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02/01/2002 Archived Entry: "Computers"

In a welcome change from my usual schedule of molecular cell biology practicals which involve using pipettes to move bits of liquid from one place to another and centrifuge them, I instead had a two hour bioinformatics practical this morning. Bioinformatics is basically the use of computers and other mathematical techniques to analyse biological information, usually but not always in the form of DNA sequences.

As I navigated my way through the crumbling remains of the Department of Genetics building in Cambridge, passing overloaded trolleys and walls with holes in them, I remarked to myself that it was surprising that they still managed to do decent research there. I made it to the computer lab on the second floor fine, and it immediately struck me as looking like no computer lab I'd ever seen before. It was a medium sized room with a motley assortment of ageing SGI and PC hardware lining the walls, all running Linux. Small plastic figurines decorated all available surfaces, I could see at least two fridges humming away along with three coffee machines and countless genetics and computer books sitting on rickity bookshelves.

There was a single non-student there, tapping away on a Linux box, with a resplendent dark beard, black T-shirt and mournful blues music piping out of some computer speakers. I noticed that there was a lot of blues music in the room. The non-student - the instructor - alas, was not wearing a Linux T-shirt.

The purpose of the practical was relatively straightforward, we had to compare a given protein sequence with a library of known protein sequences from other animals to determine homology and possible function. What I found really fun though was that I'd finally found a non computer science place in the university that was home to a few true Linux fanatics. For example, he went into a long digression about the use of conflicting standards in bioinformatics programs - e.g. how different brackets do different things, and bitterly talked about the need for standardisation. I nodded sagely, recognising the sign of a veteran unix hacker.

It was interesting to actually use the genetic comparision programs and see how simple and yet powerful a tool it was. To any experienced Perl or C programmer, the stuff we were doing was kids play - looking for particular patterns or probabilities - but then most biologists don't really know about what possibilities are available. I had a bit of fun looking at the homology between human and chimpanzee protein sequences and seeing the sad state of secondary structure predicting algorithms. Roll on IBM's Blue Gene, say I.

And then during another talk, he bemoaned the slow performance of a particular Java program on his beloved yet ageing SGI Indy and PC Linux boxen, and then promised that next year's class would have a far more advanced experience. While showing us an open source program he was using to demonstrate how you could find the 'turning point' in a membrane-spanning protein, the thing went mad on him and was clearly bug-ridden. He then began a muttered diatribe, in addition to an earlier one he made about another program which couldn't do multiple outputs simultaneously. "We've told him about the problem, but he won't listen, so we've just given up."

Ahh... open source programs, SGI boxes, programs that use lots of impressive looking DNA sequences and make pretty graphs and Linux hackers - what more could you ask from a practical?