Ubuntu Linux: “You can have your sandwich any way you like, but recently we started wrapping it in this really ugly wrapper. Still yummy though, and you can ask for a different wrapper. But you have to ask”. Mac OSX: “We only serve ham & cheese on white bread. If you don’t like it, go [...]
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 [...]
Warning: NSFW language. Brainfuck is a Turing-complete programming language consisting of eight commands, each of which is represented as a single character. > Increment the pointer. < Decrement the pointer. + Increment the cell at the pointer. – Decrement the cell at the pointer. . Output the ASCII value of the cell at the pointer. [...]
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 [...]
Postdoctoral Research Scientist Rutgers University Joint Appointment: Institute of Marine and Coastal Sciences, BioMaPS and Dept. of Biochemistry and Microbiology Two 2-3 year Postdoctoral Research Scientist positions are available. We are looking for young scholars with experience in the areas of computational biology. In the scope of this project, we will uncover how the metal-containing [...]
So you received your mate-paired reads in two different files, and you need to merge them for your assembler. Here is a quick Python script to do that. You will need Biopython installed. #!/usr/bin/env python from Bio import SeqIO import itertools import sys import os # Copyright(C) 2011 Iddo Friedberg # Released under Biopython [...]
I have recently been invited to Google+, (thanks Ruchira!) and as social timesucks go, it is quite enjoyable. Here are my first impressions about g+. In a nutshell: g+’s attempt at compartmentalized communication is laudable, but falls short of the mark. Mainly because, no social network can emulate the real-life way we communicate (or not) with [...]
Nearly a year ago, I posted about the Critical Assessment of Function prediction with which I am involved. The original post from July 22, 2010 is in the block quote. After that, an update about the meeting which will be held in exactly 2 weeks. The trouble with genomic sequencing, is that it is too [...]
For some time now, NERC has been providing us with Bio-Linux. If you don’t want to be bothered with installing all the essential bioinformatic software for your Ubuntu box, you can install Bio-Linux, either as a a Linux distro for installation from scratch, or as a set of packages for an already existing Debian or Ubuntu [...]
Some time ago an article in Linux Journal discussed the adoption of free/open course software (FOSS) by the general public. The article (I can’t seem to find it now) talked about the people that do not care about the distinction between Free as in Free Beer vs. Free as in Freedom (libre). They want software [...]
The Genome Center at University of California Davis and researchers at UC Santa Cruz are organizing a genome assembly competition which they call The Assemblathon. They have released two simulated genomes for competing groups to assemble as best they can. Assemblies are due February 6th, 2011. So there is still time, if you would like [...]
This seems very promising: two consecutive workshops on biological Wikis in Naples. If you have a life-science related wiki, plan on doing one, or just want to learn about how collaborative authoring can help your work, this would be a great place to do so. Thanks to Paolo Romano for the information. Joint NETTAB 2010 [...]
