Documentation

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==== Papers ====
 
==== Papers ====
  
*Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
+
Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
 
:[http://biopython.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.org/DIST/docs/acm/ACMbiopy.pdf PDF]
 
:[http://biopython.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.org/DIST/docs/acm/ACMbiopy.pdf PDF]
*The Bio.PDB module is described in this Bioinformatics article:
+
The Bio.PDB module is described in this Bioinformatics article:
 
<biblio>
 
<biblio>
#Hamelryck pmid=14630660
+
HamelryckAndManderick2003 pmid=14630660
 
</biblio>
 
</biblio>
*The Bio.Cluster module is described in a Bioinformatics article:
+
The Bio.Cluster module is described in a Bioinformatics article:
 
<biblio>
 
<biblio>
#de-Hoon pmid=14871861
+
DeHoonEtAl2004 pmid=14871861
 
</biblio>
 
</biblio>
*Python for Bioinformatics PLOS tutorial featuring Biopython:
+
GenomeDiagram which has now been integrated in Biopython is described in a Bioinformatics article:
 
<biblio>
 
<biblio>
#Bassi pmid=18052533
+
PritchardEtAl2006 pmid=16377612
 
</biblio>
 
</biblio>
  

Revision as of 12:27, 3 March 2009

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
  • 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:
  • Writing Tests for Biopython: See chapter 13 in the current developer's version of the Biopython Tutorial and Cookbook:
HTML
  • The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
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/ (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

Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.

HTML | PDF

The Bio.PDB module is described in this Bioinformatics article:

  1. Hamelryck T and Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics 2003 Nov 22; 19(17) 2308-10. pmid:14630660. PubMed HubMed [HamelryckAndManderick2003]

The Bio.Cluster module is described in a Bioinformatics article:

  1. 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. PubMed HubMed [DeHoonEtAl2004]

GenomeDiagram which has now been integrated in Biopython is described in a Bioinformatics article:

  1. 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. PubMed HubMed [PritchardEtAl2006]

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

Documentation for Developers

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