling Data
• UPT 3.2.2 Installation Guide
• UPT 4.2.1 User/Programmer/Installation Guide
• caArray Archived Site (GForge)

caArray Knowledge Base

Find the answers to the most frequently asked questions; understand how caArray works.

• caArray FAQ and In-depth Articles
• caArray Tutorials

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

Citations

For For a list of articles that discuss caArray, visit caArray Citations.

Open-source development

• caArray Open Development Code Base (svn)
• caArray gForge Open Application Download

Integration with other tools

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The current release of geWorkbench, version 2.15.0, connects with caArray 2.35.0 , and 2.35.1, and 2.4.0.2
For more information, visit the geWorkbench project page.

The software can be downloaded.

Integration with caIntegrator

caIntegrator can extract the genomic data from caArray hosted on either a private server or the NCI site. You can:

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

The current release of caIntegrator, version 1.4, works with caArray 2.5.

You may use the publicly accessible NCI site. To install a local copy, download a copy of the software.

Integration with GenePattern

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The caArray 2.3.0 Importer module is compatible with caArray v2.3.x. You may download the caArray2.3.0Importer.

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.

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 to learn more.

You may also download GenePattern.

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.