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E-grāmata: System Modeling in Cellular Biology – From Concepts to Nuts and Bolts: From Concepts to Nuts and Bolts

Edited by , Edited by (ETH Zürich), Edited by
  • Formāts: 464 pages
  • Sērija : The MIT Press
  • Izdošanas datums: 14-May-2014
  • Izdevniecība: MIT Press
  • ISBN-13: 9780262257060
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  • Formāts: 464 pages
  • Sērija : The MIT Press
  • Izdošanas datums: 14-May-2014
  • Izdevniecība: MIT Press
  • ISBN-13: 9780262257060
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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.
Preface vii
I. GENERAL CONCEPTS
1(50)
The Role of Modeling in Systems Biology
3(16)
Douglas B. Kell
Joshua D. Knowles
Complexity and Robustness of Cellular Systems
19(22)
Jorg Stelling
Uwe Sauer
Francis J. Doyle III
John Doyle
On Modules and Modularity
41(10)
Zoltan Szallasi
Vipul Periwal
Jorg Stelling
II. Modeling Approaches
51(148)
Bayesian Inference of Biological Systems: The Logic of Biology
53(20)
Vipul Periwal
Stoichiometric and Constraint-based Modeling
73(24)
Steffen Klant
Jorg Stelling
Modeling Molecular Interaction Networks with Nonlinear Ordinary Differential Equations
97(28)
Emery D. Conrad
John J. Tyson
Qualitative Approaches to the Analysis of Genetic Regulatory Networks
125(24)
Hidde de Jong
Delphine Ropers
Stochastic Modeling of Intracellular Kinetics
149(28)
Johan Paulsson
Johan Elf
Kinetics in Spatially Extended Systems
177(22)
Karsten Kruse
Johan Elf
III. MODELS AND REALITY
199(114)
Biological Data Acquisition for System Level Modeling---An Exercise in the Art of Compromise
201(20)
Zoltan Szallasi
Methods to Identify Cellular Architecture and Dynamics from Experimental Data
221(22)
Rudiyanto Gunawan
Kapil G. Gadkar
Francis J. Doyle III
Using Control Theory to Study Biology
243(26)
Brian P. Ingalls
Tau-Mu Yi
Pablo A. Iglesias
Synthetic Gene Regulatory Systems
269(28)
Mads Koern
Ron Weiss
Multilevel Modeling in Systems Biology: From Cells to Whole Organs
297(16)
Denis Noble
IV. COMPUTATIONAL MODELING
313(66)
Computational Constraints on Modeling in Systems Biology
315(16)
Vipul Periwal
Numerical Simulation for Biochemical Kinetics
331(24)
Daniel T. Gillespie
Linda R. Petzold
Software Infrastructure for Effective Communication and Reuse of Computational Models
355(24)
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
Hiroaki Kitano
A Software Tools for Biological Modeling 379(6)
References 385(50)
Contributors 435(4)
Index 439