Validation service for SBGN PD maps

[ugurdogrusoz]

Background

Systems Biology Graphical Notation (SBGN) [1] is a standard language for representing biological pathways with SBGNML being the exchange and storage format for SBGN. SBGN PD (process description) maps are represented with well-defined XML based representations that are syntactically correct but might be logically invalid.

[1] N. Le Novère et al., "The Systems Biology Graphical Notation", Nature Biotechnology, 27, pp. 735-741, 2009.

Goal

The goal here is to take SBGNML maps (files) and construct a static image of these maps (performing an automatic layout where needed) with any invalid issues highlighted on the image. If desired, the service will try to fix these errors when possible.

Difficulty Level: Hard

This project requires knowledge of the standard and related libraries as well as a good level of both front and back-end development experience.

Size and Length of Project

• large: 350 hours

Skills

Essential skills: Java, JavaScript, Cytoscape.js
Nice to have skills: SBGN knowledge

Public Repository

libSBGN

Potential Mentors

Ugur Dogrusoz

[AryanBakliwal]

Hello @ugurdogrusoz, I'm Aryan Bakliwal, a Computer Science and Engineering student at Manipal University. I possess five years of substantial experience in JavaScript and have a solid understanding of object-oriented programming through my work with Java. I'm enthusiastic about learning more about your project. Additionally, I've begun experimenting with Cytoscape to familiarize myself with it. I'm open to working on any preliminary assignments to showcase my expertise. Your guidance in this matter would be greatly appreciated, enabling me to start contributing promptly.

[jagpreetrahi]

Hey @ugurdogrusoz, I hope you're doing well. My name is Jagpreet Singh, and I’m a JavaScript developer interested in contributing to this issue. Since I’m new to the project, I’d appreciate it if you could help me understand the issue in more detail and possibly assign me a specific part to work on. Looking forward to your guidance.