GMOD
News/GMOD Evo Hackathon Report
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.
Posted to the GMOD News on 2010/12/20