This week we started testing on a new set of data called the TESS set. This set was compiled by Janet Thornton and Andrew Wallace at the University College in London to test a similar program they had written. We wanted to run the same set of proteins through GeoHash to see if we could match or even improve upon their results. My job was to automate the new set of tests. Originally it did not seem like that big a job, but I ended up running into a few bugs that took some time. I was having problems with using "push" in Perl to push values into an array. It seemed to push them into index 1 instead of index 0. Eventually I just set the values to the appropriate index without pushing them. It was very odd.
We also met with Olivier, our collaborator over at Baylor Medical Center this week. I spent a good deal of time preparing graphs of all the tests I had been running to show to him. In the end he liked the graphs I had made, but could not really understand their relevance. Brian and I think that the tests were relevant but offer more help in writing the code than in offering any biological information.
I am scheduled to give a presentation next Wednesday, so I have also started to think about that. Near the end of the week we were assigned our topics. My topic is to present on the work I have done this summer. The presentation should be around 20 minutes and include slides. We usually present to everyone in the lab group, so up to fifteen people.