[Gmod-help] [Gmod] GMOD Evo Hackathon Open Call for Participation
Sidibe bocs Stephanie
stephanie.sidibe-bocs at cirad.fr
Mon Sep 13 17:57:00 EDT 2010
Dear Dave,
How are you ?
Sorry not to contact you earlier. I asked my hierarchy but I do not have
a clear response (august is very quiet & september very busy) but first
I wanted to know it is still possible to apply even if the deadline is
out ? In the frame of the GNPAnnot project we are very interested to
participate to this hackaton but in practice you know how genomes &
informatics are going ...
By the way, will you be to genome informatics conference this week ? may
be you will see Fabrice and may be you can contact me on my skype
account if you have time to discuss (I will be more available this
thursday & friday).
All the best, Stéphanie.
Le 01/08/2010 19:03, Dave Clements, GMOD Help Desk a écrit :
> We are seeking participants for the GMOD Tools for Evolutionary
> Biology Hackathon, held November 8-12, 2010 at the US National
> Evolutionary Synthesis Center (NESCent) in Durham, NC.
>
> This hackathon targets three critical gaps in the capabilities of the
> GMOD toolbox that currently limit its utility for evolutionary research:
> 1. Visualization of comparative genomics data
> 2. Visualization of phylogenetic data and trees
> 3. Support for population diversity and phenotype data
>
> If you are interested in these areas and have relevant expertise, you
> are strongly encouraged to apply. Relevant areas of expertise include
> more than just software development: if you are a GMOD power user,
> visualization guru, domain expert (comparative, phylogenetics,
> population, ...), or documentation wizard, then your skills are needed!
>
> How To Apply:
> Fill out the online application form at http://bit.ly/gmodevohack.
> Applications are due August 25.
>
> About GMOD:
> GMOD is an intercompatible suite of open-source software components
> for storing, managing, analyzing, and visualizing genome-scale data.
> GMOD includes many widely-used software components: GBrowse and
> JBrowse, both genome viewers; GBrowse_syn, a comparative genomics
> viewer; Chado, a generic and modular database schema; CMap, a
> comparative map viewer; as well as many other components including
> Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the
> functionality of existing GMOD components, and integrate new
> components as well.
>
> About Hackathons:
> A hackathon is an intense event at which a group of programmers with
> different backgrounds and skills collaborate hands-on and face-to-face
> to develop working code that is of utility to the community as a
> whole. The mix of people will include domain experts and
> computer-savvy end-users.
>
> More details about the event, its motivation, organization,
> procedures, and attendees, as well as URLs to the hackathon and
> related websites are included below.
>
> Sincerely,
>
> The GMOD EvoHack Organizing Committee (and project affiliations as
> relevant):
>
> Nicole Washington, Chair (LBNL, modENCODE, Phenote)
>
> Robert Buels (SGN, Chado NatDiv)
>
> Scott Cain (OICR, GMOD)
>
> Dave Clements (NESCent, GMOD)
>
> Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)
>
> Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)
>
>
> -----------------------------
>
>
> About the GMOD Evo Hackathon
>
>
> Overview
>
>
> We are organizing a hackathon to fill critical gaps in the
> capabilities of the Generic Model Organism Database (GMOD)
> toolbox that currently limit its utility for evolutionary
> research. Specifically, we will focus on tools for 1) viewing
> comparative genomics data; 2) visualizing phylogenomic data;
> and 3) supporting population diversity data and phenotype
> annotation.
>
> The event will be hosted at NESCent and bring together a group of
> about 20+ software developers, end-user representatives, and
> documentation experts who would otherwise not meet. The participants
> will include key developers of GMOD components that currently lack
> features critical for emerging evolutionary biology research,
> developers of informatics tools in evolutionary research that lack
> GMOD integration, and informatics-savvy biologists who can represent
> end-user requirements.
>
> The event will provide a unique opportunity to infuse the GMOD
> developer community with a heightened awareness of unmet needs in
> evolutionary biology that GMOD components have the potential to fill,
> and for tool developers in evolutionary biology to better understand
> how best to extend or integrate with already existing GMOD components.
>
>
> Before the Event
>
>
> Discussion of ideas and sometimes even design actually starts
> well before the hackathon, on mailing lists, wiki pages, and
> conference calls set up among accepted attendees. This
> advance work lays the foundation for participants to be
> productive from the very first day. This also means that
> participants should be willing to contribute some time in
> advance of the hackathon itself to participate in this
> preparatory discussion.
>
>
> During the Event
>
>
> Typically, hackathon participants use the morning of the first
> day of the event to organize themselves into working groups of
> between 3 and 6 people, each with a focused implementation
> objective. Ideas and objectives are discussed, and attendees
> coalesce around the projects in which they have the most
> experience or interest.
>
>
> Deliverables / Event Results
>
>
> The meeting’s attendance, working groups, and outcomes will be
> fully logged and documented on the GMOD wiki
> (http://gmod.org). Each working group during the event will
> typically have its own wiki page, linked from the main EvoHack
> page, where it documents its minutes and design notes, and
> provides links to the code and documentation it produces.
> Also, since GMOD and NESCent are both committed to open
> source principles, all code and documentation produced by
> participants during the hackathon must be published under an
> OSI-approved open source license. As contributions to
> existing GMOD tools, all hackathon products will most likely
> satisfy this requirement automatically.
>
>
> NESCent
>
> This event is sponsored by the US National Evolutionary Synthesis
> Center (NESCent, http://www.nescent.org) through its Informatics
> Whitepapers program
> (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes
> the synthesis of information, concepts and knowledge to address
> significant, emerging, or novel questions in evolutionary science and
> its applications. NESCent achieves this by supporting research and
> education across disciplinary, institutional, geographic, and
> demographic boundaries (see http://www.nescent.org/science/proposals.php).
>
>
> Links
>
>
> Main GMOD EvoHack page, and full proposal:
> http://gmod.org/wiki/GMOD_Evo_Hackathon
>
> NESCent: http://www.nescent.org/
> GMOD: http://gmod.org <http://gmod.org/>
> Similar past NESCent events, see: http://hackathon.nescent.org/
> GMOD hackathon application: http://bit.ly/gmodevohack
>
> --
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/GMOD_Europe_2010
> http://gmod.org/wiki/Help_Desk_Feedback
>
>
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