Meeting with the SIB Education Board

Ela and I also had a meeting with members of the SIB education board, Marc Robinson-Rechavi, Patricia Palagi and Frederique Lisacek. They have shown us what the SIB has organized until now. They have several pages where the education activities in Bioinformatics in all of Switzerland are easily accessible:

There are basically three levels of courses: the regular Masters classes (per semester), PhD courses (semester or summerschools) and courses for further education which can be just a couple of days or a week.

The agreement was that for Bioinformatics we (SyBIT and in general) simply attach ourselves to these pages, ie. if we plan courses we will advertise them here or if someone asks for courses we direct them there as well. We are going to actively suggest to our partners to do the same.

We will keep close contact to exchange information about education needs, and I offered our help to disseminate information about these pages in Zurich and Basel, or also prepare and create courses should some need arise that we could address.

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SyBIT Presentation, Lausanne

Today I had a presentation in Lausanne for Sebastian Maerkl’s group (DynamiX project). It was the same kind of presentation as in Bern earlier the same week, describing what SyBIT is about and what we are doing. Jacques Rougemont was also there and most of his group, as well as Ela.

Sebastian gave us a tour of his lab after the talk and explained how their data acquisition and analysis works. They have a very similar data management challenge as the screening community, producing large numbers of images and videos that need to be analyzed using image analysis methods. They have their own cluster in the laboratory for the analysis. We will look at possibilities to help them with the metadata management in a followup meeting next week.

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I attended those two conferences in Lausanne, 22-26 March 2010. ICDT is a database theory conference while EDBT focuses on practical database topics, with less theory and more papers involving the benchmarking of new algorithms and solutions which at some later stage get incorporated into software products. The conference featured keynotes, regular papers and demos, and several workshops. The most interesting keynotes in my opinion were by Ian Horrocks on scalable semantic systems – those systems are not currently scalable at all, and by Pierre Fraigniaud on the importance of succinct labeling in XML data storage in databases. The demo session featured a B-Fabric demo by Fuat Akal et al., B-Fabric: The Swiss Army Knife for Life Sciences. This was a very comprehensive presentation of the rich set of databases supporting biological data analysis at the FGCZ in Zurich. I also attended some talks on the efficient querying of workflows, data provenance and data integration. New trends in databases include also the use of new architectures. I found a tutorial by the ETH Systems group to be of particular interest – on the use of FPGAs in databases, and a paper on the use of multicores in suffix tree construction. The PhD workshop had an interesting talk on web page archiving (by French Television/Radio) and also a talk on research funding by Moira Norrie of the ETH. Via informal discussions I also learned about some interesting databases and tools which could be used for prototyping in work, in particular I liked the BaseX from Konstanz.

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