View source for Dbhack2 proposal

= Overview =

NESCent has some funds and is open to the idea of another hackathon.  Past hackathons have been 15 to 20 people from outside NESCent, along with a handful from inside NESCent.

= Locations =

== Montpellier ==

* Cost per person:
** $ 900 from major US airport to Montpellier
** $ 110 per night lodging
* Meeting facilities:
** essentially free
* Synergies:
** TDWG annual meeting in Montpelier (http://www.tdwg.org/) November 9 to 13
** TDWG attendees would need lodging costs
** CDAO group in Strasbourg (Julie Thompson); collaborator Pontarotti in Marseilles has developed an ontology of "genetic events" in evolution.
** Ontologies group at U. Manchester is a cheap flight away.
** some names
*** Roger Hyam
*** John Wieczorek, Berkeley (Darwin core http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome)
*** Bob Morris (Biological Descriptions: http://www.tdwg.org/activities/bd/)
*** Rich Pyle (taxonomic names and concepts http://www.tdwg.org/activities/tnc/)
*** Markus Dorin (GBIF http://www.gbif.org)
*** Cynthia Parr (EOL)
*** Matt Jones (Observational Data/NSF-DataOne http://wiki.tdwg.org/Observational/)

== NESCent ==

* Cost per person:
* Meeting facilities:
* Synergies:
** NESCent: Vision, Lapp, Balhoff, Swofford, Scherle

== New Mexico ==

* Cost per person:
* Meeting facilities:
* Synergies:
** Tucson, AZ is 3 or 4 hr away by car (iPlant Collaborative; Maddison will have moved to Oregon by Nov; Mike Worobey in EEB does viral phylogenetics)
** Los Alamos (LANL HIV db) is 3 hr away by car)
** NMSU is home of Pontelli, Chisham
* challenges or disadvantages
** airport is an hour away

= Hackathon-related ideas =

Projects focused on consolidating our gains and serving the community of users:
# polish up demo projects from dbhack1.   The dbhack1 projects were promising but incomplete.  Solid well documented demonstration projects are needed to expose our interop technologies.
# set up an EvoIO portal (translation, data set curation, etc)
# develop an online course complete with information resources, demos, and assignments

Projects focused on building foundations and serving the community of developers:
# widen the domain by including viral phylogenetics and molecular epidemiology
# ontology, including sticky problems (CDAO relations and upper-level categories) and annotation support (names of programs and file formats)
# [[Transition_Model_Language|transition model language]]

== phylo interop portal ==

the strategic focus of the portal would be interop, but the portal could support other community-building activities such as blogs, bookmarking, forums, etc.
* objectives
** provide users with centralized resources
** demonstrate useful, working aspects of interop technologies
** illustrate benefits of integrative or large-scale analyses
** testbed for trying out new concepts and  for debugging
** increase exposure of project to increase chances of funding
* features
** format interconversion
** triple store for download
** visualization - second
** data set integration wizard
** annotation support for curation, metadata
** analysis operations (implemented by reasoner)
* how to get this done with limited resources
** get more players involved by conceiving this broadly
** provide hosting to some projects where mutually beneficial
** use the hackathon mechanism to get started
** use CREST funds to hire graduate student
** prepare in advance to take advantage of GSoC mechanism
** work with NSF PIs to get interop-related supplements (e.g., MrBayes)

== polish up projects ==

Sheldon:
;phylowidget/viz improvements
:clean up and generalize interface; complete modularization
:integrate with other projects with an outward facing PhyloWS interface
:write-back capability via PhlyoWS

== models ==

transition models

= Proposal =