Survival Analysis - Theory and Application

Last week I experienced a summer school from the other end. Together with Hans Soelkner we gave a two day course on survival analysis focusing on its application. This was a  satelite workshop of the 19th Animal Science Days in Primosten, Croatia. The attendance was surprisingly good! :) We had 30 participants from 6-8 countries!

The view from the course venue...

As always the theory behind is important, so Hans spent the mornings with explaining the stuff right from the beginning. Afterwards it was my responsibility to turn it into practice, using the Survival Kit v6, a program package capable to analyze large databases. For those who know me the software choice is not such a surprise :)
(For those who wonder: I a involved in its development, so it is kind of an obvious choice.)

What can I tell... The course went ok, at least according to the written (and of course anonymous) feedback after the course. One thing I would do differently is that originally I planned much more for day 1, but ended up skipping half of the stuff. I could provide the basics of usage, one or two examles but nothing more. Hans warned me before but I thought it will be ok. Well... It was on the edge, to be honest.

On day 2 we started with an example repeating the approach from the previous day. This was done by the participants themselves, so I was very happy that most of them did it without any assistence, and those who required some advice got the results soon after the "early birds". So the first day was reasonably ok, I guess... After this one we continued the day with examples on including random effects and relationship matrices, eventually ending at breeding value estimations.

In overall the conference which followed aftervards was a very nice event. A number of presentations mostly from the Central/Eastern European region, providing a good overview about the work being done on participating universities.

Last but not least I would like to express my great thanks to Ino Curik and all organizers for the invitation and the very nice time in Croatia! Hope to return one day!? ;-)

Post publication note:
Attaching my Delicious bookmarks on survival analysis. More on Google...

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.