Open Genome Informatics
Open Genome Informatics represents the efforts of many bioinformatics projects.
The Open Genome Informatics group is organizing the joint efforts of Dockstore, Galaxy, GBrowse, GMOD, Informatics and Bio-computing (OICR), JBrowse, and Reactome. This is a great opportunity for students to contribute to the work of these established bioinformatics projects.
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). Link: http://dockstore.org/.
Galaxy: An open, web-based platform for accessible, reproducible, and transparent computational biomedical research. Link: https://galaxyproject.org/.
Generic Model Organism Database (GMOD): An open source project to develop a complete set of software for creating and administering a model organism database. Link: http://gmod.org/wiki/Main_Page.
GBrowse: The Generic Genome Browser (GBrowse) is a web application for searching and displaying annotations on genomes. Link: http://gmod.org/wiki/GBrowse.
Informatics and Bio-computing (OICR): The Informatics and Bio-computing group at the Ontario Institute for Cancer Research (OICR) develops new algorithms, software, databases, visualization tools and other necessary components to interpret genome datasets. Link: http://oicr.on.ca/informatics-and-bio-computing/.
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: http://jbrowse.org/.
Reactome: A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. Link: http://www.reactome.org/.
SequenceServer is a BLAST server for individual use or for sharing datasets with colleagues and community. Its minimalist, modern and thoughtful design lets user focus on the Biology and getting things done. Link: http://sequenceserver.com.