Phylohackathon 1/Agenda
From NESCent Informatics Wiki
This page lists the agenda and logistics information for the 1st Phyloinformatics Hackathon. held at NESCent in Dec 2006.
Contents |
Documents
- Jim Balhoff, User Story (PDF)
- Brian Sidlauskas, User Story (PDF)
- Alisha Holloway, User Story (PDF)
- Jason Stajich, User Story (PDF)
- Stefanie Hartmann, User Story (PDF)
- Amy Bouck, User Story (PDF)
- Rutger Vos, BioPhylo (PDF)
- Arlin Stoltzfus, Core EIG Use Cases (PDF)
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):
- Data and data types that tree node annotation is typically comprised of
- 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
