Difference between revisions of "GSOC Groups"

Revision as of 21:13, 19 February 2015

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

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.

Mouse Genome Informatics (MGI) 

MGI is the authoritative international bioinformatics database on the laboratory mouse, annotating data and building tools that allow researchers to access comprehensive, integrated information on mouse genes, alleles, phenotypes, disease models, and gene expression in order to facilitate the study of human health and disease. Data within MGI is curated from the primary research literature, or loaded from large-scale projects or other research resources. These data are organized using structured vocabularies (gene function, mutant phenotype descriptions, anatomy) and unique identifiers making all information accessible to computational as well as traditional approaches.

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.

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]

WebApollo 

Web Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process.

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.