Software:Firegoose, Gaggle, and PIPE
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Description
The Firegoose is a Firefox pluggin that effectively turns the Firefox browser into a "Goose" that can communicate with other "Geese" as part of the Gaggle. A goose is any piece of software that has been slightly modified to accept and send small messages defined by the Gaggle standards. The Gaggle allows a user to leverage software tools developed independently and created specifically for different computational tasks in order to analyze their data through different means and gain greater insight.
The PIPE
The PIPE(Protein Information and Property Explorer) was developed as a first next step after TPP processing of mass-spec data has been performed. Once protein identifiers have been established, the PIPE can perform several different operations on the list of IDs, including: mapping to other IDs (entrez gene, unigene, uniprot, etc.), Gene Ontology enrichment calculations (to see what biological processes are overrepresented in the list), annotation of the list to specific GO terms, and more. The PIPE can also serve as a data management tool, saving lists with user specified metadata.
Reference
The Gaggle: An open-source software system for integrating bioinformatics software and data sources Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga BMC Bioinformatics 2006, 7:176
