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Assessment of International Research and Development in Systems Biology

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Final report


The final report on Systems Biology is now available in PDF format.
Individual chapters are also available.

U.S. Final Workshop held at NSF March 11th, 2005

Purpose

The goal of this study is to gather information on the worldwide status and trends in systems biology: “Network Behavior in Biological Systems” and to disseminate it to government decision makers and the research community

The study panelists will gather information on systems biology abroad useful to the U.S. government in its own R&D programs, and will critically analyze and compare the research in the United States with that being pursued in Japan, Europe, or other major industrialized countries. This information will serve the following purposes:

Scope

For the past 40 years the paradigm for predicting phenotype has focused on single gene defects.

This extraordinarily powerful approach has been the major contributor to an understanding of the function of individual genes and proteins. It seems less likely that it will yield an understanding of complex biological behavior, from individual cellular activities such as motility to the operation and integration of organ systems. Indeed, the underlying assumption for all the excitement surrounding systems biology is that phenotype is governed by the behavior of networks, rather than simply the consequence of individual gene action. In its essence systems biology is the development of approaches to the understanding of biological networks and consequently to the determination of biological phenotype. Furthermore, although a variety of tools may be used to identify the components and connectivity of the networks, a key approach of systems biology is to understand the operation of networks through the application of computational methods (simulation and modeling). Understanding input-output behavior of the network, i.e. the relationship of initiating signals to the phenotypic outcome, is more effectively reached through the systems approach, since network behavior is more complex than can be understood intuitively. The models are then modified to account for new experimental results. This iterative process can yield models which may ultimately be queried in ways that are difficult or impossible to accomplish experimentally.

A primary goal of this study is to evaluate the state of the art in using computational approaches to understand the behavior of biological networks in determining phenotype. A related goal is to examine the effectiveness of approaches for linking experimentally determined (in vivo) parameters with computational models (in silico) of network behavior. This study will include examination of issues such as modularity, robustness, motifs, and topology of networks, as well as tools to determine temporal and spatial relationships. The results of the applications of systems biology will be of interest to illustrate effective methods.

The following selection of topics may be suitable to cover the scope of the study to achieve the above goals. Each may stand as specific chapters in the panel’s report.

Finally, beyond the above issues, the study may also address the following topics:

U.S. Workshop held at NSF June 4th, 2004 


Overseas Site Visits

Host Presentations

United Kingdom

Germany

The Netherlands

Free University Amsterdam (Vrije Universitaet)

EU Projects Workshop


EU Projects Workshop Report on Systems Biology (December 2004)

Panelists

[photo: Marvin
	   Cassman]
Marvin Cassman
(panel chair)
  • Consultant
    875 Haight Street
    San Francisco, CA 94117
  • e-mail: mcassman <at> sbcglobal.net
[photo: Adam
	   Arkin]
Adam Arkin
  • Assistant Professor of Bioengineering & Chemistry
    University of California, Berkeley
    College of Chemistry, Bioengineering Department
    Mail Stop: Calvin Lab
    Berkeley, CA 94720
    USA
  • Email: APArkin <at> lbl.gov
  • Web site: Arkin Lab
[photo: Frank Doyle]
Frank Doyle
  • Department of Chemical Engineering
    University of California
    Santa Barbara, CA 93106-5080 USA
  • Email: doyle <at> engineering.ucsb.edu
[photo:
	   Fumiaki Katagiri]
Fumiaki Katagiri
  • Department of Plant Biology
    University of Minnesota
    250 Biological Sciences Center
    1445 Gortner Avenue
    St. Paul, MN 55108
  • Email: katagiri <at> umn.edu
[photo:
	   Douglas A. Lauffenburger]
Douglas A. Lauffenburger
  • Co-Director, Biological Engineering Division
    Director, Biotechnology Process Engineering Center
    Whitaker Professor of Biological Engineering, Chemical Engineering, and Biology
  • Research group web site
  • Email: lauffen <at> mit.edu
[photo: Cynthia
	   L. Stokes]
Cyndi Stokes
  • Principal Scientist, Immunologic Diseases
    In Silico R&D
    Entelos, Inc.
    110 Marsh Drive
    Foster City, CA 94404