Biopython - User contributions [en]

Talk:Biopython

2012-11-04T00:46:48Z

Jason:

Testing edit access to biopython wiki -- --[[User:Chrisdag|Chrisdag]] 08:16, 1 July 2008 (EDT)
Testing x2 --[[User:Jason|jason]] 00:46, 4 November 2012 (UTC)

SeqIO dev

2007-04-13T20:41:19Z

Jason: /* Possible additional formats */ -- updated links with interwiki prefixes to bioperl site

This page is aimed at any developers or coders interesting in understanding or extending the new Sequence Input/Output interface for BioPython, [[SeqIO]].

The code has now been checked into [http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SeqIO/?cvsroot=biopython#dirlist CVS]. Related [http://bugzilla.open-bio.org/show_bug.cgi?id=2059 Bug 2059] has been resolved.

The code is already available in BioPython 1.43.

== Reading new file formats ==

'''Note:''' The details are still subject to change

To add support for reading a new file format, you must implement an iterator that expects a just file handle and returns SeqRecord objects. You may do this using:

* An iterator class subclassing something from Bio.SeqIO.Interfaces
* A generator function (using the yield keyword; suitable for simple formats)
* An ordinary function which returns an iterator. For example, you could build a list of SeqRecords and then turn it into an iterator using the iter() function.

You may accept additional ''optional'' arguments (an alphabet for example). However there ''must'' be one and only one required argument (the input file handle).

What you use as the SeqRecord's id, name and description will depend on the file format. Ideally you would use the accesion number for the id. This id should also be unique for each record (unless the records in the file are in themselves ambiguous).

When storing any annotations in the record's annotations dictionary follow the defacto standard laid down by the GenBank parser... I should try and document this more.

If the supplied file seems to be invalid, raise a SyntaxError exception.

== Writing new file formats ==

'''Note:''' The details are still subject to change

To add support for writing a new file format you should write a sub class of one of the writer objects in Bio.SeqIO.Interfaces

Then, the new format must be added to the relevant dictionary mappings in Bio/SeqIO/__init__.py so that the '''Bio.SeqIO.parse''' and '''Bio.SeqIO.write''' functions are aware of it.

If the supplied records cannot be written to this file format, raise a ValueError exception. Where appropriate, please use the following wording:

<python>
raise ValueError("Must have at least one sequence")
raise ValueError("Sequences must all be the same length")
raise ValueError("Duplicate record identifier: %s" % ...)
...
</python>

ToDo - Defined standard exceptions in Bio.SeqIO itself?

== Possible additional formats ==

There are existing parsers in BioPython for the following file formats, which could be integrated into Bio.SeqIO if appropriate.

=== NBRF / PIR format ===

Bio.NBRF has a Martel parser for [[bp:PIR sequence format|PIR sequence format]], which is similar to the [[bp:FASTA sequence format|FASTA format]]. It would need addition work to return SeqRecords. It might be easier to extend to reuse the Bio.SeqIO fasta code instead.

There is also [http://www.psc.edu/general/software/packages/seq-intro/nbrffile.html PSC documentation].

=== KEGG format ===

Can Bio.KEGG parse files in [[bp:KEGG sequence format|KEGG format]]?

=== PHD sequencing files from PHRED ===

Bio.Sequencing.PHD has a Martel parser for [[bp:PHD sequence format|PHD format]], also used by the tools PHRAP and CONSED.

=== MASE alignment format ===

Bio.IntelliGenetics seems to use Martel parse MASE format files into its own record object. It could be extended to return SeqRecord objects. See:

http://pbil.univ-lyon1.fr/help/formats.html

=== MEME format ===

Bio.MEME has a parser for this file format, which at first glance looks like it could be treated like an alignment format.

http://meme.sdsc.edu

=== BLAST results ===

Pairwise alignments from the BLAST suite could be turned into two SeqRecord objects with gapped sequences. Is this useful?

=== COMPASS pairwise alignment format ===

Bio.Compass can parse the pairwise alignments from COMPASS. The output is similar to BLAST in many ways. Again, is getting the results as SeqRecord objects useful?

SeqIO dev

2007-04-13T20:35:54Z

Jason: /* NBRF / PIR format */

This page is aimed at any developers or coders interesting in understanding or extending the new Sequence Input/Output interface for BioPython, [[SeqIO]].

The code has now been checked into [http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SeqIO/?cvsroot=biopython#dirlist CVS]. Related [http://bugzilla.open-bio.org/show_bug.cgi?id=2059 Bug 2059] has been resolved.

The code is already available in BioPython 1.43.

== Reading new file formats ==

'''Note:''' The details are still subject to change

To add support for reading a new file format, you must implement an iterator that expects a just file handle and returns SeqRecord objects. You may do this using:

* An iterator class subclassing something from Bio.SeqIO.Interfaces
* A generator function (using the yield keyword; suitable for simple formats)
* An ordinary function which returns an iterator. For example, you could build a list of SeqRecords and then turn it into an iterator using the iter() function.

You may accept additional ''optional'' arguments (an alphabet for example). However there ''must'' be one and only one required argument (the input file handle).

What you use as the SeqRecord's id, name and description will depend on the file format. Ideally you would use the accesion number for the id. This id should also be unique for each record (unless the records in the file are in themselves ambiguous).

When storing any annotations in the record's annotations dictionary follow the defacto standard laid down by the GenBank parser... I should try and document this more.

If the supplied file seems to be invalid, raise a SyntaxError exception.

== Writing new file formats ==

'''Note:''' The details are still subject to change

To add support for writing a new file format you should write a sub class of one of the writer objects in Bio.SeqIO.Interfaces

Then, the new format must be added to the relevant dictionary mappings in Bio/SeqIO/__init__.py so that the '''Bio.SeqIO.parse''' and '''Bio.SeqIO.write''' functions are aware of it.

If the supplied records cannot be written to this file format, raise a ValueError exception. Where appropriate, please use the following wording:

<python>
raise ValueError("Must have at least one sequence")
raise ValueError("Sequences must all be the same length")
raise ValueError("Duplicate record identifier: %s" % ...)
...
</python>

ToDo - Defined standard exceptions in Bio.SeqIO itself?

== Possible additional formats ==

There are existing parsers in BioPython for the following file formats, which could be integrated into Bio.SeqIO if appropriate.

=== NBRF / PIR format ===

Bio.NBRF has a Martel parser for this file format, which is similar to the FASTA format. It would need addition work to return SeqRecords. It might be easier to extend to reuse the Bio.SeqIO fasta code instead.

* BioPerl description of [[bp:PIR_sequence_format|PIR sequence format]]
* [http://www.psc.edu/general/software/packages/seq-intro/nbrffile.html PSC documentation]

=== KEGG format ===

Can Bio.KEGG parse these files?

http://www.bioperl.org/wiki/KEGG_sequence_format

=== PHD sequencing files from PHRED ===

Bio.Sequencing.PHD has a Martel parser for this file format, also used by the tools PHRAP and CONSED.

http://www.bioperl.org/wiki/PHD_sequence_format

=== MASE alignment format ===

Bio.IntelliGenetics seems to use Martel parse MASE format files into its own record object. It could be extended to return SeqRecord objects. See:

http://pbil.univ-lyon1.fr/help/formats.html

=== MEME format ===

Bio.MEME has a parser for this file format, which at first glance looks like it could be treated like an alignment format.

http://meme.sdsc.edu

=== BLAST results ===

Pairwise alignments from the BLAST suite could be turned into two SeqRecord objects with gapped sequences. Is this useful?

=== COMPASS pairwise alignment format ===

Bio.Compass can parse the pairwise alignments from COMPASS. The output is similar to BLAST in many ways. Again, is getting the results as SeqRecord objects useful?

News

2006-06-05T15:21:46Z

Jason:

Our News/blog server is available at [http://biopython.org/news/ biopython.org/news/].

There is also a (currently separate) news server for all the [[obf:OBF|OBF]] projects at [http://news.open-bio.org news.open-bio.org].

{| border="1" width="800px"
|- style="background-color:#ccccff; text-align:center"
! Biopython News
|-
| [http://biopython.org/news/feed RSS feed]
|-
| <rss>http://biopython.org/news/feed|date|charset=utf-8|max=10</rss>
|- style="background-color:#ccccff; text-align:center"
! Recent [[Mailing lists|Mailing list]] posts
|-
|}

MediaWiki:Sidebar

2006-06-05T15:18:22Z

Jason:

MediaWiki:Sidebar

2006-06-05T15:18:13Z

Jason: remove the donations page and upcase Do

Documentation

2006-06-05T15:14:38Z

Jason: /* Papers */

==== Documentation ====

* 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]
* 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.org/DIST/docs/tutorial/Tutorial.html HTML] | [http://biopython.org/DIST/docs/tutorial/Tutorial.pdf PDF]
* 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]
* 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:
:*Converting GenBank (and other formats) to Fasta.
::[http://biopython.org/DIST/docs/cookbook/genbank_to_fasta.html HTML] | [http://biopython.org/DIST/docs/cookbook/genbank_to_fasta.pdf PDF]
:*Writing Tests for Biopython.
::[http://biopython.org/DIST/docs/cookbook/biopython_test.html HTML] | [http://biopython.org/DIST/docs/cookbook/biopython_test.pdf PDF]
:*Logistic Regression supervised learning.
::[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]
:*Working with restriction enzymes.
::[http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]

==== API Documentation ====

* Documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc].
:[http://biopython.org/DIST/docs/api/public/trees.html HTML]

==== 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/
* 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.
: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 ====

*Thomas wrote an applications note<cite>Hamelryck</cite> for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
<biblio>
#Hamelryck pmid=14630660
</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 ====

* 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]
* 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]
* General talk about scripting with Biopython based example of a primer design program.
:[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.
:[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 ====

* Details about the biopython.org [[website]].
* How to [[Contributing|contribute code]] to Biopython.
* Instructions for [[building a release]] of Biopython.

Documentation

2006-06-05T15:13:04Z

Jason: /* Documentation for Developers */

==== Documentation ====

* 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]
* 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.org/DIST/docs/tutorial/Tutorial.html HTML] | [http://biopython.org/DIST/docs/tutorial/Tutorial.pdf PDF]
* 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]
* 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:
:*Converting GenBank (and other formats) to Fasta.
::[http://biopython.org/DIST/docs/cookbook/genbank_to_fasta.html HTML] | [http://biopython.org/DIST/docs/cookbook/genbank_to_fasta.pdf PDF]
:*Writing Tests for Biopython.
::[http://biopython.org/DIST/docs/cookbook/biopython_test.html HTML] | [http://biopython.org/DIST/docs/cookbook/biopython_test.pdf PDF]
:*Logistic Regression supervised learning.
::[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]
:*Working with restriction enzymes.
::[http://biopython.org/DIST/docs/cookbook/Restriction.html HTML]

==== API Documentation ====

* Documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc].
:[http://biopython.org/DIST/docs/api/public/trees.html HTML]

==== 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/
* 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.
: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 ====

*Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
:[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.
:[http://biopython.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.org/DIST/docs/acm/ACMbiopy.pdf PDF]

==== Presentations ====

* 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]
* 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]
* General talk about scripting with Biopython based example of a primer design program.
:[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.
:[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 ====

* Details about the biopython.org [[website]].
* How to [[Contributing|contribute code]] to Biopython.
* Instructions for [[building a release]] of Biopython.

Biopython

2006-06-05T15:11:58Z

Jason: /* Download Current Release */

=== About the Biopython project ===

The Biopython Project is an international association of developers of freely available [http://www.python.org Python] tools for computational molecular biology.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the [http://www.biopython.org/DIST/LICENSE Biopython License], which is extremely liberal and compatible with almost every license in the world. We work along with the [http://open-bio.org Open Bioinformatics Foundation], who generously provide web and CVS space for the project.

=== Download Current Release ===

The latest release is Biopython 1.41, released on 28 Oct 2005. Get it from our [[Download]] page.

See the [[News|News page]] as well.

Mailing lists

2006-05-30T14:42:36Z

Jason: main mailing list host is 'lists.open-bio.org' although biopython.org is alias (but due to current in-between with hostnames lists.open-bio is the appropriate one)

=== Announcement List ===
[mailto:biopython-announce@biopython.org biopython-announce@biopython.org]

Low volume moderated list, providing announcements of major Biopython releases and upgrades.

[http://lists.open-bio.org/mailman/listinfo/biopython-announce/ List Website] | [http://lists.open-bio.org/pipermail/biopython-announce/ Web Archive]

=== Discussion List ===
[mailto:biopython@biopython.org biopython@biopython.org]

Unmoderated list for use, comments, help, and other things related to Biopython.

[http://lists.open-bio.org/mailman/listinfo/biopython/ List Website] | [http://lists.open-bio.org/pipermail/biopython/ Web Archive]

=== Development List ===
[mailto:biopython-dev@biopython.org biopython-dev@biopython.org]

Unmoderated list for Biopython developers and interested people.

[http://lists.open-bio.org/mailman/listinfo/biopython-dev/ List Website] | [http://lists.open-bio.org/pipermail/biopython-dev/ Web Archive]

=== Searching ===
[http://search.open-bio.org/cgi-bin/mail-search.cgi Search the mailing list archives.]

Documentation

2006-05-30T14:40:07Z

Jason: URL does not need to contain 'static'

==== Documentation ====

* Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.
:[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.
:[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.
:[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.
:[http://biopython.open-bio.org/DIST/docs/cluster/cluster.pdf PDF]
* Cookbook-style documentation:
:*Converting GenBank (and other formats) to Fasta.
::[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.
::[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.
::[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.
::[http://biopython.open-bio.org/DIST/docs/cookbook/biopdb_faq.pdf PDF]
:*Working with restriction enzymes.
::[http://biopython.open-bio.org/DIST/docs/cookbook/Restriction.html HTML]

==== API Documentation ====

* Documentation for Biopython modules is generated directly from source code comments using [http://epydoc.sourceforge.net/ Epydoc].
:[http://biopython.open-bio.org/DIST/docs/api/public/trees.html HTML]

==== 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/
* 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.
: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 ====

*Thomas wrote an applications note for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
:[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.
:[http://biopython.open-bio.org/DIST/docs/acm/ACMbiopy.html HTML] | [http://biopython.open-bio.org/DIST/docs/acm/ACMbiopy.pdf PDF]

==== Presentations ====

* March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.
:[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.
:[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.
:[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.
:[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 ====

* Details about the biopython.org website.
:[[website|HTML]]
* How to contribute code to Biopython.
:[[Contributing|HTML]]
* Instructions for building releases of Biopython.
:[[Building a release|HTML]]

Talk:Download

2006-05-30T14:25:44Z

Jason:

You could also just link to the [http://biopython.open-bio.org/DIST DIST] directory and let that webserver provide the list of files rather than having to keep the list of old releases up to date. --[[User:Jason|Jason]] 10:25, 30 May 2006 (EDT)

Download

2006-05-30T14:25:00Z

Jason: don't put 'static' in the URL that is handled by apache

= Current Release -- 1.41 -- 28 Oct 2005 =

=== Installation Instructions ===

* [http://biopython.open-bio.org/DIST/docs/install/Installation.html HTML Installation Instructions]
* [http://biopython.open-bio.org/DIST/docs/install/Installation.pdf PDF Installation Instructions]

=== Files ===

* Source Tarball -- [http://biopython.open-bio.org/DIST/biopython-1.41.tar.gz biopython-1.41.tar.gz] 3,718 Kb
* Source Zip File -- [http://biopython.open-bio.org/DIST/biopython-1.41.zip biopython-1.41.zip] 4,240 Kb
* Windows Installer for Python 2.3 -- [http://biopython.open-bio.org/DIST/biopython-1.41.win32-py2.3.exe biopython-1.41.win32-py2.3.exe] 1,038 Kb
* Windows Installer for Python 2.4 -- [http://biopython.open-bio.org/DIST/biopython-1.41.win32-py2.4.exe biopython-1.41.win32-py2.4.exe] 1,042 Kb

=== Required Software ===

* [http://www.python.org Python 2.3 or above]
* [http://www.python.org/doc/current/inst/inst.html A C compiler -- you need a C compiler supported by distutils. gcc will work fine on UNIX-like platforms]
* [http://www.lemburg.com/files/python/mxTextTools.html mxTextTools]
* [http://sourceforge.net/projects/numpy Numerical Python (version 24.2 recommended)]

=== Optional Software ===

* [http://www.reportlab.org/downloads.html ReportLab -- for pdf graphics code]
* [http://sourceforge.net/projects/mysql-python MySQLdb]

= Biopython-corba =

=== Files ===

* Source tarball -- [http://biopython.open-bio.org/DIST/biopython-corba-0.3.0.tar.gz biopython-corba-0.3.0.tar.gz] 344Kb
* Source Zip File -- [http://biopython.open-bio.org/DIST/biopython-corba-0.3.0.zip biopython-corba-0.3.0.zip] 378Kb

=== Required Software ===

* [http://omniorb.sourceforge.net omniORBpy]
* [http://fnorb.sourceforge.net Fnorb]
* [http://sourceforge.net/projects/orbit-python orbit-python]

= Old Releases =

* [http://biopython.open-bio.org/DIST/biopython-1.40b.tar.gz biopython-1.40b.tar.gz] 3,437 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.40b.zip biopython-1.40b.zip] 3,267 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.40b.win32-py2.3.exe biopython-1.40b.win32-py2.3.exe] 1,019 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.40b.win32-py2.4.exe biopython-1.40b.win32-py2.4.exe] 1,023 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.30.tar.gz biopython-1.30.tar.gz] 3,186 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.24.tar.gz biopython-1.24.tar.gz] 3,081 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.24.zip biopython-1.24.zip] 3,623 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.24.win32-py2.2.exe biopython-1.24.win32-py2.2.exe] 892 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.24.win32-py2.3.exe biopython-1.24.win32-py2.3.exe] 894 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.23.tar.gz biopython-1.23.tar.gz] 2,241 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.23.zip biopython-1.23.zip] 2,719 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.23.win32-py2.2.exe biopython-1.23.win32-py2.2.exe] 833 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.23.win32-py2.3.exe biopython-1.23.win32-py2.3.exe] 842 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.22.tar.gz biopython-1.22.tar.gz] 2,214 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.22.zip biopython-1.22.zip] 2,691 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.21.tar.gz biopython-1.21.tar.gz] 2,214 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.21.zip biopython-1.21.zip] 2,897 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.21.win32-py2.2.exe biopython-1.21.win32-py2.2.exe] 770 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.21.win32-py2.3.exe biopython-1.21.win32-py2.3.exe] 832 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.20.tar.gz biopython-1.20.tar.gz] 2,101 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.20.zip biopython-1.20.zip] 2,602 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.10.tar.gz biopython-1.10.tar.gz] 1,811 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.10.zip biopython-1.10.zip] 2,300 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.10.win32-py2.2.exe biopython-1.10.win32-py2.2.exe] 1,199 Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a4.tar.gz biopython-1.00a4.tar.gz] 1,739Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a4.zip biopython-1.00a4.zip] 2,121Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a4.win32-py2.0.exe biopython-1.00a4.win32-py2.0.exe] 835Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a4.win32-py2.1.exe biopython-1.00a4.win32-py2.1.exe] 837Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a4.win32-py2.2.exe biopython-1.00a4.win32-py2.2.exe] 838Kb
* [http://biopython.open-bio.org/DIST/MacBiopython-1.00a4.sit MacBiopython-1.00a4.sit] 2.2Mb
* [http://biopython.open-bio.org/DIST/biopython-1.00a3.tar.gz biopython-1.00a3.tar.gz] 1,816Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a3.zip biopython-1.00a3.zip] 2,165Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a3.win32-py2.0.exe biopython-1.00a3.win32-py2.0.exe] 583Kb
* [http://biopython.open-bio.org/DIST/biopython-1.00a3.win32-py2.1.exe biopython-1.00a3.win32-py2.1.exe] 585Kb
* [http://biopython.open-bio.org/DIST/Macbiopython-1.00a3.sit.bin Macbiopython-1.00a3.sit.bin] 1926Kb

Download

2006-05-30T14:22:58Z

Jason: /* Files */ - don't put static in the URL this is handled by the URL rewrite

= Current Release -- 1.41 -- 28 Oct 2005 =

=== Installation Instructions ===

* [http://biopython.open-bio.org/DIST/docs/install/Installation.html HTML Installation Instructions]
* [http://biopython.open-bio.org/DIST/docs/install/Installation.pdf PDF Installation Instructions]

=== Files ===

* Source Tarball -- [http://biopython.open-bio.org/DIST/biopython-1.41.tar.gz biopython-1.41.tar.gz] 3,718 Kb
* Source Zip File -- [http://biopython.open-bio.org/DIST/biopython-1.41.zip biopython-1.41.zip] 4,240 Kb
* Windows Installer for Python 2.3 -- [http://biopython.open-bio.org/DIST/biopython-1.41.win32-py2.3.exe biopython-1.41.win32-py2.3.exe] 1,038 Kb
* Windows Installer for Python 2.4 -- [http://biopython.open-bio.org/DIST/biopython-1.41.win32-py2.4.exe biopython-1.41.win32-py2.4.exe] 1,042 Kb

=== Required Software ===

* [http://www.python.org Python 2.3 or above]
* [http://www.python.org/doc/current/inst/inst.html A C compiler -- you need a C compiler supported by distutils. gcc will work fine on UNIX-like platforms]
* [http://www.lemburg.com/files/python/mxTextTools.html mxTextTools]
* [http://sourceforge.net/projects/numpy Numerical Python (version 24.2 recommended)]

=== Optional Software ===

* [http://www.reportlab.org/downloads.html ReportLab -- for pdf graphics code]
* [http://sourceforge.net/projects/mysql-python MySQLdb]

= Biopython-corba =

=== Files ===

* Source tarball -- [http://biopython.open-bio.org/static/DIST/biopython-corba-0.3.0.tar.gz biopython-corba-0.3.0.tar.gz] 344Kb
* Source Zip File -- [http://biopython.open-bio.org/static/DIST/biopython-corba-0.3.0.zip biopython-corba-0.3.0.zip] 378Kb

=== Required Software ===

* [http://omniorb.sourceforge.net omniORBpy]
* [http://fnorb.sourceforge.net Fnorb]
* [http://sourceforge.net/projects/orbit-python orbit-python]

= Old Releases =

* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.tar.gz biopython-1.40b.tar.gz] 3,437 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.zip biopython-1.40b.zip] 3,267 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.win32-py2.3.exe biopython-1.40b.win32-py2.3.exe] 1,019 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.win32-py2.4.exe biopython-1.40b.win32-py2.4.exe] 1,023 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.30.tar.gz biopython-1.30.tar.gz] 3,186 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.tar.gz biopython-1.24.tar.gz] 3,081 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.zip biopython-1.24.zip] 3,623 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.win32-py2.2.exe biopython-1.24.win32-py2.2.exe] 892 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.win32-py2.3.exe biopython-1.24.win32-py2.3.exe] 894 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.tar.gz biopython-1.23.tar.gz] 2,241 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.zip biopython-1.23.zip] 2,719 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.win32-py2.2.exe biopython-1.23.win32-py2.2.exe] 833 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.win32-py2.3.exe biopython-1.23.win32-py2.3.exe] 842 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.22.tar.gz biopython-1.22.tar.gz] 2,214 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.22.zip biopython-1.22.zip] 2,691 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.tar.gz biopython-1.21.tar.gz] 2,214 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.zip biopython-1.21.zip] 2,897 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.win32-py2.2.exe biopython-1.21.win32-py2.2.exe] 770 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.win32-py2.3.exe biopython-1.21.win32-py2.3.exe] 832 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.20.tar.gz biopython-1.20.tar.gz] 2,101 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.20.zip biopython-1.20.zip] 2,602 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.10.tar.gz biopython-1.10.tar.gz] 1,811 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.10.zip biopython-1.10.zip] 2,300 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.10.win32-py2.2.exe biopython-1.10.win32-py2.2.exe] 1,199 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.tar.gz biopython-1.00a4.tar.gz] 1,739Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.zip biopython-1.00a4.zip] 2,121Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.win32-py2.0.exe biopython-1.00a4.win32-py2.0.exe] 835Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.win32-py2.1.exe biopython-1.00a4.win32-py2.1.exe] 837Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.win32-py2.2.exe biopython-1.00a4.win32-py2.2.exe] 838Kb
* [http://biopython.open-bio.org/static/DIST/MacBiopython-1.00a4.sit MacBiopython-1.00a4.sit] 2.2Mb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.tar.gz biopython-1.00a3.tar.gz] 1,816Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.zip biopython-1.00a3.zip] 2,165Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.win32-py2.0.exe biopython-1.00a3.win32-py2.0.exe] 583Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.win32-py2.1.exe biopython-1.00a3.win32-py2.1.exe] 585Kb
* [http://biopython.open-bio.org/static/DIST/Macbiopython-1.00a3.sit.bin Macbiopython-1.00a3.sit.bin] 1926Kb

Download

2006-05-30T14:22:12Z

Jason: /* Installation Instructions */

= Current Release -- 1.41 -- 28 Oct 2005 =

=== Installation Instructions ===

* [http://biopython.open-bio.org/DIST/docs/install/Installation.html HTML Installation Instructions]
* [http://biopython.open-bio.org/DIST/docs/install/Installation.pdf PDF Installation Instructions]

=== Files ===

* Source Tarball -- [http://biopython.open-bio.org/static/DIST/biopython-1.41.tar.gz biopython-1.41.tar.gz] 3,718 Kb
* Source Zip File -- [http://biopython.open-bio.org/static/DIST/biopython-1.41.zip biopython-1.41.zip] 4,240 Kb
* Windows Installer for Python 2.3 -- [http://biopython.open-bio.org/static/DIST/biopython-1.41.win32-py2.3.exe biopython-1.41.win32-py2.3.exe] 1,038 Kb
* Windows Installer for Python 2.4 -- [http://biopython.open-bio.org/static/DIST/biopython-1.41.win32-py2.4.exe biopython-1.41.win32-py2.4.exe] 1,042 Kb

=== Required Software ===

* [http://www.python.org Python 2.3 or above]
* [http://www.python.org/doc/current/inst/inst.html A C compiler -- you need a C compiler supported by distutils. gcc will work fine on UNIX-like platforms]
* [http://www.lemburg.com/files/python/mxTextTools.html mxTextTools]
* [http://sourceforge.net/projects/numpy Numerical Python (version 24.2 recommended)]

=== Optional Software ===

* [http://www.reportlab.org/downloads.html ReportLab -- for pdf graphics code]
* [http://sourceforge.net/projects/mysql-python MySQLdb]

= Biopython-corba =

=== Files ===

* Source tarball -- [http://biopython.open-bio.org/static/DIST/biopython-corba-0.3.0.tar.gz biopython-corba-0.3.0.tar.gz] 344Kb
* Source Zip File -- [http://biopython.open-bio.org/static/DIST/biopython-corba-0.3.0.zip biopython-corba-0.3.0.zip] 378Kb

=== Required Software ===

* [http://omniorb.sourceforge.net omniORBpy]
* [http://fnorb.sourceforge.net Fnorb]
* [http://sourceforge.net/projects/orbit-python orbit-python]

= Old Releases =

* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.tar.gz biopython-1.40b.tar.gz] 3,437 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.zip biopython-1.40b.zip] 3,267 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.win32-py2.3.exe biopython-1.40b.win32-py2.3.exe] 1,019 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.40b.win32-py2.4.exe biopython-1.40b.win32-py2.4.exe] 1,023 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.30.tar.gz biopython-1.30.tar.gz] 3,186 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.tar.gz biopython-1.24.tar.gz] 3,081 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.zip biopython-1.24.zip] 3,623 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.win32-py2.2.exe biopython-1.24.win32-py2.2.exe] 892 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.24.win32-py2.3.exe biopython-1.24.win32-py2.3.exe] 894 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.tar.gz biopython-1.23.tar.gz] 2,241 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.zip biopython-1.23.zip] 2,719 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.win32-py2.2.exe biopython-1.23.win32-py2.2.exe] 833 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.23.win32-py2.3.exe biopython-1.23.win32-py2.3.exe] 842 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.22.tar.gz biopython-1.22.tar.gz] 2,214 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.22.zip biopython-1.22.zip] 2,691 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.tar.gz biopython-1.21.tar.gz] 2,214 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.zip biopython-1.21.zip] 2,897 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.win32-py2.2.exe biopython-1.21.win32-py2.2.exe] 770 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.21.win32-py2.3.exe biopython-1.21.win32-py2.3.exe] 832 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.20.tar.gz biopython-1.20.tar.gz] 2,101 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.20.zip biopython-1.20.zip] 2,602 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.10.tar.gz biopython-1.10.tar.gz] 1,811 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.10.zip biopython-1.10.zip] 2,300 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.10.win32-py2.2.exe biopython-1.10.win32-py2.2.exe] 1,199 Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.tar.gz biopython-1.00a4.tar.gz] 1,739Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.zip biopython-1.00a4.zip] 2,121Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.win32-py2.0.exe biopython-1.00a4.win32-py2.0.exe] 835Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.win32-py2.1.exe biopython-1.00a4.win32-py2.1.exe] 837Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a4.win32-py2.2.exe biopython-1.00a4.win32-py2.2.exe] 838Kb
* [http://biopython.open-bio.org/static/DIST/MacBiopython-1.00a4.sit MacBiopython-1.00a4.sit] 2.2Mb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.tar.gz biopython-1.00a3.tar.gz] 1,816Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.zip biopython-1.00a3.zip] 2,165Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.win32-py2.0.exe biopython-1.00a3.win32-py2.0.exe] 583Kb
* [http://biopython.open-bio.org/static/DIST/biopython-1.00a3.win32-py2.1.exe biopython-1.00a3.win32-py2.1.exe] 585Kb
* [http://biopython.open-bio.org/static/DIST/Macbiopython-1.00a3.sit.bin Macbiopython-1.00a3.sit.bin] 1926Kb

User:Jason

2006-05-07T17:29:36Z

Jason:

My page on [[bp:User:Jason|bioperl site]].

Sandbox

2006-05-07T17:25:34Z

Jason: some interwiki linking examples

==Some examples==
Demonstrate links to wikipedia [[wp:DNA|DNA]] and BioPerl [[bp:BLAST|BLAST]] and wikiomics [[wikiomics:BLAST|BLAST]].

User:Idoerg

2006-05-07T17:19:28Z

Jason:

Iddo Friedberg

User:Mdehoon

2006-05-07T17:18:50Z

Jason:

Michiel De Hoon

Biopython

2006-01-28T18:41:28Z

Jason:

==Welcome==
See the [http://biopython.open-bio.org/news News page] as well.

Wiki software successfully installed.

Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]
and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.

User:Jason

2006-01-28T18:37:09Z

Jason:

#REDIRECT [[bp:Jason Stajich]]