http://www.thomasmargraf.org/wordpress ...where's my blog? Fri, 02 Oct 2009 00:19:40 +0000 http://backend.userland.com/rss092 en I just started an argument with a lady from the green party who was collecting signatures for a petition to outlaw genetically modified organisms (GMOs). I agree with most of the problems they are trying to tackle with that petition, particularly those related to patents on GMOs and the practice ... http://www.thomasmargraf.org/wordpress/?p=49 I've just been informed by Tom Goddard from the UCSF Chimra team that my plugin to support the 3dConnexion 3d Input devices on Linux has been merged and will be included in future builds. If you have any problems with the plugin, please do get in touch. Otherwise, Enjoy! http://www.thomasmargraf.org/wordpress/?p=48 A postironic postmaterialist to be precise. Chances are I'm post-modern, too. With the world being post- everything, it sounds like we're past everything important, interesting or fun; -although materialism can't possibly have been any fun. Still, that's an unacceptable state of things. I was going to proclaim the pre-futurist movement ... http://www.thomasmargraf.org/wordpress/?p=46 The paper about our SALAMI server has been published. It will appear in Nucleic Acids Research's Webserver issue. You can get the advance access version here. Also, I will be speaking at 3dSIG in Stockholm at the end of June. The Topic will be multiple alignments and phylogenies of protein structures. ... http://www.thomasmargraf.org/wordpress/?p=45 As I found out recently, Endnote's bibtex export feature doesn't really produce bibtex files, but some weird bibtex wannabe format. The biggest problem is that it doesn't assign cite-keys. If you run into the problem that bib files exported by endnote, you might find this script useful. It simply assigns ... http://www.thomasmargraf.org/wordpress/?p=38 If you dig the Raconteurs or the White Stripes, The Black Keys are going to blow you away! They've been on my list of bands to check out for years, and I'm seriously disappointed that I've not listened to their stuff sooner. Give them a listen. They're brilliant! http://www.thomasmargraf.org/wordpress/?p=37 "As economics is known as 'the miserable science', software engineering should be known as 'the doomed discipline', doomed because it cannot even approach its goal since its goal is self-contradictory. Software engineering presents itself as another worthy cause, but that is eyewash: if you carefully read its literature and analyse ... http://www.thomasmargraf.org/wordpress/?p=36 Last week, I took a couple of hours to implement a simple toy force field in perl. A 100 lines of code (plus UCSF Chimera and POVRay) and a couple hours of CPU time resulted in the following animation: Essentially, the system simulates 780 particles with identical masses which are ... http://www.thomasmargraf.org/wordpress/?p=35 Normally, I don't publicise this kind of thing, but this one is too good to keep to myself: "Hey baby, do you want to explore black holes with my large particle accelerator?" This is of course in reference to the start of the LHC experiments at CERN. If you try this as ... http://www.thomasmargraf.org/wordpress/?p=33 Using MPI, I've just managed to get a speedup of about 6 for protein structure searches on 8 CPUs without even thinking about optimizations. If that scales across multiple nodes, the SALAMI server might soon become fast enough for interactive use... MPI in general, and the Perl Parallel::MPI::Simple module are pretty ... http://www.thomasmargraf.org/wordpress/?p=32