fastqEngine

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

Inspiration

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
• Example:

A publicly available Paired-end Illumina HiSeq2000 MCF7 breast cancer cell line sample can be used as a test case.

How I built it

• Use a whiteboard to brainstorm!

• Present my idea/progress periodically to other participants and sponsors

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

• Filling in the gaps and debugging in cross-language
• Scalability
• Implementation on remote computer cluster & cloud platform
• Adaptabiility as new experimental platforms come up