Notes from the life of a bioinformatician
|
There’s something very English about this story.
“I’ve refereed at Euro 2000, the 2002 World Cup and the 2006 World Cup, none have gone right for me for various reasons,” he said. “If one thing goes wrong it’s unlucky, if two things go wrong it’s really unlucky, if three things go wrong you have to look at yourself and say something isn’t right.
This will be my only World Cup post, promise.
read more »
Regular readers know of my endless quest for the perfect reference management/bibliography system that 100% Linux people can use. Another step in the right direction is the Bibliophile website. It’s a SourceForge-hosted initiative run by the developers of Wikindx, RefBase and PHPBibMan and is aimed at unifying the sorry mess that is open-source bibliographic software. There’s a lot of useful stuff there.
I like the look of BibORB. That may change of course :)
read more »
Recently I installed Bad Behavior, a set of PHP scripts to deal with blog comment spam. It works very well and I’m pleased with it. It keeps a log of denied access, most of which feature standard server responses such as “403: A User-Agent is required but none was provided”. Today I spotted a custom response that made me laugh: “412: I know you and I don’t like you, dirty spammer”.
It was something of a struggle, but we finally squeezed out some work looking at secreted proteins in the Antarctic archaeon M. burtonii. It should be online at Journal of Proteome Research in the next week or so and I added it to the list.
What’s this, a useful method with practical application in Bioinformatics? (Just kidding guys).
The article describes CD-HIT (so no bonus points for a catchy name). It’s the algorithm that RCSB/PDB and UniProt use to cluster their sequences into non-redundant datasets. Fast, by all accounts, though I’m not sure that a dual Xeon with 4 GB RAM is everyone’s workstation. Perhaps I need to be pushier with my boss. Anyway, the article is open access.
There’s an ongoing discussion between myself and Matthias underneath this post on reference management. It’s great to see active development in this area – go check it out.
I don’t normally write long “how to” articles, but I’ve been having so much fun using BioPerl’s Bio::Graphics module recently that I thought I’d write up a tutorial, of sorts. It’s quite long and assumes a reasonable knowledge of Perl and BioPerl. There may be errors – let me know if you spot any.
read more »
It’s that time of year again, when the IWC meet in some exotic location and discuss the politics of whaling. Their website is quite informative and worth a visit.
I admit that when it comes to this issue, I remove my scientist hat. One of my favourite activities at this time of year is taking a trip to Cape Solander in Botany Bay National Park and watching migrating humpback whales. My simple viewpoint is that shooting beautiful, intelligent creatures in the head with an exploding harpoon is wrong. End of story. I don’t really care if certain populations are “sustainable”. I have no time at all for the Japanese “research” argument, which is so obviously a cover for their whale meat industry. And I don’t buy the cultural “we’ve always done it” argument either. Not so long ago, hanging people for petty theft and sending small children to work in chimneys was part of my culture. We stopped those things because society decided that they were wrong.
A spider web and prey, fossilised in amber some 110 million years ago, make this weeks science news. The find is reported in Science, although the abstract rambles on about silk expression libraries, phylogeny and something vague named biomaterials.
Which really misses the point – that this sort of find is just cool. There’s something magical about fossils in amber – it’s like a snapshot of a long-gone world, with the realisation that living things were going about their business much as now, yet unimaginably long ago. I just love it.
I’ve not posted much in the Research Diary blog category of late, largely because I’ve moved to a new system for keeping a daily record of research activity. In our group we are using Twiki as a private lab intranet solution and it’s working pretty well. Read on for my thoughts on Twiki. I’ll probably post the occasional Research Diary article here if it’s worth sharing (e.g. a handy BioPerl tip).
read more »
