Duuude…

The Green Party October 2, 2009

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 of using GMO seeds in order to sell pesticides. However, after hearing Theo van Hintum’s talk about using biotechnology in order to fight world hunger at GCB 2009 on Tuesday, I couldn’t bring myself to sign such a broad petition. Germany may be able to afford the luxury of being able to ban GMO’s, but most of the world simply won’t be able to sustain its population without the use of GMOs. If the petition had been about prohibiting the use of GMOs as a vehicle for selling pesticides, or the fact that farmers aren’t allowed to use part of their crop as seeds for the next growing season, I would have been more than happy to sign. Since that wasn’t the case however, I was hoping to have an informed discussion with the lady collecting the signatures about her reasons to support this cause. After all, it doesn’t happen very often that I meet someone who is both knowledgeable and passionate about the same topic as me and also disagrees with my views.
Sadly, the lady turned out to be all passion and no knowledge. After about a minute in which I tried to explain what the basics of molecular biology and the concept of plasmids, she began to ignore me and instead started to rant incessantly at the others at the table. When I did get a word in, my arguments were duely ignored, and she continued spewing unfounded incoherent pseudoscientific arguments at my friends.
It saddens me to think that the people I voted for (despite disagreeing with the two main issues in their campaign) are just as ignorant and ill informed as those campaigning for them. My only consolation is that they lost the election and won’t be doing much harm in government over the next years. However, I fear that those who are in government may be even worse.
I need a new ideology. Radically pragmatic humanism doesn’t work for me.

SpaceNavigator support in Chimera on Linux August 18, 2009

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!

Baby, I’m an anarch postmaterialist July 13, 2009

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 now, but as it turns out, that’s already been done. Bummer! Its a shame it’s got such a narcissistic twist on it beacuse some of the ideas are pertty decent.

Published May 24, 2009

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. I can’t wait…

Generating Bibtex Cite-Keys February 2, 2009

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 ascending numbers as cite-keys.

There was also a problem with missing braces in certain publication types, but in my case that was rare enough to be fixed by hand. Vim’s bracket matching and syntax highlighting is quite useful for that kind of thing. Anyway, here is the script. If you find it useful and you would like to extend it to handle the bracket issue, please do get in touch. Of course, the Endnote folks fixing their exporter would also solve the problem…

#!/usr/bin/perl
#
open(MYINPUTFILE, "<$ARGV[0]"); # open for input
my(@lines) = ;
my $counter = 0;
foreach my $line (@lines){
    if ($line =~ /\@article{\n/ | $line =~ /\@incollection{\n/  ){
        $line =~ s/\n/$counter,\n/;
        print $line;
        $counter++;
    }
    else{
        print $line;
    }
}

The Black Keys December 4, 2008

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!

Quote of the day December 2, 2008

“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 what its devotees actually do, you will discover that software engineering has accepted as its charter ‘How to program if you cannot’.”

– Edsger Dijkstra

Ain’t it cool? September 26, 2008

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 connected by invisible springs with varying lengths and stiffness. Initially, the masses are placed at random positions. In order to get the system to settle, the force field includes a thermostat which cools the system down quite quickly.

Over the next few weeks, I’ll put up a series of posts which try to explain what I’m working on and why this animation and the code which produces it isn’t just qute, but also interesting and useful.

Innuendo of the day September 9, 2008

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 a pickup line, let me know how it went…

UPDATE:

This seems fitting, too:

I love MPI September 4, 2008

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 neat APIs. However, despite its name, MPI::Simple still follows the standard MPI API quite closely and is thus not as “simple” as it could be. For many applications, a process manager would already be sufficient. Such a module would create and manage a pool of worker processes and distribute tasks in a round robin fashion.
Both apple and the Qt library offer something similar for thread pools, so why not do the same for MPI processes?

Surely, many others before me have tackled embassasingly parallel tasks before. However, CPAN seems to offer nothing like this. Is such a module simply too trivial so that nobody has bothered publishing their code? Looking at CPAN in general, this doesn’t seem to have stopped folks in the past…

I’ll probably try to cook something up tomorrow.