The GMOD Tools for Evolutionary Biology Hackathon wiki

This is a snapshot of the GMOD Tools for Evolutionary Biology Hackathon wiki taken in June 2015. The wiki was originally live at https://www.nescent.org/wg_gmodevohackathon/Main_Page

GMOD held a hackathon November 8-12, 2010, at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. This hackathon focused on improving GMOD's support for evolutionary biology.

The Open Call for Participation went out on August 1, 2010, and remained open until August 25. Participants were selected based on their applications.

Post-Hackathon Updates: Robert Buels gave a poster on the hackathon at the Plant & Animal Genome XVIII conference (PAG) in January 2011.

Synopsis

This hackathon aimed 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 focused on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation.

The event brought together a group of about 30 software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants included 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.

This hackathon provided a unique opportunity to infuse the community of GMOD developers 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.

Background 

The GMOD project is a confederation of intercompatible open-source projects developing software tools for storing, managing, curating, and publishing biological data. Although the GMOD project originated from the goal of developing a generic tool set for common needs among model organism databases, GMOD tools are meanwhile used by many large and small, collaborative and single-investigator biological database projects for the dissemination of experimental results and curated knowledge.

GMOD's software tools provide a powerful and feature-rich basis for working with biological, in particular genomic and other molecular data. However, due to GMOD's historical emphasis on single-genome projects many GMOD tools still lack features that are critical to effectively support the comparative, phylogenetic, and natural diversity-oriented questions frequently asked in evolutionary research.

Recent developments have given rise to a window of opportunity for forging collaborations towards filling this gap. In particular, the cost of collecting comparative molecular data on a large or even genomic scale has recently dropped dramatically, primarily thanks to next-generation high-throughput sequencing technologies. This has enabled evolutionary researchers to bring genome-scale molecular data to bear on key evolutionary questions. It has also allowed single organism-focused molecular biology labs, who represent GMOD's traditional user base, to broaden out to multi-organism comparative approaches. Bringing these two communities with increasingly shared interests and complementary scientific and technical expertise together offers an opportunity to start filling GMOD's gaps in these areas while building on its existing strengths. In addition, such direct interaction will heighten future awareness of needs of evolutionary researchers among GMOD developers who have so far mostly supported its traditional user base, and can in the long term increase the ranks of GMOD contributors from a field it was not originally designed to serve.

The hackathon format is ideally suited to realize this opportunity. Its strengths lie in facilitating face-to-face interaction among people with complementary expertise, and collaborative work on tangible products that can form the basis of continued partnerships long beyond the end of the meeting.

Specific Objectives 

Organizers have identified the following broad themes for focusing work at the event. Before and at the hackathon, the participants will refine and distill these and other options into concrete implementation targets. 

• Viewing tools for comparative genomics data
• Visualization of phylogenetic data and trees
• Population Diversity and Phenotype support

Hackathon Structure 

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 this wiki. Relevant content will be copied to the GMOD wiki after the event. Each working group during the event will typically have its own wiki 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.

Sponsorship 

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.