GSOC Project Ideas 2024
Got an idea for GSOC 2024?’
Then please post it. You can either
- 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.
Contents
Proposed project ideas for 2024
MP-BioPath Perturation Analysis / Stein Lab
- Brief explanation: MP-BioPath is a computational tool designed to
predict the effects of perturbations on biological pathways. Utilizing
Reactome’s pathway models, MP-BioPath employs an optimization model.
Our objective is to develop pipelines and tools that integrate
MP-BioPath results with genomic data.
- Expected results: As a result of this project, we aim to develop
tools and pipelines capable of handling diverse genomic datasets.
Additionally, we anticipate the generation of novel biologically
significant insights.
- Project Home Page URL:
Reactome
MP-BioPath
- Project paper reference and URL:
“Evaluating the predictive accuracy
of curated biological pathways in a public knowledgebase”
- Knowledge prerequisites: Python, R, Julia
- Skill level: Medium
- Project Time: 175-hour approximately 8 weeks
- Mentors: Adam Wright <adam.wright@oicr.on.ca>
Pathway Reasoning with LLM / Stein Lab
- Brief explanation: Reactome houses a meticulously curated repository
of human biological pathways. Our current initiative focuses on
crafting a RAG chat application optimized for intuitive interaction
with the Reactome web portal. Our primary aim is to empower the
application to interpret user queries and leverage the LLM (Language
Model) to delve deep into pathway structures, enabling the generation
of comprehensive and insightful responses for users.
- Expected results: expected outcomes include the application’s
ability to effectively handle a diverse range of user queries and to
expand its capabilities to accommodate an increased number of use
cases. Furthermore, the application is expected to leverage advanced
reasoning capabilities powered by the LLM, thereby providing more
insightful and comprehensive responses tailored to each user’s inquiry
- Project Home Page URL:
Reactome
- Project paper reference and URL:
- Knowledge prerequisites: Python, RAG
- Skill level: Medium
- Project Time: 175-hour approximately 8 weeks
- Mentors: Adam Wright <adam.wright@oicr.on.ca>, Wei Jiao
<wei.jiao@oicr.on.ca>
Project template
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.
- Project Time: 90-hour, 90, 175 or 350 hours that are a standard 8
weeks long and no longer than 12 weeks.
- Mentors: name + contact details of the lead mentor, name + contact
details of 1 or 2 backup mentors.
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