The SBML discrete stochastic models test suite

Good test suites (and benchmark suites) are important for software (and model) development, but can be pretty hard to come up with for stochastic models or software relying on probabilistic algorithms.In this issue of Bioinformatics there is an application note describing such a test suite:

The SBML discrete stochastic models test suite
Evans, Gillesipe and Wilkinson
Bioinformatics 2008 24(2):285-286.

Their approach is pretty simple: compare your simulations with the expected value and see if it falls outside the expected range (from known or previously simulated sd). As such, there is not really that to it. The models are also pretty simple, so while they will be useful for catching obvious bugs in a general simulator, I am not sure they will help catching more complex bugs. Of course, you do need to have the simple stuff working before you can tackle the harder problems, so it could still be useful.

Anyway, I am not planning on implementing a general SBML simulator, so it is not that much use to me, except that I am teaching a Systems Biology class where we are using Wilkinson’s book so the models in the test suite matches the exercises I am giving my students, and I can use the test suite to test their programming. Neat.

Citation, for Research Blogging:Evans, T.W., Gillespie, C.S., Wilkinson, D.J. (2007). The SBML discrete stochastic models test suite. Bioinformatics, 24(2), 285-286. DOI: 10.1093/bioinformatics/btm566

And it just keeps getting cheaper…

Yesterday I mentioned how the price keeps dropping on genome re-sequencing, and already today I spot yet another post (on CLC Bio’s “Next Generation Sequencing” blog) on the very topic. Now VisiGen will start selling genome re-sequencing for $1000 — what I would consider the price at which you will start using re-sequencing rather than SNP typing — at the end of 2009.

Will we see the first re-sequencing association mapping studies in 2010?

Joining the DNA Network

Today I received an email from Hsien-Hsien Lei from Eye on DNA, inviting me to join the DNA Network (read a description of this network here). So now I have.

The DNA Headlines

I wasn’t even aware that this existed, but I am happy to learn about it. There is lots of interesting blogs there to follow (and I am a bit addicted to blog reading).

I am just a bit nervous if I have anything much to contribute to all this, but hey, if you don’t like my blog just stop reading it, right?

Dirt cheap whole genome re-sequencing

When writing grant applications I’ve been saying that we could expect whole genome re-sequencing in association mapping studies to be cost effective within the decade. I’m beginning to think that a decade is rather pessimistic.

The cost of re-sequencing is now down to $100,000.

Sure, that is about a factor of 100 more than just getting the SNPs covering your genome and probably tagging most interesting genetic factors we know about, but I would no longer be surprised if the cost would drop to $1000 for re-sequencing within a year, and $1000 was cheap enough for chip based whole genome association mapping studies, so it will be cheap enough for re-sequencing studies.

You can find more on the dropping cost of re-sequencing on Eye on DNA: Whole Genome Sequencing Costs Continue to Drop.

I’d better get cracking on developing analysis methods that can then actually analyse such data…

Next generation sequencing blog

CLC Bio has started a new blog on “next generation sequencing” — whatever they mean by that. Check it out here and see the announcement here.

CLC Bio is a bioinformatics company here in Aarhus and I have several old friends working there. The software they develop looks very nice, but I haven’t really used it myself. It doesn’t really match the problems I work with myself. What’s cooler, though, is that they also develop custom hardware for computationally intensive bioinformatics tasks: The Cube and The Cell.

I’m not really sure what’s supposed to go on their new blog, but since I’m a sucker for science blogs I’ll probably subscribe to it for a while and find out.