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Ten years of coding with the snake
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...
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Short bioinformatics hacks, ch. 2: chunk it.
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...
View ArticleClosing gaps
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....
View ArticleBioinformatics Open Source Conference 2010 (and a poll)
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...
View ArticleThe 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...
View ArticleShort 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 =...
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And I should go because?
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...
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Short note on getting students busy
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...
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The Bio* projects: a history in graphs
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...
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