Revision as of 14:03, 25 July 2013 by Peter
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.
- 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 using Epydoc.
- Wiki documentation,
- Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.
- Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface.
- Cookbook-style documentation:
- Cookbook documentation (on the wiki)
- The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
- Working with restriction enzymes.
Documentation for Developers
- List of Active projects to get involved with.
- How to contribute code to Biopython.
- Deprecation policy
- Instructions for building a release of Biopython.
- Details about the biopython.org website.
Online Course Notes
- Andrew Dalke taught an introduction to programming for Bioinformatics in Python class at the National Bioinformatics Network in South Africa.
- Ravinder Singh and Scott Kelley teach a Bioinformatics course using Biopython at the University of Colorado.
- 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.
- Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3. doi:10.1093/bioinformatics/btp163 pmid:19304878.
This application note covers the whole of Biopython
- Chapman BA and Chang JT. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000 Aug; 20, 15-19. HTML | PDF
This served as the official project announcement.
- 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.
- 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.
- 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.
- Cock PJ, Fields CJ, Goto N, Heuer ML, and Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010 Apr; 38(6) 1767-71. doi:10.1093/nar/gkp1137 pmid:20015970.
This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS
- Talevich E, Invergo BM, Cock PJ, and Chapman BA. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 2012 Aug 21; 13 209. doi:10.1186/1471-2105-13-209 pmid:22909249.
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.