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Dynamic Systems Biology Modeling and Simulation

2015-01-10 Science
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Release : 2015-01-10
Genre : Science
Kind : eBook
Book Rating : 932/5 ( reviews)

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Book Synopsis Dynamic Systems Biology Modeling and Simulation by : Joseph DiStefano III

Download or read book Dynamic Systems Biology Modeling and Simulation written by Joseph DiStefano III. This book was released on 2015-01-10. Available in PDF, EPUB and Kindle. Book excerpt: 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 - 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: [email protected]

Systems Biology

2021
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Release : 2021
Genre :
Kind : eBook
Book Rating : 345/5 ( reviews)

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Book Synopsis Systems Biology by : Jinzhi Lei

Download or read book Systems Biology written by Jinzhi Lei. This book was released on 2021. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses the mathematical simulation of biological systems, with a focus on the modeling of gene expression, gene regulatory networks and stem cell regeneration. The diffusion of morphogens is addressed by introducing various reaction-diffusion equations based on different hypotheses concerning the process of morphogen gradient formation. The robustness of steady-state gradients is also covered through boundary value problems. The introduction gives an overview of the relevant biological concepts (cells, DNA, organism development) and provides the requisite mathematical preliminaries on continuous dynamics and stochastic modeling. A basic understanding of calculus is assumed. The techniques described in this book encompass a wide range of mechanisms, from molecular behavior to population dynamics, and the inclusion of recent developments in the literature together with first-hand results make it an ideal reference for both new students and experienced researchers in the field of systems biology and applied mathematics.

Biological Modeling and Simulation

2008-07-25 Science
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Release : 2008-07-25
Genre : Science
Kind : eBook
Book Rating : 396/5 ( reviews)

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Book Synopsis Biological Modeling and Simulation by : Russell Schwartz

Download or read book Biological Modeling and Simulation written by Russell Schwartz. This book was released on 2008-07-25. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.

Modeling Dynamic Biological Systems

2012-12-06 Science
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Release : 2012-12-06
Genre : Science
Kind : eBook
Book Rating : 510/5 ( reviews)

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Book Synopsis Modeling Dynamic Biological Systems by : Bruce Hannon

Download or read book Modeling Dynamic Biological Systems written by Bruce Hannon. This book was released on 2012-12-06. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Measurements, Modelling and Simulation of Dynamic Systems

2009-12-30 Technology & Engineering
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Release : 2009-12-30
Genre : Technology & Engineering
Kind : eBook
Book Rating : 88X/5 ( reviews)

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Book Synopsis Measurements, Modelling and Simulation of Dynamic Systems by : Edward Layer

Download or read book Measurements, Modelling and Simulation of Dynamic Systems written by Edward Layer. This book was released on 2009-12-30. Available in PDF, EPUB and Kindle. Book excerpt: The development and use of models of various objects is becoming a more common practice in recent days. This is due to the ease with which models can be developed and examined through the use of computers and appropriate software. Of those two, the former - high-speed computers - are easily accessible nowadays, and the latter - existing programs - are being updated almost continuously, and at the same time new powerful software is being developed. Usually a model represents correlations between some processes and their interactions, with better or worse quality of representation. It details and characterizes a part of the real world taking into account a structure of phenomena, as well as quantitative and qualitative relations. There are a great variety of models. Modelling is carried out in many diverse fields. All types of natural phenomena in the area of biology, ecology and medicine are possible subjects for modelling. Models stand for and represent technical objects in physics, chemistry, engineering, social events and behaviours in sociology, financial matters, investments and stock markets in economy, strategy and tactics, defence, security and safety in military fields. There is one common point for all models. We expect them to fulfil the validity of prediction. It means that through the analysis of models it is possible to predict phenomena, which may occur in a fragment of the real world represented by a given model. We also expect to be able to predict future reactions to signals from the outside world.

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