The practice of systems biology depends upon many software tools, operating on many kinds of data from many different sources. The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data. Read more about the Gaggle.

Gaggle API

Important Notice! Read about what's new in the latest (2007-04) release of the Gaggle API. You may need to reinstall Firegoose and R Goose.

Software Tools and Databases

Currently supported geese include:

• BRM: Bioinformatics Resource Manager. A general purpose data management, analysis and integration environment for systems biology.
• Cytoscape -- the standard software for the graphical exploration of networks.
• DataMatrixViewer for loading &: navigating, and plotting high-throughput experimental data (microarray, proteomics, MPSS, ...).
• Firegoose -- a Firefox toolbar that enables data exchange between web resources and the Gaggle framework. Firegoose supports:
  • KEGG Pathway maps and pathway modules
  • EMBL STRING functional protein association networks
  • DAVID functional annotation tools
• Genome Browser - plot data in genomic context.
• MeV: MultiExperiment Viewer, a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering and visualization.
• PIPE Protein Information and Property Explorer.
• R -- an indispensible tool for statistics, graphics, and data manipulation.

Gaggle is designed to enable interoperability of bioinformatics applications including those developed by third parties.