Integrate the CausalPath Algorithm with the existing CausalPath Cytoscape App

[cannin]

Background

Last year, we developed a Cytoscape app for visualizing results from the CausalPath algorithm (https://github.com/cannin/causalpath_cytoscape_app and https://apps.cytoscape.org/apps/causalpathcytoscapeapp). The app currently takes as input two files that result from running CausalPath separately to produce a visualization.

Goal

Integrate the CausalPath algorithm with the existing CausalPath app (i.e., CausalPath algorithm should run in cytoscape which will produce the output and will be used by the existing app for visualization).

Getting Started

• Install the Cytoscape app found here (https://github.com/cannin/causalpath_cytoscape_app) to see how things currently work
• Check ongoing issues with the Cytoscape app: https://github.com/cannin/causalpath_cytoscape_app/issues this may give a understanding of the current code status
• Focus your attention on the main issue of importance for Cytoscape app (https://github.com/cannin/causalpath_cytoscape_app/issues/10). Your goal is to write a proposal to address this issue

Difficulty Level: Medium

The difficulty should be medium for the following reason.

To get a clear understanding of Cytoscape from the documentation will be time consuming and challenging; a lot of debugging will be required for beginners. Integrating the CausalPath algorithm with the existing app will be challenging as we might need to implement new interfaces for the existing algorithm.

Size and Length of Project

It is a medium length project with the following details

• Medium: 175 hours
• 12 weeks

Skills :

Essential skills: Java, Cytoscape

Public Repository

• Main Code link: https://github.com/cannin/causalpath_cytoscape_app
• CausalPath Algorithm Link: https://github.com/PathwayAndDataAnalysis/causalpath
• Dataset link: https://www.biorxiv.org/highwire/filestream/83268/field_highwire_adjunct_files/4/258855-5.zip
• Cytoscape App Development Manual: https://github.com/cytoscape/cytoscape/wiki/Cytoscape-3.0-App-Development

Potential Mentors

• Augustin Luna (aluna@jimmy.harvard.edu)
• Pritam Saha
• Ozgun Babur

[Umang03]

My name is Umang Gupta and I am a third-year undergraduate student pursuing engineering at Maharaja Agrasen Institute of Technology. I am very interested in this project for the summer and making contributions to the code. I am familiar with JavaScript, React.js, Java, Node,js, HTML, CSS, and BootStrap. Plz guide me more about this Project .

[cannin]

@Umang03 You'll need to submit a proposal. See details here: https://nrnb.org/gsoc.html Refer to the Goal/Getting Started section to give you ideas of the content that you need to address.

[Umang03]

Ok. I'll work on it.

[AlexanderPico]

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[khanspers]

Closing in preparation for GSoC 2023.