Assembling the Tree  of Life

Meeting Agenda:

Friday, November 19th:

FDIC - L. William Seidman Center, 3501 Fairfax Drive, Room 3086, Arlington, Virginia Main Auditorium

time name   speakers
1:00pm Welcome   Dr. Michael Willig, Division Director (DEB), Dr. Penny Firth, Acting Division Director, (DEB) and Dr. James Woolley, Program Director (AToL)
1:15pm Introduction [pdf] Dr. Brent Mishler, University of California, Berkeley
1:20pm 10 min. talks by the PI (or designate) of each of the 22 main funded projects, with three 20 minute break/discussion periods. Each to outline general scientific goals (leaving the details to the poster presentations), plus their group's approaches to project management, coordination, outreach, and training.
2001 Cohort: talk poster
Annelids – Dr. Damhnait McHugh [pdf] [jpg]
Arthropods – Dr. Jerry Regier [pdf] [pdf]
Chloroplast genomics – Dr. Robert Jansen    
Hexapods – Dr. Mark Clement [pdf]  
2002 Cohort: talk poster
Archosaurs - Dr.Mark Norell [pdf]  
Bacteria – Dr. Jonathan Eisen [pdf] [pdf]
Birds – Dr. Shannon Hackett [pdf] [pdf]
Fungi - Dr. David Hibbett [pdf] [1][2]
Green Plants – Dr. Charles O'Kelly [pdf] [pdf]
Nematodes – Dr. David Fitch [pdf] [pdf]
Spiders – Dr. Ward Wheeler   [pdf]
2003 Cohort: talk poster
Amphibians – Dr. David Cannatella [pdf]  
Diptera – Dr. Brian Wiegmann [pdf] [pdf]
Hymenoptera – Dr. John Heraty [pdf] [1][2]
Marine Symbiosis – Dr. Mary Beth Saffo [pdf] [pdf]
Phylogenomics Toolbox – Dr. Mike Sanderson [pdf] [pdf]
Protostomes – Dr. Gonzalo Giribe [pdf] [pdf]
Squamates - Dr. John Weins [pdf]  
2004 Cohort: talk poster
Ants - Dr. Phil Ward [pdf] [pdf]
Angiosperms – Dr. Mike Donoghue [pdf]  
Cypriniform fishes – Dr. Richard Mayden [pdf]  
Microbial Eukaryotes - Dr. Laura Katz [pdf] [pdf]

Saturday, November 20th:

Emphasis on informatics (NSF, Stafford I, Room 375)

time name   speakers
7:30am Refreshments – Foyer outside of Room 375 CIPRES in Relation to AToL – Room 375
8:00am General introduction to CIPRES by the lead PI Bernard Moret   poster: [pdf]
8:10am Database group [pdf] Dr. Dan Miranker
8:20am Simulation group [pdf] Dr. Junhyong Kim
8:30am Algorithm group [pdf] Dr. Tandy Warnow
8:40am Software development group [pdf] Dr. Dave Swofford
8:50am Central resource, San Diego Supercomputer Center [pdf] Dr. Mark Miller
9:00am Break    
9:15am Discussion of how to develop linkages between CIPRES and the individual AToL projects.    
10:00am Break    

Presentations of AToL-associated Informatics Approaches – Room 375

time name   speakers
10:15am The bioinformatic structure of Assembling the Fungal Tree of Life (AFTOL) [pdf] Drs. Frank Kauff, Cymon Cox and François Lutzoni
10:30am The uBio project - an internet based biological name server and how it can be used to
organize information about organisms on the internet.
[pdf] Drs. Dave Remsen and David Patterson
10:45am An organellar annotation program (DOGMA) and a Chloroplast Genome database.   Dr. Robert Jansen
11:00am Bioinformatics at TIGR in support of AToL [pdf] Dr. Jonathan Badger
11:15am Visualizing phylogenetic trees, and linking them to databases [pdf] Dr. Brent Mishler and Rebecca Shapley
11:30am Modeling reticulate evolution [pdf] Dr. Randy Linder
11:45am Digital Library of Vertebrate Morphology (   Dr. Tim Rowe
12:00pm Lunch on your own.    
  Database Workshop:   Organizer: Dr. Susanne Schulmeister
Reports on recent workshops held elsewhere, and presentation of existing projects on phylogenetic databasing.
1:00pm Introduction to databases; data standards [pdf] Dr. Dan Miranker
1:40pm Report on the Tallahassee workshop and its results   Dr. Frederik Ronquist
2:05pm Report on the Gainesville workshop and software of the Angiosperm AToL   Dr. Reed Beaman
2:30pm MorphoNet [pdf] Dr. John Heraty
2:55pm Break    
3:10pm MorphoBank   Dr. Maureen O'Leary
3:35pm MorphBank   Dr. Frederik Ronquist
4:00pm A database for the Archosauria AToL   Dr. Mark Norell
4:25pm General Discussion    
6:00pm Meeting adjourns for the evening.    

Sunday, November 21st:

Data, analysis, documentation, external relationships NSF, Stafford I, 3rd Floor

time name   speakers
7:30am Refreshments – Foyer outside of Room 375    
  Data and analysis issues:
A series of 9 discussions, led and moderated by pairs of people who are interested in the area, yet have different perspectives. Moderators will present short, informal, and provocative points of view, followed by open discussion.
8:00am Integrating morphological, DNA sequence, and genomic data   Moderators: Drs. Dave Cannatella and Paul Wolf
  Integrating fossils into phylogenetics   Moderators: Drs. Peter Makovicky and Tim Rowe
  Integrating parsimony, likelihood, and Bayesian approaches   Moderators: Drs. Joel Cracraft and Dick Olmstead
9:10am Break    
9:25am Concatenating analyses done at different phylogenetic scales   Moderators: Drs. Brent Mishler and Mike Sanderson
  The effect of horizontal transfer on phylogenetic reconstruction and tree representation   Moderators: Drs. Jonathan Eisen and Randy Linder
  The effects of convergence and parallelism on phylogenetic reconstruction, and how
to include in simulations?
  Moderators: Drs. Junhyong Kim and Jack Sites
10:35am Break    
10:50am Interfacing tree of life projects with "traditional" monographic systematics   Moderators: Drs. Shannon Hackett and Phil Ward
  New approaches to electronic publishing, and how that will affect AToL   Moderators: Drs. Susanne Schulmeister and Dina Mandoli
  Data-mining for analysis from large databases   Moderators: Drs. Amy Driskell and David Hibbett


Lunch on your own.    
  Plenary Session: Data Analysis and Issues – Room 375    
1:00pm Reports from each discussion. Discussion, opportunities for comments and synthesis.
  Plenary Session: Management Issues:
A series of seven open discussions on selected topics, with attendees asked to share their experiences (good and bad), plans, and expectations. These will be moderated by members of the workshop steering committee.
3:40pm How best to coordinate an AToL project? What mechanisms work, and what don't?   Moderator: Dr. Dina Mandoli
4:00pm How best to coordinate across AToL projects? Do we need a general AToL website (and who will run it!). When should the next meeting be?   Moderator: Dr. Brent Mishler
4:20pm How best to accomplish training within the AToL and in the scientific community as a whole?   Moderator: Dr. Paula Mabee
4:40pm What is or should be the relationship between AToL projects and museums and herbaria (in terms of documentation by vouchers and other physical materials)?   Moderator: Dr. Francois Lutzoni
5:00pm How do we involve the public? How do we reach out to under-represented groups in science?   Moderator: Dr. Laura Katz
5:20pm How do we reach out to other communities of researchers (i.e., ecology, physiology, genomics?)   Moderator: Dr. Jon Eisen
5:40pm How do we further develop relationships with international colleagues?   Moderator: Dr. Gustavo Hormiga
6:00pm Meeting Adjourns    
Official NSF Assembling the Tree of Life Project webpage.
We acknowledge NSF funding under award #0502081

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