Google Summer of Code 2025 - Contribute to cy3sbml: A Cytoscape App for SBML Visualization!

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Matthias König

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Feb 5, 2025, 1:46:52 AMFeb 5

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Google Summer of Code 2025 - Contribute to cy3sbml: A Cytoscape App for SBML Visualization!

Do you have Java experience and a passion for computational biology? Ready to help improve a powerful Cytoscape app and work on cutting-edge biological network visualizations? Google Summer of Code 2025 is the perfect opportunity to dive into the cy3sbml project!

About the Project: cy3sbml is a Cytoscape app that integrates Systems Biology Markup Language (SBML) into biological network visualizations. This app provides a powerful tool for representing computational models and simulations within Cytoscape, making it a vital part of modern biological research.

The project includes:

SBML model visualization within a network context
Direct import from repositories like BioModels
Integration with annotation resources like MIRIAM and Ontology Lookup Service (OLS)

What’s New in 2025: We're preparing a new release of cy3sbml that will introduce key improvements:

Support for the Automation API
Enhanced SBML graph visualization
Updated Ontology Lookup Service (OLS) version 4

The Goal: You’ll help us resolve existing bugs, update core libraries, and integrate the latest API features—an exciting and impactful challenge for anyone with an interest in computational biology and Java development.

Skills You’ll Need:

Essential: Java, Maven
Bonus: Familiarity with SBML

Project Details:

Estimated effort: 175 hours
Duration: 12 weeks
Difficulty: Medium

Get Involved: This project is ideal for students with a solid background in Java development, Maven, and Cytoscape. By joining this project, you'll have the chance to work on a well-established open-source tool and contribute to the future of biological network modeling.

How to Apply:

Get in contact with Matthias König (koni...@googlemail.com)
Response to the issue for the project https://github.com/nrnb/GoogleSummerOfCode/issues/256

Mentor:
Matthias König (koni...@googlemail.com)

Apply for Google Summer of Code 2025 now and become a part of a cutting-edge project in the world of systems biology! 🌍