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
http://www.broad.mit.edu/cancer/software/genepattern/.
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
worldwide.
For more information, contact:
Scott Turner or Michelle Nhuch
617.252.1064
news at broad.mit.edu
