Symbolic Approaches To Modeling And Analysis Of Biological Systems

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Symbolic Approaches to Modeling and Analysis of Biological Systems

Cedric Lhoussaine,Elisabeth Remy
Symbolic Approaches to Modeling and Analysis of Biological Systems Book PDF

Author : Cedric Lhoussaine,Elisabeth Remy
Publisher : John Wiley & Sons
Page : 404 pages
File Size : 52,9 Mb
Release : 2023-07-31
Category : Computers
ISBN : 9781394229079

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Symbolic Approaches to Modeling and Analysis of Biological Systems by Cedric Lhoussaine,Elisabeth Remy Pdf

Systems Biology is an approach to biology that involves understanding the complexity of interactions among biological entities within a systemic whole. The goal is to understand the emergence of physiological or functional properties. Symbolic Approaches to Modeling and Analysis of Biological Systems presents contributions of formal methods from computer science for modeling the dynamics of biological systems. It deals more specifically with symbolic methods, i.e. methods that can establish the qualitative properties of models. This book presents different approaches related to semantics, language, modeling and their link with data, and allows us to examine the fundamental problems and challenges that biological systems are facing. The first part of the book presents works that rely on various available data to build models, while the second part gathers contributions surrounding issues of semantics and formal methods.

Analysis of Biological Systems

Corrado Priami,Melissa J Morine
Analysis of Biological Systems Book PDF

Author : Corrado Priami,Melissa J Morine
Publisher : World Scientific
Page : 432 pages
File Size : 43,9 Mb
Release : 2015-01-29
Category : Science
ISBN : 9781783266890

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Analysis of Biological Systems by Corrado Priami,Melissa J Morine Pdf

Modeling is fast becoming fundamental to understanding the processes that define biological systems. High-throughput technologies are producing increasing quantities of data that require an ever-expanding toolset for their effective analysis and interpretation. Analysis of high-throughput data in the context of a molecular interaction network is particularly informative as it has the potential to reveal the most relevant network modules with respect to a phenotype or biological process of interest. Analysis of Biological Systems collects classical material on analysis, modeling and simulation, thereby acting as a unique point of reference. The joint application of statistical techniques to extract knowledge from big data and map it into mechanistic models is a current challenge of the field, and the reader will learn how to build and use models even if they have no computing or math background. An in-depth analysis of the currently available technologies, and a comparison between them, is also included. Unlike other reference books, this in-depth analysis is extended even to the field of language-based modeling. The overall result is an indispensable, self-contained and systematic approach to a rapidly expanding field of science. Contents:Algorithmic Systems BiologySetting the ContextSystems and ModelsStatic Modeling TechnologiesDynamic Modeling TechnologiesLanguage-based ModelingDynamic Modeling ProcessSimulationPerspectives and ConclusionsAppendix A: Basic MathAppendix B: Probability and StatisticsAppendix C: Semantics of Modeling Languages Readership: Graduate students in computer science, physics, mathematics or engineering or biology-related fields who want to better understand how to develop and use models of biological systems. Practitioners in systems biology who want to understand algorithmic modeling and algorithmic systems biology. Key Features:The book jointly deals with static (statistical) and dynamic (simulation) technologies making it a strong reference for who wants to approach real systems biology problemsThe content of the book is the result of more than ten years application of the material in university courses and to industrial-level problems in systems pharmacology and systems nutritionThere is no reference work available for the field of language-based modeling that is studied in depth in this bookKeywords:Modeling;Simulation;Network Analysis;Systems Biology;Systems Nutrition;Systems Pharmacology;Stochastic Models;Programming Biology;Multivariate Analysis

Symbolic Systems Biology

M. Sriram Iyengar
Symbolic Systems Biology Book PDF

Author : M. Sriram Iyengar
Publisher : Biological Science (Jones and
Page : 0 pages
File Size : 42,9 Mb
Release : 2011
Category : Science
ISBN : 076375370X

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Symbolic Systems Biology by M. Sriram Iyengar Pdf

Mathematical and computational modeling of biological processes and pathways.

Systems Biology

Andreas Kremling
Systems Biology Book PDF

Author : Andreas Kremling
Publisher : CRC Press
Page : 379 pages
File Size : 51,7 Mb
Release : 2013-11-12
Category : Mathematics
ISBN : 9781466567900

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Systems Biology by Andreas Kremling Pdf

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

Dynamical Systems for Biological Modeling

Fred Brauer,Christopher Kribs
Dynamical Systems for Biological Modeling Book PDF

Author : Fred Brauer,Christopher Kribs
Publisher : CRC Press
Page : 482 pages
File Size : 51,5 Mb
Release : 2015-12-23
Category : Mathematics
ISBN : 9781498774048

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Dynamical Systems for Biological Modeling by Fred Brauer,Christopher Kribs Pdf

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

Formal Modeling: Actors; Open Systems, Biological Systems

Gul Agha,Olivier Danvy,José Meseguer
Formal Modeling Actors Open Systems Biological Systems Book PDF

Author : Gul Agha,Olivier Danvy,José Meseguer
Publisher : Springer Science & Business Media
Page : 465 pages
File Size : 49,7 Mb
Release : 2011-10-13
Category : Computers
ISBN : 9783642249327

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Formal Modeling: Actors; Open Systems, Biological Systems by Gul Agha,Olivier Danvy,José Meseguer Pdf

This Festschrift volume, published in honor of Carolyn Talcott on the occasion of her 70th birthday, contains a collection of papers presented at a symposium held in Menlo Park, California, USA, in November 2011. Carolyn Talcott is a leading researcher and mentor of international renown among computer scientists. She has made key contributions to a number of areas of computer science including: semantics and verification of progamming languages; foundations of actor-based systems; middleware, meta-architectures, and systems; Maude and rewriting logic; and computational biology. The 21 papers presented are organized in topical sections named: Essays on Carolyn Talcott; actors and programming languages; cyberphysical systems; middleware and meta-architectures; formal methods and reasoning tools; and computational biology.

Modeling Biological Systems:

James W. Haefner
Modeling Biological Systems Book PDF

Author : James W. Haefner
Publisher : Springer Science & Business Media
Page : 500 pages
File Size : 49,9 Mb
Release : 2005-05-06
Category : Science
ISBN : 0387250115

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Modeling Biological Systems: by James W. Haefner Pdf

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

Harvey J. Gold
Mathematical Modeling of Biological Systems Book PDF

Author : Harvey J. Gold
Publisher : John Wiley & Sons
Page : 392 pages
File Size : 54,5 Mb
Release : 1977
Category : Biological models
ISBN : UCAL:B4285115

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Mathematical Modeling of Biological Systems by Harvey J. Gold Pdf

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.

Automated Reasoning for Systems Biology and Medicine

Pietro Liò,Paolo Zuliani
Automated Reasoning for Systems Biology and Medicine Book PDF

Author : Pietro Liò,Paolo Zuliani
Publisher : Springer
Page : 474 pages
File Size : 49,7 Mb
Release : 2019-06-11
Category : Computers
ISBN : 9783030172978

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Automated Reasoning for Systems Biology and Medicine by Pietro Liò,Paolo Zuliani Pdf

This book presents outstanding contributions in an exciting, new and multidisciplinary research area: the application of formal, automated reasoning techniques to analyse complex models in systems biology and systems medicine. Automated reasoning is a field of computer science devoted to the development of algorithms that yield trustworthy answers, providing a basis of sound logical reasoning. For example, in the semiconductor industry formal verification is instrumental to ensuring that chip designs are free of defects (or “bugs”). Over the past 15 years, systems biology and systems medicine have been introduced in an attempt to understand the enormous complexity of life from a computational point of view. This has generated a wealth of new knowledge in the form of computational models, whose staggering complexity makes manual analysis methods infeasible. Sound, trusted, and automated means of analysing the models are thus required in order to be able to trust their conclusions. Above all, this is crucial to engineering safe biomedical devices and to reducing our reliance on wet-lab experiments and clinical trials, which will in turn produce lower economic and societal costs. Some examples of the questions addressed here include: Can we automatically adjust medications for patients with multiple chronic conditions? Can we verify that an artificial pancreas system delivers insulin in a way that ensures Type 1 diabetic patients never suffer from hyperglycaemia or hypoglycaemia? And lastly, can we predict what kind of mutations a cancer cell is likely to undergo? This book brings together leading researchers from a number of highly interdisciplinary areas, including: · Parameter inference from time series · Model selection · Network structure identification · Machine learning · Systems medicine · Hypothesis generation from experimental data · Systems biology, systems medicine, and digital pathology · Verification of biomedical devices “This book presents a comprehensive spectrum of model-focused analysis techniques for biological systems ...an essential resource for tracking the developments of a fast moving field that promises to revolutionize biology and medicine by the automated analysis of models and data.”Prof Luca Cardelli FRS, University of Oxford

Mathematical Modeling of Complex Biological Systems

Abdelghani Bellouquid,Marcello Delitala
Mathematical Modeling of Complex Biological Systems Book PDF

Author : Abdelghani Bellouquid,Marcello Delitala
Publisher : Springer Science & Business Media
Page : 194 pages
File Size : 52,9 Mb
Release : 2006-08-17
Category : Science
ISBN : 9780817643959

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Mathematical Modeling of Complex Biological Systems by Abdelghani Bellouquid,Marcello Delitala Pdf

This book describes the evolution of several socio-biological systems using mathematical kinetic theory. Specifically, it deals with modeling and simulations of biological systems whose dynamics follow the rules of mechanics as well as rules governed by their own ability to organize movement and biological functions. It proposes a new biological model focused on the analysis of competition between cells of an aggressive host and cells of a corresponding immune system. Proposed models are related to the generalized Boltzmann equation. The book may be used for advanced graduate courses and seminars in biological systems modeling.

Mathematical Modeling of Biological Systems, Volume II

Andreas Deutsch,Rafael Bravo de la Parra,Rob J. de Boer,Odo Diekmann,Peter Jagers,Eva Kisdi,Mirjam Kretzschmar,Petr Lansky,Hans Metz
Mathematical Modeling of Biological Systems Volume II Book PDF

Author : Andreas Deutsch,Rafael Bravo de la Parra,Rob J. de Boer,Odo Diekmann,Peter Jagers,Eva Kisdi,Mirjam Kretzschmar,Petr Lansky,Hans Metz
Publisher : Springer Science & Business Media
Page : 386 pages
File Size : 45,8 Mb
Release : 2007-10-12
Category : Mathematics
ISBN : 9780817645564

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Mathematical Modeling of Biological Systems, Volume II by Andreas Deutsch,Rafael Bravo de la Parra,Rob J. de Boer,Odo Diekmann,Peter Jagers,Eva Kisdi,Mirjam Kretzschmar,Petr Lansky,Hans Metz Pdf

Volume II of this two-volume, interdisciplinary work is a unified presentation of a broad range of state-of-the-art topics in the rapidly growing field of mathematical modeling in the biological sciences. Highlighted throughout are mathematical and computational apporaches to examine central problems in the life sciences, ranging from the organization principles of individual cells to the dynamics of large populations. The chapters are thematically organized into the following main areas: epidemiology, evolution and ecology, immunology, neural systems and the brain, and innovative mathematical methods and education. The work will be an excellent reference text for a broad audience of researchers, practitioners, and advanced students in this rapidly growing field at the intersection of applied mathematics, experimental biology and medicine, computational biology, biochemistry, computer science, and physics.

Computer Modeling and Simulations of Complex Biological Systems, 2nd Edition

S. Sitharama Iyengar
Computer Modeling and Simulations of Complex Biological Systems 2nd Edition Book PDF

Author : S. Sitharama Iyengar
Publisher : CRC Press
Page : 212 pages
File Size : 53,6 Mb
Release : 1997-11-20
Category : Medical
ISBN : 0849379628

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Computer Modeling and Simulations of Complex Biological Systems, 2nd Edition by S. Sitharama Iyengar Pdf

This unique text explores the use of innovative modeling techniques in effecting a better understanding of complex diseases such as AIDS and cancer. From a way of representing the computational properties of protein-folding problems to computer simulation of bimodal neurons and networks, Computer Modeling and Simulations of Complex Biological Systems examines several modeling methodologies and integrates them across a variety of disciplines. This interdisciplinary approach suggests new ways to solve complex problems pertaining to biological systems. Written in clear and simple terms appropriate for both the novice and the experienced researcher, the book presents a step-by-step approach to the subject and includes numerous examples that explain the concepts presented in the text.

Methods in Bioengineering

Arul Jayaraman,Juergen Hahn
Methods in Bioengineering Book PDF

Author : Arul Jayaraman,Juergen Hahn
Publisher : Artech House
Page : 329 pages
File Size : 49,5 Mb
Release : 2009
Category : Science
ISBN : 9781596934061

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Methods in Bioengineering by Arul Jayaraman,Juergen Hahn Pdf

"This cutting-edge volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to: design of state-of-the art methods for analyzing biological systems Implement experimental approaches for investigating cellular behavior in health and disease; use algorithms and modeling techniques for quantitatively describing biomedical problems; and integrate experimental and computational approaches for a more complete view of biological systems." --Book Jacket.

Dynamic Models and Control of Biological Systems

Vadrevu Sree Hari Rao,Ponnada Raja Sekhara Rao
Dynamic Models and Control of Biological Systems Book PDF

Author : Vadrevu Sree Hari Rao,Ponnada Raja Sekhara Rao
Publisher : Springer Science & Business Media
Page : 279 pages
File Size : 46,5 Mb
Release : 2009-07-30
Category : Science
ISBN : 9781441903594

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Dynamic Models and Control of Biological Systems by Vadrevu Sree Hari Rao,Ponnada Raja Sekhara Rao Pdf

Mathematical Biology has grown at an astonishing rate and has established itself as a distinct discipline. Mathematical modeling is now being applied in every major discipline in the biological sciences. Though the field has become increasingly large and specialized, this book remains important as a text that introduces some of the exciting problems which arise in the biological sciences and gives some indication of the wide spectrum of questions that modeling can address.

Stochastic Models in Biology

Narendra S. Goel,Nira Richter-Dyn
Stochastic Models in Biology Book PDF

Author : Narendra S. Goel,Nira Richter-Dyn
Publisher : Elsevier
Page : 282 pages
File Size : 53,8 Mb
Release : 2016-01-26
Category : Science
ISBN : 9781483278100

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Stochastic Models in Biology by Narendra S. Goel,Nira Richter-Dyn Pdf

Stochastic Models in Biology describes the usefulness of the theory of stochastic process in studying biological phenomena. The book describes analysis of biological systems and experiments though probabilistic models rather than deterministic methods. The text reviews the mathematical analyses for modeling different biological systems such as the random processes continuous in time and discrete in state space. The book also discusses population growth and extinction through Malthus' law and the work of MacArthur and Wilson. The text then explains the dynamics of a population of interacting species. The book also addresses population genetics under systematic evolutionary pressures known as deterministic equations and genetic changes in a finite population known as stochastic equations. The text then turns to stochastic modeling of biological systems at the molecular level, particularly the kinetics of biochemical reactions. The book also presents various useful equations such as the differential equation for generating functions for birth and death processes. The text can prove valuable for biochemists, cellular biologists, and researchers in the medical and chemical field who are tasked to perform data analysis.