Documentation

Revision as of 14:28, 22 September 2008

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
• 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.

HTML | PDF

• Logistic Regression supervised learning.

HTML | PDF

• 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/

• 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

• Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.

HTML | PDF

• The Bio.PDB module is described in this Bioinformatics article:

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

• The Bio.Cluster module is described in a Bioinformatics article:

2. 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. PubMed HubMed [de-Hoon]

• Python for Bioinformatics PLOS tutorial featuring Biopython:

3. Bassi S. A primer on python for life science researchers. PLoS Comput Biol 2007 Nov; 3(11) e199. doi:10.1371/journal.pcbi.0030199 pmid:18052533. PubMed HubMed [Bassi]

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.
• Instructions for building a release of Biopython.