So how did the workshop go? I thought it went a bit better than the first day, but, hey, I’m a bit biased. To get a better idea I sent the participants a similar questionnaire to the one I sent to the Software Carpentry workshop I organised before. Nearly all the participants (95%) agreed with the statement “I enjoyed the Software Carpentry workshop” which is great, but I guess the aim is to help people change how they use computers to do research.
Today I’ve been instructing on a Software Carpentry workshop at the Wellcome Trust Centre for Human Genetics in Oxford; it’s the first time I’ve been lead instructor on a bootcamp. Today Kwasi Kwakwa and myself covered the shell and basic python; more python, then git and SQL tomorrow. So what went well? I was very pleased to find we had no installation issues, even though everyone had brought their own laptop and so we had a mixture of Macs, Windows and the odd Linux machine! I had four USB sticks with the Anaconda etc installers and we didn’t use a single one so the standard installation instructions must be working.
GROMACS is an optimised molecular dynamics code, primarily used for simulating the behaviour of proteins. To compile GROMACS you need, well, some compilers. I install gcc using MacPorts. Note that this requires you to first install Xcode. Then it is easy to install
gcc version 4.9 by
sudo port install gcc49
I’m teaching a short tutorial on how to analyse membrane protein simulations next week at the University of Bristol as part of a series arranged by CCPBioSim. As it is only 90 minutes long, it only covers two simple tasks but I show how you can do both with MDAnalysis (a python module) or in Tcl in VMD. Rather than write something and just distribute it to the people who are coming to the course, I’ve put the whole tutorial, including trajectory files and all the example code here on Github. Please feel free to clone it, make changes and send a pull request (or just send me any comments).
When I first started in Oxford our lab was based on the top floor of the Hans Krebs tower. Since 2008 we have been in the imaginatively named “New Biochemistry Building” which is actually only half a building, but that is another story. To make room for the other half, the Hans Krebs Tower is finally being demolished. In celebration and/or memory I’ve posted a stop motion video I took from my desk out of the 7th floor back in January 2008. You can see several of the characteristic spires of Oxford as well as the plumes from Didcot power station. This too has recently succumbed – 3 of the 6 cooling towers of the old Didcot A power station were demolished three weeks ago.
In an earlier paper we showed that the closed state of Kir1.1, a important potassium ion channel found in the kidneys, was stabilised by a single hydrogen bond. This paper builds on that work by looking for any interactions that stabilise either the open or closed state of the channel by systematically mutating the majority of the residues to alanine. We were surprised to find that 47 mutations destabilised the open state but only 2 destabilised the closed state, one of which was the one we’d found before. Modelling suggests that this is because open conformations of the channel are more optimised and compact hence mutations tend to be more disruptive. The work was partly funded by the Wellcome Trust and hence the paper is free to download.
Our lab has recently bought two Drobo 5Ds to give us some large storage. They work out of the box with Macs but getting them to play nicely with Linux, specifically Ubuntu 12.04, has been a bit more work so I thought I’d share the recipe that, for us at least, appears to work. Much of this has been cobbled together from the drobo-utils page and also from a very helpful earlier blog post. One thing I could not get to work, unfortunately, is USB3. There appeared to be problems with USB3 and Linux when I was trying this out. Finally I should mention that the Drobo here was setup on a Mac, so was formatted HFS+ to begin with and, of course, follow these commands at your own risk. They worked for me, but they might not work for you..