Talk Biopython

Presented by Peter Cock in Scientific track 2010 on 2010/07/10 from 16:00 to 16:30 in room Dussane
Abstract

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.

This talk will briefly cover the current state and capabilities of the Biopython project, described in a application note published last year in the journal Bioinformatics (Cock et al 2009). It is a long running distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics and computational biology. Biopython celebrated its 10th Birthday last year, and has now been cited or referred to in over 150 scientific publications (a list is included on our website).

Some examples of working with sequence data (DNA, RNA and protein) will be shown, including manipulating important file formats like FASTA, FASTQ and SFF used in current genome sequencing work. Other areas supported by Biopython already will also be covered briefly, including working with 3D protein structures from the Protein Data Bank (PDB), querying biological databases online, and visualising genomic information. The talk with wrap up with an overview of recently contributed or new and in progress code, including Google Summer of Code work on phylogenetic.

Our source code is hosted on github.com under under the very liberal MIT-style Biopython License. Please see biopython.org for more information.