Previous Meetings
"From the genome to the tree of life"
San Diego, California
11-12 February 2001
Sonoma, California
17 February

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


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 ( or (
(Host) Alison Withey, Assistant Director, SDSC
(Data Intensive Computing Environments)
Chaitan Baru
Amarnath Gupta
Bertram Ludaescher
Arcot Rajasekar
(Scientific Visualization)
Mike Bailey
(Computational Molecular Biology)
Michael Gribskov
(Alliance for Cell Signaling/Biology Workbench)
Brian Saunders

UC Berkeley
(Co-Host) Brent Mishler (Comparative Genomics/ Deep Gene)

UCSB/Aberdeen University
Mike Freeston (Digital Libraries)

Leiden University
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 & Deep Gene
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 archives

12:30 - 1:00 Working lunch and discussion

1:00 - 1:30 Amarnath Gupta/Bertram Ludaescher - Databases and semantic mediation
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 in phyloinformatics.

General goals
(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 agenda.

(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.

Phylogenetics goals
(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 plant phylogeny.

(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

Informatics goals
(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 computing techniques.

(4) The group agreed to emphasize the development of innovative and scalable database techniques for the representation and querying of large tree structures.

(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, for example).

(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.

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