Documentation
From Biopython
Contents |
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.
- 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,
- 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.
- 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.
- 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- http://www.pasteur.fr/recherche/unites/sis/formation/python/ (slightly out of date)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.
- 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.
Papers
We have a separate list of publications citing or using Biopython. If you use Biopython in a scientific publication, please cite the application note [1] and/or one of the other listed papers:
- 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
Presentations
- 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).
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