Table Of ContentP A C I F I C SYMPOSIUM O N
BBIOCCOMPUTING 2004
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P A C I F I C SYMPOSIUM O N
BIOCOMPUTING 2004
Hawaii, USA
6-1 0 January 2004
Edited by
Russ 6. Altman
Stanford University, USA
A. Keith Dunker
Indiana University, USA
Lawrence Hunter
University of Colorado Health Sciences Center, USA
Tiffany A. lung
Stanford University, USA
Teri E. Klein
Stanford University, USA
\: World Scientific
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BIOCOMPUTING
Proceedings of the 2004 Pacific Symposium
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PACIFIC SYMPOSIUM ON BIOCOMPUTING 2004
Last spring the PSB organizers engaged in an e-mail conversation on the origins
of our field. This led to the following brief study. According to the Oxford
English Dictionary, biocomputing is defined as the application of computing in
biological research, especially the analysis of statistical data and molecular
structures, and the modeling of biological processes, while bioinformatics is
defined as the science of information and information flow in biological systems,
especially the use of computational methods in genetics and genomics.
Furthermore, the same dictionary indicates that an advertisement in Science,
December 2, 1977, contained the first documented use of biocomputing and that
a biographical sketch in Simulation volume 31, 1978, contained the first
documented use of bioinformatics. The sketch referred to Paulien Hogeweg of
the University of Utrecht as having her main field of research in bioinformatics.
To this day, this university maintains a research group described as “Theoretical
Biology/Bioinformatics,” and Professor Hegeweg continues to publish in this
field.
For the period up until the eve of the first PSB, biocomputing was, by a
slight margin, the most widely used term for our field. For example, for the
period up until December 31, 1995, PubMed searches give 27 hits for the term
computational biology, 14 hits for bioinformatics, and 32 hits for biocomputing.
The picture is quite different now: on the eve of the ninth PSB, computational
biology gives 4,452 hits, bioinformatics gives 4,773 hits, and biocomputing a
mere 147 hits.
An e-mail conversation with Jean Michel Claverie provides an interesting
hypothesis regarding the popularity of the term bioinformatics. Being unaware
of Professor Hogeweg’s use of “bioinformatics,” Professor Claverie
independently coined the term “la bioinformatique molecularie” [Claverie, J. M.,
Caudron, B., and Gerard, 0. (1984) Le systeme d’analyse de sequences de
1’Institute Pastuer (S.A.1.S.P) Biofutur, Juin 35-37]. In the following years, the
term picked up quite well in France. Professor Claverie tells that
“It became increasingly difficult for me and my French colleagues,
when giving seminars in English, to switch back to the accepted English
terms of the time: “computational biology” or “biocomputing.” During
seminars, my tongue slipped many times, such as “I am going to present
some of our new developments in Bioinformatics -sorry-
Biocomputing.. .” One of the clearest instances of this happening many
times over, was in one of the first Waterville Valley meetings
[Macromolecules, Genes and Computers. These important meetings
were organized by Temple Smith. The first one was in August of 19861,
where I first met with people like Lipman, Wilbur, Temple Smith,
Staden, well, all the people from the early NAR special issues, but that
V
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was also well attended (for the first time) by Europeans (Saccone,
Gautier, Grantham, myself, and a few others). I remember some of the
attendance asking me the exact meaning and origin of
“Bioinformatics” ... (Also because I had such a bad French accent!) I
think I remember (this is S O 0 0 old), some Americans being quite
enthusiastic about it, AND THIS IS IMPORTANT, as a way to
distinguish the computational use of computers (when you do calculus
and compute things) from the more “textual”u se of them (sequence text
analysis, sequence alignment, databases, etc), and thus, a great way to
denote the ‘new wave’ from the old computer application
(computational biology, biocomputing, theoretical biology). I think it is
this new ecological niche that made the term quickly popular in
English.”
Despite the gaining popularity of the term bioinformatics, PSB will retain the use
of biocomputing: its definition conveys the breadth of topics embraced by this
meeting. -A. Keith Dunker
PSB 2004 has again been supported by grants from the U.S.
Department of Energy and the National Library of Medicinemational Institutes
of Health. The International Society for Computational Biology and Applied
Biosystems continue to sponsor PSB, and as a result, meeting participants will
once again benefit from travel grants from their generous support.
We look forward to the key addresses by Debbie Nickerson and by
Henry T. Greely. Tiffany Jung again carried out a yeoman’s work of creating
the printed and online proceedings while also providing the backbone for the
administration of the meeting.
Each year we thank the session organizers. Their unselfish and tireless
work gives PSB its special flavor.
Trey Ideker, Eric Neumann, and Vincent Schachter
Computational and Symbolic Systems Biology
Alexander Hartemink and Elan Segal
Joint Learning from Multiple Types of Genomic Data
Hui Wang, Ueng-cheng Yang, and Chris Lee
Alternative Splicing
Francisco de la Vega, Kenneth Kidd, and Andrew Collins
Computational Tools for Complex Trait Gene Mapping
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Olivier Bodenreider, Joyce A. Mitchell, and Alexa T. McCray
Biomedical Ontologies
Sean D. Mooney, Philip E. Bourne, and Patricia C. Babbitt
Informatics Approaches in Structural Genomics
PSB 2004 will also host four tutorials Systems Biology Host/Pathogen
and Other ’Community’ Interactions by Christian Forst, Creating Web Services
for Bioinformatics by Michael D. Jensen, Timothy B. Patrick, and Joyce A.
Mitchell, Network (Reticulated)E volution: Biology, Models, and Algorithms by
C . Randal Linder, Bernard M.E. Moret, and Tandy Warnow, and Modeling
Genetic and Metabolic Networks: Design of High Throughput Experiments by
Kenneth Kauffman, Babatunde A. Ogunnaike, and Jeremy S. Edwards
Again we acknowledge the crucial assistance of those who capably
reviewed the submitted manuscripts. The partial list on the following pages does
not include those who have been left of the list inadvertently or who wished to
remain anonymous,
Participants and those who haven’t yet attended PSB are encouraged to
submit proposals for sessions and tutorials for future meetings. Well-conceived
submissions are vital to the continuing success of PSB.
Aloha!
Pacific Symposium on Biocomputing Co-C hairs October 1, 2003
Russ B. Altman
Department of Genetics & Stanford Medical Informatics, Stanford University
A. Keith Dunker
Center for Computational Biology & Bioinformatics, Indiana University School
of Medicine
Lawrence Hunter
Department of Pharmacology, University of Colorado Health Sciences Center
Teri E. Klein
Department of Genetics & Stanford Medical Informatics, Stanford University
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Thanks to reviewers ...
Finally, we wish to thank the scores of paper reviewers. PSB requires that every
paper in this volume be reviewed by at least three independent referees. Since there
is a large volume of submitted papers, paper reviews require a great deal of work
from many people. We are grateful to all of you listed below and to anyone whose
name we may have accidentally omitted or who wished to remain anonymous.
Frank Alber Melissa Cline Li Jin
Serkan Apaydin Greg Cooper Mike Jones
Manny Ares Ronald Cornet Tommy Kaplan
Gil Ast Nancy Cox Kevin Karplus
Gary Bader Olivier Dameron Jim Kent
Keith Ball Doris Damian Kristian Kersting
D. Rey Banatao David Danks Giselle Knudsen
Ziv Bar-Joseph Warren Delano David Konerding
Serafim Batzoglou Jon Dugan B alaji Krishnapuram
Doug Black Keith Dunker Alain Laederach
Judith Blake Jeremy Edwards Douglas
John Blume Eleazar Eskin Lauffenberger
Olivier Bodenreider Xiangdong Fu Chris Lee
Michael Boehnke Irene Gabashvili Christina Leslie
Erich Bornberg-Bauer Aldo Gangemi Mike Liang
Jim Bowie John Gennari Zhen Lin
Heinz Breu Georg Gerber Ken Lind
Michael Brudno Warren Gish Ross Lippert
William Bruno Chern-Sing Go Irene Liu
Jeremy Buhler Catherine Grasso Jeffrey Long
Martha Bulyk Brenton Graveley Joanne Luciano
Roland Care1 Mike Gruninger Jean MacCluer
Michelle Carillo Brian Haas Nik Maniatis
Simon Cawley Bjarni V. Halldorsson Marc Marti-Renom
Joseph Chang Amir Handzel Hideo Matsuda
Alan Cheng Midori Harris Alexa McCray
Steve Chervitz Steffen Heber Robin McEntire
Derek Chiang Win Hide Loralyn Mears
John Chodera Xiaolan Hu Elaine Meng
Lonnie Chrisman Conrad Huang Eric Minch
Andrew Clark Trey Ideker Joyce Mitchell
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