I am currently attending the ISMB conference in Vienna, my first ISMB after a 3 year hiatus. As usual, a packed program that does not leave much time for blogging. My group is not presenting anything, so we can enjoy the 200 talks and 1000 posters. ISMBs are always a good occasion to meet people – yesterday I met a guy I had last seen 1991 during my first bioinformatics conference ever.
This year, I am particularly interested in text mining – not that i want to start doing text mining myself, but I am interested to see what resources based on text-mining efforts are available. Yesterday, I attended a tutorial called “automatic text analysis based on web services“, which looked just right for my interest. Although the presenter, EBI’s Dietrich Rebholz-Schuhmann, did quite a good job explaining the text mining concepts, I was nevertheless disappointed. Most of the tutorial was just like all the other text mining talks I have heard in recent years: many slided explaining why text mining is important (which I already know), many more slides on how complicated text mining can be (which is the reason why I am not doing it myself). Every self-respecting text miner has a collection of slides showing how difficult it is to recognize a gene name (or a chemical name) in a scientific text, and what the pitfalls are. Apparently, there is a drosophila gene called ‘how’, with the alternative name ‘who’. Unfortunately, the tutorial was rather short on what kind of ‘web services’ actually are available, and how they can be used. There were a couple of links, though. I will try them when i am back in the office – in case any of this turns out to be useful, I will write about it.
Today, we heard a very lively keynote talk by Michal Eisen, the brother of the equally famous Jonathan Eisen. The talk was mostly about patterning genes in the fly embryo, and how to find the relevant transcription factor binding sites. At the end, Michael surprised the audience with the recommendation that bioinformaticians should stop writing software for microarray analysis, as in two years time nobody will be using microarrays anyway. And that we should either publish in open access journals or die. I am not sure if I agree with his first suggestion (disclaimer: I am working for a microarray company). The latter suggestion made me think of Pierre’s nightmare #9 (with me, wearing an Elsevier T-shirt).
More on ISMB when I find the time. Got to sleep now – the meeting starts at 8.15 (yuck)