Scientists at Broad Release GenePattern Analysis Software
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.
