Modeling Biological Systems

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Modeling Biological Systems

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Author : James W. Haefner
language : en
Publisher: Springer Science & Business Media
Release Date : 2005-05-06

Modeling Biological Systems written by James W. Haefner and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-05-06 with Science categories.

I Principles 1 1 Models of Systems 3 1. 1 Systems. Models. and Modeling . . . . . . . . . . . . . . . . . . . . 3 1. 2 Uses of Scientific Models . . . . . . . . . . . . . . . . . . . . . . . . 4 1. 3 Example: Island Biogeography . . . . . . . . . . . . . . . . . . . . . 6 1. 4 Classifications of Models . . . . . . . . . . . . . . . . . . . . . . . . 10 1. 5 Constraints on Model Structure . . . . . . . . . . . . . . . . . . . . . 12 1. 6 Some Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1. 7 Misuses of Models: The Dark Side . . . . . . . . . . . . . . . . . . . 13 1. 8 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2 The Modeling Process 17 2. 1 Models Are Problems . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2. 2 Two Alternative Approaches . . . . . . . . . . . . . . . . . . . . . . 18 2. 3 An Example: Population Doubling Time . . . . . . . . . . . . . . . . 24 2. 4 Model Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 2. 5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 3 Qualitative Model Formulation 32 3. 1 How to Eat an Elephant . . . . . . . . . . . . . . . . . . . . . . . . . 32 3. 2 Forrester Diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 3. 3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 3. 4 Errors in Forrester Diagrams . . . . . . . . . . . . . . . . . . . . . . 44 3. 5 Advantages and Disadvantages of Forrester Diagrams . . . . . . . . . 44 3. 6 Principles of Qualitative Formulation . . . . . . . . . . . . . . . . . . 45 3. 7 Model Simplification . . . . . . . . . . . . . . . . . . . . . . . . . . 47 3. 8 Other Modeling Problems . . . . . . . . . . . . . . . . . . . . . . . . 49 viii Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3. 9 Exercises 53 4 Quantitative Model Formulation: I 4. 1 From Qualitative to Quantitative . . . . . . . . . . . . . . . . . Finite Difference Equations and Differential Equations 4. 2 . . . . . . . . . . . . . . . . 4. 3 Biological Feedback in Quantitative Models . . . . . . . . . . . . . . . . . . . . . . . . . . 4. 4 Example Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4. 5 Exercises 5 Quantitative Model Formulation: I1 81 . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 1 Physical Processes 81 . . . . . . . . . . . . . . . 5. 2 Using the Toolbox of Biological Processes 89 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 3 Useful Functions 96 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 4 Examples 102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 5 Exercises 104 6 Numerical Techniques 107 . . . . . . . . . . . . . . . . . . . . . . . 6. 1 Mistakes Computers Make 107 . . . . . . . . . . . . . . . . . . . . . . . . . . 6. 2 Numerical Integration 110 . . . . . . . . . . . . . . . . 6. 3 Numerical Instability and Stiff Equations 115 . . . . . . . . . . . . . .

Mathematical Modeling Of Biological Systems

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Author : Harvey J. Gold
language : en
Publisher: John Wiley & Sons
Release Date : 1977

Mathematical Modeling Of Biological Systems written by Harvey J. Gold and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 1977 with Biological models categories.

The modeling process - an overview. Dimension and similarity. Probability models. Dynamic processes. Interacting dynamic processes. Feedback control and stability of biological systems. Curve fiting: estimating the parameters. Computing.

Modeling Biological Systems

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Author : James W Haefner
language : en
Publisher:
Release Date : 1996-07-01

Modeling Biological Systems written by James W Haefner and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1996-07-01 with categories.

Systems Biology

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Author : Andreas Kremling
language : en
Publisher: CRC Press
Release Date : 2013-11-12

Systems Biology written by Andreas Kremling and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-12 with Mathematics categories.

Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are sy

Dynamic Systems Biology Modeling And Simulation

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Author : Joseph DiStefano III
language : en
Publisher: Academic Press
Release Date : 2015-01-10

Dynamic Systems Biology Modeling And Simulation written by Joseph DiStefano III and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-01-10 with Science categories.

Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author’s own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics; PLUS ....... The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of “math modeling” with life sciences. Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization. Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models. A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course. Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content. The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: joed@cs.ucla.edu

Stochastic Modelling For Systems Biology Third Edition

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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2018-12-07

Stochastic Modelling For Systems Biology Third Edition written by Darren J. Wilkinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-07 with Mathematics categories.

Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Computational Modeling Of Biological Systems

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Author : Nikolay V Dokholyan
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-02-12

Computational Modeling Of Biological Systems written by Nikolay V Dokholyan and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-02-12 with Science categories.

Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Modeling Dynamic Biological Systems

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Author : Bruce Hannon
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06

Modeling Dynamic Biological Systems written by Bruce Hannon and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Science categories.

Models help us understand the dynamics of real-world processes by using the computer to mimic the actual forces that are known or assumed to result in a system's behavior. This book does not require a substantial background in mathematics or computer science.

Investigating Biological Systems Using Modeling

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Author : Meryl E. Wastney
language : en
Publisher: Academic Press
Release Date : 2012-12-02

Investigating Biological Systems Using Modeling written by Meryl E. Wastney and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-02 with Computers categories.

Investigating Biological Systems Using Modeling describes how to apply software to analyze and interpret data from biological systems. It is written for students and investigators in lay person's terms, and will be a useful reference book and textbook on mathematical modeling in the design and interpretation of kinetic studies of biological systems. It describes the mathematical techniques of modeling and kinetic theory, and focuses on practical examples of analyzing data. The book also uses examples from the fields of physiology, biochemistry, nutrition, agriculture, pharmacology, and medicine. Contains practical descriptions of how to analyze kinetic data Provides examples of how to develop and use models Describes several software packages including SAAM/CONSAM Includes software with working models

Dynamical Systems For Biological Modeling

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Author : Fred Brauer
language : en
Publisher: CRC Press
Release Date : 2015-12-23

Dynamical Systems For Biological Modeling written by Fred Brauer and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-12-23 with Mathematics categories.

Dynamical Systems for Biological Modeling: An Introduction prepares both biology and mathematics students with the understanding and techniques necessary to undertake basic modeling of biological systems. It achieves this through the development and analysis of dynamical systems.The approach emphasizes qualitative ideas rather than explicit computa