Supportive Courses for Bioinformatics?

Per Christian Henden asks: "I`m aiming for a masters degree in bioinformatics, and I`m uncertain which courses would be good to follow (and my counselor doesn't know, either). There are of course some courses that 'belong' to this degree, and I`ll take those, but I get to choose a number of additional courses. I want to ask people working in bioinformatics 'What (CS) subjects are important or especially useful in bioinformatics?' I`m planning on choosing 'Large Datasets', 'Parallel Programming', 'Image Classification', and 'Subsymbolic AI', because I think those are important, but I`m really not sure what is useful or not in real life bioinformatics." Other Ask Slashdot articles, which have touched on bioinformatics, have dealt with magazines, books and graduate schools.

Comments

Take Biology

[biodork]

I work for a Bioinformatics company. Biology Biology Biology Biology!!! We have, and they are not doing as well, several people who with more of a CS background. They don't understand what it is that they are writing programs/algorithms about. We have found it easier to take Biologists who know computers and get good work from them than to do the converse. Make sure you get a VERY good grounding in basic biology. If you don't know what the data you are looking at mean, in the biological sense, then you will make the same mistake a lot do. Just because an algorithm is cool doesn't mean it makes sense. Only by understanding the Biology can you understand the difference.

Re:Take Biology

[Alan Shutko]

But remember that having a good grounding in CS is also essential. I've met too many bioinformaticists whose code was horrid.

Really, I think that it's easier to get good work from a good CS type in close collaboration with a bio type than a bio type who's picked up the usual smattering of CS. My wife (biologist) agrees.

Your experience may be different, but I'd bet you just haven't hired good CS types. Instead, your company probably hired according to buzzwords (like so many other companies in IT) and if your buzzset included Perl (like so much bioinfomatics) your hiring practices probably tended towards the bottom anyway, because the people best at eliciting requirements from domain specialists and picking up enough of the domain to be useful are not usually the people with lots of perl experience. (OTOH, they can generally code in perl quite well.)

ask a professor

[Goldsmith]

Your first problem is asking a counselor.

Find a professor at your University doing this, or interested in this, and get his advice. Better yet, start working for him.

That's just generally good advice for anyone who wants to go to grad school in science or engineering.

Check out the Human Brain Project

[MrBlic]

I recently visited the Human Brain Project yearly conference at the NIH in Bethesda Maryland. It answers all your questions. There was one computer person giving a talk for every three researchers' talks.

The big buzzword this year was Bayseian Filtering. People were using it to model probabilities that genetic sequences would correspond to: Behavior, electcrical signals in specific cells, pathology.

Lots of people were using Java. a few more people using PHP, Python and Perl... no mention of C# or other microsoft stuff. Two projects were using Qt extensively, although they were a little disapponted with something to do with Jpeg image stuff on OS X. I got the impression that they didn't see Qt as being perfect.

They're mostly Mac people And there are a _lot_ of linux enthusiasts. I had dinner with a handfull of people who seemed like 50+ year old administrators. When the subject of Linux came up things got animated. One gentleman runs every SuSE on every desktop in his department. (using Crossover plugin for MS office)

Lots of people are putting together very large databases, and trying to model lots of complex interactions. Others were trying to standardize cross-database communication.

Henry Markram from Switzerland stole the show with a Neocortical microcircuit database. He has measured electrical signals from thousands of living brain cells, traced the cells using Neurolucida, and found corresponding factors between genetic sequences and patterns of electrical activity.

It's clear there's still a lot of excitement (and a little money) in bioinformatics. The important thing is to make sure it's being driven by science.

Almost all of the work that's being done (in this field) is being done in Academia by cheap graduate students... so the complaint is that the programmers rarely stay with the project for more than a year or two.

-Jim