Open Genome Informatics
Association of open access genomics and bioinformatics projects.
Since 2011, the Open Genome Informatics group has served as an umbrella organization that represents a number of open-source and open-access bioinformatics projects worldwide, including GMOD and its software projects -- JBrowse, Apollo, Chado, Galaxy etc.; OICR; DockStore; Reactome; WormBase; and Bioconda.
This is a great opportunity for students to contribute to the work of these established bioinformatics projects:
Galaxy: An open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
Generic Model Organism Database (GMOD): An open-source project to develop a complete set of software for creating and administering a model organism database).
Informatics and Bio-computing (OICR): 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.
WormBase: An international consortium of biologists and computer scientists providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.
Please refer to the Open Genome Informatics GSoC page to find out more about the software projects being developed.
Open Genome Informatics 2020 Projects
Building functional and performant DataTable for WormBaseWormBase is a comprehensive research knowledge base on the genetics, genomics and biology of C. elegans and related nematodes. Biologists access...
GraphQL Interface For Querying Reactome DataReactome currently uses a REST-based API that allows end-users to obtain specific data from a set of predefined end-points. To provide better...
JBrowse 2 - Ensembl VEP integrationThis project aims to integrate Ensembl VEP into the developing JBrowse 2. For this to happen, every component feature of this project must be...
Phylogenetic tree viewer for JBrowse 2It is a Phylogenetic tree viewer for the JBrowse 2 in the most dynamic way possible. With the help of Reactjs, it will be much more efficient than...
Query Reactome Data in RR has been extensively used in bioinformatics research. However, there is still no direct way to obtain Reactome’s information in R. This project...