Active projects

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(Current projects: Multiple Sequence Alignments)
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=== Phylo ===
 
=== Phylo ===
  
[[User:EricTalevich|Eric]] is working on a new module for phylogenetics, [[Phylo|Bio.Phylo]]. It grew out of a Google Summer of Code 2009 [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798969 project], mentored by Brad, to add support for [http://www.phyloxml.org/ phyloXML] to Biopython; it also refactors part of Bio.Nexus. Most of the code has been pushed to the main development branch on GitHub already, but new features appear first on Eric's [http://github.com/etal/biopython/tree/phyloxml phyloxml branch].
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[[User:EricTalevich|Eric]] is working on a new module for phylogenetics, [[Phylo|Bio.Phylo]]. It grew out of a [[Google Summer of Code]] 2009 [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798969 project], mentored by Brad, to add support for [http://www.phyloxml.org/ phyloXML] to Biopython; it also refactors part of Bio.Nexus. Most of the code has been pushed to the main development branch on GitHub already, but new features appear first on Eric's [http://github.com/etal/biopython/tree/phyloxml phyloxml branch].
  
=== Biogeography (GSoC) ===
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=== Biogeography ===
  
[[Matzke|Nick]] is working on developing a Biogeography module for BioPython.  This work is funded by [http://socghop.appspot.com/program/home/google/gsoc2009 Google Summer of Code 2009] through NESCENT's [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Phyloinformatics Summer of Code 2009]. See the project proposal at: [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250 Biogeographical Phylogenetics for BioPython]. The mentors are [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd].  The code currently lives at the Bio/Geography directory of the [http://github.com/nmatzke/biopython/tree/Geography Geography fork of the nmatzke branch on  GitHub], and you can see a timeline and other info about ongoing development [[BioGeography|here]]. The new module is being documented on this wiki as [[BioGeography]].
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[[Matzke|Nick]] is working on developing a Biogeography module for BioPython.  This work was funded by a [[Google Summer of Code]] 2009 [http://socghop.appspot.com/program/home/google/gsoc2009 project] through NESCENT's [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Phyloinformatics Summer of Code 2009]. See the project proposal at: [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250 Biogeographical Phylogenetics for BioPython]. The mentors are [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd].  The code currently lives at the Bio/Geography directory of the [http://github.com/nmatzke/biopython/tree/Geography Geography fork of the nmatzke branch on  GitHub], and you can see a timeline and other info about ongoing development [[BioGeography|here]]. The new module is being documented on this wiki as [[BioGeography]].
  
 
=== Roche 454 SFF parsing in Bio.SeqIO ===
 
=== Roche 454 SFF parsing in Bio.SeqIO ===
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=== Multiple Sequence Alignments ===
 
=== Multiple Sequence Alignments ===
  
Peter is working on a new alignment class for sequence alignments (not the kind in next gen sequencing), see:
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Peter is working on a new alignment class for sequence alignments (not the kind in next gen sequencing), the core of which was recently merged into the trunk and should be included in Biopython 1.54 onwards.
http://github.com/peterjc/biopython/commits/alignment-obj
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=== Open Enhancement Bugs ===
 
=== Open Enhancement Bugs ===

Revision as of 14:23, 10 March 2010

This page provides a central location to collect references to active projects. This is a good place to start if you are interested in contributing to Biopython and want to find larger projects in progress. For developers, use this to reference git branches or other projects which you will be working on for an extended period of time. Please keep it up to date as projects are finished and integrated into Biopython.

Contents

Current projects

Population Genetics development

Giovanni and Tiago are working on expanding population genetics code in Biopython. See the PopGen development page for more details.

GFF parser

Brad is working on a Biopython GFF parser. Source code is available from git hub. Documentation is in progress at GFF Parsing. See blog posts on the initial implementation and MapReduce parallel version.

Phylo

Eric is working on a new module for phylogenetics, Bio.Phylo. It grew out of a Google Summer of Code 2009 project, mentored by Brad, to add support for phyloXML to Biopython; it also refactors part of Bio.Nexus. Most of the code has been pushed to the main development branch on GitHub already, but new features appear first on Eric's phyloxml branch.

Biogeography

Nick is working on developing a Biogeography module for BioPython. This work was funded by a Google Summer of Code 2009 project through NESCENT's Phyloinformatics Summer of Code 2009. See the project proposal at: Biogeographical Phylogenetics for BioPython. The mentors are Stephen Smith (primary), Brad Chapman, and David Kidd. The code currently lives at the Bio/Geography directory of the Geography fork of the nmatzke branch on GitHub, and you can see a timeline and other info about ongoing development here. The new module is being documented on this wiki as BioGeography.

Roche 454 SFF parsing in Bio.SeqIO

See Bug 2837, based on code from Jose Blanca. Recently merged into the trunk and should be included in Biopython 1.54 onwards.

Multiple Sequence Alignments

Peter is working on a new alignment class for sequence alignments (not the kind in next gen sequencing), the core of which was recently merged into the trunk and should be included in Biopython 1.54 onwards.

Open Enhancement Bugs

This Bugzilla Search will list all open enhancement bugs (any filed by core developers are fairly likely to be integrated, some are just wish list entries).

Project ideas

Please add any ideas or proposals for new additions to Biopython. Bugs and enhancements for current code should be discussed though our bugzilla interface.

  • Use SQLAlchemy, an object relational mapper, for BioSQL internals. This would add an additional external dependency to Biopython, but provides ready support for additional databases like SQLite. It also would provide a raw object interface to BioSQL databases when the SeqRecord-like interface is not sufficient. Brad and Kyle have some initial code for this.

Enhancement list

Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our bugzilla page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.

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