Documentation

Documentation

New to BioPython? Check out the Getting Started page, or follow one of the links below.

• Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.

HTML | PDF

• The Biopython Tutorial and Cookbook contains the main bulk of Biopython documentation. It provides information to get you started with Biopython, in addition to specific documentation on a number of modules.

HTML | PDF

• Wiki documentation,

• Seq and SeqRecord objects
• Bio.SeqIO - sequence input/output
• Bio.AlignIO - alignment input/output
• Bio.PopGen - population genetics
• Biopython's BioSQL interface

• Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.

HTML | PDF

• Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface.

PDF

• Cookbook-style documentation:

• Writing Tests for Biopython: See chapter 13 in the current developer's version of the Biopython Tutorial and Cookbook:

HTML

• The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).

PDF

• Working with restriction enzymes.

HTML

API Documentation

• Documentation for Biopython modules is generated directly from source code comments using Epydoc.

HTML

Online Course Notes

• Andrew Dalke taught an introduction to programming for Bioinformatics in Python class at the National Bioinformatics Network in South Africa.

http://www.dalkescientific.com/writings/NBN/

• Katja Schuerer and Catherine Letondal teach a Bioinformatics course in Python at the Pasteur Institute.

http://www.pasteur.fr/recherche/unites/sis/formation/python/ (slightly out of date)

• Ravinder Singh and Scott Kelley teach a Bioinformatics course using Biopython at the University of Colorado.

http://mcdb.colorado.edu/courses/6440/index.html

• Katja Schuerer, Catherine Letondal and Eric Deveaud have an online course that covers getting started in programming with Python. It's aimed at biologists that want to learn programming.

http://www.pasteur.fr/formation/infobio/python/

Papers

We have a separate list of publications citing or using Biopython, the following are key papers you may wish to cite:

1. Chapman BA and Chang JT. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000 Aug; 20, 15-19. HTML | PDF

   This serves as the official project announcement.

2. Hamelryck T and Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics 2003 Nov 22; 19(17) 2308-10. pmid:14630660.

   The Bio.PDB module is described here.

3. de Hoon MJ, Imoto S, Nolan J, and Miyano S. Open source clustering software. Bioinformatics 2004 Jun 12; 20(9) 1453-4. doi:10.1093/bioinformatics/bth078 pmid:14871861.

   The Bio.Cluster module is described here.

4. Pritchard L, White JA, Birch PR, and Toth IK. GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 2006 Mar 1; 22(5) 616-7. doi:10.1093/bioinformatics/btk021 pmid:16377612.

   This describes GenomeDiagram, which has now been integrated into Biopython.

Presentations

• BOSC 2008 presentation "Biopython Project Update"

PDF | Flash version

• BOSC 2007 presentation "Biopython Project Update"

PDF | Flash version

• March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.

PDF | tarball with LaTeX source

• BOSC 2003 presentation about Biopython and using it for Laboratory Analysis Pipelines.

PDF | tarball with LaTeX source

• General talk about scripting with Biopython based example of a primer design program.

PDF | tarball with LaTeX source

• Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython.

PDF | tarball with LaTeX source

Documentation for Developers

• Details about the biopython.org website.
• How to contribute code to Biopython.
• Deprecation policy
• Instructions for building a release of Biopython.