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Author : Michel Kana
Publisher :
ISBN 13 : 9788001044919
Total Pages : 145 pages
Book Rating : 4.0/5 (449 download)
Download or read book Tutorial for Modeling and Simulation of Biological Processes written by Michel Kana and published by . This book was released on 2010 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :
Publisher :
ISBN 13 : 9789736208652
Total Pages : 99 pages
Book Rating : 4.2/5 (86 download)
Download or read book Modeling and Simulation of Biological Processes written by and published by . This book was released on 2011 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Joseph DiStefano III
Publisher : Academic Press
ISBN 13 : 0124104932
Total Pages : 886 pages
Book Rating : 4.1/5 (241 download)
Download or read book Dynamic Systems Biology Modeling and Simulation written by Joseph DiStefano III and published by Academic Press. This book was released on 2015-01-10 with total page 886 pages. 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]
Author : James W. Haefner
Publisher : Springer Science & Business Media
ISBN 13 : 9780387250113
Total Pages : 500 pages
Book Rating : 4.2/5 (51 download)
Download or read book Modeling Biological Systems: written by James W. Haefner and published by Springer Science & Business Media. This book was released on 2005-05-06 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 . . . . . . . . . . . . . .
Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262195844
Total Pages : 403 pages
Book Rating : 4.2/5 (621 download)
Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. 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.
Author : Andrea Unger
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (72 download)
Download or read book Visual Support for the Modeling and Simulation of Cell Biological Processes written by Andrea Unger and published by . This book was released on 2010 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Avner Friedman
Publisher : Springer
ISBN 13 : 3319083147
Total Pages : 152 pages
Book Rating : 4.3/5 (19 download)
Download or read book Mathematical Modeling of Biological Processes written by Avner Friedman and published by Springer. This book was released on 2014-09-19 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.
Author : Philippe Tracqui
Publisher :
ISBN 13 :
Total Pages : 293 pages
Book Rating : 4.:/5 (592 download)
Download or read book Modelling and Simulation of Biological Processes in the Context of Genomics written by Philippe Tracqui and published by . This book was released on 2002 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Robert E. Keen
Publisher : Wiley-Liss
ISBN 13 :
Total Pages : 524 pages
Book Rating : 4.E/5 ( download)
Download or read book Computer Simulation in Biology written by Robert E. Keen and published by Wiley-Liss. This book was released on 1992 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt: Role of modeling and computer simulation in biology; Simple model equations; Analytical models based on differential equations; Analytical models based on stable states; Estimating model coefficients from experimental data; Planning and problems of programming; Numerical solution of rate equations; Models with multiple components; Kinetics of biochemical reactions; Models of homogeneous populations of organisms; Simple models of microbial growth; Population models based on age-specific events; Simulations of population genetics; Models of light and photosynthesis; Temperature and biological activity; Compartmental models of biogeochemical cycling; Diffusion models; Compartmental models in Physiology; Application of matrix methods to simulations; Physiological control systems; Probabilistic models; Monte Carlo modeling of simple stochastic processes; Modeling of sampling processes; Random walks and related stochastic processes; Markov chain simulations in biology; Supplementary models; Models of cellular function; Models of development and morphogenesis; Models of epidemics; Appendixes; Literature cited; Index.
Author : David J. Barnes
Publisher : Springer
ISBN 13 : 1447167627
Total Pages : 347 pages
Book Rating : 4.4/5 (471 download)
Download or read book Guide to Simulation and Modeling for Biosciences written by David J. Barnes and published by Springer. This book was released on 2015-09-01 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt: This accessible text presents a detailed introduction to the use of a wide range of software tools and modeling environments for use in the biosciences, as well as the fundamental mathematical background. The practical constraints presented by each modeling technique are described in detail, enabling the researcher to determine which software package would be most useful for a particular problem. Features: introduces a basic array of techniques to formulate models of biological systems, and to solve them; discusses agent-based models, stochastic modeling techniques, differential equations, spatial simulations, and Gillespie’s stochastic simulation algorithm; provides exercises; describes such useful tools as the Maxima algebra system, the PRISM model checker, and the modeling environments Repast Simphony and Smoldyn; contains appendices on rules of differentiation and integration, Maxima and PRISM notation, and some additional mathematical concepts; offers supplementary material at an associated website.
Author : Gregory R. Bock
Publisher : John Wiley & Sons
ISBN 13 :
Total Pages : 280 pages
Book Rating : 4.3/5 (91 download)
Download or read book 'In Silico' Simulation of Biological Processes written by Gregory R. Bock and published by John Wiley & Sons. This book was released on 2002 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over recent decades vast amounts of biological data have been accumulated. However, it is becoming increasingly difficult to apply traditional theoretical methods to the formulation of coherent pictures of cell and organ function because it is no longer possible for a human theorist to integrate all of the available information. Instead, computer technologies must now be used to perform this integration. This book brings together contributions from many different fields to summarize the current status of computer-assisted modelling of biological processes. The initial chapters deal with fundamental developments in hardware, software and mathematics that underlie current approaches to biological modelling. Next, different approaches to collating data on gene structure and function are presented. These databases form a vital resource for any investigator trying to construct an integrated picture of particular biological systems. Cell signalling systems form a particularly complicated aspect of all cellular function and are important both in the understanding of basic cellular processes and in selecting targets for drugs. Recent approaches to integrating data on cell signalling into computer models are covered. Further chapters build on these approaches to show how computerized models of intact cells can be developed. Finally, approaches to the computer modelling of whole organs such as the heart are presented. The role of computer modelling in drug design is the subject of the final chapter and is also touched on throughout the discussions. !-- end body copy --
Author : Elmar Heinzle
Publisher : John Wiley & Sons
ISBN 13 : 3527824421
Total Pages : 560 pages
Book Rating : 4.5/5 (278 download)
Download or read book Biological Reaction Engineering written by Elmar Heinzle and published by John Wiley & Sons. This book was released on 2021-04-06 with total page 560 pages. Available in PDF, EPUB and Kindle. Book excerpt: Die Dynamik biotechnologischer Produktionsprozesse ist äußerst komplex. Ziel des Buches ist es, diese Vorgänge durch systematische Modellbildung und Computersimulation verständlich und durchschaubar zu machen. Es werden ohne viel mathematisches Rüstzeug Grundprinzipien erklärt und anhand von zahlreichen praxisrelevanten Beispielen alle wichtigen Aspekte der Bioverfahrenstechnik ausführlich beschrieben. Modellierte biologische Systeme reichen vom einzelnen Enzym bis zu ganzen metabolischen Netzwerken und Multi-Organismen Systemen. Die kinetischen Modelle werden mit Reaktormodellen kombiniert, was oft mit verschiedenen Konfigurationen von Zu- und Abläufen und Stofftransportprozessen kombiniert ist. In vielen Beispielen werden Regelung und Optimierung der Prozesse behandelt. Die Simulationsbeispiele reichen von theoretischen Schulbeispielen bis zu aktuellen Forschungsarbeiten. Die verwendete Simulationssprache Berkeley Madonna erlaubt nach einer sehr kurzen Einarbeitung ein schnelles interaktives Üben. Der Leser kann die vorgegebenen Beispiele beliebig verändern, um sie seinem Problemfall anzupassen. Die langjährige Lehrerfahrung der Autoren an Hochschulen und Weiterbildungskursen spiegelt sich in dem Buch wider und macht es geeignet für alle Biochemiker, Biotechnologen, Bioingenieure und Verfahrenstechniker, die an Modellierung und Simulation interessiert sind. Die eingesetzte Software Berkeley Madonna für Mac und PC kann direkt von der Berkeley Madonna Webseite bezogen werden: www.berkeleymadonna.com Zusätzliches Online Material, d.h. Programme für alle Simulationsbeispiele, eine kurze Beschreibung der Verwendung der eingesetzten Simulationssoftware Berkeley Madonna und Lösungen von Übungsaufgaben kann als Zusatzmaterial (Zip-Datei) direkt von dieser Webseite heruntergeladen werden. Alle Beispiele können auch mit der kostenlosen Demo-Version von Berkeley Madonna benützt werden. Für Käufer des Buches ist Berkeley Madonna zu einem reduzierten Preis erhältlich. Hinweise dazu gibt es im Anhang des Buches.
Author : Bruce Hannon
Publisher : Springer
ISBN 13 : 3319056158
Total Pages : 419 pages
Book Rating : 4.3/5 (19 download)
Download or read book Modeling Dynamic Biological Systems written by Bruce Hannon and published by Springer. This book was released on 2014-07-05 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many biologists and ecologists have developed models that find widespread use in theoretical investigations and in applications to organism behavior, disease control, population and metapopulation theory, ecosystem dynamics, and environmental management. This book captures and extends the process of model development by concentrating on the dynamic aspects of these processes and by providing the tools such that virtually anyone with basic knowledge in the Life Sciences can develop meaningful dynamic models. Examples of the systems modeled in the book range from models of cell development, the beating heart, the growth and spread of insects, spatial competition and extinction, to the spread and control of epidemics, including the conditions for the development of chaos. Key features: - easy-to-learn and easy-to-use software - examples from many subdisciplines of biology, covering models of cells, organisms, populations, and metapopulations - no prior computer or programming experience required Key benefits: - learn how to develop modeling skills and system thinking on your own rather than use models developed by others - be able to easily run models under alternative assumptions and investigate the implications of these assumptions for the dynamics of the biological system being modeled - develop skills to assess the dynamics of biological systems
Author : Gerda de Vries
Publisher : SIAM
ISBN 13 : 0898718252
Total Pages : 307 pages
Book Rating : 4.8/5 (987 download)
Download or read book A Course in Mathematical Biology written by Gerda de Vries and published by SIAM. This book was released on 2006-07-01 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the only book that teaches all aspects of modern mathematical modeling and that is specifically designed to introduce undergraduate students to problem solving in the context of biology. Included is an integrated package of theoretical modeling and analysis tools, computational modeling techniques, and parameter estimation and model validation methods, with a focus on integrating analytical and computational tools in the modeling of biological processes. Divided into three parts, it covers basic analytical modeling techniques; introduces computational tools used in the modeling of biological problems; and includes various problems from epidemiology, ecology, and physiology. All chapters include realistic biological examples, including many exercises related to biological questions. In addition, 25 open-ended research projects are provided, suitable for students. An accompanying Web site contains solutions and a tutorial for the implementation of the computational modeling techniques. Calculations can be done in modern computing languages such as Maple, Mathematica, and MATLAB?.
Author : Stephen L. Campbell
Publisher : Springer
ISBN 13 : 3030048853
Total Pages : 447 pages
Book Rating : 4.0/5 (3 download)
Download or read book Modeling and Simulation with Compose and Activate written by Stephen L. Campbell and published by Springer. This book was released on 2018-12-19 with total page 447 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a tutorial in the use of Altair Compose and Altair Activate, software packages that provide system modeling and simulation facilities. Advanced system modeling software provide multiple ways of creating models: models can be programmed in specialized languages, graphically constructed as block-diagrams and state machines, or expressed mathematically in equation-based languages. Compose and Activate are introduced in this text in two parts. The first part introduces the multi-language environment of Compose and its use for modeling, simulation and optimization. The second describes the graphical system modeling and optimization with Activate, an open-system environment providing signal-based modeling as well as physical system component-based modeling. Throughout both parts are applied examples from mechanical, biological, and electrical systems, as well as control and signal processing systems. This book will be an invaluable addition with many examples both for those just interested in OML and those doing industrial scale modeling, simulation, and design. All examples are worked using the free basic editions of Activate and Compose that are available.
Author : Koon Heng Ivan Teo
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (18 download)
Download or read book Methods for Increasing Model Accuracy and Simulation Time Scales of Biological Processes with Molecular Dynamics written by Koon Heng Ivan Teo and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Andreas Deutsch
Publisher : Birkhäuser
ISBN 13 : 1489979808
Total Pages : 470 pages
Book Rating : 4.4/5 (899 download)
Download or read book Cellular Automaton Modeling of Biological Pattern Formation written by Andreas Deutsch and published by Birkhäuser. This book was released on 2018-03-09 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text explores the use of cellular automata in modeling pattern formation in biological systems. It describes several mathematical modeling approaches utilizing cellular automata that can be used to study the dynamics of interacting cell systems both in simulation and in practice. New in this edition are chapters covering cell migration, tissue development, and cancer dynamics, as well as updated references and new research topic suggestions that reflect the rapid development of the field. The book begins with an introduction to pattern-forming principles in biology and the various mathematical modeling techniques that can be used to analyze them. Cellular automaton models are then discussed in detail for different types of cellular processes and interactions, including random movement, cell migration, adhesive cell interaction, alignment and cellular swarming, growth processes, pigment cell pattern formation, tissue development, tumor growth and invasion, and Turing-type patterns and excitable media. In the final chapter, the authors critically discuss possibilities and limitations of the cellular automaton approach in modeling various biological applications, along with future research directions. Suggestions for research projects are provided throughout the book to encourage additional engagement with the material, and an accompanying simulator is available for readers to perform their own simulations on several of the models covered in the text. QR codes are included within the text for easy access to the simulator. With its accessible presentation and interdisciplinary approach, Cellular Automaton Modeling of Biological Pattern Formation is suitable for graduate and advanced undergraduate students in mathematical biology, biological modeling, and biological computing. It will also be a valuable resource for researchers and practitioners in applied mathematics, mathematical biology, computational physics, bioengineering, and computer science. PRAISE FOR THE FIRST EDITION “An ideal guide for someone with a mathematical or physical background to start exploring biological modelling. Importantly, it will also serve as an excellent guide for experienced modellers to innovate and improve their methodologies for analysing simulation results.” —Mathematical Reviews
