Week 5

Project Progress

It was a short week this week with Fourth of July giving us off on Friday and most people taking off on Thursday for a long weekend. I’m almost done with the pipeline that can be used for the whole library – I have been working on the querying modules the past few days and am moderately happy with them. There are options to which cutoff to put for the scoring of top genes per compounds and whether or not to only take genes associated with functional terms as well. When you query all of the top however many genes for a compound, you could get about 20% of the genes associated with a structure, so to account for that, we search for paralogs and then human homologs for associated structure under the notion that if it binds strongly to a protein with similar structure, than that’s a good sign for that gene. That increased our gene structure hit rate to about 1 in 3. Now, I just need to find a way to recycle memory and store the data in an efficient way, and learn how to submit a job to the super computer. Another really cool resource is that once we get the results, we can submit some requests to our partner wet lab and have them actually run the genetic experiments.


Outside Research

Yesterday was Fourth of July, so we embraced America by eating burgers and ice cream, and then joining a crowd of red, white, and blue for fireworks over the Mississippi. Aside from that, it’s been pretty chill around the dorm, filled with biking, guitar, and lots and lots of coffee.