I’m back in the Bay Area now. Exhausted, but safe and sound. The phyloinformatics course at NESCent was great. Dave Maddison was our instructor for the first two days. He gave us a nice overview of Mesquite‘s capabilities. At first, I was pretty excited – thinking that I was going to be writing new modules for Mesquite to do all sorts of cool things – but I know now that I probably won’t. Mesquite modules are written in Java, and I don’t know Java, and based on what I heard from the folks in the Java tract of this course, it’s not straightforward to write these modules even if you do know Java. But, Mesquite is pretty powerful as it is, so I’m glad to know more about it, and creating macros in Mesquite is very easy, and it can be run from the command line (although I wish we’d spent more time on this) so I will definitely keep it in mind for future analyses. Also, we used Eclipse to run Mesquite, so I was introduced to that as well.
For the next two days, Sergei Pond and Spencer Muse introduced us to HYPHY. We learned how to partition a multiple sequence alignment, define substitution models, perform relative rate tests, and simulate trees for bootstrapping. Sergei introduced us to the HYPHY batch programming language at the end of the first day. The second day, I took off. I really needed a day off at this point, and since we were in class from 9am-9pm every day for ten days, I had to just pick a day, and this was it. So, I missed out on the nuts and bolts of the HYPHY batch language, but I feel comfortable enough with HYPHY now to use it when I need it.
Then, the class split into two tracts, Java and Perl. The Java folks went off to do whatever it is that Java people do 😉 and Jason Stajich and Rutger Vos spent the next four days with us installing BioPerl on our laptops.
Just kidding! It didn’t take four days to do the installation. But, it was a headache. I’ve spent days trying to get BioPerl running on my computer in the past, so I must admit to the sweet, sweet schadenfreude I felt watching the experts struggle with it. Finally, though, I can use BioPerl modules in my perl scripts – yay! Jason walked us through many of the features in BioPerl. Rutger introduced us to Bio::Phylo, which is a powerful tool for analyzing/manipulating phylogenetic trees. Invaluable, all of it.
For the final two days of the course, Hilmar Lapp and Bill Piel, the course organizers, taught us how to use PostgreSQL and how to use the DBI module to interface with databases in our perl scripts.
There’s no way that in ten days I could walk away from this course a fully-functional bioinformatician, but I really do feel more empowered to become one. And, my future efforts to write the kinds of analysis pipelines that I’ve struggled with in the past are going to be much more efficient.