Bio::Blogs #2

Welcome to Bio::Blogs #2. This edition comes to you from Brisbane, state capital of Queensland, Australia.
Brisbane is a thriving city, currently the fastest growing in Australia. It has much to commend it: a year-round lively cultural scene based largely along the Brisbane River, a pleasant subtropical climate and easy access to many nearby national parks.

Queensland has long been our “sunshine state” – a holiday destination of beaches, rainforest, islands and of course, the Great Barrier Reef. In recent years it’s acquired a new nickname – the "smart state". This state government strategy has led to a lot of bioscience investment, exemplified by the Queensland Bioscience Precinct based here at UQ. This area houses the Institute for Molecular Bioscience, where bioinformatics and computational biology are closely integrated with wet labs. If you’re looking for a world-class environment for bioinformatics, bioscience and daily life, you could do a lot worse than here.

If this is your first time at my little blog – welcome. It’s a bit of a mish-mash; mostly science, which is mostly biological and often computational, with occasional rambling about whatever else is in my head that day.

Now that I’ve done my PR for UQ and the Australian Tourist Board – on with the science!

Bio::Blogs business
Just before we start – Bio::Blogs needs a host for September, otherwise the next edition won’t be until October. Volunteers can email bioblogs <at> gmail <dot> com. If you don’t have your own hosted blog, you can always use Nodalpoint, I guess.
We had 8 submissions this month, plus a few extras – more of those later.

Conferences
There was a spate of excellent conference blogging this month. Roland Krause, aka Spitshine, braved the flat swamps of Cambridgeshire to attend DILS06, a workshop on data integration in the life sciences. He writes about it over at Notes from the Biomass: here are his thoughts on day 1, day 2 and day 3. “All in all, the workshop exceeded my expectations. The talks delivered much more than buzzwords”, he writes. Let’s hope to hear lots more about this important topic in the near future.
Nodalpoint regular Duncan Hull was at AAAI06, an artificial intelligence conference in Boston. He blogged his experiences over at Nodalpoint, including an amusing account of lively debate between Tim Berners-Lee and Peter Norvig, of Google Labs. Duncan also presented a paper (PDF link) on matching web requests to appropriate services.
As Greg noted at Nodalpoint, “it was like attending two conferences at once, without the poisonous black conference coffee”. It takes real commitment and enthusiasm to blog from conferences, so congratulations and thanks are in order.
Pedro, from Public Rambling, also noted that SBMC06, a systems biology conference in Heidelberg, have their live talks online.

Primers and Reviews
Sandra from Discovering Biology in a Digital World submitted a couple of nice posts on measures of sequence quality: am I really related to Cleopatra? and who is this phred and what is his formula?. If you’re a student looking for introductory information on bioinformatics or molecular biology or an educator looking for project ideas, check out her blog.

Blog articles
Jacob Tennessen at Salamander Candy sends in an excellent post on what you might call “amateur bioinformatics”, entitled Lowering the Ivory Tower with Molecular Evolution. I’ve mused about something similar before, but his post is a better read.
Glyn Moody’s blog is enigmatically titled Open… – you’ll see why when you get there. He points out that we are all now in a position to subject Craig Venter to genetic analysis. No doubt Craig himself is already on the case.
Dan Rhoads writes on biology at Migration and submitted a thoughtful post on a recent Cell paper which used comparative oncogenomics. This was a new term to me, yet another -omics and is well worth a read.
Chris Patil has just started a new blog, Ouroboros, for ageing researchers. By which we mean researchers who study ageing, of course. One of his early posts concerns Human Ageing Genomic Resources, or HAGR for short. Make sure to pop over and support Chris’s efforts.
Ricardo Vidal blogs at My Biotech Life, another relatively new blog and he points us to some biotechnology podcasting resources.
Staying with the biotech theme, Deepak Singh’s blog, business|bytes|genes|molecules features more ruminations on data integration. He has some other good material too, particularly on molecular dynamics and computational chemistry. Go and have a read.
Last but certainly not least is that man Pedro again. If you believe that the future of research means online collaboration, open access, science 2.0 and other goodness of that nature, check out many of his posts at Public Rambling. Pedro is interested in protein-protein interactions and his latest post on the human interactome presents preliminary results which he hopes to establish as an open project. Go Pedro!

Editor’s pick
I kept a few posts up my sleeve in case there were no submissions this month, but I think we did pretty well. Here’s just a couple that I enjoyed in the past month. Target? TARGET? We don’t need no stinkin’ Target! is an excellent presentation using genetic algorithms in the service of bashing creationists, over at The Panda’s Thumb. Pierre Lindenbaum’s excellent blog YAKAFOKON illustrates an unusual use for the C language: defining bioinformatic functions in MySQL. And those bemused physicists struggling with biology from BioCurious have a few thoughts on the economics of open-access publishing.

That’s your lot for this month. I trust that I didn’t forget anyone – if you spot omissions or errors, please let me know. I hope you enjoyed this round-up, may there be many more to come.