WebGenomics

WebGen is hosted on GitHub Pages at web4bio.github.io/webgen/main/html

View our May 2020 interactive presentation at web4bio.github.io/webgen/presentationPoster/

Conference call via Zoom Fridays at 11:45AM EST

Background

Precision Medicine requires an ever-growing biomedical big data reference. This growth is particularly striking for pathologies with a genomic basis, like cancer. Accordingly, NIH/NCI has spearheaded the establishment of an interoperable multi-petabyte-sized Genomic Data Commons (PMC5683428) as a data ecosystem that the scientific community, including the citizen-scientist, can populate with analytical applications. The goal of this project is to explore this new data-rich landscape by developing nimble Web applications (apps) that help find novel associations between genomic features and cancer phenotypes.

How to Contribute

This is a public, open-source project, as well as a project that students may receive academic credit for through the Stony Brook University VIP program.

1. Create a GitHub account, request access to this project, and add your name/GitHub username to the participants table below.
2. Create a WebGen Observable notebook using your Github credentials, and publish it.
3. Have a look at freecodecamp.org as reference for JS learning.
4. Start checking your fellow participants' notebooks and GitHub activity.
5. Study the GDC API and note how easy it is to retrieve data. The next step is to start doing just that in the middle of your own notes. Have a look at mine.
6. Study the FireBrowse API.
7. Report issues or requests for new features.
8. Create a fork or a branch, and make a pull request.

Participants

Name & GitHub ID	Individual folder or notebook	Observable	Other links
Richard Moffitt	Folder, js Sandbox	Notebook homepage, WebGen page, Simple GDC query tool	Faculty website
Jonas Almeida	Folder, js Sandbox	Sandbox	Firebrowse
Carolyn Bremer	Fall 2019 Log, Spring 2020 Log, Fall 2020 Log	Sandbox
Erika Nemeth	Fall 2019 Log, Spring 2020 Log, Fall 2020 Log	WebGen Background	Interactive Plots
Zhenghao (Kevin) Zhu	Spring 2020 Log, Fall 2020 Log	Sandbox
Adit Anand	Spring 2020 Log, Fall 2020 Log	Observable
Yuwei Zhang	Fall 2020 Log	Histology Sandbox
Luke Torre-Healy	Fall 2020 Log	Sandbox	SBU
Kevin Murgas		Sandbox
Soma Kobayashi	Fall 2020 Log	Histology Sandbox
Eric Ruan	Fall 2020 Log	Sandbox
Jillian Unkenholz	Fall 2020 Log	Sandbox
Chowdhury An-Noor	Fall 2020 Log	Sandbox

Alumni

• Ethan Earlie: Sandbox, Web App
• Hunter Jimenez: Histology Sandbox
• Ki Oh: Sandbox
• Anthony Xiang: Histology Sandbox
• Anthony Li: Sandbox
• Shweta Sankaranarayanan: Sandbox
• Nayan Pasari: Sandbox
• Tony Jin: Sandbox
• Chinonso Nwabueze
• Fenghsi Yu: Sandbox
• Wen Cheng: Sandbox
• Sam Wang: Sandbox
• Anuki Liyanage: Sandbox
• Kevin Chang: Sandbox
• Jonathan Krog: Sandbox
• Chantelle Dsilva: Sandbox

APIs

• GDC https://api.gdc.cancer.gov
  • Documentation
  • Example
• FireBrowse http://firebrowse.org
  • Documentation
  • Example
• All of Us https://public.api.researchallofus.org
  • [Documentation] ?
  • [Example] ?

---

Course Information

• Participation in this project may count for SBU students as part of the VIP program, or BMI 530 Software Development in Biomedical Informatics, or under another listing in your home department.

• Issues: Cancer Genomics, Web Technologies, JavaScript, Artificial Intelligence, scalable distributed computing, social coding, patient-centered cancer prevention and treatment.

• Methods & Technologies: Web Technologies (JavaScript, Apps), Cancer Genomics, Computational Statistics, Artificial Intelligence, Precision Medicine

• Disciplines: Applied Mathematics and Statistics, Biomedical Engineering, Biomedical Informatics, Computer Engineering, Computer Science

• Interests / Preparation by Major: Pre-existing knowledge of programming, particularly JavaScript, will be favored as it indicates an innate interest in social coding (user-facing application development). This is applicable to all students, regardless of focus being on Mathematics or Molecular Biology.

• Faculty:

  • Richard Moffitt (Department of Biomedical Informatics)
  • Jonas S Almeida (Department of Biomedical Informatics)

• Team Established: Spring 2019

• Meeting Time: Friday 11:45am-12:50pm

• Meeting Location: Zoom

• Contact: richard . moffitt @ stonybrookmedicine . edu

Links

• Related work
  • cBioPortal
  • Regulome explorer
  • IntOGen
  • Xena
  • TCGA Splicing Variation Database GitHub
  • OncoJS
• Active friends of the project
  • SBU's Integrative Informatics workshop Wiki
  • NCI Division of Cancer Epidemiology and Genetics
    • cloud4bio GitHub and Wiki
    • episphere GitHub and Observable
• Previous related work
  • https://github.com/mathbiol/gdc
  • https://github.com/mathbiol/gdcfun
  • https://beta.observablehq.com/@youdymoo/gdcfun
  • http://bit.ly/tcgascope
  • http://bit.ly/loadsparcs
  • http://bit.ly/pqiSuffolk

---

Edit this page at source.