Detailed notes from the hackathon meeting

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Detailed notes from the hackathon meeting

Day 1 meeting notes

Introductory session

  • Welcome (Hilmar Lapp, NESCent)
  • Introduction to NESCent activities (Todd Vision, NESCent informatics director)
  • Staff introductions (Danielle)
    • Jack D'Ardenne - IT support
    • Danielle Wilson - logistics
    • Lori Slack - accounting (reimbursements)
    • Candace Brown - front desk
  • Evaluation survey (Jonathon Cummings)
    • questions or comments to Jonathon at his email address (<first>.<last>
  • Participant introductions (all)
  • Reminder of interop technologies
    • phyloWS - Hilmar, Rutger
    • CDAO - Arlin, Enrico, Brandon
    • nexml - Rutger
  • IRC channel

Open Space Pitches

rule: you're either learning, or contributing; if not, move on

Hilmar : integrated database of trees
  • technology
    • integration db possibly BioSQL
  • nexml exchange format
  • phyloWS access
  • purposes: facilitates integration
  • problems to solve: nexml --> db (use bio::phylo and biosql?)
Rutger : Java API library to nexml
Vivek : API for CDAO using semantic framework
  • go from xml to CDAO, then use reasoner
  • use Jena library
  • create a viewer
Bill : clarify OTU concept to specify search interface

aka "intelligence for OTU labels"

  • how to support queries like "give me all trees where bats are monophyletic"
  • how to make taxonomy glue work better
Sheldon : high-level UI to mash-up tree metadata
  • exploit integrative technology developed here
  • e.g., web app based on Perl-CGI, PhyloWidget, AJAX etc.
Ryan : middleware to expose phyloWS

generic middleware end implementation of phylows for which we can

Mark : mashup of LANL HIV data
  • markup clinical pathogen sequence data
  • create queries based on ontologies
  • adapt technology such as bioperl to respond to queries
Greg : visualizing trees and metadata
  • e.g., demo app
  • or create standard for visualizations, like google's charts api
Roger : integrating classifications with phylogenetic data
  • a meta-pitch across many projects
  • working with taxonomies not phylogenetically based
  • e.g., take catalog of life and integrate with CDAO or nexml
Arlin : taxonomy resolution service
  • see mailing list
Matt Y: taxonomy mapping methods
  • map one taxonomy to another based on content
Matt K: defining what data users want and how to deliver it
  • the PaleoDB as a resource - What data do non-paleontologists want and should the PaleoDB make that available?

Subgroup reports

See Subgroups for details on each.

See revision 5099 of this page for Arlin's original notes. These notes were moved to the subgroups' individual pages.

Report on logistics


Boot camp session I

  • Syntax and semantics (Arlin) (presentation: File:Syntax and semantics.ppt)
  • nexml (Rutger) (presentation)
    • quick links to resources
    • a walk throught the schema and its main elements (uses nexml project page)
      • root element
      • discussion: versioning the namespace
      • characters, states
      • sequences
      • discussion: symbol uniqueness in states element (ought to require symbols to be unique)
      • validating if a "sequence" is a sequence
      • trees are collections of nodes and edges
      • discussion: what are restrictions on tree topology implied by schema?
      • sets ("class" elements and class attributes)

Day 2 meeting notes

Tuesday, March 10, 1009.

Boot camp session II

First work session (programming)

See the individual Subgroups' pages for their Standup reports.

Day 3 Meeting Notes

Wednesday, March 11, 2009.