Direct GitHub Integration from PathVisio to WikiPathways

[mkutmon]

Background

WikiPathways (https://www.wikipathways.org/) is a collaborative platform for pathway curation in biology, supporting community-contributed models of biological processes. Recently, WikiPathways migrated its entire database and website to GitHub (https://github.com/wikipathways), embracing a more open and modern infrastructure.

However, the current pathway curation workflow in PathVisio, the desktop pathway editor, is still tied to outdated systems. This project proposes developing a new PathVisio plugin that directly connects to the GitHub-hosted WikiPathways repository. It will allow users to commit new pathways and edits directly to GitHub from within PathVisio, streamlining the contribution process and supporting the future infrastructure of WikiPathways.

Goal

The end result will be a new PathVisio plugin that:

• Authenticates users via GitHub
• Enables users to create commit requests with new or edited pathway models (GPML files) directly from PathVisio
• Interacts with the GitHub API to create pull requests against the appropriate WikiPathways repository
• Optionally, integrates GitHub Actions to validate submissions (e.g., file format checks, metadata completeness)
• Provides clear UI/UX for biologist users unfamiliar with Git systems

The plugin will align with the workflow of the new GitHub-based WikiPathways platform, replacing the legacy submission mechanism.

Difficulty Level: Medium

The project requires Java development experience, understanding of GitHub API interactions, and some knowledge of Git workflows. It is moderately complex due to handling authentication, GitHub API requests, and integration into an existing Java-based desktop application.

Size and Length of Project:

• medium: 175 hours
• 12 weeks

Skills

Essential Skills:

• Java (PathVisio plugin development)
• GitHub API usage
• Basic understanding of Git workflows

Nice to have Skills:

• Familiarity with GitHub Actions
• Experience with biological data or pathway models (GPML format)
• UI/UX design for non-technical users

Public Repository

The new plugin will be developed under the PathVisio GitHub organization, e.g.:
https://github.com/PathVisio/WP-GitHub-Plugin (new repo to be created)

Reference to legacy plugin: https://github.com/PathVisio/WP-plugin

Potential Mentors

Martina Summer-Kutmon

[Bhaskar1612]

Hi @mkutmon,

I have drafted my GSoC proposal for the PathVisio GitHub Plugin project and would love to get your feedback.

What would be the best way to share it for review? Should I send it via email or another channel?

Thanks in advance! Looking forward to your guidance. 😊

Best regards,

Bhaskar
GitHub: https://github.com/Bhaskar1612

[mkutmon]

@Bhaskar1612, thanks for reaching out! Feel free to drop me an email, then I can have a look!

Hi @mkutmon,

I have drafted my GSoC proposal for the PathVisio GitHub Plugin project and would love to get your feedback.

What would be the best way to share it for review? Should I send it via email or another channel?

Thanks in advance! Looking forward to your guidance. 😊

Best regards,

Bhaskar GitHub: https://github.com/Bhaskar1612

[lakshya-pratap-singh-chauhan]

@mkutmon
i've not done so much open source but i have done GSSOC 2024 , i've gained experience and i would like to contribute in your project . i've also raise issue about the wikipathways how we can fix it hope you consider my application in gsoc 2025. i've sove real worls problems in GSSOC 2024.

[harkirath1511]

Hi @mkutmon
I'm very interested in the "Direct GitHub Integration from PathVisio to WikiPathways" project for GSoC. I would like to send you my proposal for review, but I couldn't find your email. Could you please share it?
Thank you!

[mkutmon]

@mkutmon i've not done so much open source but i have done GSSOC 2024 , i've gained experience and i would like to contribute in your project . i've also raise issue about the wikipathways how we can fix it hope you consider my application in gsoc 2025. i've sove real worls problems in GSSOC 2024.

Nice!! Let me know if I can help with anything!

[mkutmon]

Hi @mkutmon I'm very interested in the "Direct GitHub Integration from PathVisio to WikiPathways" project for GSoC. I would like to send you my proposal for review, but I couldn't find your email. Could you please share it? Thank you!

Sure! You can send it to martina.kutmon@maastrichtuniversity.nl