GSOC Groups

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These bioinformatics groups are hoping to participate in Google Summer of Code 2015:

;Generic Model Organism Database (GMOD) : An open source project to develop a complete set of software for creating and administering a model organism database. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. This project is collaboration of several database projects, including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database. Links: Website, GMOD Blog
GBrowse
The Generic Genome Browser (GBrowse) is a web application for searching and displaying annotations on genomes. GBrowse was designed from the bottom up for portability, extensibility, and modularity. It relies on no proprietary software, but only readily available open source software such as MySQL and the BioPerl libraries. GBrowse is implemented in Perl. Link: Website.
JBrowse
JBrowse is being developed as the successor to GBrowse. It is a modern, fast genome browser implemented almost entirely in JavaScript, with some server-side formatting code in Perl. Link: Website.
Reactome 
A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. The Reactome data model describes diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, signal transduction, and high-level processes, such as the cell cycle. Reactome software uses only freely available (and often open source) components and has been created with cross-platform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programming language. The Reactome team is composed of individuals who are both biologists and programmers at the Ontario Institute for Cancer Research, New York University Langone Medical Center, Cold Spring Harbor Laboratory, and The European Bioinformatics Institute. Links: Website, ReactomeWiki .
SeqWare
SeqWare is a multi-faceted project that includes a developer-friendly workflow development and execution engine (SeqWare Pipeline) along with a NoSQL variant database (SeqWare Query Engine). The system is used by OICR to automate the analysis of a large percentage of the NGS samples processed by the institute. It's our intention to share these workflow with the community and we're using the SeqWare workflow format and reference VM on Amazon to do this. For the GSoC we're interested in integrating the project with Galaxy to use that terrific application as a frontend. We also are interested in exposing the Query Engine HBase variant database through a nice REST API and web app for interacting with this highly scalable variant storage and analysis system. The SeqWare team is based at OICR and includes developers at UNC, Nimbus Informatics, Garvin, and other locations. Links: [1]
WormBase 
An online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis. WormBase is a collaboration among the Wellcome Trust Sanger Institute, Ontario Institute for Cancer Research, Washington University in St. Louis, and the California Institute of Technology. Links: Website.

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