Dynamic Systems Biology Modeling And Simulation
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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 - 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]
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.
Systems Biology Simulation Of Dynamic Network States
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Author : Bernhard Ø. Palsson
language : en
Publisher: Cambridge University Press
Release Date : 2011-05-26
Systems Biology Simulation Of Dynamic Network States written by Bernhard Ø. Palsson and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-05-26 with Science categories.
Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard Ø. Palsson shows how network reconstructions that are based on genomic and bibliomic data, and take the form of established stoichiometric matrices, can be converted into dynamic models using metabolomic and fluxomic data. The Mass Action Stoichiometric Simulation (MASS) procedure can be used for any cellular process for which data is available and allows a scalable step-by-step approach to the practical construction of network models. Specifically, it can treat integrated processes that need explicit accounting of small molecules and protein, which allows simulation at the molecular level. The material has been class-tested by the author at both the undergraduate and graduate level. All computations in the text are available online in MATLAB® and Mathematica® workbooks, allowing hands-on practice with the material.
Biological Modeling And Simulation
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Author : Russell Schwartz
language : en
Publisher: MIT Press
Release Date : 2008-07-25
Biological Modeling And Simulation written by Russell Schwartz and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-07-25 with Science categories.
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.
Computer Assisted Simulation Of Dynamic Systems With Block Diagram Languages
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Author : Nicholas M. Karayanakis
language : en
Publisher: CRC Press
Release Date : 1993-06-24
Computer Assisted Simulation Of Dynamic Systems With Block Diagram Languages written by Nicholas M. Karayanakis and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1993-06-24 with Computers categories.
Computer-Assisted Simulation of Dynamic Systems with Block Diagram Languages explores the diverse applications of these indispensable simulation tools. The first book of its kind, it bridges the gap between block diagram languages and traditional simulation practice by linking the art of analog/hybrid computation with modern pc-based technology. Direct analogies are explored as a means of promoting interdisciplinary problem solving. The reader progresses step-by-step through the creative modeling and simulation of dynamic systems from disciplines as diverse from each other as biology, electronics, physics, and mathematics. The book guides the reader to the dynamic simulation of chaos, conformal mapping, VTOL aircraft, and other highly specialized topics. Alternate methods of simulating a single device to emphasize the dynamic rather than schematic features of a system are provided. Nearly-forgotten computational techniques like that of integrating with respect to a variable other than time are revived and applied to simulation and signal processing. Actual working models are found throughout this eminently readable book, along with a complete international bibliography for individuals researching subjects in dynamic systems. This is an excellent primary text for undergraduate and graduate courses in computer simulation or an adjunct text for a dynamic systems course. It is also recommended as a professional reference book.
Applications Of Dynamical Systems In Biology And Medicine
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Author : Trachette Jackson
language : en
Publisher: Springer
Release Date : 2015-07-06
Applications Of Dynamical Systems In Biology And Medicine written by Trachette Jackson and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-06 with Mathematics categories.
This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control. Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction. Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation.
Dynamic Biosystem Modeling Simulation Methodology Integrated Accessible
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Author : Joseph Distefano, 3rd
language : en
Publisher:
Release Date : 2019-09-16
Dynamic Biosystem Modeling Simulation Methodology Integrated Accessible written by Joseph Distefano, 3rd and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-16 with categories.
This textbook is uniquely crafted for use in teaching undergraduate students in the life, math, computer and other sciences and engineering. It is INTRODUCTORY LEVEL, for students who have taken or are currently completing their undergraduate math requirements, and are acquiring analytical-thinking and doing skills, along with introductory biology, chemistry and physics subject matter. It's about learning HOW to model and simulate dynamic biological systems, which also makes it useful for graduate students and professional researchers who want a more rigorous treatment of introductory life science math modeling, integrated with the biology. It brings together the multidisciplinary pedagogy of these subjects into a SINGLE INTRODUCTORY MODELING METHODOLOGY COURSE, crystalizing the experience of an author who has been teaching dynamic biosystems modeling and simulation methodology for the life sciences for more than 50 years. DiStefano maximizes accessibility and "systems-math-biology" integration - without diminishing conceptual rigor. Minimally essential applied math and SYSTEMS ENGINEERING METHODS are included, along with a synopsis of the biology and physiology underlying dynamic biosystem modeling, all in a modeling pedagogy context. This textbook fills a major need in the training of contemporary biology students.Dynamic biosystems modeling methodology is presented over 12 distinctive chapters, primarily with systems diagrams and simple differential equations and algebra for expressing them quantitatively, integrated with the biology. Solving and analyzing (quantifying) the biomodels are then accomplished by simulation, using a facile control system simulation language Simulink, a GUI/Matlab toolbox that emulates control systems diagramming, rather than by "coding" the model in a standard computer programming language. Students see and work with the system model - not the code - a big plus. Higher math and complex analytical solutions are avoided.Each chapter begins with a list of LEARNING GOALS, to help with both perspective for the chapter material, and retrospective, to measure learning. EXERCISES for the student at the end of each chapter are designed to test and reinforce learning. A SOLUTIONS MANUAL for chapter exercises is available to qualified instructors from the author, as are LECTURE SLIDES and LAB ASSIGNMENTS AND SOLUTIONS, for courses that adopt the textbook for student use.
Stochastic Dynamics In Computational Biology
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Author : Stefanie Winkelmann
language : en
Publisher: Springer Nature
Release Date : 2021-01-04
Stochastic Dynamics In Computational Biology written by Stefanie Winkelmann and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-01-04 with Mathematics categories.
The aim of this book is to provide a well-structured and coherent overview of existing mathematical modeling approaches for biochemical reaction systems, investigating relations between both the conventional models and several types of deterministic-stochastic hybrid model recombinations. Another main objective is to illustrate and compare diverse numerical simulation schemes and their computational effort. Unlike related works, this book presents a broad scope in its applications, from offering a detailed introduction to hybrid approaches for the case of multiple population scales to discussing the setting of time-scale separation resulting from widely varying firing rates of reaction channels. Additionally, it also addresses modeling approaches for non well-mixed reaction-diffusion dynamics, including deterministic and stochastic PDEs and spatiotemporal master equations. Finally, by translating and incorporating complex theory to a level accessible to non-mathematicians, this book effectively bridges the gap between mathematical research in computational biology and its practical use in biological, biochemical, and biomedical systems.
Modeling In Systems Biology
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Author : Ina Koch
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-10-21
Modeling In Systems Biology written by Ina Koch 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 2010-10-21 with Computers categories.
The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.
E Cell System
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Author : Satya Nanda Vel Arjunan
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-05-13
E Cell System written by Satya Nanda Vel Arjunan 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 2013-05-13 with Science categories.
The interdisciplinary field of molecular systems biology aims to understand the behavior and mechanisms of biological processes composed of individual molecular components. As we gain more qualitative and quantitative information of complex intracellular processes, biochemical modeling and simulation become indispensable not only to uncover the molecular mechanisms of the processes, but to perform useful predictions. To this end, the E‐Cell System, a multi‐algorithm, multi‐timescale object‐oriented simulation platform, can be used to construct predictive virtual biological systems. Gene regulatory and biochemical networks that constitute a sub‐ or a whole cellular system can be constructed using the E‐Cell System to perform qualitative and quantitative analyses. The purpose of E‐Cell System: Basic Concepts and Applications is to provide a comprehensive guide for the E‐Cell System version 3 in terms of the software features and its usage. While the publicly available E‐Cell Simulation Environment version 3 User's Manual provides the technical details of model building and scripting, it does not describe some of the underlying concepts of the E‐Cell System. The first part of the book addresses this issue by providing the basic concepts of modeling and simulation with the E‐Cell System.