nodalpoint.org

Alkes Price

The talk is on "De Novo Identification of Repeat Families in Large Genomes", Alkes Price is giving the presentation. The slides are available here. A repeat family is a collection of similar sequence which appear many times in the genome e.g. Alu repeats. Pull out Alu sequences, align them, consensus. We don't know the regions, we don't know the boundaries, repeats don't appear of full copies only partial. Eddy concludes that the problem is messy.

Why do this ? Repeats are biological meaningful, genome rearrangements, drivers of evolution etc. For pragmatic reasons we need repeat masking. Why ? to do comparative genomics. You need to mask repeats before alignment, RepeatMasker is effective only if you know the library of repeats. So how do you identify the repeat families in large genomes.

So I've been here at the conference for a week now and it is becoming more and more like science reality TV. My veins are pumping pure coffee just to maintain sanity. This update is a little more live, the previous to posts were from yesterdays sessions. Again I just didn't have the mental energy to tidy up my notes and post them after the poster session. My poster got a fairly good response, it seems that biological XML standards and the semantic web is starting to get more recognition.

I also spoke to the Director of Operations at BioMed Central, Matthew Cockerill. I asked him about the BMC backend, whether they are planning to add more RSS to the site, make comments more prominent, allow track-backs etc. he was definitely open minded and enthusiastic about all these kinds of technologies (after all the have RSS already) but because they run a fairly serious productions site (with their own software) so these things will need to be considered. A good response, and he's also following the ISMB posts here.

I'm now in the main hall for the final keynote presentation. The hall is packed with people, currently there is a promotional video for Brazil, which is where ISMB2006 will be held. I'm definitely requesting travel funds for that, but then again, I'll have to travel with the boss... We have the governer of Michigan here apparently, Jennifer Granholm, will appere ? She's here, she talked, we discovered that Michigan is shaped like a hand.

Pavel Pevzner's key note has just started. He's talking on the topic of genome rearrangements

Six grueling days and I still have the conference dinner and my poster session to go. I haven't found any of the presentations today particularly interesting so I've skipped most of the sessions. I will get along tonight to the key note at 5:10pm.

I've walled into the IBM demo 40 min late, it goes for two hours, looks like I've just caught the end of the technical introduction. Basically IBM are pushing something called the DB2 "graph extender" (google doesn't seem to have anything on "graph extender"), which by the looks of the last few slides is basically turning DB2 into a graph database. She runs through some of the queries, doesn't look like it is based on RDF or any of the semantic web technologies.

I'm sitting in on the BioDASH demo, Eric Neumann is giving a broad strokes introduction to the semantic web, resources need metadata, basically if we can share and aggregate data and everything will be wonderful.

Now he's talking about semantic lenses, this I think is Haystack specific, he's talking about FOAF now. The slide he's using is the same one that was used in the bio-ontologies, for links see the comments here.