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==== Documentation ====
 
==== Documentation ====
 +
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 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
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:* [[SeqIO|Bio.SeqIO]] - sequence input/output
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:* [[AlignIO|Bio.AlignIO]] - alignment input/output
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:* [[PopGen|Bio.PopGen]] - population genetics
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:* 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:
:*Converting GenBank (and other formats) to Fasta.
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:*[[:Category:Cookbook|Cookbook documentation]] (on the wiki)
::[http://biopython.org/DIST/docs/cookbook/genbank_to_fasta.html HTML] | [http://biopython.org/DIST/docs/cookbook/genbank_to_fasta.pdf PDF]
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:*The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).  
:*Writing Tests for Biopython.
+
::[http://biopython.org/DIST/docs/cookbook/biopython_test.html HTML] | [http://biopython.org/DIST/docs/cookbook/biopython_test.pdf PDF]
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:*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.  
+
 
::[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]
  
==== 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]
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* 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 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:
:[http://bioinformatics.oupjournals.org/cgi/content/abstract/19/17/2308 Abstract and links to full text]
+
 
*Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
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<biblio>
:[http://biopython.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.org/DIST/docs/acm/ACMbiopy.pdf PDF]
+
#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
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// This describes the Bio.Phylo and Bio.Phylo.PAML modules.
 +
</biblio>
  
 
==== 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"
 +
:[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]].
:[[website|HTML]]
+
* How to contribute code to Biopython.
+
:[[Contributing|HTML]]
+
* Instructions for building releases of Biopython.
+
:[[Building a release|HTML]]
+

Revision as of 17:57, 23 August 2012

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:

  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 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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