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.
PhyloXML driver (GSoC)
Eric is working on supporting the PhyloXML format, as a project for Google Summer of Code 2009. Brad is mentoring this project. The code lives on a branch in GitHub, and you can see a timeline and other info about ongoing development here. The new module is being documented on this wiki as PhyloXML.
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 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.
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.
- 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 has 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.
- Roche 454 SFF support in Bio.SeqIO is being discussed on the mailing lists.
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.