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.
Population Genetics development
Giovanni and Tiago are working on expanding population genetics code in Biopython. See the PopGen development page for more details.
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.
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.
Nick is working on developing a Biogeography module for BioPython. This work is funded by Google Summer of Code 2009 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), see: http://github.com/peterjc/biopython/commits/alignment-obj
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).
Please add any ideas or proposals for new additions to Biopython. Bugs and enhancements for current code should be discussed though our bugzilla interface.
- 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
- 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.
- Revamp the GEO SOFT parser, drawing on the ideas used in Sean Davis' GEOquery parser in R/Bioconductor. See also this page.
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.