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项目作者： web4bio

项目描述 ：
WebGen Vertically Integrated Project
高级语言： JavaScript
项目地址: git://github.com/web4bio/webgen.git
创建时间： 2019-02-01T14:40:50Z
项目社区：https://github.com/web4bio/webgen
开源协议：
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Join the chat at https://gitter.im/web4bio/webgen

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 @jonasalmeida/webgen">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 @rmoffitt?tab=notebooks">Notebook homepage, @rmoffitt/webgen">WebGen page, @rmoffitt/tcgaplots">Simple GDC query tool Faculty website
Jonas Almeida Folder, js Sandbox @jonasalmeida/webgen">Sandbox Firebrowse
Alisa Yurovsky @ayurovsky">Observable Faculty website
Adit Anand Spring 2020 Log, Fall 2020 Log, Spring 2021 Log, Fall 2021 Log @19aanand">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 @amaraim22/webgen">Observable
Erika Nemeth Fall 2019 Log, Spring 2020 Log, Fall 2020 Log, Spring 2021 Log @enemeth19/webgen">WebGen Background Interactive Plots
Uday Turakhia Fall 2023 Log NASA Events API, State VS Covid

Alumni

APIs

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

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