[Biopython-dev] BOSC 2012 - Biopython Update

Eric Talevich eric.talevich at gmail.com
Fri Apr 13 14:31:08 UTC 2012

Thanks for this. I'll keep it as LaTeX, since it already looks nice.

1. Several parts say "[to be revised prior to BOSC]" -- I take it we
have the option of updating our abstract shortly before BOSC, and this
is a note to the conference organizers that we intend to do so? To
save space and reduce distraction, should this be a footnote instead?

2. To save space: Do we need the line "Bioinformatics Open Source
Conference (BOSC) ..." after the author names?

3. Again to save space, and make room to cite the Phylo paper: can we
drop the citation for TogoWS, and add a few words of description in
the main text where it's mentioned? (We don't cite PAML, HMMer, etc.)

4. How do you feel about dropping inline citations, and just have a
list of \nocite references at the bottom? In a one-page abstract, it
should be easy enough for readers to figure out what's what.


On Fri, Apr 13, 2012 at 7:31 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.)
> Yep.
>> * GenomeDiagram improvements:
>> New, pretty features. Eye candy for the slides.
> Yep. Maybe even an example in the abstract?
>> * TogoWS
> Yep.
>> * 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.
> Peter

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