Summary of the Phyloinformatics Workshop
February 11 and 12, 2001
Sponsored by the San Diego Supercomputer Center, UCSD
and the Deep Gene RCN
La Jolla, California
PURPOSE OF THE WORKSHOP
In an effort to further the recommendations of three recent NSF workshops
convened to advance the construction of the Tree of Life, a group of researchers
gathered at the San Diego Supercomputer Center to identify relevant phyloinformatics
research challenges. At present, the lack of appropriate tools and technologies
for accessing, archiving, querying, and visualizing phylogenetic information
is a fundamental impediment to constructing the Tree of Life. The workshop
was designed to bring together a small, multidisciplinary group of experts
to share ideas and to develop a phyloinformatics research agenda relevant
to the proposed NSF Tree of Life Initiative.
SDSC/UCSD (www.sdsc.edu) or (www.npaci.edu)
(Host) Alison Withey, Assistant Director, SDSC
(Data Intensive Computing Environments)
(Computational Molecular Biology)
(Alliance for Cell Signaling/Biology Workbench)
(Co-Host) Brent Mishler (Comparative Genomics/ Deep Gene)
Mike Freeston (Digital Libraries)
Bill Piel (Tree Base)
Utah State University
Paul Wolf (Organellar Genomics)
John Hanks (Bioinformatics)
February 11, Sunday
9:00 - 9:15 Alison Withey - Welcome and introductions
9:15 - 9:45 Brent Mishler - Introduction to phylogenetic systematics &
9:45 - 10:15 Paul Wolf - Organellar genome biocomplexity project
10:15 - 10:45 Bill Piel - Introduction to Tree Base
10:45 - 11:00 Break
11:00 - 11:30 Michael Gribskov - Phylogenetic databases
11:30 - 12:00 Mike Freeston - Databases/indexing/digital libraries
12:00 - 12:30 Arcot Rajasekar - SDSC Storage Resource Broker and data
12:30 - 1:00 Working lunch and discussion
1:00 - 1:30 Amarnath Gupta/Bertram Ludaescher - Databases and semantic
1:30 - 2:00 Chaitan Baru - Data mining
2:00 - 2:30 Brian Saunders - Demonstration of the Biology Workbench
2:30 - 2:45 Break
2:45 - 5:30 Discussion of potential research agenda and funding opportunities.
6:30 - 8:30 Working Dinner
February 12, Monday
9:00 - 9:30 Mike Bailey - Visualization
9:30 - 12:00 Discussion
12:00 Meeting adjourned.
Based on workshop presentations and subsequent discussion, the group
was able to articulate the following objectives relevant to future research
(1) The group agreed that multidisciplinary research was critical to advancing
a phyloinformatics research agenda.
(2) The group agreed it was important to include the greater phylogenetics
community, educators, and others with a practical need for understanding
phylogenetic relationships (including, for example, those who wish to
use the information for forensic analysis or as a guide to the discovery
of new pharmaceuticals) in the development of the phyloinformatics research
(3) The group agreed that there was a need to train a new generation
of researchers to develop and maintain the tools and technologies that
form the foundation of phyloinformatics.
(1) The group articulated a need to develop a comparative database of
organellar genomic data.
(2) The group expressed a desire to further scientific understanding
of the molecular evolution of organelles.
(3) The group agreed to focus on the resolution of key sections of green
(4) The group agreed that it would be important to focus on the theory
of analysis and issues of scale relating to the spectrum ranging from
total evidence to super trees, with the compartmentalization approach
somewhere in between
(1) The group articulated a need to develop formal metadata standards
to describe phylogenetic data.
(2) The group expressed interest in developing interoperable archives
of phylogenetic data sets, trees and associated software tools based on
the metadata standard.
(3) The group agreed it was important to develop tools to support large-scale
phylogenetic analyses using distributed computing resources and parallel
(4) The group agreed to emphasize the development of innovative and scalable
database techniques for the representation and querying of large tree
(5) The group agreed to focus on the development of tools for data mining
and visualization--within the structure of the Tree of Life, within the
character data from which the tree is derived, and between the Tree of
Life and databases of associated information (such as museum voucher information,
(6) The group articulated a need to build a virtual phylogenetic "workbench"
or "laboratory" consisting of a one-stop, user friendly internet
portal designed to deliver not only the raw data, but also the analytical
and visualization tools required by researchers, educators, and others
with a practical need to understand phylogenetic relationships.