Organizing your computational biology projects

There’s a nice piece recently in PLoS Computational Biology on organizing your projects:

A quick guide to organizing computational biology projects

William S. Nobel

PLoS Computational Biology 2009

I can’t say I’m following all the advice here.  I generally tend to leave a bit of a mess in my projects and every time I’ve completed one I’m vowing to do better next time, but here at least are some advice to keep in mind…


Last week in the blogs








Generally speaking, I am pro-copyright.  I think people should be protected when they create something.  I don’t want people to just copy my work and presenting it as their own, but there is something wrong with the current law on copyrights.

Copyright, yes, but reduce the time where the rights are held.

Same goes for patents.

A pharma company spends millions or billions on creating a new drug.  They wouldn’t if they wouldn’t hold the patent’s right on it.  So we need patents to promote creating inventions.  What we do not need is laws that prevents innovations.

Software patents are particularly bad.  You spend more time checking if your ideas are patented than actually coming up with the ideas.  That is just not right.

Sorry for ranting.  I was discussing this with Molegro Mikael just the other day, so it’s been on my mind lately.

I really don’t know what the right balance is between public domain and copyrights, but I strongly feel that the current situation is just wrong.


It’s time to get on the GPU wagon

Nvidia’s CEO predicts that GPU performance will increase by 570x over the next six years, compared to only 3x for CPUs.  So if you are running time intensive computations, it might be worth thinking about ways of porting them to the graphics cards.

Personally, I want my hidden Markov models to run on GPUs and I’ve just submitted a grant application to get a PhD student and a postdoc to work on that.

Speaking of GPUs, now that Snow Leopard is out it is also time to look at OpenCL.  I haven’t gotten hold of Snow Leopard myself yet, but my student who works on our HMM framework has, so I hope we get around to that soon.

In the meantime I am going to look at these tutorials: