[Bioperl-l] reminder: Aug 25 deadline for GMOD Hackathon application

Robert Buels rmb32 at cornell.edu
Thu Aug 19 13:09:45 EDT 2010

Hi all,

This is your one-week reminder: the deadline for open applications to 
the GMOD Evo hackathon is Wednesday, August 25th.



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.


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


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

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.


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).


Main GMOD EvoHack page, and full proposal:

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


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