Gaggle Components
Data Standards

Welcome to the Gaggle web site!

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Workshop 2012

Gaggle Workshop 2012!

Bringing software developers and scientists together to promote interoperability in software for systems biology.

Sept. 10th & 11th, 2012

Gaggle News

Read the latest Gaggle news here.

Gaggle Developers

Send us information about your Gaggle-enabled applications and we will feature it prominently on our site! Read more.

New! ChromeGoose is available now! ChromeGoose is a Chrome browser plugin for integration of bioinformatics analysis scripts, visualization tools and desktop and web resources by enabling seamless data exchange between all the components. More

Important Notice! The latest update to Java caused Gaggle to stop working. A fix is avaiable as follows:

Install Firegoose from

It is important that you MUST upgrade to Java 7u51 here so that Firegoose will function properly.

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 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.
  • BioTapestry -- an interactive tool for building, visualizing, and simulating genetic regulatory networks.
  • N-Browse -- a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data.

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

© 2006, Institute for Systems Biology, All Rights Reserved