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

Montpelier

• Cost per person:
  • $ 900 from major US airport to Montpelier
  • $ 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)
    • 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

Ideas

Projects focused on consolidating our gains and serving the community of users:

1. 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.
2. set up an EvoIO portal (translation, data set curation, etc)
3. develop an online course complete with information resources, demos, and assignments

Projects focused on building foundations and serving the community of developers:

1. widen the domain by including viral phylogenetics and molecular epidemiology
2. ontology, including sticky problems (CDAO relations and upper-level categories) and annotation support (names of programs and file formats)
3. 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

widen the domain

molecular epidemiology

models

transition models