I am a student of the School of Electrical Engineering, University of Belgrade majoring in Software Engineering. The Summer of HPC programme was introduced to me by my Professor who attended it a few years ago, and who thought it was an awesome experience. After looking at the offered projects, I got pretty excited, as most of them deal with real problems and data, and on a large scale too.
So far, the people I’m with in Ostrava, which is where I’m situated, have been nothing but amazing. I think I got lucky with my mentor, Martin, as he’s very responsive to any questions I have, whether it’s about the project or simply getting to know the surroundings. He’s away for a few days now, but I’m getting him a beer as soon he comes back. The other student, James, who’s with me in Ostrava for the summer is this really laidback guy – extremely easy to talk to. So yeah, I’d say I’m in pretty good company for the weeks to come.
As for the project, I’m dealing with software that assembles genome from a large amount of short DNA sequences. In other words, there’s lots and lots of data and it can take days to finish processing. This is where I come in – my main job is to improve the efficiency of the implementation, whether by making small improvements with DNA file readers or making sure that as many stages of the assembly are running in parallel, multithreaded and multiprocessed. The whole bioinformatics field is absolutely new to me, so initially it took me a bit of time to get myself acquainted with the mechanics of algorithms being used and various new terms. I’d say it has paid off, though, as the approaches used to handle DNA data are rather clever, particularly from an engineering perspective.
As far as I’m concerned, this is a good start and I’ll be updating with new information as the situation progresses.