Documentation

(Difference between revisions)
Jump to: navigation, search
(Presentations: Adding my recent NextGenBUG talk)
m (Presentations: Adding BOSC 2009 slides)
Line 63: Line 63:
 
==== Presentations ====
 
==== Presentations ====
  
* Scottish NextGenBug meeting - Second generation sequence data and Biopython
+
* BOSC 2009 presentation "Biopython Project Update"
 +
:[http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2009.pdf PDF] | [http://www.slideshare.net/bosc/cock-biopython-bosc2009 Flash version]
 +
* Scottish Bioinformatics Forum NextGenBug meeting - Second generation sequence data and Biopython
 
:[http://biopython.org/DIST/docs/presentations/Biopython_NextGenBUG_June2009.pdf PDF]
 
:[http://biopython.org/DIST/docs/presentations/Biopython_NextGenBUG_June2009.pdf PDF]
 +
* Laptop session at "2009 Biología Computacional de Proteínas workshop" at Quilmes National University
 +
:[http://www.bioinformatica.info/biopython/ HTML] (requires Crunchy to try the code online)
 
* BOSC 2008 presentation "Biopython Project Update"
 
* BOSC 2008 presentation "Biopython Project Update"
 
:[http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2008.pdf PDF] | [http://www.slideshare.net/bosc_2008/antao-biopython-bosc2008/ Flash version]
 
:[http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2008.pdf PDF] | [http://www.slideshare.net/bosc_2008/antao-biopython-bosc2008/ Flash version]
Line 73: Line 77:
 
* BOSC 2003 presentation about Biopython and using it for Laboratory Analysis Pipelines.
 
* BOSC 2003 presentation about Biopython and using it for Laboratory Analysis Pipelines.
 
:[http://biopython.org/DIST/docs/presentations/bosc_biopython.pdf PDF] | [http://biopython.org/DIST/docs/presentations/bosc_biopython.tar.gz tarball with LaTeX source]
 
:[http://biopython.org/DIST/docs/presentations/bosc_biopython.pdf PDF] | [http://biopython.org/DIST/docs/presentations/bosc_biopython.tar.gz tarball with LaTeX source]
* General talk about scripting with Biopython based example of a primer design program.
+
* General talk about scripting with Biopython based example of a primer design program (old).
 
:[http://biopython.org/DIST/docs/presentations/scripting.pdf PDF] | [http://biopython.org/DIST/docs/presentations/scripting.tar.gz tarball with LaTeX source]
 
:[http://biopython.org/DIST/docs/presentations/scripting.pdf PDF] | [http://biopython.org/DIST/docs/presentations/scripting.tar.gz tarball with LaTeX source]
* Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython.
+
* Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython (old).
 
:[http://biopython.org/DIST/docs/presentations/biopython.pdf PDF] | [http://biopython.org/DIST/docs/presentations/biopy_group.tar.gz tarball with LaTeX source]
 
:[http://biopython.org/DIST/docs/presentations/biopython.pdf PDF] | [http://biopython.org/DIST/docs/presentations/biopy_group.tar.gz tarball with LaTeX source]
* Laptop session at "2009 Biología Computacional de Proteínas workshop" at Quilmes National University :[http://www.bioinformatica.info/biopython/ HTML] (requires Crunchy to try the code online)
 
  
 
==== Logo ====
 
==== Logo ====
  
 
Read more about the [[Logo|Biopython logo]].
 
Read more about the [[Logo|Biopython logo]].

Revision as of 11:09, 7 July 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 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
  • API documentation for Biopython modules is generated directly from source code comments using Epydoc.
HTML
  • 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:
  • Cookbook documentation (on the wiki)
  • The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
PDF
  • Working with restriction enzymes.
HTML

Documentation for Developers

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. If you use Biopython in a scientific publication, please cite the application note [1] and/or one of the other listed papers:

  1. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3. doi:10.1093/bioinformatics/btp163 pmid:19304878. PubMed HubMed [CockEtAl2009]
    This application note covers the whole of Biopython
  2. Chapman BA and Chang JT. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000 Aug; 20, 15-19. HTML | PDF [ChapmanAndChang2000]
    This served as the official project announcement.
  3. 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.
  4. 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.
  5. 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 2009 presentation "Biopython Project Update"
PDF | Flash version
  • Scottish Bioinformatics Forum NextGenBug meeting - Second generation sequence data and Biopython
PDF
  • Laptop session at "2009 Biología Computacional de Proteínas workshop" at Quilmes National University
HTML (requires Crunchy to try the code online)
  • 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 (old).
PDF | tarball with LaTeX source
  • Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython (old).
PDF | tarball with LaTeX source

Read more about the Biopython logo.

Personal tools
Namespaces
Variants
Actions
Navigation
Toolbox