Web-Based Interactive Visualization to integrate Geneset Analysis with DBRetina

[MoHelmy]

Background

DBRetina is a high-performance bioinformatics command-line tool (CLI) designed to compute pairwise distances among large collections of gene sets, enabling the generation of comprehensive similarity networks. Its computational efficiency eliminates the need to rely on outdated gene sets, allowing users to seamlessly integrate and curate the latest versions of various molecular databases. In addition, DBRetina allows users to incorporate their own gene sets into the network, offering unprecedented resolution for enrichment analysis and unlocking new insights.

Challenge

As a CLI tool, users still have to download the gene sets from suitable molecular databases, transform them into a Gene Set Database Format to be suitable for processing by DBRetina, and explore the outputs in suitable visualization tools. Therefore, we propose a unified web interface to streamline gene set analysis by integrating DBRetina’s computational power, biomedical database interoperability, and Cytoscape-based network visualization. This platform will democratize access to advanced genomic comparisons while ensuring scalability and user-friendliness.

Goal

To develop an interactive visualization for datasets in DBRetina with the following core functionalities:

1. Biomedical Database Integration
2. User Geneset Upload & Validation
3. In-Browser DBRetina Execution
4. Interactive Network Visualization

Difficulty Level: Easy/Medium

Size and Length of Project

• medium: 175 hours
• 12-16 weeks

Skills

Essential skills: Cytoscape.JS, HTML, CSS, JS
Nice to have skills: web development experience

Public Repository

• DBRetina: https://dbretina.github.io/DBRetina/
• Cytoscape.js: https://js.cytoscape.org/
• WebAssembly: https://webassembly.org/
• Gene Set Formats: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

Potential Mentors

Tamer Mansour
Mohamed Helmy

[SHUBHAM-410]

Hi Helmy, I am interested in working on this project. Could you please guide me on how and where to get started?

[MoHelmy]

Hi Helmy, I am interested in working on this project. Could you please guide me on how and where to get started?

Thanks for your interest. Please email Tamer and me on the provided addresses to further discuss the project.

[ankushthedeveloper]

Hi Helmy , I explored and researched about the project and i really liked the baseline of the project and i have all the required skills to work on this project ,I would like to work with you on the project

[MoHelmy]

@ankushthedeveloper Thanks for your interest. Please email Tamer and me on the provided addresses to further discuss the project.

[PalashChitnavis]

Hey @MoHelmy @drtamermansour, I am interested in contributing to this project and would love the opportunity to collaborate. I have sent you an email from palashchitnavis@gmail.com regarding the same.

[MridulBatra1]

Hi @MoHelmy @drtamermansour I am really interested in working in this project and collaborate with you. Can you please guide me on where to get started

[MoHelmy]

@MridulBatra1 Thanks for your interest. Please email Tamer and me on the provided addresses to further discuss the project.