Documentation

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==== Documentation ====
 
==== Documentation ====
  
:* Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself. HTML | PDF
+
:* Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.  
:* 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. HTML | PDF
+
::HTML | PDF
:* Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL. HTML | 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.  
:* Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface. PDF
+
::HTML | PDF
 +
:* 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-style documentation:
:**Converting GenBank (and other formats) to Fasta. HTML | PDF
+
:**Converting GenBank (and other formats) to Fasta.  
:**Writing Tests for Biopython. HTML | PDF
+
:::HTML | PDF
:**Logistic Regression supervised learning. HTML | PDF
+
:**Writing Tests for Biopython.  
:**The Biopython Structural Bioinformatics FAQ. PDF
+
:::HTML | PDF
:**Working with restriction enzymes. HTML
+
:**Logistic Regression supervised learning.  
 +
:::HTML | PDF
 +
:**The Biopython Structural Bioinformatics FAQ.  
 +
:::PDF
 +
:**Working with restriction enzymes.  
 +
:::HTML
  
 
==== API Documentation ====
 
==== API Documentation ====
Line 18: Line 27:
 
==== Online Course Notes ====
 
==== Online Course Notes ====
  
    * 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/
    * Katja Schuerer and Catherine Letondal teach a Bioinformatics course in Python at the Pasteur Institute.
+
:* 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://www.pasteur.fr/recherche/unites/sis/formation/python/
+
:* 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/
    * 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
+
==== Papers ====
  
    * Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
+
:*Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures. Abstract and links to full text
      Abstract and links to full text
+
:* Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000. HTML | PDF
    * Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
+
      HTML | PDF
+
  
Presentations
+
==== Presentations ====
  
    * 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.
      PDF | tarball with LaTeX source
+
::PDF | 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.
      PDF | tarball with LaTeX source
+
::PDF | 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.
      PDF | tarball with LaTeX source
+
::PDF | 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.
      PDF | tarball with LaTex source
+
::PDF | tarball with LaTex source
  
Documentation for Developers
+
==== Documentation for Developers ====
  
    * Details about the biopython.org website.
+
:* Details about the biopython.org website.
      HTML
+
::HTML
    * How to contribute code to Biopython.
+
:* How to contribute code to Biopython.
      HTML
+
::HTML
    * Instructions for building releases of Biopython.
+
:* Instructions for building releases of Biopython.
      HTML
+
::HTML

Revision as of 19:44, 13 March 2006

Contents

Documentation

  • Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.
HTML | 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.
HTML | PDF
  • 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:
    • Converting GenBank (and other formats) to Fasta.
HTML | PDF
    • Writing Tests for Biopython.
HTML | PDF
    • Logistic Regression supervised learning.
HTML | PDF
    • The Biopython Structural Bioinformatics FAQ.
PDF
    • Working with restriction enzymes.
HTML

API Documentation

  • Documentation for Biopython modules is generated directly from source code comments using Epydoc. HTML

Online Course Notes

Papers

  • Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures. Abstract and links to full text
  • Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000. HTML | PDF

Presentations

  • 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.
PDF | tarball with LaTeX source
  • Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython.
PDF | tarball with LaTex source

Documentation for Developers

  • Details about the biopython.org website.
HTML
  • How to contribute code to Biopython.
HTML
  • Instructions for building releases of Biopython.
HTML
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