Documentation

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Documentation

  • 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
  • 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
    • Converting GenBank (and other formats) to Fasta.
           HTML | PDF
    • Writing Tests for Biopython.
           HTML | PDF
    • Logistic Regression supervised learning.
           HTML | PDF
    • The Biopython Structural Bioinformatics FAQ.
           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

   * Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
     Abstract and links to full text
   * Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
     HTML | PDF

Presentations

   * 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.
     HTML
   * How to contribute code to Biopython.
     HTML
   * Instructions for building releases of Biopython.
     HTML
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