Reminder: Subject: GMOD Evo Hackathon Open Call for Participation

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Reminder: Subject: GMOD Evo Hackathon Open Call for Participation

Nicole Washington

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
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

How To Apply:
Fill out the online application form at
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.


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
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 (  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

This event is sponsored by the US National Evolutionary Synthesis
Center (NESCent, through its Informatics
Whitepapers program
( 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
Main GMOD EvoHack page, and full proposal:
Similar past NESCent events, see:
GMOD hackathon application:

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