Documentation

(Difference between revisions)
Jump to: navigation, search
(Papers: Adding genomediagram paper, simplifying formatting.)
(Papers)
Line 41: Line 41:
 
==== Papers ====
 
==== Papers ====
  
Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
+
We have a separate list of [[Publications|publications citing or using Biopython]], the following are key papers you may wish to cite:
:[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:
+
 
<biblio>
 
<biblio>
HamelryckAndManderick2003 pmid=14630660
+
#ChapmanAndChang2000 Chapman BA and Chang JT. ''Biopython: Python tools for computational biology.'' ACM SIGBIO Newsletter 2000 Aug; 20, 15-19. [http://biopython.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.org/DIST/docs/acm/ACMbiopy.pdf PDF]
</biblio>
+
// This serves as the official project announcement.
The Bio.Cluster module is described in a Bioinformatics article:
+
#HamelryckAndManderick2003 pmid=14630660
<biblio>
+
// The Bio.PDB module is described here.
DeHoonEtAl2004 pmid=14871861
+
#DeHoonEtAl2004 pmid=14871861
</biblio>
+
// The Bio.Cluster module is described here.
GenomeDiagram which has now been integrated in Biopython is described in a Bioinformatics article:
+
#PritchardEtAl2006 pmid=16377612
<biblio>
+
// This describes GenomeDiagram, which has now been integrated into Biopython.
PritchardEtAl2006 pmid=16377612
+
 
</biblio>
 
</biblio>
  

Revision as of 15:58, 4 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

We have a separate list of publications citing or using Biopython, the following are key papers you may wish to cite:

  1. Chapman BA and Chang JT. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000 Aug; 20, 15-19. HTML | PDF [ChapmanAndChang2000]
    This serves as the official project announcement.
  2. 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.PDB module is described here.
  3. 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]
    The Bio.Cluster module is described here.
  4. 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]
    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

Documentation for Developers

Personal tools
Namespaces
Variants
Actions
Navigation
Toolbox