Bioinformatics Australia 2007: day 2 and round-up

Some more brief notes and hyperlinks from day 2 of the Bioinformatics Australia 2007 meeting.

I enjoyed this meeting. Nothing earth-shattering, but a lot of good talks with themes that interest me: genomics, data management, data integration, bringing bioinformatics to bench biologists. I’d definitely attend again. The organisers hope that this meeting will become a major event in the Australian bioinformatics calendar, reaching into the Asia-Pacific region and attracting more interest. Bioinformaticians who fancy a trip to Australia should keep an eye on the event and wangle themselves an invitation.

Session 3: Proteomics and structural bioinformatics
Ten minutes before the session begins, a complete power failure strikes the conference centre and surrounding area. We watch the organisers minds race as they contemplate worst case scenarios. Fortunately, power is soon restored, but a few uploaded talks have vanished from the meeting room computer, prompting some hasty reorganisation. We all have a good laugh and professionalism is maintained throughout.

The role of bioinformatics in glycomics.
Nicolle Packer Home page | PubMed search
A very interesting talk on how glycomics and glycoproteomics require similar databases and web resources to the other -omics.

Predikin and PredikinDB: tools to predict protein kinase peptide specificity.
A talk by yours truly. I think it went quite well. If you’re interested, take a look here.

Unique ion signatures (UIS) and mass spectrometry: a methodology to unequivocally identify and quantify all the proteins in a proteome.
Jamie Sherman APAF home page | PubMed search for Molloy MP
In principle, UISs can unequivocally identify peptides from complete proteomes.

Angles of transmembrane helices predicted from sequences.
Zheng Yuan
I haven’t located Zheng on the web yet – his talk described SVMs that use sequence features to predict TM helix angles.

Session 4: Biological Systems

Kinetics of gene regulatory network during early stage of embryogenesis.
Tanya Soboleva JCSMR Chromatin Group | PubMed search
A talk on modelling the dynamics of mRNA and protein content in early embryonic cells.

Modelling and simulation techniques for membrane biology.
Kevin Burrage Home page | PubMed search
Using Monte Carlo simulation to model protein and lipid raft diffusion in a lipid bilayer.

A generic information model for biological data.
Christophe Roos Medicel home page | PubMed search
Christophe discussed the construction of database schemas to integrate bioinformatic data from disparate sources.

Combined in silico and metabolomic studies of Leishmania.
Vladimir Likic Home page | PubMed search
Vladimir heads the LeishCyc project, a metabolomics database for Leishmania.

Lunchtime, posters and on to the second plenary talk.

Divining the organising principle.
Winton Hide Home page | PubMed search
A tremendously entertaining overview of Win’s numerous projects in disease gene discovery.

Session 4: Comparative Genomics and Evolution
I had planned to skip the first couple of talks in this session, as I’d seen them recently at another meeting. Unfortunately some rescheduling occurred in my absence, so I ended up attending these two:

New methods of detecting violated phylogenetic assumptions: implications on comparative genomics.
Lars Jermiin Home page | PubMed search
Lars has developed diagnostic statistical tests that tell you whether you should even be attempting phylogenetic analysis with your sequence set. A longer and far better version of his ComBio 2007 talk that I saw recently.

Using comparative genomics to build the virtual sheep genome and refine the cow genome assembly.
Brian Dalrymple Home page | PubMed search
Brian had the insane idea of reconstructing the sheep genome (no sequence available but a lot of markers) using the genomes of human, dog and cow. Amazingly it works pretty well and is published in Genome Biology.