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Should research code be released as part of the peer review process?

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 […]

Can we make accountable research software?

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 […]

Oh, but to receive such a rejection letter!

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 […]

The genomics programming language

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 […]

Short bioinformatics hacks: reading mate-pairs from a fastq file

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 […]

Brainf**k while waiting for a flight

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. […]

The Friedberg Lab is Recruiting Graduate Students

  The Friedberg Lab is recruiting graduate students, for both Master’s and Ph.D. WE ARE:  A dynamic young lab  interested in gene, gene cluster and genome evolution, understanding microbial communities and microbe-host interactions by metagenomic analyses, developing algorithms for understanding gene cluster evolution, and prediction of protein function from protein sequence and structure. YOU ARE: […]

Friday fun story: extreme bug hunting on MIRA

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 […]

Postdoc positions available at Rutgers University

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 […]

Short bioinformatics hacks: merging fastq files

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 […]