Gene Matchmaker

Link to Video: https://www.powtoon.com/online-presentation/dnb7qcLjpxt/the-gene-matchmaker/?mode=movie#/

Inspiration

We, the matchmakers, wanted to help scientists better understand the intersecting regions in BED files from experiments, so we wanted to build a tool that would be easy to understand and visualize, effectively and efficiently.

What it does

It searches through BED files from experiments, creates a new file with all the regions that intersect with each other, and then outputs it as a visual on the screen. Right now, it can either output all the intersected regions chromosome by chromosome or output the intersected region and some info for a singular, user chosen, chromosome.

How we built it

We used python to build, from scratch, the algorithm to find the intersecting regions and the visual tool. Our "Region" file is an object. The visual tool is built using the graphics.py library.

Challenges we ran into

Our initial challenges were deciding what to do. There are various tools already built to search through BED files, but the software learning curve to use them were incredibly steep. Instead of using a pre-made tool, we started from scratch in python. Additionally, python is not a language we were very familiar with so we had to learn about both more of the capabilities of python, using various data structures in python, and how to use the entire graphics library.

Accomplishments that we're proud of

We are proud of everything that we've accomplished here. As high school students, we had very little idea how extensive this project would be, but we've learned a lot in these last 30 and some hours, and we're very proud that we have something that runs, and runs pretty good.

What we learned

We learned so much this weekend. We learned about BED files and what they are, how they're used, and why they're important. It was also nice to get a refresher on some of the biology we had forgotten! We also learned a lot about the python language, and all the cool things it can do, especially regarding creating and using objects.

What's next for Gene Matchmaker

What's next is to optimize our algorithm; it isn't the most efficient ever. We'd also like to combine the various visual capabilities into one user-friendly and user-interactive tool. That would probably(definitely) have to be done using a better graphics tool. Using those, we'd hope Gene Matchmaker could then incorporate a more sophisticated algorithm so it was more customizable to the scientist and their experiment, so that we can help them get as much information as possible.

Built With

• python