Nutrigenomics One Stop Shop

Our project streamlines the snp-finding process. Then, you can drag and drop the VCF file into our application, which allows you to learn all you need to know about any possible mutations.

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Inspiration

All of us on this team love science, and space is always pushing science forward. We wanted to be a part of that scientific exploration.

What it does

This application will find mutations in astronauts' DNA and allow you to run an analysis that will tell the user what that mutation might mean in terms of astronaut nutrition. Within the app you can then look up articles and have chat gtp summarise them for you to learn even more about these mutations and find food from a curated vegetable, nut, and fruit database that can help any of these nutrient deficiencies.

How we built it

The application is built in two parts that we plan to combine later. The first part is a state-of-the-art bioinformatics snake-make pipeline that takes the astronaut fasta files and aligns them using BWA, this alignment alignment is then sorted using SamTools and finally, snps are called using BcfTools. These bioinformatic tools usually each have to be downloaded separately but our pipeline creates containerized environments for each tool and activates them when necessary.
The second part of our application takes the output, a vcf file, from the pipeline and puts it into a streamlit application. This application will read the vcf file and pull out any mutations, known as snps, that can possibly affect astronaut nutrition. It will give you a short description of what such a mutation can cause. You can then look up genes in our application and have it pull up the most recent 7 articles an that gene which are then summarized by chat gtp for your convenience. Then, using our curated vegetable, fruit, and, nut database you can look up foods that are high in certain nutrients.

Challenges we ran into

Snake make upscaling and reproducing data very easy but it is harder to create piplines in it than we thought it would be. One of us had to be remote last minute and was using a hotspot on a car ride when coding. Non of us have any video making experience, this made video editing hard.

Accomplishments that we're proud of

We completed almost everything we set out to do. We learned a lot about coding and each others strengths and weaknesses. I also got to give a shout out to Marry-Francis who spent most of her time coding on the rode, rest stops, and hotels.

What we learned

Good project management and constant communication can help us cover each others weaknesses better.

What's next for Nutrigenomics One Stop Shop

Our next step to this project is integrating the bioinformatics snake-make pipeline into the streamlit application, making this truly a one stop shop. We also would like to expand our pathogenic mutation database to find more nutrigenomic snps.

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