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!

My first publication in a renown Journal has now been published. I’m quite proud of it… well, I’m not the first author, but one has to start small, eh?

I hope there will be more to come, but my diploma thesis work leading to this publication and being awarded the price for “Best Thesis Work” in BIN02 is a good start

From now on, you can officially call me “Dipl.-Ing. (FH)”!

More later, when I had some time to relax…

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.

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…

12/21: The “Winterfest” (WTF05) took place in Hagenberg. It was great fun and I hope all of the visitors enjoyed the fruits of the work Bigii and I did to make it happen. Pixx: in the gallery
as well als here as zip.

12/22: We had our presentation of our Internship. It was nice to see some of my class again and interesting to listen to what they did.

Today (and a part of yesterday) I spent mostly on various trains. Yeah, and I went to Heidelberg to visit the EMBL, where I will work on my Diploma Thesis, to talk about the specifics of my project. It was nice to get to know the people there; I really think I will enjoy my work in Heidelberg.

It looks like I will have to work real hard on this project; the math involved seems rather complicated. I will have to read more about it before I try to explain it here, in case someone is interested. The one thing that’s not so great about this project is that I won’t earn much money. Most of it will go directly into the rent for the room at the guesthouse. Well, there goes my dream of buying a new PowerBook next year…
The team is an interesting combination of nationalities: The team leader is from Greece, the one I’m working together is from Spain, and then there is another Greek, one from Palestine and one from Ireland. I hope I can practice my English some more.

A side note for anyone who understands German around here (yeah, I know, all of you do) : I have just left Augsburg Main Station and that’s what I heard on the train announcement system: “Heazlich willkommen auch den zugestigenen Fåhrgästen. Hier ist eine Person vom Bordservice zugestiegen, die ihnen bis München åm Plåtz frische Brezen und Kåffee servieren wird. Wia wünschen einen guaden Åppetit“. Tsk, those crazy Bavarians.

Later that train ride: I just arrived at Munich. It’s getting dark outside again. I feel like I had no real day today, and I’m getting really tired Stupid train rides. Well, at least I got my laptop, some power from the train and no internet…

Today, we went to Hannover to visit the “Biotechnica 2005”.
We were a group of 19 students from Hagenberg. Our train left yesterday at 10:45pm, a night train that went directly to Hannover. We arrived at 06:40am and had breakfast at the bistro directly at the train station. Then we caught our connection train to the fair grounds, which are two stations from the centre.
Once we left the train station there we were greeted by some shuttle buses which took us directly to the halls where the fair was taking place. We got there at about 08:30am and checked in and bought our tickets. The fair opened at 09:00am, and we were one of the first visitors to pass the ticket checks. At first it was a bit frustrating, because most of the booths were still finishing their decorations and fixing stuff.
We started to stroll around and to look for firms which could be of interest to us. Many companies worked on hardware and machines for working with micro arrays or micro titer plates, and we had a hard time finding companies which focused on software development. But at least I found some interesting information concerning the Affymetrix scanner I’m supposed to work with in my internship. I got some tips and will try to get the recommended software to work. I hope this will satisfy the requirements, as it looks like there is already enough software around, most of it would even be freely available to the Blutzentrale, because they bought the scanner.
Later on we started to do what all the people visiting fairs do: collecting the stuff they give away for free. You can see some pictures of the stuff I got on the webcam. Some of my colleagues were either more successful or more cheeky, because they got more stuff than me, some of them even got some cool stuff, for example a t-shirt saying “rna – the other nucleic acid” (yeah, kind of an “insider” joke) and some nice posters.
I talked to some interesting companies and got some contacts, which could be useful for some of us. One of those companies was the Fraunhofer Institute, which presented a low cost micro array scanner, in some ways similar to the machine developed by the UAR, although they use a totally different method to take the picture. They also have a department which works in the field of bioinformatics, so we’ll take a look if they are interested in cooperating or accepting interns.
Now we are on our way back to Linz (we have to change trains 3 times – in Nürnberg, Passau and in Wels). The conductor on the last train was really strange, we suspected him to be a bit drunk. He even had the wrong date on his stamp:

I just found something interesting in a Slashdot Article. It seems like some scientists managed to create proteins by designing the genes on a computer and inserting the sequence into E.coli. A short report in simple words and a detailed article in “Nature” should provide any information you want about this.