[Biopython-dev] BOSC 2012 - Biopython Update

Peter Cock p.j.a.cock at googlemail.com
Fri Apr 13 11:31:30 UTC 2012

On Thu, Apr 12, 2012 at 11:37 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> 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.

Biopython 1.57 was already covered at BOSC 2011.

> * Installation improvements:
> pip support (v.1.57); easy_install will automatically handle the numpy
> dependency (v.1.59, Feb '12)

Brad commented on this, perhaps a line in the abstract?

> * 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)

This is something I would want to cover.

> * 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.

Yep. Maybe even an example in the abstract?

> * 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

Good points - although I don't want to over promise ;)

> * 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++

We should have a summary of what they did somewhere, perhaps
as an OBF blog post? I'm hoping to get this year's GSoC students
to write weekly progress reports on a blog or at least by email to
the mailing list.

> * 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.


Here's a draft abstract - note we have to fit in a page. Having a logo
or some eye catching image is very effective for standing out in the
abstract book (on screen or on paper).

Comments welcome - but keep in mind the one page limit.

Eric - feel free to turn this into a Google Doc if you prefer.

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