Bioinformatics Australia 2007: day 1

This week, I attended Bioinformatics Australia 2007 here in Brisbane. It’s a small meeting; about 100 participants, 2 plenary talks, 2 discussion forums and 22 symposium talks (including myself), plus a smattering of posters. As the name suggests it’s a local meeting, although there are a few participants from overseas.

I enjoyed day 1 on the whole; here’s a brief round up with hyperlinks.

Session 1: Computational Biology

The Visible Cell project: changing the way we think about cells.
Mark Ragan Home page | PubMed search
A nice overview of the Visible Cell project, which aims to integrate bioinformatic data with high-resolution images of cells to provide spatial context. I recommend you visit the project website to find out more.

From Oncosystems to Oncogenes, and back… and iterate.
Pablo Moscato Home page | PubMed search
Entertaining look at the use of memetic algorithms to classify differential gene expression data from cancer cells.

Automated classification and visualisation of high-throughput subcellular localisation imaging.
Nick Hamilton Home page | Publications
Lightning summary of Nick’s work on assigning subcellular location by analysis of fluorescence microscopy images.

An automated approach to identify and annotate noncoding transcripts for functional study.
Marcel Dinger Mattick Lab | PubMed search
Well, it wouldn’t be a Queensland meeting without a talk on ncRNA. Over 30 000 now known from mice and just 20 with an assigned function.

Session 2: Methods and Tools in Bioinformatics

The impact of epigenetic modifications on genomic diversity.
Gavin Huttley ANU Computational Genomics group | PubMed search
Gavin’s group has authored some excellent software tools, including PyCogent.

Generalized linear methods for biological data analysis.
Alex Smola Home page | PubMed search
Statistical machine learning methods – way too mathematical for me to follow, but interesting nevertheless.

Detection of chimeric sequences from PCR artefacts: keeping biodiversity estimates accurate.
Thomas Huber Home page | Publications
Even some pure microbial cultures can yield chimeric PCR products – meaning that they’re not pure after all. Check out the Green Genes website.

Comprehensive analysis of alternative splicing patterns in chicken, compared to human and mouse, using a splicing graph approach.
Shoba Ranganathan Home page | PubMed search (incomplete)
Shoba described a graph method to visualise and compare alternative splicing.

Lunchtime. After lunch, a discussion forum entitled “Developing Bioinformatics Capacity within the -omics Platforms.” I skipped most of this since my solution would be “buy computers, employ people who can run them”. However, I did catch a few comments at the end in which bioinformaticians complained that engaging biologists with initiatives like HPC projects was almost impossible. Tell me about it.

On to the first plenary of the meeting.

SBML, Biomodels Database, MIRIAM, and SBO: Infrastructure projects for computational systems.
Michael Hucka Home page | PubMed search
A great talk on the past, present and future of SBML, from its chief architect.

Looking around the audience, I notice that someone has a dashboard open in their web browser. Never did figure out who they were.

Afternoon tea, then a second discussion forum that seems to be centred on bioinformatics development in Australia. These events are always rather parochial and a little sad, so I skip out early after an interesting day.