Notes from the life of a bioinformatician
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I’m off on my first vacation in years, so there’ll be nothing new here for a couple of weeks. Entertain yourselves with some old posts or a random pick.
Next week I’ll be on the world’s largest sand island, then a short break before we head for the Red Centre to see a very large rock. There should be lots of new content in my Flickr account after all that.
Last week, my imagination was captured by the story of the whale and the 19th century harpoon. If you want to explore beyond the headline, look no further than Carl Zimmer’s post over at The Loom. He’s written a short NYT piece on the evolution of ageing and points us to the AnAge database, a curated database containing age and longevity records for many species.
I have a theory. My theory is that many scientists are prone to doublethink. They believe that they are acting in a certain way when in fact, they’re doing the exact opposite.
Take data sharing.
Read the rest. . .
‘Junk’ DNA makes compulsive reading
Whatever the truth, the results pose fresh puzzles about how genes work. “It would now take a very brave person to call non-coding DNA junk,” says Greally.
It would. So stop it, New Scientist. Putting the “junk” in quotation marks doesn’t distract us from the usage of the word.
The article is a summary of recent findings from the ENCODE project (ENCyclopedia Of DNA Elements). More details in:
Way too busy for a proper blog post, here’s some links to resources that caught my eye in the past week:
Via BoingBoing comes a sorry tale of physics education in the UK. Wellington Grey, physics teacher and cartoonist has written an open letter to the Department of Education to complain about changes to the high school physics syllabus:
One question asks “why would radio stations broadcast digital signals rather than analogue signals?” An acceptable answer is:
* Can be processed by computer / ipod [sic]
Briefings in Bioinformatics is less well-known than the other bioinformatics/genomics journals, perhaps as there are only 6 issues a year, but it’s often worth a read.
The current issue is a special entitled “Knowledge Integration and Web Communities”, featuring 6 papers and focusing on semantic web technology. From one of the abstracts:
Scientists drove the early development of the World Wide Web, primarily as a means for rapid communication, document sharing and data access. They have been far slower to adopt the web as a medium for building research communities.
The articles don’t appear to be open access, unfortunately.
Every few months, my colleagues decide that electronic laboratory notebooks (ELNs) are a good idea. I go through the ritual of searching the web, bookmarking some resources and where possible downloading, installing, configuring and running packages to see how well they work. I know in advance that I’m wasting my time, because I’ve tried them all and there isn’t one free/open-source ELN that works for me.
Read the rest. . .
Science, Nature and Wiley journals will not accept Microsoft Word 2007 documents. Presumably for practical reasons (they can’t deal with them), but I’d love to think that this signals something deeper – i.e. a move towards (open?) standards in science publishing.
Staying with both science publishing and Attila’s blog, he’s going to try blog editing of his thesis. Congratulations and good luck to him.
