Monthly Archives: July 2008

ISMB 2008: it’s a wrap

ISMB 2008 wrapped up yesterday. I enjoyed it immensely and will have much more to say in the coming weeks. Right now I just wanted to say:

- It was great to meet so many of my online friends for the first time. I’ve “known” some of you for years, others for a few months and really enjoyed catching up with you all in person.

- Thanks to all who contributed to the coverage in the ISMB 2008 FriendFeed room. It was quite an experiment and I think we were all pleasantly surprised by how well it worked out. Looks like this could lead to some form of semi-official live blogging next year too, which would be excellent.

Tomorrow takes me through Chicago to Manchester, UK, then north to a little place called Carlisle – which happens to be where I was born. It’s not the most wired town in the world, so networking could be sporadic until I get back to Brissie on August 5th.

Off to ISMB 2008

ISMB 2008 poster

ISMB 2008 poster

The last major international conference that I attended was ISMB 2003. It was – right here in Brisbane, although I was living in Sydney at the time. I have to admit that I haven’t always been proactive when it comes to seeking funds to attend meetings. I’ll admit too that I have mixed feelings about conferences. Many of my best friends are scientists, but there’s something about being in a confined space with several hundred intense, academic types that unsettles me. There’s also the prospect (for Australians) of travelling for 24 hours to reach N. America or Europe.

Tomorrow, I’m jetting off to ISMB 2008 in Toronto. I’m sure that I’ll have a fine time once I get there and look forward to putting faces to those names that I’ve known for some years now. I’ll be standing next to this poster at some point too.

Look out for updates here and most likely, via FriendFeed.

More wikis in biology

Hot on the heels of WikiProteins comes:

Huss, J.W. III et al. ( 2008 )
A Gene Wiki for Community Annotation of Gene Function
PLoS Biol 6(7): e175 | Open Access

Which anyone can read, because it’s open access. It’s a realistic assessment of community annotation, focusing on the creation of gene stubs for editing within Wikipedia. Early reaction at the OpenHelix blog and a thread at FriendFeed.

Thanks to Andrew Su, who was kind enough to send me a preprint.

Update: more FriendFeed threads via this search

Thoughts on other programming languages

With respect to their potential for bioinformatics web applications:

Feature Python Ruby
Modern, clean syntax, object-oriented Yes Yes
Web framework Django (and others) Rails (and others)
Bio library BioPython BioRuby
Extensive Bio graphics library Not really – any more than this? Kind of – Bio::Graphics
Use with App Engine Yes Not yet
Well-regarded by scientific programmers Yes M. Wood, J. Badger, ??

To the novice, it looks like “much of a muchness”. Thoughts?