Dynamic Systems Biology Modeling and Simulation book cover

Dynamic Systems Biology Modeling and Simulation

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.

Audience
upper-division undergraduate, graduate level, and research level students systems biology, computational biology, biomathematics, biomedical engineering (bioengineering), pharmacology and areas using contemporary dynamical biosystem modeling and simulation methodology.

Hardbound, 884 Pages

Published: November 2013

Imprint: Academic Press

ISBN: 978-0-12-410411-2

Reviews

  •  â€œI am just in awe of your ability to start with simple ideas and use them to explain sophisticated concepts and methodologies in modeling biochemical and cellular systems (Chapters 6 and 7).  This is a great new contribution to the textbook offerings in systems biology.”
    Alex Hoffmann, Director of the San Diego Center for Systems Biology and the
    UCSD Graduate Program in Bioinformatics and Systems Biology


    “I found Chapter 1 to be a marvel of heavy-lifting, done so smoothly there was no detectable sweat.  Heavy-lifting because you laid out the big load of essential vocabulary and concepts a reader has to have to enter the world of biomodeling confidently.  In that chapter you generously acknowledge some us who tried to accomplish this earlier but, compared to your Chapter 1, we were clumsy and boring.  For me, now, Chapter 1 was a "page-turner" to be enjoyed straight through.  You have the gift of a master athlete who does impossible performances and makes them seem easy.
    “Your Chapter 9 - on oscillations and stability - is a true jewel.  I have a shelf full of books etc on nonlinear mechanics and system analyses and modeling, but nothing to match the clarity and deep understanding you offer the reader. You are a great explainer and teacher.”
    F. Eugene Yates, Emeritus Professor of Medicine, Chemical Engineering and
    Ralph and Marjorie Crump Professor of Biomedical Engineering, UCLA


     â€œChapter 4 covers many aspects of the notion of compartmentalization in the structural modeling of biomedical and biological models - both linear and nonlinear.  Developments are biophysically motivated throughout; and compartments are taken to represent entities with the same dynamic characteristics (dynamic signatures). A very positive feature of this text is the numerous worked examples in the text, which greatly help readers follow the material.  At the end of the chapter, there are further well thought out analytical and simulation exercises that will help readers check that they have understood what has been presented.
     â€œChapter 5 looks at many important aspects of multicompartmental modeling, examining in more detail how output data limit what can be learnt about model structure, even when such data are perfect. Among the many features explained are how to establish the size and complexity of a model; how to select between several candidate models; and whether it is possible to simplify a model. All of this is done with respect to the dynamic signatures in the model. As in Chapter 4, readers are helped to understand the often challenging material by means of numerous worked examples in the text, and there are further examples given at the end.”
    Professor Keith Godfrey, University of Warwick, Coventry, U.K.


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