Revision as of 20:25, 8 February 2024

Got an idea for GSOC 2024?'

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 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: 90-hour projects that are a standard 8 weeks long and no longer than 12 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: xpected 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: 90-hour projects that are a standard 8 weeks long and no longer than 12 weeks.
• Mentors: Adam Wright <adam.wright@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 projects 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.