These bioinformatics groups belong to the Genome Informatics ‘umbrella’ organization:
Dockstore
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
Quay.io/Github (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.
Galaxy
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
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.
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 .