Difference between revisions of "GSOC Project Ideas 2021"

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(Proposed project ideas for 2021)
(Proposed project ideas for 2021)
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**''Mentors:'' Sibyl Gao (sibyl@wormbase.org).
 
**''Mentors:'' Sibyl Gao (sibyl@wormbase.org).
  
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*'''Bioinformatics with Jupyter Notebooks (WormBase)'''
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**''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically.
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**''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics.
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**''Project Home Page URL:'' https://wormbase.org.
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**''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31642470/ WormBase: a modern Model Organism Information Resource]
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**''Knowledge prerequisites:'' Python or R, and bioinformatics knowledge.
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**''Skill level:'' Advanced.
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**''Mentors:'' Sibyl Gao (sibyl@wormbase.org).
  
 
== Template ==
 
== Template ==

Revision as of 00:36, 26 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
  • Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)
    • Brief explanation: The Alliance of Genome Resources is founded to unify access to research knowledge across different model organism systems (such as worms, flies, mouse, etc). It provides ways for published research knowledge to be categorized, aggregated and searched. The Alliance is founded by members that each specialize in a specific model organism system. They each have their own existing websites and user base (more detail on these members and their sites here: https://www.alliancegenome.org/) At the Alliance, we look to support the existing uses cases of the member sites while furthering usability and consistency. To achieve those goals, we need style guides that can be applied to the development of the Alliance website.
    • Expected results: Design Prototypes and guidelines resulting from several iterations of design lifecycle.
    • Project Home Page URL: https://www.alliancegenome.org/.
    • Project paper reference and URL: The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases
    • Knowledge prerequisites: Design or HCI. Knowledge of biology is preferred.
    • Skill level: Advanced.
    • Mentors: Sibyl Gao (sibyl@wormbase.org).
  • Bioinformatics with Jupyter Notebooks (WormBase)
    • Brief explanation: WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through REST API and downloadable files. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically.
    • Expected results: A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics.
    • Project Home Page URL: https://wormbase.org.
    • Project paper reference and URL: WormBase: a modern Model Organism Information Resource
    • Knowledge prerequisites: Python or R, and bioinformatics knowledge.
    • Skill level: Advanced.
    • Mentors: Sibyl Gao (sibyl@wormbase.org).

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.