How to: map protein sequence onto chromosomal coordinates using BioPerl

My coding challenge this week: given a protein sequence and its exons, how do you map single amino acid residues to a location on a DNA sequence? It’s trickier than you might think. Read on for my latest BioPerl how-to.

Best wishes to Jonathan Eisen

Just wanted to add my voice to the many congratulating Jonathan Eisen: biologist, blogger, Open Access advocate and all-round top bloke on his appointment to PLoS Biology Academic Editor in Chief. You can read his editorial to learn more about his motivation and plans for the journal.

Jonathan, you realise that you’re now the figurehead for the revolution, don’t you ;)

Web snippets of interest

• From the Google Blog: Supporting cluster computing in the research community.
• From the excellent One Big Lab: Laboratree, a new professional social networking site for scientists. At first glance, it will have difficulty competing with OpenWetWare.
• From Science Commons: Netsquared hosts data mashup challenge – win a share of $100 000 with your great data mashup idea.

FeedJournal: silly but fun

Via LifeHacker:

Web application FeedJournal turns your RSS feed(s) of choice into a newspaper-formatted PDF.

A little clunky and buggy when I tried it out, but I eventually generated this PDF from a few of my Google shared items. I’m not keen on the way articles are headed “by neilfws” – I didn’t write any of them!

What use is it? Not much – perhaps a nice way to generate a PDF for the next edition of Bio::Blogs.

OpenWetWare

This post from the OpenWetWare blog (discovered via Pedro’s shared items) has inspired me to sign up to OWW – should have done so much earlier. Here’s my user page and the beginnings of a wiki for our lab. Read the OWW mission statement if you’re not familiar with their goals.

I think the OWW site provides an excellent space for collaborative projects. Note to self: aim to set up at least one in the next couple of months or so.

Internet versus research

Yeah, that’d be right. Via BoingBoing, of course.

Post-vacation random picks

RSS feeds are very much “here and now” sources of information, aren’t they? Monitoring them as they come in is no problem at all but if you’re away for a week or two, they lose their immediacy, leading to much “marking as read”.

Anyway – a few that caught my eye on this first day back at work:

• A new computational biology blog from Lars Jensen – Buried Treasure, via Roland. Lars has written a nice summary of the increasingly infamous mitochondrial ID paper which we were alerted to by Attila.
• Bill writes on the proposal for an Open Science Session at the Pacific Symposium on Biocomputing. See One Big Lab for the details.
• Open Students. Early days for this new OA-oriented blog.
• The ever-industrious Pierre brings us a XUL tutorial and a fun Freebase project.
• Jan Aerts on custom glyphs for BioRuby’s Bio::Graphics library.
• Non-science but important and via Bosco’s blog: we finally say sorry.

It’s taken me a while, but I finally figured out the difference between starring (mark as important for later) and sharing (mark as important for others) in Google Reader! Both one-click operations too. I’m quite dense sometimes. Anyway, here are my shared items – also available as a right-sidebar widget at this blog.

That’s several thousand feed items and 150 emails dealt with – back to work I guess. New Zealand, by the way, is impossibly scenic, spectacular and beautiful. Do go there if you can.

But just before I go…

…I have to mention Carl Zimmer’s post on the quest to find English words in human protein sequences.

This game has been around as long as sequence databases have existed. I have a vague memory of a letter from the early 1990s (possibly in Trends in Biochemical Sciences Nature) in which the authors reported the results of comparing SwissProt with the Oxford English Dictionary. As I recall, the longest word that they found was ENSILISTS – meaning people who practice the art of making silage.

Anyway – here’s a quick and easy way to tackle the problem using EMBOSS and some Linux command line trickery.

Vacation

I’m going offline for a couple of weeks (Feb 3 – 17), to enjoy the scenery of our neighbours across the ditch and “tramp” along one of their famous tracks. Normal service resumes Feb 18; comments requiring moderation will be held until then. Expect lots of Flickr activity on my return.

Bio::Blogs #18

A new year, a new Bio::Blogs – edition #18. Hosted by Mike over at Bioinformatics Zen, this issue focuses on open notebook science. If you’re wondering what was hot in the bioinformatics blogosphere the past month, that’s the place to go.

Remember, hosts and monthly contributions are always welcome – details here.