An introduction and overview of system modeling in biology that is accessible to researchers from different fields, including biology, computer science, mathematics, statistics, physics, and biochemistry.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. This comprehensive introduction and overview of system modeling in biology makes the relevant background material from all pertinent fields accessible to researchers with different backgrounds.The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. This book fills that gap. It is the first to provide the necessary critical comparison of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages and disadvantages; lessons from the application of mathematical models to the study of cellular biology; and available modeling tools and datasets, along with their computational limitations.
Reihe
Sprache
Verlagsort
Verlagsgruppe
Zielgruppe
Für Beruf und Forschung
US School Grade: From College Freshman to College Graduate Student
Produkt-Hinweis
Maße
Höhe: 229 mm
Breite: 178 mm
Dicke: 25 mm
Gewicht
ISBN-13
978-0-262-19548-5 (9780262195485)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Klassifikation
Zoltan Szallasi is Professor at the Center for Biological Sequence Analysis, Technical University of Denmark.
Jörg Stelling is a faculty member of the Department of Biosystems Science and Engineering at ETH Zürich.
Vipul Periwal is with the Mathematical Cell ModelingSection, NIDDK, National Institute of Health.
Herausgeber*in
ETH Zuerich
Preface I GENERAL CONCEPTS 1 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 III and John Doyle 19 3 On Modules and Modularity Zoltan Szallasi, Vipul Periwal and Jörg Stelling 41 II MODELING APPROACHES 51 4 Bayesian Inference of Biological Systems: The Logic of Biology Vipul Periwal 53 5 Stoichiometric and Constraint-based Modeling Steffen Klamt and Jörg Stelling 73 6 Modeling Molecular Interaction Networks with Nonlinear Ordinary Differential Equations Emery D. Conrad and John J. Tyson 97 7 Qualitative Approaches to the Analysis of Genetic Regulatory Networks Hidde de Jong and Delphine Ropers 125 8 Stochastic Modeling of Intracellular Kinetics Johan Paulsson and Johan Elf 149 9 Kinetics in Spatially Extended Systems Karsten Kruse and Johan Elf 177 III MODELS AND REALITY 199 10 Biological Data Acquisition for System Level Modeling-An Exercise in the Art of Compromise Zoltan Szallasi 201 11 Methods to Identify Cellular Architecture and Dynamics from Experimental Data Rudiyanto Gunawan, Kapil G. Gadker and Francis J. Doyle III 221 12 Using Control Theory to Study Biology Brian P. Ingalls, Tau-Mi Yi and Pablo A. Iglesias 243 13 Synthetic Gene Regulatory Systems Mads Kærn and Ron Weiss 269 14 Multilevel Modeling in Systems Biology: From Cells to Whole Organs Denis Noble 297 IV COMPUTATIONAL MODELING 313 15 Computational Constraints on Modeling in Systems Biology Vipul Periwal 315 16 Numerical Simulation for Biochemical Kinetics Daniel T. Gillespie and Linda R. Petzold 331 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 355 A Software Tools for Biological Modeling 379 References Contributors Index
