Week 6

In the Lab

This was the week of supercomputing. I am both mildly frustrated that my programs can no longer run in the milliseconds like in my old cs classes and yet super grateful that supercomputers and clusters exist at all.


I am currently trying to plan out how to run the queries and docking efficiently, but to give you an idea of the scope, there are 1500 compounds which will translate to about 50,000 proteins queried from 2.5 million genes. If I run 50 trials of each (which would be better, but I have to decide how practical that is), it would be about 1.5 million trials. Each trial takes a couple minutes, so I could expect about 6 years for it to run if I were lucky! With the supercomputer, however, I'm hoping to dock everything in about 2 days (again, if I'm lucky), but definitely under a week -- I'd take that over 6 years any day.