Computer Simulation In Biology

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Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Author : Victor Bloomfield
Publisher : Springer Science & Business Media
ISBN 13 : 1441900837
Total Pages : 325 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Computer Simulation and Data Analysis in Molecular Biology and Biophysics by : Victor Bloomfield

Download or read book Computer Simulation and Data Analysis in Molecular Biology and Biophysics written by Victor Bloomfield and published by Springer Science & Business Media. This book was released on 2009-06-05 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.

Computer Simulation in Biology

Author : Robert E. Keen
Publisher : Wiley-Liss
ISBN 13 :
Total Pages : 524 pages
Book Rating : 4.E/5 ( download)

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Book Synopsis Computer Simulation in Biology by : Robert E. Keen

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.

Simulation Algorithms for Computational Systems Biology

Author : Luca Marchetti
Publisher : Springer
ISBN 13 : 3319631136
Total Pages : 245 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis Simulation Algorithms for Computational Systems Biology by : Luca Marchetti

Download or read book Simulation Algorithms for Computational Systems Biology written by Luca Marchetti and published by Springer. This book was released on 2017-09-27 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays, diffusion in space, or that are based on hybrid simulation strategies. This is a valuable self-contained resource for graduate students and practitioners in computer science, biology and bioinformatics. An appendix covers the mathematical background, and the authors include further reading sections in each chapter.

Computer Simulations with Mathematica

Author : Richard J. Gaylord
Publisher :
ISBN 13 :
Total Pages : 330 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Computer Simulations with Mathematica by : Richard J. Gaylord

Download or read book Computer Simulations with Mathematica written by Richard J. Gaylord and published by . This book was released on 1995 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of natural phenomena using computer simulation is a major new research tool in the physical, chemical, biological and social sciences. It is useful for studying simple systems, and it is essential for the study of complex systems. Using Mathematica, an integrated software environment for scientific programming, numerical analysis and visualization, this book describes computer simulations applicable to a wide range of phenomena.

Biological Modeling and Simulation

Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262303396
Total Pages : 403 pages
Book Rating : 4.2/5 (623 download)

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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 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.

Computer Simulation in Biology

Author : Robert E. Keen
Publisher : Wiley-Liss
ISBN 13 : 9780471561910
Total Pages : pages
Book Rating : 4.5/5 (619 download)

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Book Synopsis Computer Simulation in Biology by : Robert E. Keen

Download or read book Computer Simulation in Biology written by Robert E. Keen and published by Wiley-Liss. This book was released on 1991-12-27 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Offers a comprehensive, step-by-step approach to explain the development and use of computer models and simulators in biology. How to obtain equations for simple models and their utilization in generating simulation data is thoroughly covered and each chapter provides numerous helpful exercises. Also contains related software.

Computer Simulation of Biomolecular Systems

Author : W.F. van Gunsteren
Publisher : Springer Science & Business Media
ISBN 13 : 9789072199256
Total Pages : 664 pages
Book Rating : 4.1/5 (992 download)

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Book Synopsis Computer Simulation of Biomolecular Systems by : W.F. van Gunsteren

Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 1997-11-30 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.

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

Author : S. Sitharama Iyengar
Publisher : CRC Press
ISBN 13 : 9780849379628
Total Pages : 212 pages
Book Rating : 4.3/5 (796 download)

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

Download or read book Computer Modeling and Simulations of Complex Biological Systems, 2nd Edition written by S. Sitharama Iyengar and published by CRC Press. This book was released on 1997-11-20 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computational Modeling of Biological Systems

Author : Nikolay V Dokholyan
Publisher : Springer Science & Business Media
ISBN 13 : 1461421454
Total Pages : 360 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Computational Modeling of Biological Systems by : Nikolay V Dokholyan

Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Systems Biology

Author : Aleš Prokop
Publisher : Springer Science & Business Media
ISBN 13 : 9400768036
Total Pages : 569 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Systems Biology by : Aleš Prokop

Download or read book Systems Biology written by Aleš Prokop and published by Springer Science & Business Media. This book was released on 2013-08-28 with total page 569 pages. Available in PDF, EPUB and Kindle. Book excerpt: Growth in the pharmaceutical market has slowed down – almost to a standstill. One reason is that governments and other payers are cutting costs in a faltering world economy. But a more fundamental problem is the failure of major companies to discover, develop and market new drugs. Major drugs losing patent protection or being withdrawn from the market are simply not being replaced by new therapies – the pharmaceutical market model is no longer functioning effectively and most pharmaceutical companies are failing to produce the innovation needed for success. This multi-authored new book looks at a vital strategy which can bring innovation to a market in need of new ideas and new products: Systems Biology (SB). Modeling is a significant task of systems biology. SB aims to develop and use efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of biological systems, such as the networks of metabolites comprise signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes. SB involves a series of operational protocols used for performing research, namely a cycle composed of theoretical, analytic or computational modeling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.

Calculated Surprises

Author : Johannes Lenhard
Publisher : Oxford University Press
ISBN 13 : 0190873299
Total Pages : 256 pages
Book Rating : 4.1/5 (98 download)

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Book Synopsis Calculated Surprises by : Johannes Lenhard

Download or read book Calculated Surprises written by Johannes Lenhard and published by Oxford University Press. This book was released on 2019-02-18 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: If all philosophy starts with wondering, then Calculated Surprises starts with wondering about how computers are changing the face and inner workings of science. In this book, Lenhard concentrates on the ways in which computers and simulation are transforming the established conception of mathematical modeling. His core thesis is that simulation modeling constitutes a new mode of mathematical modeling that rearranges and inverts key features of the established conception. Although most of these new key features--such as experimentation, exploration, or epistemic opacity--have their precursors, the new ways in which they are being combined is generating a distinctive style of scientific reasoning. Lenhard also documents how simulation is affecting fundamental concepts of solution, understanding, and validation. He feeds these transformations back into philosophy of science, thereby opening up new perspectives on longstanding oppositions. By combining historical investigations with practical aspects, Calculated Surprises is accessible for a broad audience of readers. Numerous case studies covering a wide range of simulation techniques are balanced with broad reflections on science and technology. Initially, what computers are good at is calculating with a speed and accuracy far beyond human capabilities. Lenhard goes further and investigates the emerging characteristics of computer-based modeling, showing how this simple observation is creating a number of surprising challenges for the methodology and epistemology of science. These calculated surprises will attract both philosophers and scientific practitioners who are interested in reflecting on recent developments in science and technology.

Computer Simulation in Human Population Studies

Author : Bennett Dyke
Publisher : Academic Press
ISBN 13 : 1483264556
Total Pages : 541 pages
Book Rating : 4.4/5 (832 download)

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Book Synopsis Computer Simulation in Human Population Studies by : Bennett Dyke

Download or read book Computer Simulation in Human Population Studies written by Bennett Dyke and published by Academic Press. This book was released on 2014-05-12 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Simulation in Human Population Studies contains the proceedings of a conference held at Pennsylvania State University on June 12-14, 1972, under the sponsorship of the Social Science Research Council. The conference provided a forum for discussing the application of computer simulation techniques to human population studies and organized topics around four themes: anthropology and social systems; genetics and adaptive systems; demography; and simulation methodology. Comprised of 23 chapters, this volume begins with an analysis of two tests of computer microsimulation: the effect of an incest taboo on population viability, and the effect of age differences between spouses on the skewing of their consanguineal relationships. The reader is then introduced to computer simulation of incest prohibition and clan proscription rules in closed, finite population; an empirical perspective on simulation models of human population; and models applicable to geographic variation in humans. Subsequent chapters deal with the role of co-adapted sets in the process of adaptation; simulation of human reproduction; and the mathematics of population simulation models. This book will be of interest to anthropologists, geneticists, biologists, computer scientists, mathematicians, and social scientists.

Computational Modeling And Simulations Of Biomolecular Systems

Author : Benoit Roux
Publisher : World Scientific
ISBN 13 : 9811232776
Total Pages : 209 pages
Book Rating : 4.8/5 (112 download)

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Book Synopsis Computational Modeling And Simulations Of Biomolecular Systems by : Benoit Roux

Download or read book Computational Modeling And Simulations Of Biomolecular Systems written by Benoit Roux and published by World Scientific. This book was released on 2021-08-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).

Introduction to Computational Science

Author : Angela B. Shiflet
Publisher : Princeton University Press
ISBN 13 : 140085055X
Total Pages : 857 pages
Book Rating : 4.4/5 (8 download)

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Book Synopsis Introduction to Computational Science by : Angela B. Shiflet

Download or read book Introduction to Computational Science written by Angela B. Shiflet and published by Princeton University Press. This book was released on 2014-03-30 with total page 857 pages. Available in PDF, EPUB and Kindle. Book excerpt: The essential introduction to computational science—now fully updated and expanded Computational science is an exciting new field at the intersection of the sciences, computer science, and mathematics because much scientific investigation now involves computing as well as theory and experiment. This textbook provides students with a versatile and accessible introduction to the subject. It assumes only a background in high school algebra, enables instructors to follow tailored pathways through the material, and is the only textbook of its kind designed specifically for an introductory course in the computational science and engineering curriculum. While the text itself is generic, an accompanying website offers tutorials and files in a variety of software packages. This fully updated and expanded edition features two new chapters on agent-based simulations and modeling with matrices, ten new project modules, and an additional module on diffusion. Besides increased treatment of high-performance computing and its applications, the book also includes additional quick review questions with answers, exercises, and individual and team projects. The only introductory textbook of its kind—now fully updated and expanded Features two new chapters on agent-based simulations and modeling with matrices Increased coverage of high-performance computing and its applications Includes additional modules, review questions, exercises, and projects An online instructor's manual with exercise answers, selected project solutions, and a test bank and solutions (available only to professors) An online illustration package is available to professors

Computer Simulation Analysis of Biological and Agricultural Systems

Author : Barney K. Huang
Publisher : CRC Press
ISBN 13 : 9780849348693
Total Pages : 892 pages
Book Rating : 4.3/5 (486 download)

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Book Synopsis Computer Simulation Analysis of Biological and Agricultural Systems by : Barney K. Huang

Download or read book Computer Simulation Analysis of Biological and Agricultural Systems written by Barney K. Huang and published by CRC Press. This book was released on 1994-03-22 with total page 892 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Simulation Analysis of Biological and Agricultural Systems focuses on the integration of mathematical models and the dynamic simulation essential to system analysis, design, and synthesis. The book emphasizes the quantitative dynamic relationships between elements and system responses. Problems of various degrees of difficulty and complexity are discussed to illustrate methods of computer-aided design and analysis that can bridge the gap between theories and applications. These problems cover a wide variety of subjects in the biological and agricultural fields. Specific guidelines and practical methods for defining requirements, developing specifications, and integrating system modeling early in simulation development are included as well. Computer Simulation Analysis of Biological and Agricultural Systems is an excellent text and self-guide for agricultural engineers, agronomists, foresters, horticulturists, soil scientists, mechanical engineers, and computer simulators.

Dynamic Systems Biology Modeling and Simulation

Author : Joseph DiStefano III
Publisher : Academic Press
ISBN 13 : 0124104932
Total Pages : 886 pages
Book Rating : 4.1/5 (241 download)

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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 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]

Mathematical Modeling and Simulation in Enteric Neurobiology

Author : Roustem Miftahof
Publisher : World Scientific
ISBN 13 : 9812834818
Total Pages : 350 pages
Book Rating : 4.8/5 (128 download)

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Book Synopsis Mathematical Modeling and Simulation in Enteric Neurobiology by : Roustem Miftahof

Download or read book Mathematical Modeling and Simulation in Enteric Neurobiology written by Roustem Miftahof and published by World Scientific. This book was released on 2009 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lack of scientists equally trained and prepared to understand both mathematics and biology/medicine hampers the development and application of computer simulation methods in biology and neurogastrobiology. Currently, there are no texts for navigating the extensive and intricate field of mathematical and computational modeling in neurogastrobiology. This book bridges the gap between mathematicians, computer scientists and biologists, and thus assists in the study and analysis of complex biological phenomena that cannot be done through traditional in vivo and in vitro experimental approaches. The book recognizes the complexity of biological phenomena under investigation and treats the subject matter with a degree of mathematical rigor. Special attention is given to computer simulations for interpolation and extrapolation of electromechanical and chemoelectrical phenomena, nonlinear self-sustained electromechanical wave activity, pharmacological effects including co-localization and co-transmission by multiple neurotransmitters, receptor polymodality, and drug interactions. Mathematical Modeling and Simulation in Enteric Neurobiology is an interdisciplinary book and is an essential source of information for biologists and doctors who are interested in knowing about the role and advantages of numerical experimentation in their subjects, as well as for mathematicians who are interested in exploring new areas of applications.