[Biopython-dev] BOSC 2012 - Biopython Update

[Brad Chapman]

Eric and Peter;
Eric -- I'm glad you're taking this on. It'll be great to have a
Biopython presentation at BOSC. The points you mentioned all sound
great, although I would drop some of the more boring ones like the
installation stuff (I can pick on that, since it's mine).

My only other suggestions is to focus the talk around the people who've
provided the improvements. One of the awesome things about Biopython is
the wide contributor base and we still manage to pull everything into a
coherent package thanks to Peter's guiding hand. It would be cool to
emphasize this community as part of the update.

Thanks again for doing this,
Brad

> > Hello all,
> >
> > The BOSC abstract deadline (tomorrow) has rather crept up on me,
> > despite Nomi's reminder emails (My excuse is I've been thinking
> > more about GSoC!). For anyone thinking of submitting a talk, the
> > abstract limit is just a page - see:
> > http://www.open-bio.org/wiki/BOSC_2012
> >
> > I'm hoping to attend BOSC, but will probably not be at ISMB 2012.
> > I'd be delighted for another Biopython developer to give the project
> > update talk (and as in previous years, we'll help out with the abstract,
> > slides, etc). Anyone interested? Giving a talk can be very helpful in
> > getting travel funding ;)
> >
> > I know Eric might be a candidate as he will be in Long Beach
> > (congratulations on getting your ISMB poster accepted Eric!).
> >
> > Note that dedicated "Bioinformatics Open Source Project Updates"
> > track is new this year. The talks are likely to be at the shorter end of
> > the talk length range specified (i.e. closer to 5 minutes than 20 mins)
> > but that will partly depend on quite how full the final schedule turns
> > out to be.
> >
> > The idea (speaking with my BOSC hat on) with the update talks is
> > to try to highlight what is new and exciting, with only a minimal
> > introduction for the higher profile projects - most of the audience
> > will know roughly what BioPerl etc are, and won't be interested
> > to hear it again ;)
> >
> > So for the Biopython talk we'd probably want to cover things like
> > GSoC, work with PyPy and Python3, major new functionality, any
> > Biopython papers, etc, and a bit on future plans. The talk should be
> > short but sweet :)
> >
> > Regards,
> >
> > Peter
> 
> 
> OK, here are some potential talking points I scraped from past announcements:
> 
> * SeqIO.index_db:
> Introduced v.1.57 (Apr 2011), with improvements since then. Ideas to
> carry the index_db concept to other modules.
> 
> * Installation improvements:
> pip support (v.1.57); easy_install will automatically handle the numpy
> dependency (v.1.59, Feb '12)
> 
> * Portability:
> Python 3 compatibility (except for a couple C extension modules);
> still supporting Jython; now mostly supporting Pypy (except for
> modules that use numpy or C extensions)
> 
> * Merged Brandon Invergo's independent project pypaml under
> Bio.Phylo.PAML ((v.1.58, Aug '11). With SeqIO's new sequential Phylip
> support (v.1.59) and the existing support for phylogeny I/O under
> Phylo, we can now easily assemble and run complete workflows involving
> PAML.
> (Similarly for PhyML, with SeqIO's "phylip-relaxed" and
> Bio.Phylo.Applications.PhymlCommandline.)
> 
> * GenomeDiagram improvements:
> New, pretty features. Eye candy for the slides.
> 
> * TogoWS
> 
> * Next release & future plans:
> - Restored mmCIF support, via Lenna Peterson, a prospective GSoC student
> - Brad's GFF parser
> - Deeper future: see the other mailing list thread
> 
> * GSoC 2011 results:
> - Mikael Trellet -- Interface
> - Michele Silva -- Mocapy++ Python module; also ported two
> applications to Biopython
> - Justinas D. -- Python-based extension system for Mocapy++
> 
> * Summer of Struct:
> João and Eric are working to refactor and merge the vast amount of
> Bio.PDB-related code produced during previous GSoCs. (Includes a
> planned SeqIO-style API for structures in PDB, mmCIF and PBDML
> formats.) Improvements have been trickling in since the last BOSC;
> here comes the flood.
> 
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