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Announcement: GenePattern, a microarray analysis package

The GenePattern Team softwareworkshop at broad.mit.edu.invalid
Mon Apr 26 01:52:15 EST 2004

Scientists at the new Broad Institute have released GenePattern, a 
flexible software package that will allow biomedical researchers to 
perform custom gene expression analysis experiments, record and replay 
analyses, and use tools from many different software sources within a 
single interface.

This new microarray analysis package is freely available to researchers 
and may be downloaded at 

GenePattern addresses several hurdles facing biomedical research, 
particularly the need for interoperable tools in bioinformatics. It 
provides an accessible yet sophisticated analytical tool, with the 
ability to support novel approaches to analysis, while unifying 
investigative methods across disciplines.

Built upon a software infrastructure for interoperable informatics, 
GenePattern offers researchers the ability to exchange and use each 
other's methods and data. A researcher can use GenePattern through a 
simple user interface or a powerful scripting language. A computational 
biologist can add a software module written in any language.

"The methodologies and advanced algorithms in GenePattern are flexible 
and accessible," said Jill Mesirov, chief informatics officer and 
director of Bioinformatics and Computational Biology at the Broad 
Institute. "It provides biomedical researchers with a comprehensive and 
integrated computational biology software environment."

The rapidly increasing rate of production of biological information 
offers extraordinary prospects for insights into human disease and its 
treatment. However, much of this data awaits appropriate analysis and 
interpretation. Researchers must become more efficient at integrating 
new data into their analyses and in adopting new tools and methodologies.

GenePattern will help scientists make better use of this biological 
data. It will reduce development and integration costs and bring 
benefits to the biomedical, bioinformatics, and computational biology 
communities for both ongoing research and educational efforts.

"The cancer genomics program at the Broad Institute has long been a 
leader in the development of powerful yet user-friendly software for the 
analysis of functional genomics data," said Wing Wong, professor, 
Department of Statistics, Harvard University. "With the release of 
GenePattern, they are now providing an interoperable environment for 
both the development and application of bioinformatics tools," he said.

"GenePattern is a significant step forward compared to similar programs 
of its type," according to George M. Church, professor of genetics, 
Harvard Medical School & MIT Health Sciences & Technology & CSBi. "It is 
much more flexible, and allows for a broad range of analyses. 
Additionally, it enables analyses to be performed in a way that they can 
be replicated. I can't overstate how important that is." Church is also 
Director of the Lipper Center for Computational Genetics & the 
MIT-Harvard DOE Genomics: GTL Center.

The software platform's infrastructure supports scientists, ranging from 
the novice to the most experienced. The interface annotates each 
analysis parameter, helping inexperienced users understand how to best 
use an algorithm. Sophisticated users can write algorithms in a variety 
of programming languages and add them to the system without writing 
additional code.

"The modular structure of GenePattern allows us to plug in other tools 
or to take them out for reusing in another environment," said Michael Q. 
Zhang, professor, Cold Spring Harbor Laboratory.

"GenePattern was designed to provide a powerful integrated environment 
that is unique among microarray analysis tools," said Michael Reich, 
group leader for Cancer Genomics Informatics at the Broad Institute and 
software engineering manager for GenePattern. Among its features, 
GenePattern can be used as a standalone application on a laptop, or it 
can take advantage of the greater power of a client-server installation. 
It is packaged with a core library of analytic and visualization modules 
that can be easily connected as a pipeline or method. New modules are 
frequently released for download from the GenePattern web site.

"Researchers often have problems trying to reproduce work that others 
have published because the publishing process often leaves out necessary 
steps," said Pablo Tamayo, senior computational biologist and manager of 
Cancer Genomics Informatics at the Broad Institute. "GenePattern allows 
users to create and share scripts that will reproduce an analysis in the 
level of detail that researchers require."

In the near future, the Broad scientists plan to integrate additional 
modules into the package that will extend the scope of GenePattern into 
sequence analysis, proteomics and metabolomic methods.

Additional members of the GenePattern development team include Josh 
Gould, Charlotte Henson, Jim Lerner, Ted Liefeld, Stefano Monti, Keith 
Ohm, Ken Ross and Aravind Subramanian. The work was supported by the 
National Cancer Institute through a grant from the Biomedical 
Information Science and Technology Initiative of the National Institutes 
of Health.

The Broad Institute (rhymes with "code") is known officially as The Eli 
and Edythe L. Broad Institute. It is a research collaboration of the 
Massachusetts Institute of Technology, Harvard University and its 
hospitals and the Whitehead Institute for Biomedical Research. The 
Broad's mission is to propel genomic research, creating comprehensive 
tools for genomic medicine and making them available to scientists 

For more information, contact:
Scott Turner or Michelle Nhuch
news at broad.mit.edu

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