A web-based user interface (WUI) for getting gene expression matrix from scratch with just few clicks



What it does

  • Let user select RNA-seq raw data files (.fastq format), often from people with diseases such as cancer
  • Operates locally -- no risk of exposing data files potentially subject to privacy and/or intellectual property (IP) rights

How I built it

  • Use a whiteboard to brainstorm!
  • Present my idea/progress periodically to others

Challenges I ran into

  • Triggering execution of bash shell from html and Javascript
  • Retrieving actual vs. fakepaths based on user input

Accomplishments that I'm proud of

  • Make a solution to real-world problem that I personally encountered come true
  • Being a "solo hacker" in a hackathon for the first time

What I learned (beyond the organizational detail)

  • Efficient loading of .css and .js using the minimalized file version

What's next for fastqEngine

  • Scalability
  • Implementation on remote computer cluster
  • Implementation on cloud platform
  • Adaptabiility as new experimental platforms come up
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