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.
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.
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 (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 (seehttp://www.nescent.org/science/proposals.php).
Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application: http://bit.ly/gmodevohack
Lawrence Berkeley National Laboratory
Life Sciences Division
1 Cyclotron Rd. MS64-121
Berkeley, CA 94720