[Biopython-dev] Project ideas for GSoC (or other student projects)

Bartek Wilczynski bartek at rezolwenta.eu.org
Fri Mar 15 23:06:57 UTC 2013

Hi All,
I would add one more (old) idea for a GSoC pool, i.e. adding support
for different biological ontologies to biopython.

This was already discussed some time ago
mostly in the context of gene ontology, and to some extent this is
addressed by the development of GOAtools
(https://github.com/tanghaibao/goatools), but I think it would be
worth to have a decent support for OBO-file-based ontologies (not only
gene ontology, I'm also interested myself in anatomical ontologies,
there are also other available at obofoundry.org) in biopython.

I think it would need to include support for IO operations on both OBO
and annotation files, as well as statistical enrichment measures and
potentially some visualisation.

Would anyone be interested in co-mentoring this project? There is one
student in my department who would be interested in applying to GSoC
for this project, but I think it would be great if other people joined
the discussion on the functionality and having more people involved is
always better...

Bartek Wilczynski

On Wed, Mar 13, 2013 at 7:32 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Tue, Feb 12, 2013 at 9:08 PM, Michiel de Hoon <mjldehoon at yahoo.com>wrote:
>> It would be great to have better support for microarray analysis in
>> Biopython. Something like lumi/limma in R. Perhaps this is an option for
>> the GSoC?
>> Best,
>> -Michiel.
> I like Michiel's idea, and I'll suggest two more:
> 1. Codon alignment & analysis:
> - PAL2NAL-style conversion of unaligned nucleic acid sequences and a
> protein sequence alignment to a codon alignment. (Previously discussed)
> - dN/dS and the related functions needed to calculate it.
> - Possible AlignIO or MultipleSeqAlignment tweaks to take full advantage of
> codon alignments, including validation (testing for frame shifts etc.)
> 2. Phylo enhancements:
> 2a. Tree drawing:
> - A proper draw_unrooted function to perform radial layout, with an
> optional "iterations" argument to use Felsenstein's Equal Daylight
> algorithm -- I feel this layout approach is neglected in most libraries.
> - Better matplotlib/pylab integration, so the plot components can be
> tweaked using matplotlib functions.
> - Other common layout approaches, e.g. circular.
> 2b. A "Phylo.consensus" module:
> - strict consensus, like Bio.Nexus already implements.
> - other consensus methods, time permitting.
> 2c. A "Phylo.distance" module:
> - Robinson-Foulds distance -- though others might be working on this
> already.
> 2d. Simple tree inference:
> - Straightforward algorithms exist for neighbor-joining and parsimony tree
> estimation. For small alignments (and perhaps medium-sized ones with PyPy),
> it would be nice to run these without an external program, e.g. to
> construct a guide tree for another algorithm or quickly view a phylogenetic
> clustering of sequences.
> Any interest in either of these? Shall I add them to the wiki?
> -Eric
> --- On Tue, 2/12/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> > From: Peter Cock <p.j.a.cock at googlemail.com>
>> > Subject: [Biopython-dev] Project ideas for GSoC (or other student
>> projects)
>> > To: "Biopython-Dev Mailing List" <biopython-dev at biopython.org>
>> > Date: Tuesday, February 12, 2013, 12:51 PM
>> > Hello all,
>> >
>> > Google recently confirmed they will be running Google Summer
>> > of Code 2013,
>> > and we (Biopython and the other Bio* projects) would hope to
>> > be accepted again
>> > under the Open Bioinformatics Foundation as in previous
>> > years:
>> > http://lists.open-bio.org/pipermail/gsoc/2013/000196.html
>> >
>> > It would be great to start coming up with potential project
>> > ideas, both larger
>> > pieces of work suitable for GSoC but also smaller tasks for
>> > other project
>> > students, or 'low hanging fruit' for potential contributors
>> > to cut
>> > their teeth on.
>> >
>> > See also http://biopython.org/wiki/Active_projects
>> > and the ideas list there.
>> >
>> > Regards,
>> >
>> > Peter
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Bartek Wilczynski

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