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 W 2:30 - 3:23 PM EST Other weekly meetings here

Private folder for Spring 2024 student notebooks

Background

There is an ever-growing Biomedical BigData reference, which is particularly striking for (1) pathologies with a genomic basis, like Cancer, and (2) observational studies from electronic health records. Accordingly, NIH has spearheaded the establishment of interoperable repositories such as the Genomic Data Commons (gdc.cancer.gov) & the National Covid Cohort Collaborative (covid.cd2h.org). These data ecosystems allow the scientific community, including the citizen scientist, to generate complimentary analytical applications. The goal of this project is to explore this new data-rich landscape by developing nimble Web Applications (Apps) using these public data..

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 off of the development 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
Alisa Yurovsky		Observable	Faculty website
Adit Anand	Spring 2020 Log, Fall 2020 Log, Spring 2021 Log, Fall 2021 Log	Observable, Spring 2022 Log
Purva Shenoy	Spring 2021 Log, Fall 2021 Log, Spring 2022 Log
Amara Im	Spring 2021 Log Fall 2021 Log Fall 2022 Log Spring 2023 Log	Observable
Erika Nemeth	Fall 2019 Log, Spring 2020 Log, Fall 2020 Log, Spring 2021 Log	WebGen Background	Interactive Plots
Uday Turakhia	Fall 2023 Log	NASA Events API, State VS Covid

Alumni

• Kevin Murgas
• Luke Torre-Healy
• Eric Ruan :Sandbox
• Chowdhury An-Noor
• Yuwei Zhang
• Soma Kobayashi
• Jillian Unkenholz
• Joshua Mathew
• Will Li
• Shiying Lin
• Carolyn Bremer :Sandbox
• 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
• Jie Xi Li: Observable
• Zhenghao (Kevin) Zhu : 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] ?

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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:

  • Alisa Yurovsky (Biomedical Informatics, Stony Brook)
  • Richard Moffitt (Hematology / Medical Oncology, Biomedical Informatics, Emory University)
  • Jonas S Almeida (Naitonal Cancer Institute)

• Team Established: Spring 2019

• Meeting Time: W 10:30 -11:25 AM EST

• 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

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