You have until Friday Saturday, April 20th to submit your abstracts to the Automated Function Prediction meeting, an ISMB 2013 Special Interest Group and CAFA: Critical Assessment of Function Annotations. Keynote speakers: Patricia Babbitt, University of California, San Francisco. Protein similarity networks: Identification of functional trends from the context of sequence similarity Alex Bateman, European Bioinformatics [...]
I am not inclined to write polemic posts. I generally like to leave that to others, while I take the admittedly easier route of waxing positive over various bits of cool science I find or hear about, and yes, occasionally do myself. But WSJ editorial from E.O. Wilson has irked me so much, I have [...]
It seems like the forces of light have triumphed somewhere around September 2006: …as have their evil counterparts, April 2009: bacteria are neck-in-neck with humans: But they beat the largest creatures on Earth: Of course, you can’t beat cats:
This is romantic! So listen up! A 3D heart shape may be drawn using the following implicit function: Or, in Python: def heart_3d(x,y,z): return (x**2+(9/4)*y**2+z**2-1)**3-x**2*z**3-(9/80)*y**2*z**3 Trouble is, there is no direct way of graphing implicit functions in Python. But anything can be found on Stack Overflow. Putting it all together: #!/usr/bin/env python from mpl_toolkits.mplot3d import [...]
There has been a lot of discussion recently on this blog and others on the need for robust scientific software. Most of the discussion I have been involved in comes from bioinformaticians, because, well, I am one. There has been plenty of talk about code robustness, sharing, and replicability vs. reproduciblity. I do not want [...]
Our lab has a new project and website up. The project is BioDIG: Biological Database of Images and Genomes. BioDIG lets you combine image data and genome data of, well, just about anything which you can make images and have a genome, or partial genomic information. You can upload your image, annotate (tag) parts of [...]
My previous post on ROSALIND, a bioinformatics learning site, got picked up by the Slashdot community. A discussion came up on careers in Bioinformatics, and the Slashdot user rockmulle made some interesting observations on career paths in bioinformatics, which I have copied here. While brief and therefore omitting many important details (research at a university [...]
I just learned about this one: ROSALIND is a really cool concept in learning bioinformatics. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once [...]
I recently read this post about lacunae in Bioinformatics. One complaint was: I know that documentation is a thankless task. But some parts of the Bio[Java|Perl|Python] libraries are described only as an API? This became apparent to me when I had to teach the libraries to students. What does this module do and why does it do [...]
So there have been a few reactions to my latest post on accountable research software, including a Tweeter kerfuffle (again). Ever notice how people come out really aggressive on Twitter? Must the the necessity to compress ideas into 140chars. You can’t just write “Interesting point you make there, sir. Don’t you think that your laudable goal would [...]
Preamble: this post is inspired by a series of tweets that took place over the past couple of days. I am indebted to Luis Pedro Coelho (@LuisPedroCoelho) and to Robert Buels (@rbuels) for a stimulating, 140-char-at-a-time discussion. Finally, my thanks (and yours, hopefully) to Ben Temperton for initiating the Bioinformatics Testing Consortium. Science is messing around with [...]
It is with no inconsiderable degree of reluctance that I decline the offer of any Paper from you. I think, however, you will upon reconsideration of the subject be of opinion that I have no other alternative. The subjects you propose for a series of Mathematical and Metaphysical Essays are so very profound, that there [...]
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 [...]
