GMOD Evo Hackathon Report

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GMOD Evo Hackathon Report

Dave Clements

Hello all,

The GMOD Evo Hackathon was held November 8-12 at NESCent. The 30 participants self-organized into eight groups with at least one group addressing each of the event's three objectives. The outcomes for each group are summarized below.

GMatchbox
Worked on establishing a common database backend and JSON-based API for comparative genomics data, using several visualization tools (including JBrowse and GBrowse_syn) as targets. Will enable sharing of comparative data in multiple tools from multiple sources.
GBrowse_syn2
GBrowse_syn is built on and takes advantage of the GBrowse genome browser code and config files. However, it did not work well with GBrowse2, due to significant architectural changes. This group refactored GBrowse2 to naturally support GBrowse_syn. This work will also enable several other GBrowse1-only applications (SynView, Primer Designer, ...) to be ported to GBrowse2 as well. Two participants also became core GBrowse_syn developers.
JBrowse_syn
This group set out to extend JBrowse to be a comparative genomics browser. The group removed the existing "single genome" assumption from the code and successfully displayed several genomes in parallel. Several participants also became familiar with JBrowse code and architecture.
PhyloBox
PhyloBox is a flexible and fast web based tree visualization program. At the hackathon the PhyloBox team extended PhyloBox in numerous ways to make it a "widget" that can interact with other widgets. PhyloBox documentation was also created.
Integration PhyloBox JBrowse Integration
The group is the perfect example of the interaction that can happen at a hackathon. They worked with the JBrowse_syn, PhyloBox and GMatchbox groups to enable integration of these three technologies. This group was very helpful at getting teams to work together.
Natural Diversity and Phenotypes in Chado
This group focused on two outcomes, both relating to Chado. The first was a prototype Rails application that provided a web interface to the new Natural Diversity module in Chado. This was built on top of the emerging Chado on Rails project. The second was a better understanding, slight refactoring, and updated documentation for Chado's phenotype module.
Galaxy + HyPhy
Galaxy is both a workflow system and a means of persisting computational pipelines and results. This group worked on improving Galaxy's ability to integrate interactive tools, using HyPhy as the prototype application. The Galaxy and HyPhy code bases were modified to support this.
BioPerl
This subgroup worked on improving tree handling in BioPerl. Specifically, they addressed the handling of very large trees or large numbers of small trees. BioPerl now supports storing such trees in a lightweight database instead of in memory.

Dave Clements
GMOD Help Desk


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