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 Other weekly meetings here
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.
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.
- Create a GitHub account, request access to this project, and add your name/GitHub username to the participants table below.
- Create a WebGen Observable notebook using your Github credentials, and publish it.
- Have a look at freecodecamp.org as reference for JS learning.
- Start checking your fellow participants' notebooks and GitHub activity.
- 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.
- Study the FireBrowse API.
- Report issues or requests for new features.
- Create a fork or a branch, and make a pull request.
- 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
- GDC https://api.gdc.cancer.gov
- FireBrowse http://firebrowse.org
- All of Us https://public.api.researchallofus.org
- [Documentation] ?
- [Example] ?
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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.
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Issues: Cancer Genomics, Web Technologies, JavaScript, Artificial Intelligence, scalable distributed computing, social coding, patient-centered cancer prevention and treatment.
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Methods & Technologies: Web Technologies (JavaScript, Apps), Cancer Genomics, Computational Statistics, Artificial Intelligence, Precision Medicine
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Disciplines: Applied Mathematics and Statistics, Biomedical Engineering, Biomedical Informatics, Computer Engineering, Computer Science
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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.
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Faculty:
- Richard Moffitt (Department of Biomedical Informatics)
- Jonas S Almeida (Department of Biomedical Informatics)
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Team Established: Spring 2019
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Meeting Time: Friday 11:45am-12:50pm
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Meeting Location: Zoom
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Contact: richard . moffitt @ stonybrookmedicine . edu
- Related work
- 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
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