NetBoxR Updates: Develop a Galaxy Platform Entry for NetBoxR, Pipeline for Processing cBioPortal Data, and Module Analysis Features

[cannin]

Background

netboxr (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234669) is an R package for the automated discovery of biological process modules by network analysis.

Goals

This project has multiple goals (proposals should discuss at least 2 of these; they are ordered from most to least important):

• Add additional analysis features into netboxr, specifically (the following). This additionally will involve making use of module (community) detection algorithms in igraph (https://igraph.org/r/html/latest/communities.html)

  1. The ability to support weighted nodes in the module detection
  2. The ability to parameterize the sizes of returned modules

• Make netboxr more widely available. The Galaxy platform (https://galaxyproject.org/) is a platform to make tools more widely available. The goal would be to make netboxr available on Galaxy (https://galaxyproject.org/admin/tools/add-tool-tutorial/).

• Process datasets from cBioPortal with netboxr (https://github.com/cBioPortal/datahub/tree/master/public) following the package vignette (https://bioconductor.org/packages/release/bioc/vignettes/netboxr/inst/doc/netboxrTutorial.html).

Getting Started

Eventually, you'll need to write a proposal (see details: https://nrnb.org/gsoc). Elements of this proposal should include:

1. Demonstrated understanding (code samples help) of what steps are involved in making a Galaxy tool
2. Try out netboxr on different sets of data from cBioPortal given the instructions in the tutorial
3. An understanding of the igraph community methods

Getting Help

Post issues if you encounter bugs in the tutorial here: https://github.com/mil2041/netboxr/issues

Difficulty Level: Easy

Navigating the documentation for the Galaxy platform may have some difficulty.

Size and Length of Project

Size: 175 hours

Length: 12 weeks

Skills

• Essential skills: R, XML

Public Repository

• https://github.com/mil2041/netboxr

Potential Mentors

Augustin Luna Eric Minwei Liu

[sajo25]

Hi! My name is Sara and I'm really interested in applying for one of the netboxr projects. I have a background in biomedical sciences and 7 months of experience with R, but I'm very new to open source. I wanted to reach out and let you know that I've started working on some of the introductory tasks for this project and will let you know if I encounter any problems. Please let me know if you have any additional tips or guidance! Thank you.

[cannin]

@sajo25 Thanks for the interest. Take a look the "Getting Started" section above.

[pramitsahoo]

Hi @cannin , I am Pramit and i'm currently pursuing Bachelor's in Pharmaceutical Technology and i want to contribute to this project.. can you please guide me ?

[cannin]

@pramit026 Look at the "Getting Started" section.

[khanspers]

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.

[AlexanderPico]

IMPORTANT REMINDER: GSoC 2022 is for new “beginners” to open source.

Applicants are expected to review eligibility requirements prior to applying. We can not accept applications from contributors with prior open source development experience. From the GSoC FAQ https://developers.google.com/open-source/gsoc/faq:

Can someone already participating in open source be a GSoC Contributor?

The goal of GSoC is to bring new contributors into open source organizations. GSoC can also help beginner contributors learn the ins and outs of open source while being mentored by experienced community members. GSoC is for new and beginner contributors to open source, it is not for experienced contributors to open source.

[khanspers]

Closing because this is an active project for GSoC 2022.