GSOC Groups

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These bioinformatics groups belong to the Genome Informatics 'umbrella' organization:

An open source project to bring together bioinformatics tools encapsulated in Docker with machine- and human-readable descriptions in the Command Workflow Language (CWL) or the Workflow Definition Language (WDL). This system lets you combine the great features of (autobuilding of Docker containers, versioning, hosting for the world) with a standardized, programmatic description of how to call a tool in a given Docker container. Together, this lets the research community create, share, search, and automatically run Docker containers designed to process genomics data in a way that hopefully is popular with multiple projects and embraced by groups like the Global Alliance for Genomics and Health.
An open, web-based platform for accessible, reproducible, and transparent computational biomedical research. Website.
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
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 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.
Genome Sequence Informatics (OICR) 
Ontario Institute for Cancer Research (OICR) is an innovative translational research institute dedicated to research on the prevention, early detection, diagnosis and treatment of cancer. The Genome Sequence Informatics group develops new algorithms, software, databases, visualization tools and other necessary components to interpret genome datasets.
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 .