GenePattern receives Bio-IT World Best Practices award
The GenePattern team
Left to right: Charlotte Henson, Josh Gould, Jill Mesirov, Michael Reich, Ted Liefeld, and Pablo Tamayo.
Not pictured: Gad Getz, Jim Lerner, Stefano Monti, Ken Ross, and Aravind Subramanian
GenePattern, a gene expression analysis software package developed by researchers from the Broad Institute, was chosen for an Editor's Choice award at the 2005 Bio-IT World Best Practices celebration on June 28. The freely available application was selected for this award from 33 different submissions by a panel of computational biology experts.
"We are thrilled by this honor. Improving research practices is one of GenePattern's basic goals," said Michael Reich, manager of cancer informatics development and group leader for GenePattern. "As this tool helps accelerate genomic research, we look forward to its results — a quickened pace of scientific discovery and insight into biological processes and the causes of disease."
The GenePattern software package allows researchers to use a wide variety of methodologies to analyze gene expression data. It is also part of a larger architecture that addresses more general challenges in computational genomic research: the need to add new analysis tools quickly and easily, the need to reproduce the results of complex in silico analyses that require the coordination of different tools, and the need for a range of interfaces that make analyses accessible to non-programming researchers without limiting the full power of a tool to more experienced users.
GenePattern was recently selected by the Harvard Medical School-Partners Healthcare Center for Genetics and Genomics (HPCGG) for integration with their GIGPAD (Gateway for Integrated Genomics-Proteomics Application and Data) informatics system. "GenePattern is the best solution for integrating bioinformatics processing capabilities into GIGPAD's research and clinical process flows. We've been very pleased with GenePattern's functionality and well thought out implementation," said Samuel Aronson, director of information technology at the HPCGG. GIGPAD also received a 2005 Bio-IT World Best Practices award.
"This is a well-deserved reward for the GenePattern team," said Jill Mesirov, principal investigator and director of Computational Biology and Bioinformatics at the Broad Institute. "They made our vision for GenePattern — ease of use, interoperability, reproducibility, and flexibility — a reality."
Broad researchers recently released GenePattern 1.4, an enhanced version of the software package. For a comprehensive list of new features and fixes, and free access to the software, visit the GenePattern web site http://www.broad.mit.edu/genepattern.
The 2005 Bio-IT World Best Practices celebration took place at the National Press Club in Washington, D.C. Submissions for the awards came from academic institutions, pharmaceutical and biotech companies.
Originally made available to the scientific community in 2004, there are currently 1,100 GenePattern users, including more than 500 institutions and 30 pharma-biotech companies across 35 countries worldwide.
In addition to Mesirov and Reich, members of the GenePattern development team include: Gad Getz, Josh Gould, Charlotte Henson, Jim Lerner, Ted Liefeld, Stefano Monti, Ken Ross, Pablo Tamayo, and Aravind Subramanian.
The work was supported by the National Institutes of Health.
