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.

Just a quick note to let everyone know that the University in Taiwan where nodalpoint is hosted has been having various network problems, which is why the site has been unavailable for the past 24 hrs. I don't know what the specific problem was or if the fix is permanent.

Yeast hub

This is the talk I was genuinely interested in seeing, it is supposedly all about semantic web...

- Time is right for using the semantic web...

So the introduction is fairly general, the web is full of heterogeneous data and access methods, we need metadata and we need a standard format to put our metadata in which in this case is RDF.

The speaker is now talking about the proliferation of all the different BioXML standards, for example MAGE-ML, SBML, etc. The problem in pathway databases is particularly bad with many formats describing the same thing. So according to the speaker we should unify on RDF/XML. Then we get all the so-called "stuff for free" e.g. inference, integration etc.

So now I'm way at the back of the main conference all because my laptop battery is not what it used to be...

- Annotations are made by different annotation groups
- How do you maintain consistency
- GO aims to maintain consistency
- Standards, best practice, training

- After the annotations how do we check the consistency ?

- Compare annotations (curated orthologs) across species ?

- Measure of annotation consistency: e.g. Mouse, human and rat annotation of PAX8, how do they compare ?

- Collect data, cluster annotations and make comparison
- Use curated ortholog sets from MGI about 15000

I'm sitting in on the ontologies and database track at ISMB today, the wireless isn't working in the main conference room, I'm a little fuzzy from drinking German beer last night, but thankfully I didn't find myself wearing my lanyard to the bar or taking my laptop to dinner. Not that I can say the same for others...

Data integration introduction

- How do we control people ?
- How do we maintain consistency ?
- Theme of data integration has been around for a while (early 90s)
- Talking about RDF and data integration
- Raving on basically...

The presenter is Finnish, his accent is a little funny, kind of like listening to the chef from the muppets give a scientific talk, he's cool though...

One of the crucial aspects of any 6 day marathon conference is plentiful strong coffee, ISMB2003 got this right, however ISMB2005 coffee leaves a lot to be desired. Anyway on to more weighty matters. I'm sitting in on the BioOntologies panel discussion, they seem to have a jokey kind of vibe going on here which is cool. The participants on the panel are Mark Musen (MM), Larry Hunter (LH), Judith Blake (JB) and Eric Neumann (EN), they are trying to get input on the following statements (responses follow):