[Bio-software] GMOD Evo Hackathon Open Call for Participation

Dave Clements via bio-soft%40net.bio.net (by clements from nescent.org)
Sun Aug 1 12:22:38 EST 2010

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 tha=
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 generi=
and modular database schema; CMap, a comparative map viewer; as well as man=
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 mi=
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.


The GMOD EvoHack Organizing Committee (and project affiliations as

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 fil=
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. Th=
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

The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary biolog=
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 tim=
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
/ Event Results The meeting=92s attendance, working groups, and outcomes wi=
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, linke=
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 Nationa=
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
Links Main GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application:  http://bit.ly/gmodevohack


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