Phylohackathon 1/Agenda

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This page lists the agenda and logistics information for the 1st Phyloinformatics Hackathon. held at NESCent in Dec 2006.

Documents

Agenda

Participants arrive on Sunday, Dec 10.

Monday, Dec 11

  • 8.00am - Shuttle from hotel to NESCent
  • 8.15am - Coffee & Cookies
  • 8.30am - Introductions to NESCent (10mins each)
NESCent (Kathleen K. Smith)
Education and Outreach (Jory Weintraub)
Informatics (Todd Vision)
  • 9.00am - Participant introductions
  • 9.30am - User stories told by evolutionary biologists (10min each)
Jim Balhoff, NESCent postdoc
Brian Sidlauskas, NESCent postdoc (videocast)
Amy Zanne, NESCent postdoc
  • 10.00am - Coffee Break
  • 10.20am - User stories told by evolutionary biologists, cont'd
Jason Stajich, UC Berkeley, postdoc with J. Taylor, Fungal genome User Story
Stefanie Hartmann: reconciling trees, UNC, postdoc with T. Vision
Alisha Holloway: genomic sequence & expression data, UC Davis, postdoc with D. Begun
Dave Des Marais, Duke, postdoc with M Rausher
Amy Bouck, Determining the genome-wide distribution of Ks, UNC/Duke, postdoc with T. Vision & J. Willis
David Kidd, NESCent postdoc
  • 11.20am - Examples for re-usable phylogenetic libraries (10mins each)
Sendu Bala: Bio::Tree and friends
Rutger Vos: Bio::Phylo
Aaron Mackey: Character data and trees (Bio::CDAT)
  • 12.30pm - Lunch Break
Tobias Thierer: JEBL, PAL
Mark Holder: CIPRES architecture
Sergei Kosakovsky Pond: HyPhy: Simple script plug-in architecture for statistical sequence analyses
  • 1.45pm - Examples for re-usable phylogenetic libraries (10mins each)
  • 2.30pm - Prioritization of use cases
  • 3.45pm - Coffee Break
  • 4.20pm - Toolkit-specific identification of targets of opportunity
  • 5.30pm - Shuttle back to hotel
  • 6.30pm - Shuttle to dinner restaurant(s)

Tuesday, Dec 12

  • 8.15am - Shuttle from hotel to NESCent
  • 8.30am - Coffee & Cookies
  • 9.00am - Standard exchange format for character data, trees, and analytic parameters
David Swofford, Mark Holder, Paul Lewis, Bill Piel, Derrick Zwickl, Rutger Vos: NEXUS format
Chris Zmasek: PhyloXML format
Open discussion
  • 10.00am - Coffee Break
  • 10.20am - Stand-ups on toolkit-specific targets of opportunity
  • 10.40am - Programmming in groups
  • 12pm - Lunch Break
  • 1.30pm - Programming in subgroups
  • 3.00pm - Coffee Break
  • 3.20pm - Programming in subgroups
  • 5.30pm - Shuttle back to hotel
  • 6.30pm - Shuttle to dinner restaurant(s)

Wednesday, Dec 13

  • 8.15am - Shuttle from hotel to NESCent
  • 8.30am - Coffee & Cookies
  • 9.00am - Background and Outlook presentation (30mins)
Bill Piel: Storing phylogenies in RDMSs and querying on tree topology
  • 9.30am - Open round-table discussion (led by Bill Piel):
  1. Data and data types that tree node annotation is typically comprised of
  2. How to represent distributions of trees
  • 10.00am - Coffee Break
  • 10.20am - Programming in subgroups
  • 12pm - Lunch Break
  • 1.30pm - Programming in subgroups
  • 3.00pm - Coffee Break
  • 3.20pm - Programming in subgroups
  • 5.00pm - Reception with NESCent resident scientists
  • 6.00pm - Shuttle back to hotel
  • 7.00pm - Shuttle to dinner restaurant(s)

Thursday, Dec 14

  • 8.15am - Shuttle from hotel to NESCent
  • 8.30am - Coffee & Cookies
  • 9.00am - Programming in subgroups
  • 10.00am - Coffee Break
  • 10.20am - Programming in subgroups
  • 12pm - Lunch Break
  • 1.30pm - Programming in subgroups
  • 3.30pm - Coffee Break
  • 4.00pm - Programming in subgroups
  • 5.30pm - Shuttle back to hotel
  • 6.30pm - Shuttle to dinner restaurant(s)

Friday, Dec 15

  • 8.15am - Shuttle from hotel to NESCent
  • 8.30am - Coffee & Cookies
  • 9.00am - Programming in subgroups
  • 10.30am - Coffee Break
  • 10.50am - Programming in subgroups
  • 12pm - Lunch Break
  • 1.00pm - Report back from subgroups
  • 3pm - Wrap-up, future and follow-up plans
  • 4pm - Adjourn