Thursday, August 25, 2011

One week, five countries

Most of the time I try to post some stuff here that might be interesting to some of you (or at least I hope). But as you might have noticed I write some “personal” notes as well from time to time, about things that I want to keep in mind or not want to forget. This post is one of the personal ones as well.

Last week I had the opportunity to visit 5 European countries in 7 daysIt was a nice experience worth to remember, so I am posting it here with some accompanying photos.

Monday: Munich, Germany – actually I was the whole previous week there on the Synbreed Summer School The lake was not integral part of the  course, but I like the photo :) My work... One of the best so far I guess...
Monday evening: Wageningen, The Netherlands – The EMABG Welcome event was running, and I had 2 presentations there. Good time! (p.s. This is the main building of the animal breeding people there, but they will move to new locarion soon dubbed as the "New Zodiac", so likely it was my last visit in this building.)
Thursday: Vienna, Austria – I spent the shortest time here from the 5, basically landing by plane going through the city to the train station, but it counts ;)

Thursday evening: Slovakia – home sweet home

Friday: Budapest, Hungary – finally some leisure trip with my family to the Tropicarium (said to be the biggest in central Europe) 

Sunday: Slovakia, a "ranch" neaby Galanta. Family time again :)

Monday, August 22, 2011

Next Generation Sequencing: Departure to New Frontiers

Last week I have competed the Synbreed Summer School called “Next Generation SequenceAnalysis: Practice and Departure to New Frontiers. It was organized in Herrsching am Ammersee, Germany which is a place just near Munchen. The main organizers were animal breeding people from Technical University Munchen and researchers from the Helmholz Zentrum

I have to say: It was an exceptionally good summer school!

There were several thing in the course that were “out of the ordinary”, yet contributed for the course success (at least for my viewpoint).
1.       Focus on practical data handling: I liked this part very much. We went through everything, starting for the installation of the software up to imputation. It is not easy, but manageable.
2.       Usage of free software: I mean all software, including the operating system. Actually I had to install the Ubuntu Linux because of this. But now I am glad I did. The main interface is far from the command line feeling, which often keeps people from installing Linux. At least with this new Ubuntu graphical interface I had the feeling I am browsing a smartphone… Of course the things can become pretty complicated, depending on the actual aims of the user, but the basic navigation is without problems.
3.       Course given by PhD students: I was realizing this just by the end of the summer school. Not that PhD students are not good enough (in fact they were excellent), but I would expect somebody older “by default”. But I guess this was the strategy of the course to bring in people who are working with these things on daily basis,as they are the most qualified ones to introduce the techniques to us.
4.       Evening sessions: After the daily workload we often went for a beer-or-two, often ending in the billiard room. Good time! 

Except from the practical sessions there were also presenteres, who contributed to afternoon sessions. They were specialist in their fields highlighting various possibilities of sequence data. The list is as follows: Mario Caccamo and Jared Simpson on De novo assembly, Paul Kersey on Genome browsers and databases, Ben Hayes on Genomic selection, Agricultural genome projects and Perspectives of using sequence data, and last but not least Karl Schmid on  Next generation population genomics.

The list of software and other useful links:
  • Burrows Wheeler Aligner - for alligning short sequence reads
  • SAMtools - various utilities to manipulate allignments
  • SEQanswers - all-around forum for sequencing issues. They have a wiki too with the list of most popular software. If you are into sequencing, this is the place to dive deeper. 
Be sure to check out the "World map of sequencing" too. Well... I think it displays the number of sequencers by region, consequently the amount of effort put into sequencing everything what comes around. As of August 2011 it seems that the most powerfull players are the US and China as individual states. Europe comes third if we look at total sums.