Documentation

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Contents

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

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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