I just received an email from Julian Gough , one of last year’s CAFA participants. He started a Wikipedia initiative on protein function prediction, which are barely stubs at the moment. EDIT: He alerted me to the fact that protein function prediction has virtually no presence on Wikipedia. So all you protein function predictors out there, please contribute. Yes, [...]
In Chapter 3 of The House at Pooh Corner, Rabbit organizes a search for Small, “One of my friends and relations.” Like a good manager (or scientist) Pooh lays out a program: As soon as Rabbit was out of sight, Pooh remembered that he had forgotten to ask who Small was, and whether he was the [...]
Prepared by daughter. Not to scale. Species not yet identified. Delicious.
Man is the only animal that laughs and weeps, for he is the only animal that is struck with the difference between what things are and what they ought to be. – William Hazlitt We like to think that we are the only species capable of emotional self-awareness and therefore the only “animal that laughs [...]
Genomics is a new and exciting programming language based on Brainfsck. Here are the commands: g Move pointer to the right. e Move pointer to the left. n Increment the cell at the pointer. o Decrement the cell at the pointer. m Jump forward past the matching i if the cell at the current pointer [...]
If you have a merged file of paired-end reads, here is a quick way to read them using Biopython: from Bio import SeqIO from itertools import izip_longest # Loop over pairs of reads readiter = SeqIO.parse(open(inpath), “fastq”) for rec1, rec2 in izip_longest(readiter, readiter): print rec1.id # do something with rec1 print rec2.id # do something [...]
The Dead Body That Claims It Isn’t: I’m not dead. The Dead Collector: What? Large Man with Dead Body: Nothing. There’s your ninepence. The Dead Body That Claims It Isn’t: I’m not dead. The Dead Collector: ‘Ere, he says he’s not dead. Large Man with Dead Body: Yes he is. The Dead Body That [...]
The IgNobel prizes were awarded this week. Yes, the Nobel prizes too, but the IgNobels are the really interesting ones. (For an thoughtful piece about why the Nobel Prizes in the sciences do not enhance or may even hurt scientific recognition, read Carl Zimmer’s piece at The Loom) . The IgNobel prizes are awarded annually for [...]
Good news: Press Release 2011-10-03 The Nobel Assembly at Karolinska Institutet has today decided that The Nobel Prize in Physiology or Medicine 2011 shall be divided, with one half jointly to Bruce A. Beutler and Jules A. Hoffmann for their discoveries concerning the activation of innate immunity and the other half to Ralph M. Steinman [...]
Hats off to Jonathan Eisen for hosting this activity on his blog. (I’ll keep mine on, thank you. It’s raining cats and dogs here right now). A couple of weeks ago I posted a discussion about two papers that challenged the ortholog conjecture. Briefly, both papers stated that orthologs may not be such great [...]
An original viral (or rather, fungal and bacterial) marketing campaign for the movie Contagion. Although the film tells the story of a fictional viral outbreak, the marketers of Warner Brothers Canada kept it in the realm of microbiology by teaming up with 25 microbiologists and creating what is probably the first agar-plated billboard, which they [...]
MIRA is a really cool sequence assembly software, developed and maintained by Bastien Chevreux. MIRA has a large and active community, led by the funny and gracious Bastien, for whom no problem is too small, or too large. Recently MIRA seemed to have developed a stochastic bug, one of those which are a serious headache [...]
