[BioRuby] BioRuby GSoC 2011 ideas?

Wed Feb 23 13:20:35 UTC 2011

I'm available too for mentoring or co-mentoring with Raoul, particularly on
NGS plugins.
In these days I'm working on the main NGS plugin and I think one interesting
topic will be to develop a workflow plugin to handle multiple (and parallel)
NGS tasks and also other type of bio-analyses, as discussed during the last
IRC call. OBF GSoC could be a good opportunity to develop such a plugin.

Cheers
Francesco

On Wed, Feb 23, 2011 at 13:10, Raoul Bonnal <bonnalraoul at ingm.it> wrote:

> Dear All,
> I remind you about the irc meeting for live discussion, I think the main
> topic can be GSoC 2011
>
> I'd like to have some update about Semantic Web its reliability and if we
> (bioruby) are going to use it. Where?
>
> I'm available for mentoring on OBF GSoC projects.
>
> On 23/feb/2011, at 08.43, Toshiaki Katayama wrote:
>
> > Hi all,
> >
> > I just discussed with Rutger about Google Summer of Code (GSoC) 2011.
> > If you are interested in to mentor/participate GSoC this year, please put
> your ideas on this list.
> >
> > Attached is an announcement from NESCent, which is focused on
> phloinformatics.
> > I heard that Open Bio Foundation (OBF) is also considering to organize
> GSoC again (not confirmed, though).
> >
> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
> > http://www.open-bio.org/wiki/Google_Summer_of_Code
> >
> > Some ideas from our side are:
> >
> > for NESCent GSoC,
> > - compile phyloinfo plugins for BioRuby (based on NEXML
> https://github.com/rvosa/bio-nexml, forester
> http://code.google.com/p/forester/ etc.) to make analysis pipeline
> available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully
> ;)
> >
> > for OBF GSoC,
> > - develop NGS-related plugins
> > - develop a generic framework for workflow management and parallel
> execution of tasks
> > - develop plugins for Semantic Web (RDF utilities, SPARQL query
> interface, handling ontologies etc.)
> >
> > Regards,
> > Toshiaki Katayama
> >
> > Begin forwarded message:
> >
> >> From: Hilmar Lapp <hlapp at nescent.org>
> >> Date: 2011年2月22日 03:55:52JST
> >> To: PhyloSoC Announcements <phylosoc-announce at googlegroups.com>
> >> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors
> >> Reply-To: phylosoc-announce at googlegroups.com
> >>
> >> Over the next 3 weeks we will be pulling together NESCent's application
> to the 2011 Google Summer of Code as a mentoring organization. This is a
> call for all prospective mentors, primary and secondary, to step forward.
> >>
> >> Participating as an organization is competitive. Over the last years the
> acceptance rate for organizations has been around 30-35%. The most important
> component of organization applications is the Ideas page, and specifically
> the quality and suitability of the project ideas. These project ideas are
> contributed by you, our mentors. In the past we have had a strong, diverse
> and well-documented portfolio of ideas with different degrees of difficulty,
> from different participating open-source projects, using different
> programming languages.
> >>
> >> If you can fancy yourself serving as a mentor, or helping someone else
> mentoring a student as a secondary mentor, or would like to help out in
> other capacities, please contact us as soon as you can at
> phylosoc-admin at nescent.org. If you have not been a mentor with us in
> previous years, we'll send you guidance on what doing so involves, and how
> you can contribute to our participation. We will also add everyone who is
> interested in serving to our (private) mentors mailing list (at least those
> who aren't already).
> >>
> >> If you are new to Summer of Code and wonder what it takes or what it is
> like to be a mentor for us, don't hesitate to ask questions or to contact
> previous mentors (see URLs below for projects that got selected). Being a
> mentor does require time (see http://bit.ly/soc2011-mentortime), but our
> past mentors have pretty much unanimously found it a fun and rewarding
> experience. That's aside from the code a student could contribute to your
> project, and, possibly most important of all in the long run, the chance to
> gain a new developer.
> >>
> >> The initial skeleton of our 2011 Ideas page is now up here and ready for
> adding project ideas and mentors(*).
> >>
> >>
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
> >>
> >> We will send further guidance on drafting project ideas, but for now you
> can see examples of the format and scope of project ideas on the Ideas pages
> from previous years (click on "Ideas"):
> >>
> >>
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010
> >>
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009
> >>
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008
> >>
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007
> >>
> >> Dates:
> >> ======
> >>
> >> Submission of organization applications starts Feb 28 and closes on
> March 11. For project ideas to contribute to the strength of our application
> they must be in reasonable shape by the morning of March 11. *If* we are
> accepted, ideas can be refined (or added) between March 18-27.
> >>
> >> Students apply March 28-April 8, and selected students are announced
> April 25. The coding period runs from May 23 to August 22. See
> >> http://bit.ly/soc2011-timeline for a full timeline of the whole
> program.
> >>
> >> Cheers, and we look forward to hearing from you!
> >>
> >>       Karen Cranston
> >>       Hilmar Lapp
> >>
> >> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon
> wiki) requires you to login. We had to disable local account creation due to
> spam getting out of control. The wiki is still open, though - just login
> with your OpenID. If you don't have an OpenID, the "Login with OpenID" page
> has information on you can easily get one, and if you have a Google account,
> you're all set to go.
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> >> Groups "Phyloinfomatics Summer of Code Announcements" group.
> >> To unsubscribe from this group, send email to
> >> phylosoc-announce+unsubscribe at googlegroups.com
> >> For more options, visit this group at
> >> http://groups.google.com/group/phylosoc-announce?hl=en
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
> --
> Ra
>
>
>
>
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

-- 

Francesco