Documentation

From Biopython
(Difference between revisions)
Jump to: navigation, search
m (Documentation: Tweak MediaWiki markup)
 
(9 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
==== Documentation ====
 
==== Documentation ====
New to BioPython? Check out the [[Getting_Started|Getting Started]] page, or follow one of the links below.
+
New to Biopython? Check out the [[Getting_Started|Getting Started]] page, or follow one of the links below.
  
* Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.  
+
* Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.
:[http://biopython.org/DIST/docs/install/Installation.html HTML] | [http://biopython.org/DIST/docs/install/Installation.pdf PDF]
+
*: [http://biopython.org/DIST/docs/install/Installation.html HTML] | [http://biopython.org/DIST/docs/install/Installation.pdf 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.
+
* 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
:[http://biopython.org/DIST/docs/tutorial/Tutorial.html HTML] | [http://biopython.org/DIST/docs/tutorial/Tutorial.pdf PDF]
+
*: [http://biopython.org/DIST/docs/tutorial/Tutorial.html HTML] | [http://biopython.org/DIST/docs/tutorial/Tutorial.pdf PDF]
 
* API documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc].
 
* API documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc].
:[http://biopython.org/DIST/docs/api HTML]
+
*: [http://biopython.org/DIST/docs/api HTML]
 
* Wiki documentation,
 
* Wiki documentation,
:* [[Seq]] and [[SeqRecord]] objects
+
** [[Seq]] and [[SeqRecord]] objects
:* [[SeqIO|Bio.SeqIO]] - sequence input/output
+
** [[SeqIO|Bio.SeqIO]] - sequence input/output
:* [[AlignIO|Bio.AlignIO]] - alignment input/output
+
** [[AlignIO|Bio.AlignIO]] - alignment input/output
:* [[PopGen|Bio.PopGen]] - population genetics
+
** [[PopGen|Bio.PopGen]] - population genetics
:* Biopython's [[BioSQL|BioSQL interface]]
+
** [[The Biopython Structural Bioinformatics FAQ|Bio.PDB]] - structural bioinformatics
* Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.  
+
** Biopython's [[BioSQL|BioSQL interface]]
:[http://biopython.org/DIST/docs/biosql/python_biosql_basic.html HTML] | [http://biopython.org/DIST/docs/biosql/python_biosql_basic.pdf PDF]
+
* 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.  
+
*: [http://biopython.org/DIST/docs/biosql/python_biosql_basic.html HTML] | [http://biopython.org/DIST/docs/biosql/python_biosql_basic.pdf PDF]
:[http://biopython.org/DIST/docs/cluster/cluster.pdf PDF]
+
* Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface.
 +
*: [http://biopython.org/DIST/docs/cluster/cluster.pdf PDF]
 
* Cookbook-style documentation:
 
* Cookbook-style documentation:
:*[[:Category:Cookbook|Cookbook documentation]] (on the wiki)
+
**[[:Category:Cookbook|Cookbook documentation]] (on the wiki)
:*The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).  
+
**The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
::[http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf PDF]
+
*: [http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf PDF]
:*Working with restriction enzymes.  
+
**Working with restriction enzymes.
::[http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]
+
*: [http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]
  
 
==== Documentation for Developers ====
 
==== Documentation for Developers ====
Line 36: Line 37:
  
 
* Andrew Dalke taught an introduction to programming for Bioinformatics in Python class at the National Bioinformatics Network in South Africa.
 
* 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/
+
*: http://www.dalkescientific.com/writings/NBN/
 
* Ravinder Singh and Scott Kelley teach a Bioinformatics course using Biopython at the University of Colorado.
 
* Ravinder Singh and Scott Kelley teach a Bioinformatics course using Biopython at the University of Colorado.
:http://mcdb.colorado.edu/courses/6440/index.html
+
*: 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.
 
* 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/
+
*: http://www.pasteur.fr/formation/infobio/python/
  
 
==== Papers ====
 
==== Papers ====
Line 59: Line 60:
 
#CockEtAl2009b pmid=20015970
 
#CockEtAl2009b pmid=20015970
 
// This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS
 
// This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS
 +
#TalevichEtAl2012 pmid=22909249
 +
// This describes the Bio.Phylo and Bio.Phylo.PAML modules.
 
</biblio>
 
</biblio>
  
 
==== Presentations ====
 
==== Presentations ====
  
 +
 +
* BOSC 2013 presentation "Biopython Project Update"
 +
*: [http://www.open-bio.org/bosc2013/day1/BOSC2013_Biopython_Update_-_Peter_Cock.pdf PDF] | [http://www.slideshare.net/pjacock/biopython-update-bosc2013/ Flash version]
 +
* BOSC 2012 presentation "Biopython Project Update"
 +
*: [http://www.slideshare.net/jandot/e-talevich-biopython-projectupdate Flash version]
 +
* BOSC 2011 presentation "Biopython Project Update"
 +
*: [http://www.slideshare.net/bosc2011/talk6-biopython-bosc2011 Flash version]
 +
* BOSC 2010 presentation "Biopython Project Update"
 +
*: [http://www.slideshare.net/chapmanb/biopython-at-bosc-2010 Flash version]
 
* July 2010 - EuroSciPy2010, Paris
 
* July 2010 - EuroSciPy2010, Paris
:[http://biopython.org/DIST/docs/presentations/Biopython_EuroSciPy2010.pdf PDF]
+
*: [http://biopython.org/DIST/docs/presentations/Biopython_EuroSciPy2010.pdf PDF]
 
* February 2010 Biopython workshop at the University of Georgia
 
* February 2010 Biopython workshop at the University of Georgia
:[http://etal.myweb.uga.edu/biopywork.pdf PDF] | [http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga Flash version]
+
*: [http://etal.myweb.uga.edu/biopywork.pdf PDF] | [http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga Flash version]
 
* BOSC 2009 presentation "Biopython Project Update"
 
* 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]
+
*: [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 June 2009 - Second generation sequence data and Biopython
 
* Scottish Bioinformatics Forum NextGenBug meeting June 2009 - 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
 
* 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)
+
*: [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]
 
* BOSC 2007 presentation "Biopython Project Update"
 
* BOSC 2007 presentation "Biopython Project Update"
:[http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2007.pdf PDF] | [http://www.slideshare.net/bosc/biopython Flash version]
+
*: [http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2007.pdf PDF] | [http://www.slideshare.net/bosc/biopython Flash version]
 
* March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.
 
* March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.
:[http://biopython.org/DIST/docs/presentations/biopython_exelixis.pdf PDF] | [http://biopython.org/DIST/docs/presentations/biopython_exelixis.tar.gz tarball with LaTeX source]
+
*: [http://biopython.org/DIST/docs/presentations/biopython_exelixis.pdf PDF] | [http://biopython.org/DIST/docs/presentations/biopython_exelixis.tar.gz tarball with LaTeX source]
 
* 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 (old).
 
* 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 (old).
 
* 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]
  
 
==== Logo ====
 
==== Logo ====
  
 
Read more about the [[Logo|Biopython logo]].
 
Read more about the [[Logo|Biopython logo]].

Latest revision as of 19:09, 8 March 2015

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

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:

Error fetching PMID 19304878:
Error fetching PMID 14630660:
Error fetching PMID 14871861:
Error fetching PMID 16377612:
Error fetching PMID 20015970:
Error fetching PMID 22909249:
  1. Error fetching PMID 19304878: [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. Error fetching PMID 14630660: [HamelryckAndManderick2003]
    The Bio.PDB module is described here.

  4. Error fetching PMID 14871861: [DeHoonEtAl2004]
    The Bio.Cluster module is described here.

  5. Error fetching PMID 16377612: [PritchardEtAl2006]
    This describes GenomeDiagram, which has now been integrated into Biopython.

  6. Error fetching PMID 20015970: [CockEtAl2009b]
    This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS

  7. Error fetching PMID 22909249: [TalevichEtAl2012]
    This describes the Bio.Phylo and Bio.Phylo.PAML modules.

All Medline abstracts: PubMed HubMed

Presentations

  • BOSC 2013 presentation "Biopython Project Update"
    PDF | Flash version
  • BOSC 2012 presentation "Biopython Project Update"
    Flash version
  • BOSC 2011 presentation "Biopython Project Update"
    Flash version
  • BOSC 2010 presentation "Biopython Project Update"
    Flash version
  • July 2010 - EuroSciPy2010, Paris
    PDF
  • February 2010 Biopython workshop at the University of Georgia
    PDF | Flash version
  • BOSC 2009 presentation "Biopython Project Update"
    PDF | Flash version
  • Scottish Bioinformatics Forum NextGenBug meeting June 2009 - 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