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 hackathontargets 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
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!
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
details about the event, its motivation, organization, procedures, and
attendees, as well as URLs to the hackathon and related websites are
The GMOD EvoHack Organizing Committee (and project affiliations as relevant):
Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)
About the GMOD Evo Hackathon
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
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.
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
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
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
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.