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 main bulk of Biopython documentation. It provides information to get you started with Biopython, in addition to specific documentation on a number of modules.
- 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:
- Converting GenBank (and other formats) to Fasta.
- Writing Tests for Biopython.
- Logistic Regression supervised learning.
- The Biopython Structural Bioinformatics FAQ.
- Working with restriction enzymes.
API Documentation
- Documentation for Biopython modules is generated directly from source code comments using Epydoc.
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.
- 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
- Thomas wrote an applications note[1] for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
- Hamelryck T and Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics 2003 Nov 22; 19(17) 2308-10. pmid:14630660.
- Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
Presentations
- 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.
- Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython.
Documentation for Developers
- Details about the biopython.org website.
- How to contribute code to Biopython.
- Instructions for building a release of Biopython.
