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Main documentation site for NRNB GSoC project ideas and resources
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Adding visualization of protein-complex interaction to openPIP #188

Closed MoHelmy closed 2 years ago

MoHelmy commented 2 years ago

OVERVIEW

The Open Source Protein Interaction Platform (openPIP) is an open-source software package for hosting protein-protein interaction (PPI) data based on the PSI-MI-TAB format. openPIP provides a PPI database and a customizable web interface that enables searching and visualizing the interactions as well as downloading the search results in different formats. The whole system is a ready-to-use virtual machine that can be imported to VMware. openPIP was used to build the portals f two major PPI project, The Human Reference Protein Interactome Mapping (HuRI) Project (Luck at el, Nature, 2020) and The Yeast Protein Interactome Mapping (YeRI) Project (Under review).

Focus

This project aims to add several new features and enhancements to openPIP.

Goals

1- Adding visualization of protein complex interactions. We had made a prototype in a previous GSoC project. It needs to be finished. 2- Adding default download options through the automatic creation of download link for each interactions dataset or interactions from the same publication). 3- Adding a custom download option (similar to STRING). 4- Adding organism level: so far, openPIP can host multiple datasets from different sources and in the search results it keeps track of all the differences (publishes/unpublished, experimental/predicted...). However, they are all from the same organism. We need to add support to the use in the use case of hosting interactions from different organisms. 5- Test and refine the setup process for new instances e.g. hosting the docker container on DockerHub for more convenient access.

Coding Skills

PHP, JavaScript, HTML/CSS, Symfony

Acceptance Criteria

Students interested in working on this project will be asked to provide their CV and school transcript then the short-listed students will be asked to do an evaluation task that will be used for assessing their fitness for the project.

Public Repository

openPIP at GitHub

Difficulty Level: Medium

Size and Length of Project

Mentors

Gary Bader, Mohamed Helmy

alvinuday commented 2 years ago

Hi Sir, my name is Alvin Adarsh Kumar , I'm a second year CS undergrad with prior experience in front end development with HTML,CSS,JS , React and Vue. I wanted work on this issue with an enthusiasm to learn as well. I was hoping you could guide me further as to how i could get started with this issue?

khanspers commented 2 years ago

A reminder that the application period opens on Monday April 4. Proposals to NRNB must be submitted on the official GSoC Site (https://summerofcode.withgoogle.com/) before April 19, 18:00 UTC to be considered, and contributors are encouraged to submit proposals in draft format early, so that mentors can give feedback directly at the GSoC site.

khanspers commented 2 years ago

Closing because this is an active project for GSoC 2022.