Der Bioinformatiker

This is just a short test posting from my iPod touch…
Oh yeah, btw. I’m married now. Pixx will follow soon, from the wedding and from the honeymoon too.

Well, it’s been a long time since I wrote something here. So I’ll fix up anything that’s broken, and write a recap of what has happened in my life since the last posts.

And then, hopefully, I’ll blog more often. Somehow I feel I got something to say again. But maybe that’s because of twitter.

A quick shout out to any fellow wordpress users: if you are currently running version 2.1.1, urgently update to 2.1.2. It seems that the previous release was compromised by a hacker.

Great. Paranoia++.

WordPress has been updated – again. However, this time it’s the big one. 2.1 is released. Go update!

First a small hint for all fellow Wordpress users: upgrade to 2.0.6!

The second part of this short entry is the announcement that – now that work related stress is going down – I will have more free time. And how better to spend this time than to invest it in the blog?

I plan to update my blog more frequently – let’s see how long this motivation holds; somehow it feels kinda similar to these new-year-resolutions…

In case you haven’t noticed yet, I put my recent tracks from last.fm down there, on the bottom of the sidebar on the left.

I just got my reward for finishing bioinformatics: a brand new, shiny MacBook Pro 15.4″!

I’m really satisfied with it. The only drawback I have noticed so far is that it gets quite warm, but that is usual with modern laptops, I think. I spent the last days installing stuff, setting up Windows XP in a parallels-VM (yeah, I figure I will have to work with Windows stuff), setting up Windows XP using Apple boot camp (for those programs that don’t run in a VM) and installing more stuff.

I also upgraded my RAM myself, because the Mac Ram is ridiculously overpriced. I read in a review that Apple used “world’s tiniest screws” for the cover. I really have to confirm this. Fortunately I also own “world’s tiniest screwdriver” .

I also updated my blog, but I seem to have lost the pictures I had uploaded. Sorry for that…

I am happy to announce that the RSS feeds are working again. It was a problem with the permalink-structure of my blog, it seems that Wordpress changed something in the last update.

I also chose a new theme, I hope you like it. I will continue tweaking stuff, maybe I can find some useful additions.

EDIT: I fixed the flickr-fscked page structure too. Now I can display this proudly:

Finally, I found some time to update my blog. Much has happened, not all of it really worthy to write down, but I will give my audience a short update what is now going on in my life.

First, a short technical note: since my last security update, I seem to have screwed the newsfeeds. I hope I will find some time soon to fix them.

My work here at the EMBL Heidelberg is nearing its end. Today, I managed to get the major part of my program working, now I’m much more relaxed. All I have to do now is some fine-tuning and data collection for my thesis.

I guess I’ll explain what I am working on here. It is not classical bioinformatics, at least not how I solved the problem The group I’m working in is researching in the field of Cryo-Electron-Tomography.

• Tomography is a technique to get 3D data. It is based on taking transmission images (with X-ray for humans, for example) from different angles (preferrably evenly spaced around the 360°). This data can be reconstructed to a 3D density model.
• The “Electron” signifies the use of an electron microscope
• “Cryo” is added to point out the sample preparation technique: the sample is shock-frozen in water, in a way to get amorphous ice, which is frozen water that did not form ice crytals and therefore does not destroy the sample

The resulting technique allows us to generate 3D images of a cells interiour, in a next-to-natural state and high resolution. The resolution is high enough to detect bigger proteins and get good data on the exact organization of a cell.

My work is/was to work on the reconstruction. I get the projection data and feed it to my program, which then calculates (and calculates and calculates…) to reconstruct the 3D structure. Because it is so computationally expensive, parallelizing the work is a solution to get the results faster. Although we have access to a big cluster of high-performance machines, it would be nice to use these for other parts (for example the things Bernhard Knapp, the other bioinformatician from Hagenberg here, is working on – finding and clustering the particles in the data) and fortunately we had a great idea – why not use the graphics card? (Well, to be honest, the idea was found by another company, but their product does not quite fit our needs…) – so I researched a lot and started programming. My first prototype (which we tested before easter) was around 10 times faster than the calculation on a CPU. Now, I finished the second prototype and I’m about to run some speed tests… I hope that it will be not much slower now. If anyone is interested how this speedup can be reached, take a look at the GPGPU website or ask me…

As I surfed the other blogs of some “Hagenberger” colleagues, I noticed a significant (100%) trend to writing/ranting in English. So well, I’ll be lame and join the crowd.
blog.Language = "English"

…den die Welt nicht braucht.

Diesen Teil meiner Webseite möchte ich einer Art “Zeitung” für Bioinformatiker widmen. Falls jemand ungeahnte kreative Abgründe Fähigkeiten hat und gerne ein bisschen (pseudo-)publizistisch tätig sein möchte, nur melden! Ich würde mich echt freuen.