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System Modeling in Cellular Biology
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System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Zoltan Szallasi, Jorg Stelling, and Vipul Periwal

Abstract

Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines. The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. The book provides the necessary critical comparison of co ... More

Keywords: systems biology, computer science, statistics, biochemistry, system modeling, cellular biology, robustness, modularity, biological systems, mathematical models

Bibliographic Information

Print publication date: 2006 Print ISBN-13: 9780262195485
Published to University Press Scholarship Online: August 2013 DOI:10.7551/mitpress/9780262195485.001.0001

Authors

Affiliations are at time of print publication.

Zoltan Szallasi, editor

Jorg Stelling, editor

Vipul Periwal, editor

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Contents

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Front Matter

I General Concepts

1. The Role of Modeling in Systems Biology

Douglas B. Kell, and Joshua D. Knowles

2 Complexity and Robustness of Cellular Systems

Jörg Stelling, Uwe Sauer, Francis J. Doyle, and John Doyle

3 On Modules and Modularity

Zoltan Szallasi, Vipul Periwal, and Jörg Stelling

II Modeling Approaches

5. Stoichiometric and Constraint-based Modeling

Steffen Klamt, and Jörg Stelling

8 Stochastic Modeling of Intracellular Kinetics

Johan Paulsson, and Johan Elf

9 Kinetics in Spatially Extended Systems

Karsten Kruse, and Johan Elf

III Models and Reality

11 Methods to Identify Cellular Architecture and Dynamics from Experimental Data

Rudiyanto Gunawan, Kapil G. Gadkar, and Francis J. Doyle

12 Using Control Theory to Study Biology*

Brian P. Ingalls, Tau-Mu Yi, and Pablo A. Iglesias

13 Synthetic Gene Regulatory Systems

Mads Kærn, and Ron Weiss

IV Computational Modeling

16 Numerical Simulation for Biochemical Kinetics

Daniel T. Gillespie, and Linda R. Petzold

17. Software Infrastructure for Effective Communication and Reuse of Computational Models

Andrew Finney, Michael Hucka, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John Doyle, and Hiroaki Kitano