Documentation

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==== Documentation ====
 
==== Documentation ====
New to BioPython? Check out the [[Getting_Started|Getting Started]] page, or follow one of the links below.
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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.  
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* 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]
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*: [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.
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* 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]
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*: [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]
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*: [http://biopython.org/DIST/docs/api HTML]
 
* Wiki documentation,
 
* Wiki documentation,
:* [[Seq]] and [[SeqRecord]] objects
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** [[Seq]] and [[SeqRecord]] objects
:* [[SeqIO|Bio.SeqIO]] - sequence input/output
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** [[SeqIO|Bio.SeqIO]] - sequence input/output
:* [[AlignIO|Bio.AlignIO]] - alignment input/output
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** [[AlignIO|Bio.AlignIO]] - alignment input/output
:* [[PopGen|Bio.PopGen]] - population genetics
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** [[PopGen|Bio.PopGen]] - population genetics
:* Biopython's [[BioSQL|BioSQL interface]]
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** [[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.  
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** 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]
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* 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.  
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*: [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]
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* 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)
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**[[:Category:Cookbook|Cookbook documentation]] (on the wiki)
:*The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).  
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**The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
::[http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf PDF]
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*: [http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf PDF]
:*Working with restriction enzymes.  
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**Working with restriction enzymes.
::[http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]
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*: [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/
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*: 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
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*: 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/
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*: 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]
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* 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]
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*: [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]
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*: [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]
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*: [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]
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*: [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)
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*: [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]
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*: [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]
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*: [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]
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*: [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]
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*: [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]
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*: [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]
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*: [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:

  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.

  6. Cock PJ, Fields CJ, Goto N, Heuer ML, and Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010 Apr; 38(6) 1767-71. doi:10.1093/nar/gkp1137 pmid:20015970. PubMed HubMed [CockEtAl2009b]
    This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS

  7. Talevich E, Invergo BM, Cock PJ, and Chapman BA. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 2012 Aug 21; 13 209. doi:10.1186/1471-2105-13-209 pmid:22909249. PubMed HubMed [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.

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