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nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
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Develop a Standalone CellDesigner to BioPAX Converter #177

Closed cannin closed 3 years ago

cannin commented 3 years ago

Background

CellDesigner (http://www.celldesigner.org/) is a tool for drawing and modeling biological networks. CellDesigner has a plugin (https://academic.oup.com/bioinformatics/article/27/24/3437/306597) to export networks in the BioPAX (biopax.org), a format that ignores much of the visualize styles of CellDesigner to retain just the "biological content".

Goal

The goal is to reproduce the BioPAX export plugin as a standalone tool. The Supplementary Data file from (https://academic.oup.com/bioinformatics/article/27/24/3437/306597) provides information about the mapping that needs to occur. Ideally, the project would either use Java BioPAX library (https://github.com/BioPAX/paxtools) or call it from Python using Pyjnius (https://pyjnius.readthedocs.io/) when necessary (e.g., to validate output).

Difficulty Level 2

This project will require users to become quickly familiar with two XML-based formats.

Skills

Public Repository

Potential Mentors

Augustin Luna

ballaneypranav commented 3 years ago

Hi, I'm Pranav Ballaney from India, and I would like to work on this project for GSoC 2021. I'm a Biology and Computer Science major, and I worked as part of GSoC last year with Debian on quality assurance and continuous integration of bioinformatics applications.

I've gone through the publications and resources posted here, and I've built a basic prototype for the converter here. The file I've used as input is a sample that comes with the CellDesigner installation. The converter is rudimentary and works only with this simple model. The output passes the BioPAX Validator with no errors, but some warnings are shown.

I have used a procedural approach here since it's just a prototype, but I would like to develop the software further with a more modular and object-oriented approach.

Please take a look at the prototype and let me know what you think.

Regards, Pranav

ballaneypranav commented 3 years ago

Hi, I just wanted to ask whether you had a chance to take a look yet. If you would like me to continue working on it, please let me know.

cannin commented 3 years ago

@ballaneypranav sincere apologies for the delay. I earlier did look at the code; it is an amazing start. Part of the delay has been an ongoing discussion with a potential co-mentor regarding "converter" projects: https://github.com/nrnb/GoogleSummerOfCode/issues/175 and https://github.com/nrnb/GoogleSummerOfCode/issues/177 and we still have to settle a clear direction. A meeting to settle some points is expected tomorrow.

ballaneypranav commented 3 years ago

Thanks a lot, @cannin! Have any changes been made to this project? If you would like me to continue developing this some more as an evaluation task, please let me know; otherwise, I can directly submit a proposal.

cannin commented 3 years ago

I'm closing this project in favor of #175 @ballaneypranav please see that project in case you are still interested