Documentation

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* 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 main 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].
 +
:[http://biopython.org/DIST/docs/api HTML]
 +
* Wiki documentation,
 +
:* [[Seq]] and [[SeqRecord]] objects
 +
:* [[SeqIO|Bio.SeqIO]] - sequence input/output
 +
:* [[AlignIO|Bio.AlignIO]] - alignment input/output
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:* [[PopGen|Bio.PopGen]] - population genetics
 +
:* [[The Biopython Structural Bioinformatics FAQ|Bio.PDB]] - structural bioinformatics
 +
:* Biopython's [[BioSQL|BioSQL interface]]
 
* Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.  
 
* Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.  
 
:[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/biosql/python_biosql_basic.html HTML] | [http://biopython.org/DIST/docs/biosql/python_biosql_basic.pdf PDF]
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:[http://biopython.org/DIST/docs/cluster/cluster.pdf PDF]
 
:[http://biopython.org/DIST/docs/cluster/cluster.pdf PDF]
 
* Cookbook-style documentation:
 
* Cookbook-style documentation:
:*Writing Tests for Biopython.
+
:*[[:Category:Cookbook|Cookbook documentation]] (on the wiki)
::[http://biopython.org/DIST/docs/cookbook/biopython_test.html HTML] | [http://biopython.org/DIST/docs/cookbook/biopython_test.pdf PDF]
+
:*Logistic Regression supervised learning.
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::[http://biopython.org/DIST/docs/cookbook/LogisticRegression.html HTML] | [http://biopython.org/DIST/docs/cookbook/LogisticRegression.pdf PDF]
+
 
:*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]
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::[http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]
 
::[http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]
  
==== API Documentation ====
+
==== Documentation for Developers ====
  
* Documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc].
+
* List of [[Active projects]] to get involved with.
:[http://biopython.org/DIST/docs/api/public/trees.html HTML]
+
* How to [[Contributing|contribute code]] to Biopython.
 +
* [[Deprecation policy]]
 +
* Instructions for [[building a release]] of Biopython.
 +
* Details about the biopython.org [[website]].
  
 
==== Online Course Notes ====
 
==== Online Course Notes ====
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* 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/
* Katja Schuerer and Catherine Letondal teach a Bioinformatics course in Python at the Pasteur Institute.
 
:http://www.pasteur.fr/recherche/unites/sis/formation/python/
 
 
* 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
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==== Papers ====
 
==== Papers ====
  
*Thomas wrote an applications note<cite>Hamelryck</cite> for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
+
We have a separate list of [[Publications|publications citing or using Biopython]].  If you use Biopython in a scientific publication, please cite the application note <cite>CockEtAl2009</cite> and/or one of the other listed papers:
 +
 
 
<biblio>
 
<biblio>
#Hamelryck pmid=14630660
+
#CockEtAl2009 pmid=19304878
 +
// This application note covers the whole of Biopython
 +
#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]
 +
// This served as the official project announcement.
 +
#HamelryckAndManderick2003 pmid=14630660
 +
// The Bio.PDB module is described here.
 +
#DeHoonEtAl2004 pmid=14871861
 +
// The Bio.Cluster module is described here.
 +
#PritchardEtAl2006 pmid=16377612
 +
// This describes GenomeDiagram, which has now been integrated into Biopython.
 +
#CockEtAl2009b pmid=20015970
 +
// 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>
*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]
 
  
 
==== Presentations ====
 
==== Presentations ====
  
 +
* 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
 +
:[http://biopython.org/DIST/docs/presentations/Biopython_EuroSciPy2010.pdf PDF]
 +
* 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]
 +
* 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 June 2009 - Second generation sequence data and Biopython
 +
:[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"
 +
:[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"
:PDF pending...
+
:[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.
+
* 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]
  
==== Documentation for Developers ====
+
==== Logo ====
  
* Details about the biopython.org [[website]].
+
Read more about the [[Logo|Biopython logo]].
* How to [[Contributing|contribute code]] to Biopython.
+
* Instructions for [[building a release]] of Biopython.
+

Revision as of 01:49, 26 March 2013

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/
  • 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:

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 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.

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