Active projects

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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.
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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.
  
 
== Current projects ==
 
== Current projects ==
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=== (GSOC 2010) Extending Bio.PDB ===
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João Rodrigues's Summer of Code project aims to introduce several new features to the Bio.PDB structural biology module. It will include functions for adding polar hydrogens to structures, probing for SS bridges based on structural information and annotations, renumbering residues, coarse-graining a structure, etc. A more comprehensive layout of the project is available [[GSOC2010_Joao|on this wiki]], and the code is on [http://github.com/JoaoRodrigues/biopython/tree/GSOC2010 a GitHub branch].
  
 
=== Population Genetics development ===
 
=== Population Genetics development ===
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=== GFF parser ===
 
=== GFF parser ===
  
Brad is working on a Biopython GFF parser. Source code is available from [http://github.com/chapmanb/bcbb/tree/be2f4f1714b67aa8e428b747c74c81cdd0451072/gff git hub]. See blog posts on the [http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/ initial implementation] and [http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/ MapReduce parallel version].
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Brad is working on a Biopython GFF parser. Source code is available from [http://github.com/chapmanb/bcbb/tree/master/gff git hub]. Documentation is in progress at [[GFF Parsing]]. See blog posts on the [http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/ initial implementation] and [http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/ MapReduce parallel version].
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=== Phylo ===
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[[Phylo|Bio.Phylo]], a new, mostly-stable module for working with phylogenetic trees, was released with Biopython 1.54. [[User:EricTalevich|Eric]] is currently working on bringing the Tree object methods to parity with Bio.Nexus. New features appear on [http://github.com/etal/biopython/ GitHub branches] first.
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=== Biogeography ===
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Nick Matzke developed a biogeography module for BioPython as a [[Google Summer of Code]] 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 were [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd].  The new module is documented on this wiki as [[BioGeography]].
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The code currently lives at the Bio/Geography directory of Nick's [http://github.com/nmatzke/biopython/tree/Geography Geography branch on GitHub], and Eric is preparing it for integration into the Biopython trunk on [http://github.com/etal/biopython/tree/geography another branch].
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=== RNA structure === 
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Several branches for working with RNA data have been made available by Kristian Rother. They can be used mainly for parsing RNA secondary structures [http://github.com/krother/biopython/tree/rna] and working with Bio.Sequence objects that represent modified RNA nucleotides [http://github.com/krother/biopython/tree/rna_alphabet].
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=== Open Enhancement Bugs ===
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This [http://bugzilla.open-bio.org/buglist.cgi?product=Biopython&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED&bug_severity=enhancement 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).
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=== Branches on github.com ===
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The [http://github.com/biopython/biopython/network Biopython network diagram at github.com] will show all public branches of our repository on github, and will therefore let you see things that are being worked on.
  
 
== Project ideas ==
 
== Project ideas ==
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Please add any ideas or proposals for new additions to Biopython. Bugs and enhancements for current code should be discussed though our bugzilla interface.
 
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 adds an additional library 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 has some initial code for this.
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* Build a general tool to filter sequences containing ambiguous or low quality bases. Chris Fields from BioPerl is interested in coordinating the BioPerl/Biopython implementations. See these threads on the mailing lists for discussion: http://lists.open-bio.org/pipermail/biopython/2009-July/005355.html, http://lists.open-bio.org/pipermail/biopython/2009-July/005342.html
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* 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.
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* Revamp the GEO SOFT parser, drawing on the ideas used in [http://www.bioconductor.org/packages/bioc/html/GEOquery.html Sean Davis' GEOquery parser in R/Bioconductor].  See also [http://www.warwick.ac.uk/go/peter_cock/r/geo/ this page].
  
 
== Enhancement list ==
 
== Enhancement list ==
  
Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our [http://bugzilla.open-bio.org/ 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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Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our [http://redmine.open-bio.org/projects/biopython Issue Tracker] page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.

Revision as of 05:17, 15 February 2013

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

(GSOC 2010) Extending Bio.PDB

João Rodrigues's Summer of Code project aims to introduce several new features to the Bio.PDB structural biology module. It will include functions for adding polar hydrogens to structures, probing for SS bridges based on structural information and annotations, renumbering residues, coarse-graining a structure, etc. A more comprehensive layout of the project is available on this wiki, and the code is on a GitHub branch.

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

Bio.Phylo, a new, mostly-stable module for working with phylogenetic trees, was released with Biopython 1.54. Eric is currently working on bringing the Tree object methods to parity with Bio.Nexus. New features appear on GitHub branches first.

Biogeography

Nick Matzke developed a biogeography module for BioPython as a Google Summer of Code project through NESCent's Phyloinformatics Summer of Code 2009. See the project proposal at: Biogeographical Phylogenetics for BioPython. The mentors were Stephen Smith (primary), Brad Chapman, and David Kidd. The new module is documented on this wiki as BioGeography.

The code currently lives at the Bio/Geography directory of Nick's Geography branch on GitHub, and Eric is preparing it for integration into the Biopython trunk on another branch.

RNA structure

Several branches for working with RNA data have been made available by Kristian Rother. They can be used mainly for parsing RNA secondary structures [1] and working with Bio.Sequence objects that represent modified RNA nucleotides [2].

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).

Branches on github.com

The Biopython network diagram at github.com will show all public branches of our repository on github, and will therefore let you see things that are being worked on.

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 Issue Tracker page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.

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