Tuesday, July 24, 2007

I hate computers

The PC hosting linnaeus.zoology.gla.ac.uk and darwin.zoology.gla.ac.uk has died, and this spells the end of my interest in (a) using generic PC hardware and (b) running Linux. The former keeps breaking down, the later is just harder than it needs to be (much as I like the idea). From now on, it's Macs only. No more geeky knapsacks for me.

Because of this crash a lot of my experimental web sites are offline. I'm slowly putting some back up, driven mainly by what my current interests are, what people have asked for, or things linked to by my various blogs. So far, these pages are back online:

A lot of the other stuff will have to wait.

I hate computers...

Tuesday, July 17, 2007

LSID wars

Well, the LSID discussion has just exploded in the last few weeks. I touched on this in my earlier post Rethinking LSIDs versus HTTP URI, but since then the TDWG discussion has become more vigourous (albeit mainly focussed on technical issues, although I suspect that these are symptoms of a larger problem), while public-semweb-lifesci@w3.org list for July has mushroomed into a near slugfest of discussion about URIs, LSIDs, OWL, the goals of the Semantic Web, etc. There are also blog posts, such as Benjamin Good's The main problem with LSIDs, Mark Wilkinson's numerous posts on his blog, and Pierre Lindebaum's commentary.

I have no comment to make on this, I'm merely bookmarking them for when I find the time to wade through all this...

Friday, July 13, 2007

Phyloinformatics Workshop in Edinburgh October 22-24 2007

This October 22-24 there is a phyloinformatics workshop at the e-Science Institute in Edinburgh, Scotland, hosted in conjunction with the Isaac Newton Institute for Mathematical Sciences's Phylogenetics Programme.
As phylogenetics scales up to grapple with the tree of life, new informatics challenges have emerged. Some are essentially algorithmic - the underlying problem of inferring phylogeny is computationally very hard. Large trees not only pose computational problems, but can be hard to visualise and navigate efficiently. Methodological issues abound, such as what is the most efficient way to mine large databases for phylogenetic analysis, and is the "tree of life" the appropriate metaphor given evidence for extensive lateral gene transfer and hybridisation between different branches of the tree. Phylogenies themselves are intrinsically interesting, but their real utility to biologists comes when they are integrated with other data from genomics, geography, stratigraphy, ecology, and development. This poses informatics challenges, ranging from the more general problem of integrating diverse sources of biological data, to how best to store and query phylogenies. Can we express phylogenetic queries using existing database langauges, or is it time for a phylogenetic query language? All these topics can be gathered together under the heading "phyloinformatics". This workshop brings together researchers with backgrounds in biology, computer science, databasing, and mathematics. The aim is to survey the state of the art, present new results, and explore more closely the connections between these topics. The 3 day workshop will consist of 10 talks from invited experts (45 minutes each), plus 3 group discussion sessions (45 mins - 1 hour each). A poster session will be held in the middle of the meeting for investigators who wish to present their results, and there be also be time set aside for additional discussion and interaction.

The invited speakers are:

For more details visit the web site.