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.

JBrowse: A modern, fast genome browser implemented almost entirely in JavaScript, with some server-side formatting code in Perl. Link.

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.

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Technologies

  • neo4j
  • python
  • javascript
  • react
  • r-project

Topics

comment IRC Channel
email Mailing list
mail_outline Contact email

Open Genome Informatics 2020 Projects

  • Hitonari Sato
    Building functional and performant DataTable for WormBase
    WormBase is a comprehensive research knowledge base on the genetics, genomics and biology of C. elegans and related nematodes. Biologists access...
  • Pratik Lodha
    GraphQL Interface For Querying Reactome Data
    Reactome currently uses a REST-based API that allows end-users to obtain specific data from a set of predefined end-points. To provide better...
  • Andra Vasilache
    JBrowse 2 - Ensembl VEP integration
    This project aims to integrate Ensembl VEP into the developing JBrowse 2. For this to happen, every component feature of this project must be...
  • Shreya Srivastava
    Phylogenetic tree viewer for JBrowse 2
    It 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...
  • Chi Lam Poon
    Query Reactome Data in R
    R has been extensively used in bioinformatics research. However, there is still no direct way to obtain Reactome’s information in R. This project...
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2020