Python Tools for Computational Molecular Biology
Python Tools for Computational Molecular Biology
New to Biopython? Check out the Getting Started page, or follow one of the links below.
The Biopython Tutorial and Cookbook contains the bulk of Biopython documentation. It provides information to get you started with Biopython, in addition to specific documentation on a number of modules
API documentation for Biopython modules is generated directly from source code comments Sphinx autodoc:
Biopython API (latest release), and Biopython API (in-development).
Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.
The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
Working with restriction enzymes.
Andrew Dalke taught an introduction to programming for Bioinformatics in Python class at the National Bioinformatics Network in South Africa.
Kristian Rother wrote a GitBook for learning Biopython with two case studies
Peter Cock wrote a Biopython Workshop which was used at the University of Dundee.
Tiago Antao converted and adapted a good part of the Tutorial into Notebook format.
Chris Rands wrote a separate Biopython Notebook tutorial illustrating how to characterize a small sequence like a coronavirus genome.
We have a separate list of publications citing or using Biopython. If you use Biopython in a scientific publication, please cite the application note (Cock et al., 2009) and/or one of the other listed papers:
Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423
This application note covers the whole of Biopython
Chapman BA and Chang JT (2000). Biopython: Python tools for computational biology. ACM SIGBIO Newsletter, 20, 15-19
This served as the official project announcement
Hamelryck T and Manderick B (2003) PDB file parser and structure class implemented in Python. Bioinformatics, 22, 2308-2310
The Bio.PDB module is described here
De Hoon MJ, Imoto S, Nolan J and Miyano S (2004) Open source clustering software. Bioinformatics, 20, 1454-1453
The Bio.Cluster module is described here
Pritchard L, White JA, Birch PR and Toth IK (2006) GenomeDiagram: a Python package for the visualization of large-scale genomic data. Bioinformatics, 22, 616-617
This describes GenomeDiagram, which has now been integrated into Biopython
Cock PJ, Fields CJ, Goto N, Heuer ML and Rice PM (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38, 1767-1771
This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS
Talevich E, Invergo BM, Cock PJ and Chapman BA (2012) Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics, 13, 209
This describes the Bio.Phylo and Bio.Phylo.PAML modules
BOSC 2013 presentation “Biopython Project Update”
BOSC 2012 presentation “Biopython Project Update”
BOSC 2011 presentation “Biopython Project Update”
BOSC 2010 presentation “Biopython Project Update”
July 2010 - EuroSciPy2010, Paris
February 2010 Biopython workshop at the University of Georgia
BOSC 2009 presentation “Biopython Project Update”
Scottish Bioinformatics Forum NextGenBug meeting June 2009 - Second generation sequence data and Biopython
Laptop session at “2009 Biología Computacional de Proteínas workshop” at Quilmes National University
HTML (requires Crunchy to try the code online)
BOSC 2008 presentation “Biopython Project Update”
BOSC 2007 presentation “Biopython Project Update”
March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.
BOSC 2003 presentation about Biopython and using it for Laboratory Analysis Pipelines.
General talk about scripting with Biopython based example of a primer design program (old).
Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython (old).
Read more about the Biopython logo.