Improve Genome Nexus' Command Line Interface Experience

[inodb]

Background:
Genome Nexus [1] is a tool for the annotation and interpretation of mutations in cancer. cBioPortal leverages Genome Nexus' API to for instance show how a mutation might change the protein or how often a mutation occurs in healthy populations or patients with cancer. We recently released Genome Nexus as a standalone tool and website. The workflow of how Genome Nexus related to cBioPortal is shown below:

The annotation of the inputted mutation file happens on the command line. There are several formats of mutation files, the most popular being Mutation Annotation Format and VCF. We want to make it as easy as possible for people to annotate mutation files for import into cBioPortal. Currently there a variety of different tools to help with this including (a) genome-nexus-annotation-pipeline for annotation of MAF files, (b) annotation-tools for annotation of VCF files and (c) genome-nexus-cli with a redesigned interface for both. For this project we can either create a unified command line experience under (b) if the student is familiar with Java or Python or in (c) if they prefer to work in JavaScript.

[1] de Bruijn I, Li X, Sumer SO, et al. Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. JCO Clin Cancer Inform. 2022;6:e2100144. doi:10.1200/CCI.21.00144

Goal:

• Improve the command line experience of Genome Nexus by unifying the current 3 tools into a single recommended command line interface
• Develop public documentation on how to best annotate a mutation file in MAF and VCF leveraging the new unified interface

Approach:

• Learn about mutation file formats including MAF and VCF. What does each row represent? What is single nucletiode variant (SNV), what is a deletion, what is an insertion?
• Research how to build user friendly command line interfaces
• Create a unified user friendly command line interface in either Java, Python or JavaScript

Need skills:

• Either Java, Python or JavaScript

Possible mentors:
@ao508 @inodb @leexgh @sheridancbio @averyniceday @FahimehMirhaj

[hossamelgendy1]

I'm a 3rd-year CS student interested in implementing this project with Java. can you suggest small tasks to work on meanwhile besides researching command-line interfaces and mutation files?

[ao508]

@hossamelgendy1 Hello and thank you for your interest in this project! At this time we have a couple open issues in the genome-nexus-cli repo but please feel free to begin work on the proposal. Best of luck and please reach out if you have any additional questions!

[pradhyumnj]

Hi, I'm a 3rd year biosciences students at IIT Madras. I'm interested in the GSoC project "Improve Genome Nexus' Command Line Interface Experience" in python, but I don't quite understand the problem statement clearly. Right now we have genome-nexus-annotation-pipeline for MAF and annotation-tools for VCF, and the goal is to create a CLI that is user friendly and can annotate both MAF and VCF files. Is that correct? Isn't the genome Nexus cli doing just that? So is the goal to improve it's user interface? What do students with a knowledge of python (and none of javascript) do?

[davidizzle]

Hi @ao508 ,
I'm a CS fresh postgrad who's switching jobs, and will be contributing to open-source over the summer before my next job starts. Would you guys need an extra hand? Your projects look super interesting. Feel free to reach me at [email protected] if you have any extra work in particular you'd like help with.

[Gairick52]

@inodb i am new to open source can you suggest me some beginner friendly issues

[Cardano-max]

Respected sir/madam,
I am Ateeb Taseer, a computer engineering undergrad, I have just entered my final year at NUST. I am new to open source contributions, but I am well aware of python, C++, java, JavaScript and Node.js. I am very much interested in this project as my final year project is also related to Bioinformatics and want to start my career in Bioinformatics, I would like to contribute to your organization but could you please tell me how to get started?
Hoping to hear from you sonn.
Regards
ATEEB

[harsh2929]

Hello @inodb ,@ao508, i would like to contribute in this project, kindly let me know if its still open for contribution.

[ao508]

Hello @inodb ,@ao508, i would like to contribute in this project, kindly let me know if its still open for contribution.

Hi @harsh2929, thank you for your interest in contributing to GSoC this year! I noticed that you've also expressed interest in our other GSoC project ideas. I recommend that you narrow down to just one project and include a brief summary of interest along with a link to your CV or LinkedIn profile.

[harsh2929]

@ao508 @inodb
I have attached my resume and motivation letter, please do reach out for any queries on my email mentioned in both,

(Motivation letter)--------------------------- https://docs.google.com/document/d/1bkL2-a2lSwEC5B78v5RKNaZi_yd1j4GStFryBwISV0o/edit?usp=drivesdk

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(Resume)
https://docs.google.com/document/d/1bf9J2Z_86GIYCvEfO9wmPWobPblBz3HGQRdQgNlFsw4/edit?usp=drivesdk

[bhanushri123]

Hello @inodb , @ao508 I am Bhanushri a sophomore at IIT Mandi, I am an Engineering Physics undergraduate , I am interested in contributing to open source though I am new to this but I have good experience with Python, C++ and I have good experience in Machine Learning as well.
I would like to contribute to open source .
I am attaching my resume pls reach out to me .
(RESUME)
https://docs.google.com/document/d/1fSeLuoQBTJBWqq6Uu-L9bSyiPGVNYeglf2WwiT7VMyQ/edit