Add Mutation Diagram on Study View for Enhanced Mutation Analysis

[inodb]

Background:

The cBioPortal is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets, which are collected from a multitude of sources such as published research papers, publicly available data repositories, and private data sets. Please refer to the cBioPortal home page for an overview.

The Study View of the cBioPortal provides users with powerful and interactive means for exploring clinical and genomic data in a study or cohort of samples. Follow this link to explore the Study View page for the 2017 MSKIMPACT cohort.

---

Goal:

Enhance the cBioPortal's capability for analyzing mutations by:

• Visualizing mutations in a gene with mutation diagram

  • Each gene in the Mutated Genes table can have a submenu or icons that can lead to adding a mutation diagram

• The added mutation diagram should be interactive with other charts

  • When the user selects samples with other charts, the mutation diagram will only show mutations for the selected samples
  • When selecting one or more mutations in the mutation diagram, the other charts will also reflect based on the selected samples.
  • Allow user to select a range
  • Allow zoom in

Approach:

The REACT component that is used in the Mutations tab should be reused here. Enhancement will also be necessary (e.g. zooming capability).

---

Needed skills:

Javascript, REACT

Possible mentors:

@gblaih @dippindots

[Kanha-13]

I wanted to contribute in this project can anyone help me with this?

[tanishq67]

Hi, I am Tanishq Gupta, a 3rd-year UnderGraduate pursuing Biological Sciences and Bio-Engineering from IIT Kanpur. I completed GSOC’21 under Open Bioinformatics Foundation. I have been programming since, the last 2 years, and I am very much passionate about working on projects that are related to biology. As a web-head, I with my team created this https://www.ppociitk.in/ website in react for our PPOC club from scratch.

I think, I have all the relevant skills to work on this project. Here, is my Resume for reference https://drive.google.com/file/d/1sMQU0juB2xShgKLDDQ8lqcHlJuSemvvO/view?usp=sharing I am really interested in contributing to this project for this GSoC’22. Could you please let me know if there is any sub-issue that I can first fix and put up a PR on to show my competence, or shall I start working on the proposal?

PS:- The given link cBioPortal is not working.

[tanishq67]

@Luke-Sikina @dippindots

[tanishq67]

@inodb is this issue still up for GSoC? Or is there any other mailing list that I am supposed to join? please let me know. Thank You :)

[ao508]

hi @tanishq67, thank you for your interest in this project and apologies for the delayed response! This project is still available and I know for certain Luke is still interested in being a mentor. If you have any questions please let us know.

[tanishq67]

@ao508 thank you for your reply. I wanted to know, if I can work on some subissue to show my competence or I should directly work on the project proposal.

Thank you

[ao508]

@tanishq67 At this time please feel free to start the proposal, thank you!

[tanishq67]

@ao508 sure, I am on it, will give you update in around a week :)

[MoatazNasr]

@inodb @ao508 Hey are there any issues to work on before submitting the proposal ?

[AbhishekJamhoriya]

Hi @ao508, I'm in my 3rd year at IIT Jodhpur INDIA and currently pursuing my B.tech degree in Computer Science and Technology. I wanna apply for Gsoc and feels that this project will be a great fit for me. I have a great knowledge of Javascript, HTML, CSS and MERN stack. I have done an internship where I was working on a similar thing.so if you give me a green signal I can work on the proposal part.

[ao508]

@AbhishekJamhoriya @MoatazNasr Thank you for your interest! Please feel free to begin working on the proposal and let us know if you have any additional questions.

At this time I don't believe there are any issues to work on related to the Mutation Diagram before submitting the proposal.

[aakilkhanemon]

Hi there! Is this issue still up for GSoC2022? I am interested in contributing to this project. Could anyone please let me know if there is any chance to get involved specific project? Thanks for your time.

[ao508]

Hi @aakilkhanemon - unfortunately the application period closed for GSoC 2022 on April 19th.

[MayaSatishRao]

Is this issue still open? I wanted to contribute and wanted to know if this is available for GSOC 2023?

[inodb]

@MayaSatishRao yes still open - note that GSoC 2023 participating organizations haven't been announced yet

[MayaSatishRao]

@inodb is the image in the description of the issue a mutation diagram? I am not getting what exactly is required?

[Aaryan-Musk]

@inodb Hello there, I am a second year student in computer science department. i want to contribute in this project now(2023). I have knowledge in react and javascript. I personally am really passionate to solve issues that can help cancer worriers. If i could get an email it would be extremely helpful. i really want to discuss this idea with you.

[harsh2929]

@inodb I would love to contribute in this issue, I'm a second year student doing my bachelors in CSE from NIT-K.

[Amritanshu02]

Hello everyone, I am Amritanshu, a CSE 3rd year student. I am currently pursuing my B.tech from Babu Banarasi Das Institue of Technology and Management, India. I am very interested in website building and had build a number of websites like Netflix clone, staybnb clone and many more. Recently I had also developed an interest in Open Source and I would like to contribute for the organizatons in GSoC and show case my skills. I had also participated in Hacktoberfest event and was able to make successfully 4 PRs. After carefully going through your GSoC 2023 Ideas, I had developed a keen interest for "Add Mutation Diagram on Study View for Enhanced Mutation Analysis". I being skilled in Java, HTML, CSS, JavaScript and React and also being familiar with MySQL, DBMS, Git and GitHub, believe that I will be able to make some meaningful contributions to your organizations. I will be looking forward to become a part of your organization and show case my development skills. Also I am new to this whole GSoC so I will be looking for your guidance @Luke-Sikina @dippindots. Thank you all.

GitHub: https://github.com/Amritanshu02 LinkedIn: https://www.linkedin.com/in/amritanshu-gupta-982529201/

[neeraj542]

Hello Everyone, My name is Neeraj Meena, and I'm a first-year student at NIT Bhopal. I'm excited to dive into the open-source community and contribute to meaningful projects.

As a web developer, I have experience working with the MERN stack and possess proficiency in JavaScript, C++, HTML, and CSS. Currently, I'm building websites and working with ReactJS. I'm excited about the opportunity to work on a real-life project like this and contribute to the development of cBioPortal.

I'm passionate about programming and eager to apply my skills to real-world problems.

I'm interested in contributing to this project and I would like to take on issue #87. I think interactive data visualization would be a great addition to the portal, and I have experience with JavaScript. Can you assign this issue to me, please?

In particular, I am hoping to work with mentors such as @Luke-Sikina @dippindots. I am impressed by your contributions to the open-source community and would be honored to work alongside you.

GitHub: https://github.com/neeraj542 LinkedIn: https://www.linkedin.com/in/kumar-neeraj-2019/

Thank you for your time and consideration. I look forward to hearing from you soon.