Der Bioinformatiker

So now the work-related news:

I currently work at the R&D Department of my Alma Mater, the University of Applied Sciences in Hagenberg, Austria. The project I’m workting on is not bioinformatics-related but very interesting. I got to work a lot with Python and wxPython as well as some insight into hardware development. Some possibly interesting ideas for bioinformatics may come out of this later; I have to find someone who would need it and finance it, however.

The project is planned to be finished by October, we will see what I will work on from then.

I also started working in the education part of the university. Last year, I was project coach, and this year I changed to being tutor for the Linux-For-Beginners course for bioinformatics and one half of the software engineers. Unfortunately, I may only work for 4 hours per week on education besides the research, so the other half of SE has to be taken over by someone else.

I find it very interesting to work with students. I hope there will be more opportunities in the future for that!

The project-page is now online: Hpe-desk

More info later, when something interesting is ready to be released.

I started working today! I work at the F&E in Hagenberg on a new Project. It has nothing to do with bioinformatics, but more with hardware development; It is very interesting, and I’m looking forward to this challenge.

I will write more about it once the project page is online.

By the way, my diploma thesis is now finished. It has been approved by my tutor, so I will print it tomorrow and hand it in soon afterwards. The exam will be on July 19th or 20th.

I’m home! After about 5 hours of driving – passing some nice places…

…and nearly no traffic jams I finally reached Linz again. I’m glad it’s all done now. All I have to do now is to finish writing my thesis paper…

Today was my last day at work! Tomorrow I will be driving home from Heidelberg to Linz, I can’t wait to be back close to Elke again. The only drawback of this whole situation is that my diploma thesis is not yet finished, so I will have to dedicate all my time now to writing.

I’m free! No more working from 09:00 to 19:00 with only 30 minutes lunch break! No more slavery!

Well, to be honest, it wasn’t that bad… exhausting, but very interesting work. I am a bit proud of my achievements here…
EMBL Heidelberg – I will miss it (at least a tiny bit)

oh – I nearly forgot… the speed tests I mentioned earlier (see Blog Update) showed that a speed up factor (compared to a single CPU) of 50 to 70 times was not unusual…

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…

Mein Balkon

Originally uploaded by Hannes Müller.

Yesterday was a great day, all sunny and warm. So I sat in my dark room and chatted in IRC, complaining about how much I would have liked to sit out in the sun. So JG^ told me “IKEA is still open”…
One hour and 15 minutes later, I’m back with my new table and two chairs. I even got a candle for those extra romantic nights…
The only thing I got to figure out is how to read the laptop screen in the sun.

Well, enough of these trivialities. I guess the next blog entry will be all techie and stuff again…

Frauenparkplatz
Originally uploaded by Hannes Müller.

We all know the wonders of women and parking. It seems that some clever politicians decided to make it a law to have womens parking lots – maybe to minimze damage?

Yeah, I know, that was rude. But I simply could not resist taking THAT photo.

If you dislike the “default” windows desktop like I do (and simultaneously like the OS X desktop or even own a mac and want to have the same look and feel): FlyakiteOSX – Modify . Simplify . Aquafy [The Official Site] version 3.0 was released. Version 3.1 is announced for next week, so I’ll wait for the bugfix/update. I usually would try it, but the mentioned bug (something about an error with the bootscreen) sounds like a more severe problem. And since my laptop is really important for me and my emotional and mental well being (Maybe has something to do with skyping Elke), I won’t risk that by installing that buggy version.

I had the version 2 installed but had to remove it, because it interfered with the installer/control program for the UMTS card. So if you own such a thing, you may be extra careful. But the uninstaller is very thorough, if there are problems you simply revert to an earlier stage (you all have that nice WinXP feature running, don’t ya? – well, you should, it saved me from totally reinstalling the system many times).

I also had some interesting talks at work today, concerning my diploma; we are still not fully decided, if I will work on the “safe” or the “interesting” thing. Since the “safe” one is … well … safe, I have some time (approx. until end of January) to research about the “interesting” one. I really hope that I can get this to work. More details when I get the clearance from my group.