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NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance.
This study was supported by Contract No. DE-AT01-03ER25552 between the National Academy of Sciences and the Department of Energy. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project.
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COMMITTEE ON MATHEMATICAL SCIENCES RESEARCH FOR DOE’S COMPUTATIONAL BIOLOGY
MAYNARD V. OLSON,
University of Washington,
Chair
PETER J. BICKEL,
University of California at Berkeley
JACK D. COWAN,
University of Chicago
NINA FEDOROFF,
Pennsylvania State University
LESLIE GREENGARD,
New York University
RICHARD HUDSON,
University of Chicago
JAMES KEENER,
University of Utah
ROBERT LIPSHUTZ,
Affymetrix, Inc.
JILL P. MESIROV,
Massachusetts Institute of Technology
CLAUDIA NEUHAUSER,
University of Minnesota
STANISLAV Y. SHVARTSMAN,
Princeton University
GARY D. STORMO,
Washington University
MICHAEL S. WATERMAN,
University of Southern California
PETER G. WOLYNES,
University of California at San Diego
WING H. WONG,
Stanford University
JOHN WOOLEY,
University of California at San Diego
Staff
SCOTT WEIDMAN, Director,
Board on Mathematical Sciences and Their Applications
JENNIFER SLIMOWITZ, Program Officer (through February 18, 2005)
BARBARA WRIGHT, Administrative Assistant
BOARD ON MATHEMATICAL SCIENCES AND THEIR APPLICATIONS
DAVID W. McLAUGHLIN,
New York University,
Chair
TANYA STYBLO BEDER,
Tribeca Investments, LLC
PATRICK L. BROCKETT,
University of Texas at Austin
ARAVINDA CHAKRAVARTI,
Johns Hopkins University School of Medicine
PHILLIP COLELLA,
Lawrence Berkeley National Laboratory
LAWRENCE CRAIG EVANS,
University of California at Berkeley
JOHN E. HOPCROFT,
Cornell University
ROBERT KASS,
Carnegie Mellon University
KATHRYN B. LASKEY,
George Mason University
C. DAVID LEVERMORE,
University of Maryland
ROBERT LIPSHUTZ,
Affymetrix, Inc.
CHARLES M. LUCAS,
AIG
CHARLES MANSKI,
Northwestern University
JOYCE McLAUGHLIN,
Rensselaer Polytechnic Institute
PRABHAKAR RAGHAVAN,
Verity, Inc.
STEPHEN M. ROBINSON,
University of Wisconsin-Madison
EDWARD WEGMAN,
George Mason University
DETLOF VON WINTERFELDT,
University of Southern California
Staff
SCOTT WEIDMAN, Director,
Board on Mathematical Sciences and Their Applications
JENNIFER SLIMOWITZ, Program Officer (through February 18, 2005)
BARBARA WRIGHT, Administrative Assistant
For more information on BMSA, see its Web site at http://www7.nationalacademies.org/bms
Preface
This report was commissioned by the Office of Advanced Scientific Computing Research (OASCR) at the Department of Energy (DOE). This office, which has broad responsibilities for applications of mathematics and computing to all fields of science of importance to DOE, sought advice as specified in the charge to the committee:
The study will recommend mathematical sciences research activities to the Department of Energy that will enable science to make effective use of the large amount of existing genomic information and the much larger and more diverse collections of structural and functional genomic information that are being created. The recommended activities should cover both current research needs and also include some higher-risk research that might lead to innovative approaches for the future.
In discussions with OASCR officials, it became apparent that the intent was to sponsor a broad, scientifically based view of the opportunities that now lie at the interface between the mathematical sciences and biology. “The mathematical sciences” was to be broadly defined to include statistics, computational science, and all areas of applied mathematics.1 Although the Department of Energy is an agency with deep roots in applying the mathematical sciences to the physical sciences—as well as a pioneer in selected biological applications such as protein-structure de-
termination and genome sequencing—there was no intent that the committee analyze specific DOE programs or restrict itself to DOE’s existing programmatic boundaries. Hence, the recommendations are stated in general terms and are applicable to programs at any of the funding organizations whose missions encompass the mathematical sciences, biology, and the interactions between these fields, including but not limited to DOE. The committee has worked very hard to provide substantiated guidance about the scientific opportunities that these organizations are poised to support.
This report has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with procedures approved by the NRC’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institutional standards for objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following individuals for their review of this report:
James Collins, Boston University,
Terry Gaasterland, Rockefeller University,
David Haussler, University of California at Santa Cruz,
Douglas Lauffenburger, Massachusetts Institute of Technology, and
Simon Levin, Princeton University.
Although the reviewers listed above have provided many constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by Ronald Douglas, Texas A&M University. Appointed by the National Research Council, he was responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this report rests entirely with the authoring committee and the institution.
In addition, the committee thanks Mark Daly, Avner Friedman, and Alan Perelson for their remarks and suggestions during the study process.
