System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
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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 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.
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Front Matter
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I General Concepts
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II Modeling Approaches
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4.
Bayesian Inference of Biological Systems: The Logic of Biology
Vipul Periwal
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5.
Stoichiometric and Constraint-based Modeling
Steffen Klamt andJörg Stelling
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6.
Modeling Molecular Interaction Networks with Nonlinear Ordinary Differential Equations
Emery D. Conrad andJohn J. Tyson
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7
Qualitative Approaches to the Analysis of Genetic Regulatory Networks
Hidde de Jong andDelphine Ropers
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8
Stochastic Modeling of Intracellular Kinetics
Johan Paulsson andJohan Elf
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9
Kinetics in Spatially Extended Systems
Karsten Kruse andJohan Elf
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4.
Bayesian Inference of Biological Systems: The Logic of Biology
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III Models and Reality
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10
Biological Data Acquisition for System Level Modeling—An Exercise in the Art of Compromise
Zoltan Szallasi
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11
Methods to Identify Cellular Architecture and Dynamics from Experimental Data
Rudiyanto Gunawan and others
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12
Using Control Theory to Study Biology*
Brian P. Ingalls and others
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13
Synthetic Gene Regulatory Systems
Mads Kærn andRon Weiss
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14
Multilevel Modeling in Systems Biology: From Cells to Whole Organs
Denis Noble
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10
Biological Data Acquisition for System Level Modeling—An Exercise in the Art of Compromise
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IV Computational Modeling
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End Matter
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