GSOC Project Ideas 2022

Got an idea for GSOC 2022?

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 2022

JBrowse 2 Plugins for Additional Synteny Formats

• Brief explanation: Write a new JBrowse 2 plugin to support MSPCrunch data input, BLAST results, and .coord files from MUMmer
• Expected results: a new JBrowse 2 plugin that adds support for one or more of the data formats listed above
• Project Home Page URL: JBrowse.org
• Project chat: [1]
• Knowledge prerequisites: JavaScript
• Skill level: Medium
• Project Time: 175 hours
• Mentors: JBrowse development team

JBrowse 2 Multi-way synteny visualization

• Brief explanation: JBrowse 2 can currently compare two genomes at a time, but comparing more than two genomes is common! Write new JBrowse 2 features to support this functionality using data from PAF files or other synteny pipelines.
• Expected results: a new method to compare more than two genomes at a time
• Project Home Page URL: JBrowse.org
• Project chat: [2]
• Knowledge prerequisites: JavaScript, Typescript, React
• Skill level: Difficult
• Project Time: 350 hours
• Mentors: JBrowse development team

Use Galaxy to run Reactome analysis and processes on proteomics data (Reactome)

• Brief explanation: Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Galaxy is an open, web-based platform for data-intensive biomedical research, which allows users to perform, reproduce, and share complete analyses.
• Expected results: There are two potential sub-projects. 1) Adding Reactome as a data resource in Galaxy, to enable Galaxy users to use Reactome reaction and pathway annotation data, and 2) Performing identifier mapping and over-representation analysis workflows from Reactome in Galaxy. Reactome Github.
• Project Home Page URL: if there is one.
• Project paper reference and URL: reactome.org, galaxyproject.org, ProteoRE (Proteomics Research Environment)
• Knowledge prerequisites: Galaxy, Java, web services.
• Skill level: Medium.
• Project Time: 350 hours
• Mentors: Robin Haw (robin.haw[AT]oicr.on.ca)

Centralized dashboard or metrics system (Reactome)

• Brief explanation: Reactome has both manual and automated statistical tracking of its quarterly release data. This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology. a centralized dashboard would be useful by the team for discussing metrics externally and community outreach.
• Expected results: A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals
• Project Home Page URL: reactome.org.
• Knowledge prerequisites: Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)
• Skill level: Medium.
• Project Time: 175 hours
• Mentors: Robin Haw (robin.haw[AT]oicr.on.ca)

Community access portal to Reactome Archive (Reactome)

• Brief explanation: Reactome generates new pathway and other annotation data on a quarterly basis. With each new release, the preceding data set is archived to an AWS S3 bucket. As part of our data sharing policy, we would like to develop web interface to allow users to request specific versions of archived data and to make it available to download.
• Expected results: Web interface for users to request data and download via a shareable link that either expires within a certain timeframe or after data is downloaded.
• Project Home Page URL: reactome.org.
• Knowledge prerequisites: Java, AWS, Joomla, Cloudfront
• Skill level: Medium.
• Project Time: 175 hours
• Mentors: Robin Haw (robin.haw[AT]oicr.on.ca)

Datatypes Help in Galaxy (Galaxy)

• Brief explanation: Create infrastructure for providing datatype help in Galaxy. Includes expanding datatype definitions and updating Galaxy user interface to take advantage of it.
• Expected results: Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes.
• Project Home Page URL: https://galaxyproject.org/
• Project paper reference and URL: Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434
• Knowledge prerequisites: Python and JavaScript. Will use Vue.js components in front end.
• Skill level: Basic
• Project Time: 175 hours
• Mentors: Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Galaxy Support Working Group, global.

Provide users with better quota information (Galaxy)

• Brief explanation: Publish each server's quotas in a standard way; provide users with more information about what analyses and datasets are consuming their quota allocation.
• Expected results: Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota. Users will have a clear idea of what they can expect, and what they can do to increase their available resources.
• Project Home Page URL: https://galaxyproject.org/
• Project paper reference and URL: Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434
• Knowledge prerequisites: Python and JavaScript. Will use Vue.js components in front end.
• Skill level: Medium
• Project Time: 175 hours
• Mentors: Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Galaxy Support Working Group, global.

Creating learning paths within the Galaxy Training Network

• Brief explanation: Implement and display learning paths in the Galaxy Training Material infrastructure to show learners, especially newcomers, which tutorial they should take first or which sequence of tutorials to follow to become knowledgeable about a particular topic.
• Expected results: An easy way to configure and update learning paths. Easy to understand and navigate learning paths for web site users.
• Project Home Page URL: https://training.galaxyproject.org/
• Project paper reference and URL: Batut, B., Hiltemann, S., Bagnacani, A., Baker, D., Bhardwaj, V., Blank, C., Bretaudeau, A., Brillet-Guéguen, L., Čech, M., Chilton, J., Clements, D., Doppelt-Azeroual, O., Erxleben, A., Freeberg, M. A., Gladman, S., Hoogstrate, Y., Hotz, H.-R., Houwaart, T., Jagtap, P., … Grüning, B. (2018). Community-Driven Data Analysis Training for Biology. Cell Systems, 6(6), 752-758.e1. https://doi.org/10.1016/j.cels.2018.05.012

• Knowledge prerequisites: Ruby, JavaScript (some Python).
• Skill level: Medium
• Project Time: 175 hours
• Mentors: Bérénice Batut, University of Freiburg (berenice DOT batut[at] gmail.com). Galaxy Outreach & Training Working Group, global.

Integrate MP-BioPath into Reactome FI-Viz Cytoscape plugin

• Brief explanation: MP-BioPath is a similar algorithm to the options available within the Reactome FI Viz Cytoscape plugin (https://reactome.org/tools/reactome-fiviz). We are interested in incorporating our latest algorithm MP-BioPath (https://github.com/OICR/mp-biopath) into the
• Expected results: A new version of the FI-Viz plugin that incorporates MP-BioPath with customized visualizations for MP-BioPaths pathways and results
• Project Home Page URL: https://reactome.org/tools/reactome-fiviz
• Project paper reference and URL:
• Knowledge prerequisites: JAVA programming language
• Skill level: Medium
• Project Time: 175 hours
• Mentors: Adam Wright (adam.wright@oicr.on.ca)

Converting Release Jenkins Pipeline to incorporate Continuous Integration / Continuous Deployment (CI/CD) principles and AWS services where useful

• Brief explanation: In order to display the rich displays within the Reactome portal an Extract Transform Load (ETL) - mainly Java - Jenkins pipeline(s) is currently being run. This process could be, made more robust and facilitate rapid development cycles through incorporating CI/CD principles into our existing pipelines.
• Expected results: Have Jenkins CI/CD pipelines pulling the latest changes from GitHub automatically, compiling the Java code, dockerizing each component and deploying the code after all relevant test

s have passed.

• Project Home Page URL: https://github.com/Reactome/
• Project paper reference and URL:
• Knowledge prerequisites: Groovy (pipeline code), Bash
• Skill level: Basic
• Project Time: 175 hours
• Mentors: Adam Wright (adam.wright@oicr.on.ca), Joel Weiser (joel.weiser@oicr.on.ca)

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: 175 hours or 350 hours
• Mentors: name + contact details of the lead mentor, name + contact details of 1 or 2 backup mentors.