Live at web4bio.github.io/webgen! Conference call via google meet Fridays at 11AM EST
Precision Medicine requires an ever growing Biomedical BigData reference. This growth is particularly striking for pathologies with a genomic basis, like Cancer. Accordingly, NIH/NCI has spearheaded the establishment of interoperable multi-petabyte sized Genomic Data Commons (gdc.cancer.gov, also article 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. For more information see Stony Brook University VIP page.
- Create a Github account, request access to this project, list your id with your name below.
- Create a WebGen doc at https://beta.observablehq.com (use your Github credentials). Publish it.
- Have a look at freecodecamp.org as reference for JS learning.
- Start checking your fellow participants' notebooks and Github activity.
- Study GDC (Genomics Data Commons) API and note how easy it is to retrieve data. So the next step is to start doing just that in the middle of your own notes. Have a look at mine.
- Review official GDC tools (https://gdc.cancer.gov/access-data/gdc-community-tools)
- Check out some existing work (https://github.com/oncojs)
- Tony Jin, notebook
- Chinonso Nwabueze
- Fenghsi Yu, notebook,[fenghsi.yu@stonybrook.edu]
- Wen Cheng, notebook
- Sam Wang, notebook,[sammy.wang@stonybrook.edu]
- Anuki Liyanage,notebook
- Kevin Chang,notebook,[kevin.chang.1@stonybrook.edu]
- Jonathan Krog, notebook
- Chantelle Dsilva, notebook, [chantelleeliza.dsilva]
- GDC https://api.gdc.cancer.gov
- firebrowse http://firebrowse.org
- All of us https://public.api.researchallofus.org
- [documentation] ?
- [example] ?
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 11:00-11:53am
Meeting Location: HSCENT 3-045B
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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