GenePattern

GenePattern is a freely available computational biology open-source software package developed at the Broad Institute of MIT and Harvard for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. It now has over 15,000 registered users at over 2300 commercial and non-profit organizations internationally.

Usage

GenePattern is a powerful scientific workflow system that provides access to more than 150 genomic analysis tools. Use the analysis tools as building blocks to design sophisticated analysis pipelines that capture the methods, parameters and data used to produce analysis results. Pipelines can be used to create, edit and share reproducible in silico results.

Features

• regularly updated repository of computational analysis modules that support data preprocessing, gene expression analysis, proteomics, Single nucleotide polymorphism (SNP) analysis, flow cytometry, and next-generation_sequencing
• pipelines that allow you to chain modules together to create analysis workflows
• tools to support easy creation and integration of new analysis modules
• versioning of modules and pipelines to ensure reproducible research
• web browser, application, and programmatic interfaces to make analysis modules and pipelines available to a broad range of users

See also

GenePattern Public Server - a publicly hosted instance of GenePattern utilizing the Broad Institute's compute farm as the back end.

References

GenePattern 2.0 Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & Jill P Mesirov. Nature Genetics - 38, 500 - 501 (2006)

External links

• Official Broad Institute website

Related Software:

• GeneCruiser
• Integrative Genomics Viewer