[Biopython-dev] Active projects list? (BOSC Biopython Project Update)

[Andrea Pierleoni]

> Hi all,
>
> BOSC is rapidly approaching, so I have been working on slides for the
> Biopython Project Update. One thing I would really like help with is
> listing
> current active projects, as I think the wiki is out of date here:
> http://biopython.org/wiki/Active_projects
>
> In addition to the GSoC work, my list currently has the following (in some
> cases just from looking at github - for example I don't recall Tamas
> posting
> on the mailing lists):
>
> Brad Chapman – GFF parsing
> Andrea Pierleoni - UniProt XML parsing
> Kristian Rother – Modified RNA sequences
> Chris Lasher, Kyle Ellrott, Tamás Nepusz – Gene Ontology
> Kyle Ellrott - HMMER parser
> Uri Laserson, Peter Cock - IMGT files (EMBL like)
>
> I know Michiel has mentioned some ideas for updating our BLAST parsers,
> and I have several smaller things on the side (e.g. an on disk index for
> Bio.SeqIO.index, enhancements to SeqFeature and FeatureLocation).
>
> What are we missing that should be there?
>
> Thanks,
>
> Peter
>


Dear Peter,
I'm actually working on two more projects than the XML parsing, that could
be useful in biopython.

1) together with Mauro Amico, we hare developing a graphical library very
similar to the Bio::Graphics module pf BioPerl. The project is at good
point, and will come with documentation and tutorial as a standalone
package we call BioGraPy. I know that in biopython one can already use
GenomeDiagram to draw, for example, seqrecord features, but this could
extend biopython plotting capability significantly. You can use BioGraPy
to plot a blast output (with its HTML map), to plot hydrophobicity plot
along the sequence (read as per letter annotations), mRNA and CDS with
their splicing sites, and so on... BioGrapy relies on matplotlib, so this
will be an additional external dependence, but worthwhile in my opinion.

2) Since I'm working with the web2py web framework, and I work with biosql
databases, I spent some time adapting the current BioSQL code to be used
with the web2py DAL (Database Abstraction Layer). DAL is much more simpler
(and sometimes faster) than SQLAlchemy, and its syntax and use are very
similar to SQL queries, so it was very easy to adapt the current code to
use the DAL. Main advantages of using the web2py DAL are that it can be
used on almost any DB engine. listing from the web2py site: SQLite,
PostgreSQL, MySQL, MSSQL, FireBird, Oracle, IBM DB2, Informix, Ingres, and
Google App Engine. I've succesfully tested with both Postgres and SQLite,
but should be tested for the other. Since the Web2py code is GPL2, I can
incorporate the modules needed for DAL directly into Biopython, so there
will be no external dependences. I know that Brad Chapman and some others
were working on implementing BioSQL with SQLAlchemy, so let me know if
this could be an addition to Biopython.

Cheers,

Andrea