Documentation
(Difference between revisions)
(→Documentation) |
(URL does not need to contain 'static') |
||
| Line 2: | Line 2: | ||
* 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.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/install/Installation.html HTML] | [http://biopython.open-bio.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 main 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.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/tutorial/Tutorial.html HTML] | [http://biopython.open-bio.org/DIST/docs/tutorial/Tutorial.pdf PDF] |
* 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.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/biosql/python_biosql_basic.html HTML] | [http://biopython.open-bio.org/DIST/docs/biosql/python_biosql_basic.pdf PDF] |
* Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface. | * Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface. | ||
| − | :[http://biopython.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/cluster/cluster.pdf PDF] |
* Cookbook-style documentation: | * Cookbook-style documentation: | ||
:*Converting GenBank (and other formats) to Fasta. | :*Converting GenBank (and other formats) to Fasta. | ||
| − | ::[http://biopython.open-bio.org | + | ::[http://biopython.open-bio.org/DIST/docs/cookbook/genbank_to_fasta.html HTML] | [http://biopython.open-bio.org/DIST/docs/cookbook/genbank_to_fasta.pdf PDF] |
:*Writing Tests for Biopython. | :*Writing Tests for Biopython. | ||
| − | ::[http://biopython.open-bio.org | + | ::[http://biopython.open-bio.org/DIST/docs/cookbook/biopython_test.html HTML] | [http://biopython.open-bio.org/DIST/docs/cookbook/biopython_test.pdf PDF] |
:*Logistic Regression supervised learning. | :*Logistic Regression supervised learning. | ||
| − | ::[http://biopython.open-bio.org | + | ::[http://biopython.open-bio.org/DIST/docs/cookbook/LogisticRegression.html HTML] | [http://biopython.open-bio.org/DIST/docs/cookbook/LogisticRegression.pdf PDF] |
:*The Biopython Structural Bioinformatics FAQ. | :*The Biopython Structural Bioinformatics FAQ. | ||
| − | ::[http://biopython.open-bio.org | + | ::[http://biopython.open-bio.org/DIST/docs/cookbook/biopdb_faq.pdf PDF] |
:*Working with restriction enzymes. | :*Working with restriction enzymes. | ||
| − | ::[http://biopython.open-bio.org | + | ::[http://biopython.open-bio.org/DIST/docs/cookbook/Restriction.html HTML] |
==== API Documentation ==== | ==== API Documentation ==== | ||
* Documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc]. | * Documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc]. | ||
| − | :[http://biopython.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/api/public/trees.html HTML] |
==== Online Course Notes ==== | ==== Online Course Notes ==== | ||
| Line 42: | Line 42: | ||
:[http://bioinformatics.oupjournals.org/cgi/content/abstract/19/17/2308 Abstract and links to full text] | :[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. | *Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000. | ||
| − | :[http://biopython.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.open-bio.org/DIST/docs/acm/ACMbiopy.pdf 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. | ||
| − | :[http://biopython.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/presentations/biopython_exelixis.pdf PDF] | [http://biopython.open-bio.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.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/presentations/bosc_biopython.pdf PDF] | [http://biopython.open-bio.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. | ||
| − | :[http://biopython.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/presentations/scripting.pdf PDF] | [http://biopython.open-bio.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. | ||
| − | :[http://biopython.open-bio.org | + | :[http://biopython.open-bio.org/DIST/docs/presentations/biopython.pdf PDF] | [http://biopython.open-bio.org/DIST/docs/presentations/biopy_group.tar.gz tarball with LaTeX source] |
==== Documentation for Developers ==== | ==== Documentation for Developers ==== | ||
Revision as of 14:40, 30 May 2006
Contents |
Documentation
- 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.
- 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.
- Cookbook-style documentation:
- Converting GenBank (and other formats) to Fasta.
- Writing Tests for Biopython.
- Logistic Regression supervised learning.
- The Biopython Structural Bioinformatics FAQ.
- Working with restriction enzymes.
API Documentation
- Documentation for Biopython modules is generated directly from source code comments using Epydoc.
Online Course Notes
- Andrew Dalke taught an introduction to programming for Bioinformatics in Python class at the National Bioinformatics Network in South Africa.
- 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.
- 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.
Papers
- Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
- Brad and Jeff wrote a paper for the ACM SIG-BIO newsletter back in August of 2000.
Presentations
- March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.
- BOSC 2003 presentation about Biopython and using it for Laboratory Analysis Pipelines.
- General talk about scripting with Biopython based example of a primer design program.
- Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython.
Documentation for Developers
- Details about the biopython.org website.
- How to contribute code to Biopython.
- Instructions for building releases of Biopython.
