Notes from the life of a bioinformatician
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…Odile Crick, wife of Francis. Interestingly, the illustrator of the figure depicting the DNA double helix in that Nature paper:
In his memoir, “What Mad Pursuit,” Dr. Crick recalled going home that day and telling his wife of the historic discovery. Only years later, he wrote, had Mrs. Crick told him that she did not believe a word of it, saying, “You were always coming home and saying things like that, so naturally I thought nothing of it.”
It’s almost time for the monthly compendium of bioinformatics-oriented material from the blogosphere that we call Bio::Blogs. I’ll be hosting this month so send your submissions to the usual bioblogs <at> gmail <dot> com. Remember, you can send one of your own posts or recommend someone else’s.
The official publishing date is August 1st (Wednesday), but I may delay until Friday 3rd, depending on other commitments this week.
A lot of bioinformatics consists of fetching files in various formats from databases and writing parsers to extract features. What to do when one of your trusty parsers unexpectedly fails?
Take a look at the file – use something like grep if possible to examine specific lines and see if their format has altered.
One of my more robust perl scripts is designed to examine the MOD_RES line in the feature table section of a SwissProt file for protein kinase names. Imagine my surprise when out of the blue, not a single name appeared in the ~50 000 line output file. A quick “grep MOD_RES file.dat | less” revealed this alteration:
Previous: FT MOD_RES 353 353 Phosphoserine (by MAPK12 and MAPK9) Current: FT MOD_RES 353 353 Phosphoserine; by MAPK12 and MAPK9.
Might be time to fix up your regexes if you have code that parses SwissProt format.
Once in a while, you need a “random” sequence. For instance, you might perform a simple statistical analysis on a bunch of sequences from a database and decide that it looks interesting. However, if the analysis looks the same when performed on a set of completely random sequences, it’s a fair bet that it isn’t interesting at all.
I’ve had harsh words to say about ATI Linux video drivers in the past – and I’m not withdrawing them. My advice is still do yourself a favour and buy NVIDIA. That said, I did an Ubuntu install on a work machine today (we get little choice with the specs) and finally got the proprietary fglrx driver working with Xgl and beryl, for a fancy desktop. All thanks to this very clear post; I’ve read many and this is the best.
The key points are:
Xgl can do nasty things to your fonts (this thread includes a fix for “my emacs is all squares”) and some apps, like Google Earth are difficult to run (this page contains a fix) but on the whole, things work. If you’re stuck with ATI give these tips a try.
One day either fglrx will have composite or radeon will have tv-out. Which first, I wonder?
Every year I berate myself for not getting organised in time to attend the ISMB meeting.
At least I have the blogosphere. Expect news via Nodalpoint soon. BOSC 2007 is already causing a stir thanks to the keynote talk: the seven deadly sins of bioinformatics (slideshare link – thanks Duncan).
I think it’s time for a quick Perl tutorial. This week: how to extract PDB entries based on 3 factors: a domain that interests you, the number of chains and their length.
Read the rest. . .
Stepping away from my usual content to mention in passing the Australian screening of “controversial” climate change “documentary” The Great Global Warming Swindle. Most notable not for the film but the reactions afterwards.
I set up the news aggregator over at Nodalpoint, to aggregate posts from the blogs of Nodalpoint members. Read the post there for the details.
It’s great to see some new content:
Remember, any registered Nodalpoint user can also access the wiki. If you’d like to create content but don’t have edit permission, leave a note on Nodal and someone will fix you up.
