Revision as of 03:43, 24 February 2021

Got an idea for GSOC 2021?

Then please post it. You can either

1. Add it here, by directly editing this page. Just copy, paste and update the template below. This requires that you have or create a GMOD.org login.

Projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms.

Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route. As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open-source programmers.

Proposed project ideas for 2021

• JBrowse 2 Plugins for Additional Synteny Formats
  • Brief explanation: Write a new JBrowse 2 plugin to support MSPCrunch or Mummer data input
  • Expected results: a new JBrowse 2 plugin that adds support for one of the data formats listed above
  • Project Home Page URL: JBrowse.org
  • Knowledge prerequisites: JavaScript
  • Skill level: Medium
  • Mentors: JBrowse development team

• Interactive viewer for systems-biology variant interpretation (UI)
  • Brief explanation: Develop a interactive DAG linking user-specified variant to genes, cell-type expression, disease association/known cancer mutations, known drug targets.
  • Expected results: Website powered by Cytoscape.js which shows input variants as nodes, linked to different levels of system organization.
  • Project Home Page URL: Reactome.org
  • Knowledge prerequisites: JavaScript
  • Skill level: Medium
  • Mentors: Shraddha Pai

• Interactive viewer for systems-biology variant interpretation (Server-side)
  • Brief explanation: Create server-side database and application for system-level annotation of variants/gene, to connect to interactive UI (e.g. selected single-cell marker datasets , known disease associations, drug targets).
  • Expected results: Website allows users to visualize systems-level variant/gene annotation with interactive linkouts to data sources
  • Project Home Page URL: Reactome.org
  • Knowledge prerequisites: Experience with document oriented databases (e.g. MongoDB), graphQL
  • Skill level: Medium
  • Mentors: Shraddha Pai

Template

• Project Idea Name (Project Name/Lab Name)
  • Brief explanation: Brief description of the idea, including any relevant links, etc.
  • Expected results: describe the outcome of the project idea.
  • Project Home Page URL: if there is one.
  • Project paper reference and URL: Is there a paper about the project this effort will be a part of?
  • Knowledge prerequisites: programming language(s) to be used, plus any other particular computer science skills needed.
  • Skill level: Basic, Medium or Advanced.
  • Mentors: name + contact details of the lead mentor, name + contact details of 1 or 2 backup mentors.