Sire

Happy Christmas everyone! The holidays are now here, so it's time to take a break from the keyboard and relax for a bit.

It looks like the JCP paper didn't make it in time for the December issues (it didn't make the 21st, and I don't know whether there is an issue on the 28th - surely the editorial staff would need a break?). So it looks like it will be the first of what looks like many papers for 2008. It will at the very least be joined by my review article, the draft of which is now complete (finally!). It was hard work, but worth it, as I am now pretty on top of modelling methods from quantum to continuum (I even now understand a little systems biology). The best thing though is that I can see how to implement all of this in Sire, thus showing that the design is as flexible as I planned it to be :-)

Speaking of Sire, I had a meeting with someone from DEISA last week to discuss what we will be doing with the computer time, and what we need to do to port the code to the different HPC platforms we will be using. It looks like a reasonable amount of work (a national supercomputer sure is a long way from a beowulf!) but the upside will be that Sire and my algorithms should parallelise quite well, so we will be able to use these supercomputers for something more interesting than just large MD simulations (not that large MD simulations aren't useful - it's just that there's more to biomodelling than just MD ;-). The only scary thing is that to get the code onto these machines, I have to send the source to the administrators who will compile, profile and optimise it for me. While I do write clean code with lots of comments etc., it is quite daunting thinking that someone with quite a lot of HPC experience will be going through it and pulling it to pieces... I feel like such an amateur... :-)

Anyway, enjoy the holidays - and look out for me if you are attending the CCPB conference at Bristol in January - I'll be talking about my work on the first day!