live at web4bio.github.io/webgen!

Web Genomics

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) 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.

Todo

1. Create gihub account, list you id with your name below.
2. Create a webgen doc at https://beta.observablehq.com.
3. Have a look at freecodecamp.org as reference for JS leaning.
4. Start checking your fellow participant's notebooks and github activity.
5. Study GDC (Genomics Data Commons) API and note how easy it is to retieve data. So the next step is to start doing just that in the middle of your own notes. Have a look at mine.

participants

• Jonas Almeida, notebook.
• Richard Moffitt, notebook
• Fenghsi,
• Wen Cheng
• Anthony Xiang
• Chantelle Dsilva
• Hunter Jimenez
• Chinonso Nwabueze
• Carolyn Bremer
• Erika Nemethnotebook
• SAM WANG
• ...

WebConferencing

https://global.gotomeeting.com/join/744703413

...

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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 Section: 04

Team Established: Spring 2019

Meeting Time: Friday 11:00-11:53am (Spring 2019)

Meeting Location: HSCENT 3-045B

Contact: richard . moffitt @ stonybrookmedicine . edu

Links: * 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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