Prototype COSE Network Layout Algorithm to Support Biological Context for Layouts More Intuitive to Humans

[cannin]

Background

Pathway knowledge describing interactions between proteins and other biological molecules is essential for interpreting and integrating diverse genomics data, understanding disease mechanisms and informing medical decision making. Consequently, pathway visualization is very useful for biomedical research. Researchers often visualize pathways with spatial relationships in mind (i.e., proteins on the cell surface at the top and those in the nucleus (the most cell interior) towards the bottom. This spatial information is missing from most generic graph layout algorithms.

COSE Layout

The CoSE (pron. "cosay", Compound Spring Embedder) layout for Cytoscape.js developed by i-Vis Lab in Bilkent University is a spring embedder layout with support for compound graphs (nested structures) and varying (non-uniform) node dimensions. A faster version of this layout style called fCoSE, also supporting user-defined placement constraints can be found here.
(demo, compound demo).

Citation: U. Dogrusoz, et al, "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 2009.

Video: fCOSE: https://www.youtube.com/watch?v=vRZVlwntzGY

Gene Information using Gene Ontology (GO)

The Gene Ontology knowledgebase provides a computational representation of our current scientific knowledge about the functions, localization, and involved processes for genes.

Example Gene Localization: https://www.genecards.org/cgi-bin/carddisp.pl?gene=ITGB4#localization-ptm

GO is an immense hierarchy, but it can be simplified to include a reduced set of terms:

• Cellular Compartment Hierarchy (Nucleus): https://www.informatics.jax.org/vocab/gene_ontology/GO:0005634
• GO Subsets (GO Slim): http://geneontology.org/docs/download-ontology/
• Generate a GO Slim: https://github.com/owlcollab/owltools/wiki/Map2Slim

Goal

The goal is to prototype an updated version of this algorithm that includes spatial information and makes automatic use of this information for layout purposes.

How to Start

Interested applicants should:

1. Explore libraries/sites/repos mentioned above
2. Explore code base for fCOSE
3. Develop a proposal for incorporating GO information into fCOSE

Difficulty Level: Medium

Size and Length of Project

175 hours
12 weeks

Skills

Javascript

Public Repository

• https://github.com/iVis-at-Bilkent/cytoscape.js-fcose
• https://github.com/cytoscape/cytoscape.js

Potential Mentors

• Augustin Luna ({first_name}_{last_name} AT hms.harvard.edu)
• Ugur Dogrusoz

[khanspers]

@Simer13 : Thank you for your interest. We are still in the process of applying as a mentoring organization; mentoring organizations will be announced on Feb 22. Check back after that date for more information.

[khanspers]

NRNB has been accepted as a mentoring organization for GSoC 2023! Contributor applications open on March 20. Here are some useful links:

GSoC contributor guide
NRNB project proposal template
Eligibility requirements
Full program timeline

[kunal00000]

Hi @cannin ,
I want to work upon this project, Let me know the initial steps.
I have gone through these link which Kristina mentioned.

[cannin]

@kunal00000 if still interested and have looked at the "How to Start" section then you can start working on a proposal.

[Shubhamrajgithub]

Hi @cannin @ugurdogrusoz ,
I am 3rd year college student actively interested in open source. I have gone through all the mentioned sites/repo/library, this project seems really interesting as well as challenging task. I am little confused with the proposal part, I need a little guidance.
It would be great if I can get yours email contact to get started on my proposal.

[cannin]

@Shubhamrajgithub thanks. take a look at the "How to Start"

[Shubhamrajgithub]

@cannin, Can I get your email to review my proposal.

[cannin]

@Shubhamrajgithub check project description for my contact info

[melondotdev]

Hi @cannin,

My name is Han and I'm a former biomedical researcher (highest degree: Master of Science in Physiology from the University of Alberta) who's made the decision to transition into programming as a full time career. I discovered Google Summer of Code while looking for opportunities to network and enrich my coding education, which is not very extensive and is mostly self-study using online resources other than the few computer science courses I took in Undergrad. Even so, I am a passionate learner and would love to contribute to a fantastic open source project such as yours if given the opportunity. I will be writing a proposal and hope that you find it plausible enough to give me that opportunity.

Warm regards,
Han

[cannin]

@hanhylee thanks for the interest. please work towards a strong and detailed proposal that clearly shows your idea for the project.

[ginisha02]

@cannin
Hi.. My name is Ginisha I came across to this project, and I find it really fascinating. I believe my skills and experience would be a great fit for this project. I am really interested in contributing to it, and I’ve relevant skills for contributing to it as I’ve experience in full stack web development. I’ve worked on full stack projects & 2 internships in the past months. Additionally, I have worked on various frontend and backend projects, and recently I cleared Microsoft certification.

I'm willing to learn new skills while contributing to the project for example Cytoscape.js. I’ll put my best efforts into successfully contributing to the project. Could you please give me some advice so that I can contribute.
Thanks a lot.

[cannin]

@ginisha02 Thanks; take a look at the "How to Start" section.

[rudrakushwaha]

Hey @cannin is this issue still open for contribution? I would like to contribute to it. I have basic knowledge about Javascript but Cytospace is new to me. Please guide me for further steps to start my journey.

[7070Shreyash]

Hello @cannin, I've grasped the goal, and I'm confident in my ability to accomplish it. I'm currently delving into fCose and GO. If this matter is still open for contributions, I'm eager to contribute.
Thanks.

[khanspers]

NRNB has been accepted as a mentoring organization for GSoC 2024. The contributor application period is March 18 – April 2. Here are some useful links:

GSoC contributor guide
NRNB project proposal template
Eligibility requirements
Full program timeline