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| Intended Audiences:
Biomedical researchers. Areas of focus include: Microarray Analysis, SNP Analysis, Proteomics. |
| Area of Focus:
Data Analysis and Statistical Tools |
Primary Workspace:
ICR |
Product Description:
GenePattern puts sophisticated computational methods into the hands of the biomedical research community. A simple application interface gives a broad audience access to a growing repository of analytic tools for genomic data, while an API supports computational biologists. GenePattern is a powerful analysis workflow tool developed to support multidisciplinary genomic research programs and designed to encourage rapid integration of new techniques.
GenePattern has been publicly released since January of 2003 and currently (10/07) has over 7000 users world wide. It won the Bio-IT World Best Practices Editors choice award in 2005. |
| Current Version Number: 3.1 |
Release Date of Current Version:
February 19 2008 |
Currently caGrid Enabled?
Yes
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caBIG™ Compatibility Level:
Silver
Learn more about Silver Compatibility |
| Tool Maturity Assessment:
Mature Product (Successfully Adopted) |
Installation Level:
Basic - Wizard or web browser application; minimal technical assistance required
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Architecture Type:
Desktop Application, Web Application - Remote application with data uploads/downloads through web interface |
System Requirements:
GenePattern consists of a server (that may be kept private or shared), a web application client, a desktop application client and programming language libraries (Matlab, R, Java) that can call the server. It will also soon include caGRID interfaces. GenePattern requires 256MB of system RAM and 500MB of hard drive space. Installers exist for Windows, Macintosh and Linux systems but it can also run on any other operating system with Java 1.5 support. GenePattern has three Silver level analysis services publicly available on caGrid. The GenePattern server itself qualifies as Legacy and there are several analysis modules within GenePattern at the Bronze level. |
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GenePattern is integrated with BioConductor and geWorkbench. |
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Demo Files & Exercises
GenePattern
Demonstration – 20-minute Audio over Slides and Screencast (turn speakers
on). You may also download the Power
Point slides for this demonstration.
Tutorial caArrayImportViewer Training
Documentation & Training
Access the caBIG™ Learning Management System to learn about training programs, register for classes, track your progress, and stay informed about training offerings. We invite you to explore the catalog to see what is available. You will need to create an account before registering for classes.
GenePattern Tutorial Java Client Guide Web Client Guide Programmers Guide Installation Instructions caBIG GenePattern Technical, Administration and Installation Guide caBIG GenePattern End User Manual Release Notes Frequently Asked Questions
Tool Download Files
Tool Download Page
Developer Institution(s)
The Broad Institute of MIT and Harvard
Adopter Institution(s)
Currently over 7000 users in over 500 organizations and 80 countries across the world
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