Yesterday I received an email from Kristjan Liiva, a student at RWTH Aachen University Germany. Kristjan has developed a really cool dashboard to analyze and visualize the development of collaborative OSS projects by mining their mailing lists and software repositories. (If the link doesn’t work, try again later; the project is heavily under development). The […]
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 […]
Found this in my inbox: Dear Dr.Iddo Friedberg, Greeting from OMICS Group! I came across your contribution entitled “Biopython: freely available Python tools for computational molecular biology and bioinformatics” published in the Journal of Bioinformatics and thought your expertise would be an excellent fit for Toxicology-2012 Conference that OMICS Group is hosting. I’m just wondering how many legitimate calls for […]
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 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 is coming up in Boston, July 9-10 2010. The BOSC meetings are a great get-together of a community of programmers who are like-minded in their advocacy of open source code for science, and specifically for bioinformatics. The whole thing is run by volunteers who take a […]
Geek alert: this post for coders. So you sequenced your genome, reached an optimally small number of contigs, they look sane, and now you would like to see what you need for the finishing stage. Namely, how many gaps you have and what are their sizes. UPDATE: “might just be worth clarifying this is for […]
First, a non-bioinformatic one liner, which is very relevant to most of us working on 3 different machines simultaneously, not including the 80 in our cluster. ssh-ing and giving your password each time is painful, and makes it almost impossible to do scripted file transfers, like backups. A good solution is shared key ssh in […]
Biopython is entering its 10th year; the unofficial birthday is on September, since that is when the mailing list started: September 1999. I stumbled onto that list mid-September, 1999. I believe the Python version was 1.5, I was still working on SGI Irix, and I was an 0.3 PhD candidate. Today I am coding with […]
