Documentation

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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.
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
  • API documentation for Biopython modules is generated directly from source code comments using Epydoc.
HTML
  • Wiki documentation,
  • 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:
  • Cookbook documentation (on the wiki)
  • The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
PDF
  • Working with restriction enzymes.
HTML

Documentation for Developers

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http://www.pasteur.fr/recherche/unites/sis/formation/python/ (slightly out of date)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. If you use Biopython in a scientific publication, please cite the application note [1] and/or one of the other listed papers:

Error fetching PMID 19304878:
Error fetching PMID 14630660:
Error fetching PMID 14871861:
Error fetching PMID 16377612:
  1. Error fetching PMID 19304878: [CockEtAl2009]
    This application note covers the whole of Biopython

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

    [ChapmanAndChang2000]

    This served as the official project announcement.

  3. Error fetching PMID 14630660: [HamelryckAndManderick2003]
    The Bio.PDB module is described here.

  4. Error fetching PMID 14871861: [DeHoonEtAl2004]
    The Bio.Cluster module is described here.

  5. Error fetching PMID 16377612: [PritchardEtAl2006]
    This describes GenomeDiagram, which has now been integrated into Biopython.

All Medline abstracts: PubMed HubMed

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
  • Laptop session at "2009 Biología Computacional de Proteínas workshop" at Quilmes National University :HTML (requires Crunchy to try the code online)

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