Gaggle Components
Data Standards

Third Party Geese

One of the key benefits of the Gaggle is that anyone can implement their own Geese. We hope to promote interoperability among bioinformatics applications by making this as easy as possible. Here is a (likely incomplete) list of tools and data sources that have been integrated into the Gaggle by independent labs, groups, and programmers.

Have an application you'd like to see included on this page? Please contact us by email (cbare or dtenenbaum at or through the discussion groups.

Bioinformatics Resource Manager

Bioinformatics Resource Manager. A general purpose data management, analysis and integration environment for systems biology developed at the Scientific Data Management Group at Pacific Northwest National Laboratory.


BioTapestry is a tool for visualizing circuit diagrams of developmental network models written by William Longabaugh and Hamid Bolouri of the Institute for Systems Biology.


Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Cytoscape communicates with Gaggle through the CyGoose plugin.


MeV. MeV (Multiexperiment Viewer) is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. Development of MeV is led by the Computational Biology and Functional Genomics Lab at Dana-Farber.


PDDB The Prion Disease Database (PDDB) is a public database that supports the prion disease research community created by the Institute for Systems Biology and the McLaughlin Research Institute. Gene names and expression data can be broadcast from PDDB.


Protein Information and Property Explorer (PIPE) is a starting point analysis of proteomic experimental results. This web application is a launching pad from where simple operations can be performed on this data and messages can be passed to other, more sophisticated, analysis software such as the Gaggle. PIPE was written by Hector Ramos in the Aebersold lab at ISB.

Science Service Bus

Science Service Bus by Edwin Tellman integrates the Mule Enterprise Service Bus / message broker with Gaggle. See also SSB source and docs in the Gaggle subversion repository.


SeeGraph is a graph visualization tool developed at Seelab at UT Knoxville. Exploratory work has been done towards gaggling SeeGraph.

Systems Biology Workbench

Systems Biology Workbench (SBW) is a software framework that allows heterogeneous application to communicate and use each others' capabilities via a fast binary encoded-message system. The SBW project shares the same goals as Gaggle. Interoperability between the two frameworks has been demonstrated by the SBW team in proof-of-concept mode.

Trans-proteomic pipeline

The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the Seattle Proteome Center.

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