NATIONAL COLLABORATORIES

Applying Information Technology for Scientific Research

Committee on a National Collaboratory: Establishing the User-Developer Partnership

Computer Science and Telecommunications Board

Commission on Physical Sciences, Mathematics, and Applications

National Research Council

National Academy Press
Washington, D.C. 1993



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National Collaboratories: Applying Information Technology for Scientific Research NATIONAL COLLABORATORIES Applying Information Technology for Scientific Research Committee on a National Collaboratory: Establishing the User-Developer Partnership Computer Science and Telecommunications Board Commission on Physical Sciences, Mathematics, and Applications National Research Council National Academy Press Washington, D.C. 1993

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National Collaboratories: Applying Information Technology for Scientific Research 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 competencies and with regard for appropriate balance. This report has been reviewed by a group other than the authors according to procedures approved by a Report Review Committee consisting of members of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Frank Press is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Robert M. White is president of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Kenneth I. Shine is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy's purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Frank Press and Dr. Robert M. White are chairman and vice chairman, respectively, of the National Research Council. Support for this project was provided by the National Science Foundation (Grant No. CDA-9021110). Library of Congress Catalog Card Number 93-83795 International Standard Book Number 0-309-04848-6 Copyright 1993 by the National Academy of Sciences. All rights reserved. Available from: National Academy Press 2101 Constitution Avenue, N.W. Washington, D.C. 20418 B-122 Printed in the United States of America

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National Collaboratories: Applying Information Technology for Scientific Research COMMITTEE ON A NATIONAL COLLABORATORY: DEVELOPING THE USER-DEVELOPER PARTNERSHIP VINTON G. CERF, Corporation for National Research Initiatives, Chairman ALASTAIR G.W. CAMERON, Harvard College Observatory, Vice-Chairman JOSHUA LEDERBERG, Rockefeller University CHRISTOPHER T. RUSSELL, University of California at Los Angeles BRUCE R. SCHATZ, University of Arizona PETER M.B. SHAMES, California Institute of Technology LEE S. SPROULL, Boston University ROBERT A. WELLER, Woods Hole Oceanographic Institution WILLIAM A. WULF, University of Virginia Staff MARJORY S. BLUMENTHAL, Director MONICA KRUEGER, Staff Officer ARTHUR L. McCORD, Project Assistant (through February 1993) LESLIE M. WADE, Project Assistant

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National Collaboratories: Applying Information Technology for Scientific Research COMPUTER SCIENCE AND TELECOMMUNICATIONS BOARD WILLIAM A. WULF, University of Virginia, Chairman RUZENA BAJCSY, University of Pennsylvania DAVID J. FARBER, University of Pennsylvania SAMUEL H. FULLER, Digital Equipment Corporation JAMES GRAY, Digital Equipment Corporation JOHN L. HENNESSY, Stanford University MITCHELL D. KAPOR, Electronic Frontier Foundation SIDNEY KARIN, San Diego Supercomputer Center RICHARD M. KARP, University of California at Berkeley KEN KENNEDY, Rice University ROBERT L. MARTIN, Bell Communications Research ABRAHAM PELED, IBM T.J. Watson Research Center WILLIAM PRESS, Harvard College RAJ REDDY, Carnegie Mellon University JEROME SALTZER, Massachusetts Institute of Technology CHARLES L. SEITZ, California Institute of Technology MARY SHAW, Carnegie Mellon University EDWARD SHORTLIFFE, Stanford University School of Medicine IVAN E. SUTHERLAND, Sun Microsystems LAWRENCE T. TESLER, Apple Computer Inc. MARJORY S. BLUMENTHAL, Director HERBERT S. LIN, Senior Staff Officer MONICA KRUEGER, Staff Officer GREG MEDALIE, Staff Officer FRANK PITTELLI, CSTB Consultant RENEE A. HAWKINS, Staff Associate DONNA F. ALLEN, Administrative Assistant LESLIE WADE, Project Assistant

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National Collaboratories: Applying Information Technology for Scientific Research COMMISSION ON PHYSICAL SCIENCES, MATHEMATICS, AND APPLICATIONS RICHARD N. ZARE, Stanford University, Chairman JOHN A. ARMSTRONG, IBM Corporation PETER J. BICKEL, University of California at Berkeley GEORGE F. CARRIER, Harvard University GEORGE W. CLARK, Massachusetts Institute of Technology MARYE ANNE FOX, University of Texas AVNER FRIEDMAN, University of Minnesota SUSAN L. GRAHAM, University of California at Berkeley NEAL F. LANE, Rice University ROBERT W. LUCKY, Bell Communications Research CLAIRE E. MAX, Lawrence Livermore National Laboratory CHRISTOPHER F. McKEE, University of California at Berkeley JAMES W. MITCHELL, AT&T Bell Laboratories RICHARD S. NICHOLSON, American Association for the Advancement of Science ALAN SCHRIESHEIM, Argonne National Laboratory A. RICHARD SEEBASS III, University of Colorado KENNETH G. WILSON, Ohio State University NORMAN METZGER, Executive Director

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National Collaboratories: Applying Information Technology for Scientific Research Preface On December 13, 1991, at the request of the National Science Foundation, the Computer Science and Telecommunications Board (CSTB) of the National Research Council convened the Committee on a National Collaboratory: Establishing the User-Developer Partnership. The committee was charged to study and report on the need for and potential of information technology to support collaboration in the conduct of scientific research. An increasing number of scientific problems call for or would benefit from collaboration among researchers, while improvements in the capabilities, ease of use, and availability of computing and communications systems suggest that information technology can facilitate and enable collaboration. The concept of a national collaboratory was first explored in a white paper written by William Wulf while he was assistant director of the National Science Foundation's Directorate for Computer and Information Science and Engineering.1 Dr. Wulf coined the term "collaboratory" by combining the words "collaboration" and "laboratory." Initially proposed as a single all-encompassing entity, a national collaboratory was defined in the white paper as ''a center without walls, in which the nation's researchers can perform their research without regard to geographical location—interacting with colleagues, accessing instrumentation, sharing data and computational resources, [and] accessing information in digital libraries." The proposed collaboratory depended on a network of computers to perform its functions, but it was more than a mere interconnection of computers; it was envisioned as offering a complete infrastructure of software, hardware, and networked resources to enable a full range of collaborative work among scientists. The national collaboratory concept was further explored in March 1989 at a 2-day workshop organized by biologist Joshua Lederberg and information technologist Keith Uncapher and held at the Rockefeller University. The workshop enthusiastically endorsed the concept and in general terms identified the technologies and services that would have to exist or be developed to provide the necessary infrastructure. The report of that workshop2 and the diagram of collaboratory technologies (Appendix A) produced by Mark Stefik proved valuable resources for this committee. This report is the result of a year-long effort to study the needs of scientists for computing and information technology to facilitate collaboration, and to relate those needs to the development and use of collaboratories. The members of the committee met frequently during 1992 both in face-to-face discussions and by teleconference. To obtain information about scientists' requirements for collaboration and supporting technology and to get feedback on how collaboratories and information technology might facilitate research in the sciences, the committee held three 2-day workshops in specific disciplines: molecular 1   Although Dr. Wulf became chair of CSTB in July 1992, he recused himself from CSTB oversight of this project and was not involved in discussions with the National Science Foundation about terms of the grant that supported this project. He served as assistant director for Computer and Information Science and Engineering from May 1988 to May 1990. 2   Towards a National Collaboratory, the unpublished report of an invitational workshop held at the Rockefeller University, March 17-18, 1989 (Joshua Lederberg and Keith Uncapher, co-chairs).

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National Collaboratories: Applying Information Technology for Scientific Research biology (specifically genome research), oceanography, and space physics (Appendix B). These disciplines were chosen because they represent big and small science, a wide spectrum of technical and theoretical sophistication, and a broad range of institutions and styles of research, and they derive support from a variety of sources, including the National Science Foundation, the National Institutes of Health, the National Aeronautics and Space Administration, the (Defense) Advanced Research Projects Agency, the Office of Naval Research, and the Department of Energy. The workshops provided a rare opportunity for participants—scientists actively doing research in molecular biology, oceanography, and space physics; scientists and technologists specializing in computing, communications, and information science; and a sociologist specializing in the use of computing technology by scientists—to consider together a number of issues affecting the potential to build useful collaboratories. As the study progressed, the idea of developing a single national collaboratory was replaced by the idea of developing multiple scientific collaboratories. These collaboratories would share network and computing resources, software, and infrastructure but would have unique features dictated by the needs of particular scientific disciplines. Recognition of those varying needs drove the shift in focus from a single national collaboratory to many scientific collaboratories. Much of the report writing and editing was carried out using electronic mail on the Internet. The report's first four chapters relate the needs of scientists for information technology, generally to support collaboration and specifically to develop collaboratories. Chapters 2 and 3 address collaboration challenges and opportunities in oceanography and space physics, respectively. Chapter 4 examines a computationally intensive branch of molecular biology, genome research, and provides an information technologist's perspective on the building and designing of collaboratories to support genome studies. Chapter 5 provides a synthesis of the committee's observations on collaboratories, and Chapter 6 contains the committee's recommendations. The time and talents of many people contributed to this report. The creative and thoughtful contributions of the workshop participants were essential to the committee's work. The committee thanks Tom Dickey of the University of Southern California for his substantial contributions to the report and the oceanography workshop, Bob Kahn of the Corporation for National Research Initiatives and Connie Pechura of the Institute of Medicine for their wise counsel, and the anonymous reviewers for their thought-provoking comments. The committee is also grateful to David Kingsbury of the George Washington University Medical Center; Peter Pearson of the Genome Data Base at Johns Hopkins University, who helped clarify the discussion of issues in genome research; John Wooley of the Department of Energy; and Chris Overton of the University of Pennsylvania. Of course, responsibility for the final content rests with the committee members. Vinton G. Cerf, Chairman Alastair G.W. Cameron, Vice-Chairman Committee on a National Collaboratory: Establishing the User-Developer Partnership

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National Collaboratories: Applying Information Technology for Scientific Research Contents     EXECUTIVE SUMMARY   1 1   SCIENCE, COLLABORATION, AND INFORMATION TECHNOLOGY   5     Increase in Volume of Information and Complexity,   5     Information Technology for Research and Collaboration,   6     The Collaboratory Concept,   7     This Study,   10     Notes,   11 2   BUILDING COLLABORATORIES FOR OCEANOGRAPHY   12     Oceanographic Research,   12     Field Experimentation,   13     Modeling,   16     Collaborative Research in Oceanography,   17     International Initiatives,   17     World Ocean Circulation Experiment,   17     Tropical Ocean-Global Atmosphere Program,   17     Additional Interdisciplinary Programs,   20     Using Collaboratory Components to Facilitate Research,   20     Improving Access to Colleagues,   21     Electronic Communication,   22     Educational Workshops,   23     Improving Access to Data,   24     Providing Tools for Collaboration in Oceanography,   25     TOGA Data Catalog,   25     Globe Data Catalog,   26     Tour Tool,   27     Cruise Planning Tool,   27     Ontology Tool,   28     Attributes of a Useful Collaboratory for Oceanography,   28     Interoperability,   28     Transparency,   29     Customizability,   29     Integrity and Extensibility,   29     Notes,   29 3   BUILDING COLLABORATORIES FOR SPACE PHYSICS   31     Space Physics Research,   31     Data Collection and Instrumentation,   31

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National Collaboratories: Applying Information Technology for Scientific Research     Methods and Technologies for Data Analysis,   32     Examples of Collaborative Efforts in Space Physics Research,   33     Initial and Ongoing Collaborative Programs,   33     Space Physics Analysis Network,   33     Coordinated Data Analysis Workshops,   34     Active Magnetospheric Particle Tracer Explorer/Charge Composition Explorer,   35     Sondre Stromfjord Observatory Testbed,   35     Solar-Terrestrial Energy Program,   36     Geospace Environment Modeling Program,   36     International Solar-Terrestrial Physics Program,   37     Space Physics Data System: A Collaboratory of One,   37     New Opportunities Provided by a Collaboratory for Space Physics,   38     Components of a Collaboratory Infrastructure,   39     Note,   40 4   BUILDING COLLABORATORIES FOR MOLECULAR BIOLOGY   41     Genome Research in Molecular Biology,   43     Trends in Technology to Support Collaborative Genome Research,   44     Current Database Systems,   44     MedLine,   45     GenBank,   45     Genome Data Base,   47     Future Information Systems—Toward a Working Collaboratory,   48     Basic Components and Research Prototypes,   49     Remote Analysis Servers—Blast,   49     Interconnecting Archival Databases—Entrez,   49     Community Information Systems,   51     Basic Elements and Capabilities,   51     A Model Collaboratory—Worm Community System,   52     Opportunities to Enhance Research,   53     Notes,   55 5   BUILDING AND USING NATIONAL COLLABORATORIES   56     Identifying Basic Capabilities a Collaboratory Should Support,   56     Providing Basic Capabilities—Technical Considerations,   57     Interconnecting Data Sources,   57     Sharing and Applying Programs,   58     Controlling Remote Instruments,   60     Supporting User Interaction,   60     Achieving Transparency,   62     Acknowledging Context—Social and Institutional Considerations,   63     Issues for Individual Scientists,   63     Costs for Individual Scientists of Using Computer-based Collaboration Technology,   65     Education and Training,   66     User-Developer Partnerships,   66     Issues for Individual Institutions,   68     Providing Local Infrastructure Support,   68     Managing the Results of Increased Interaction,   69

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National Collaboratories: Applying Information Technology for Scientific Research     Issues in Funding for Collaboratory Infrastructure,   70     Making a Start,   71     Notes,   71 6   PROVIDING FOR A NATIONAL COLLABORATORY PROGRAM   73     Note,   77     REFERENCES   78     APPENDIXES         A Elements of a Functional Collaboratory,   83     B Workshop Programs and Participants,   86     C Rules Governing Access to and Use of the CDAW-9 Database,   95     D Training Computational and Mathematical Biologists,   97

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