Tutorial For Modeling And Simulation Of Biological Processes

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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.

Simulation Modeling

Author : Constantin Volosencu
Publisher : BoD – Books on Demand
ISBN 13 : 1839696834
Total Pages : 268 pages
Book Rating : 4.8/5 (396 download)

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Book Synopsis Simulation Modeling by : Constantin Volosencu

Download or read book Simulation Modeling written by Constantin Volosencu and published by BoD – Books on Demand. This book was released on 2022-01-19 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book presents some recent specialized works of a theoretical and practical nature in the field of simulation modeling, which is being addressed to a large number of specialists, mathematicians, doctors, engineers, economists, professors, and students. The book comprises 11 chapters that promote modern mathematical algorithms and simulation modeling techniques, in practical applications, in the following thematic areas: mathematics, biomedicine, systems of systems, materials science and engineering, energy systems, and economics. This project presents scientific papers and applications that emphasize the capabilities of simulation modeling methods, helping readers to understand the phenomena that take place in the real world, the conditions of their development, and their effects, at a high scientific and technical level. The authors have published work examples and case studies that resulted from their researches in the field. The readers get new solutions and answers to questions related to the emerging applications of simulation modeling and their advantages.

Systems Medicine

Author : Ulf Schmitz
Publisher : Humana
ISBN 13 : 9781493932825
Total Pages : 0 pages
Book Rating : 4.9/5 (328 download)

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Book Synopsis Systems Medicine by : Ulf Schmitz

Download or read book Systems Medicine written by Ulf Schmitz and published by Humana. This book was released on 2015-12-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume guides readers through the field of systems medicine by defining the terminology, and describing how established computational methods form bioinformatics and systems biology can be taken forward to an integrative systems medicine approach. Chapters provide an outlook on the role that systems medicine may or should play in various medical fields, and describe different facets of the systems medicine approach in action. Ultimately it introduces tools, resources and methodologies from bioinformatics and systems biology, and how to apply these in a systems medicine project. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, and discuss experimental and computational approaches, methods, and tools that should be considered for a successful systems medicine project. Systems Medicine aims to motivate and provide guidance for collaborations across disciplines to tackle today's challenges related to human health and well-being.

Analysis Of Biological Systems

Author : Corrado Priami
Publisher : World Scientific
ISBN 13 : 1783266899
Total Pages : 431 pages
Book Rating : 4.7/5 (832 download)

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Book Synopsis Analysis Of Biological Systems by : Corrado Priami

Download or read book Analysis Of Biological Systems written by Corrado Priami and published by World Scientific. This book was released on 2015-01-29 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Logical Modeling of Cellular Processes: From Software Development to Network Dynamics

Author : Matteo Barberis
Publisher : Frontiers Media SA
ISBN 13 : 2889459837
Total Pages : 340 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by : Matteo Barberis

Download or read book Logical Modeling of Cellular Processes: From Software Development to Network Dynamics written by Matteo Barberis and published by Frontiers Media SA. This book was released on 2019-08-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.

A Course in Mathematical Biology

Author : Gerda de Vries
Publisher : SIAM
ISBN 13 : 0898718252
Total Pages : 307 pages
Book Rating : 4.8/5 (987 download)

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Book Synopsis A Course in Mathematical Biology by : Gerda de Vries

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?.

Molecular Modeling and Simulation

Author : Tamar Schlick
Publisher : Springer Science & Business Media
ISBN 13 : 0387224645
Total Pages : 669 pages
Book Rating : 4.3/5 (872 download)

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Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick

Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Algebraic and Discrete Mathematical Methods for Modern Biology

Author : Raina Robeva
Publisher : Academic Press
ISBN 13 : 0128012714
Total Pages : 383 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Algebraic and Discrete Mathematical Methods for Modern Biology by : Raina Robeva

Download or read book Algebraic and Discrete Mathematical Methods for Modern Biology written by Raina Robeva and published by Academic Press. This book was released on 2015-05-09 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. - Examines significant questions in modern biology and their mathematical treatments - Presents important mathematical concepts and tools in the context of essential biology - Features material of interest to students in both mathematics and biology - Presents chapters in modular format so coverage need not follow the Table of Contents - Introduces projects appropriate for undergraduate research - Utilizes freely accessible software for visualization, simulation, and analysis in modern biology - Requires no calculus as a prerequisite - Provides a complete Solutions Manual - Features a companion website with supplementary resources

Erwin-Riesch Workshop: System Analysis of Biological Processes

Author : Dietmar Möller
Publisher : Vieweg+teubner Verlag
ISBN 13 :
Total Pages : 244 pages
Book Rating : 4.:/5 (318 download)

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Book Synopsis Erwin-Riesch Workshop: System Analysis of Biological Processes by : Dietmar Möller

Download or read book Erwin-Riesch Workshop: System Analysis of Biological Processes written by Dietmar Möller and published by Vieweg+teubner Verlag. This book was released on 1987 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spine title: System analysis of biological processes.

Principles of Object-Oriented Modeling and Simulation with Modelica 3.3

Author : Peter Fritzson
Publisher : John Wiley & Sons
ISBN 13 : 1118859162
Total Pages : 1268 pages
Book Rating : 4.1/5 (188 download)

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Book Synopsis Principles of Object-Oriented Modeling and Simulation with Modelica 3.3 by : Peter Fritzson

Download or read book Principles of Object-Oriented Modeling and Simulation with Modelica 3.3 written by Peter Fritzson and published by John Wiley & Sons. This book was released on 2015-01-06 with total page 1268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fritzson covers the Modelica language in impressive depth from the basic concepts such as cyber-physical, equation-base, object-oriented, system, model, and simulation, while also incorporating over a hundred exercises and their solutions for a tutorial, easy-to-read experience. The only book with complete Modelica 3.3 coverage Over one hundred exercises and solutions Examines basic concepts such as cyber-physical, equation-based, object-oriented, system, model, and simulation

Computational Methods in Systems Biology

Author : Roberta Gori
Publisher : Springer Nature
ISBN 13 : 303171671X
Total Pages : 268 pages
Book Rating : 4.0/5 (317 download)

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Book Synopsis Computational Methods in Systems Biology by : Roberta Gori

Download or read book Computational Methods in Systems Biology written by Roberta Gori and published by Springer Nature. This book was released on with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Systems Medicine

Author :
Publisher : Academic Press
ISBN 13 : 0128160780
Total Pages : 1571 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Systems Medicine by :

Download or read book Systems Medicine written by and published by Academic Press. This book was released on 2020-08-24 with total page 1571 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information

Computational Methods in Systems Biology

Author : Jérôme Feret
Publisher : Springer
ISBN 13 : 3319674714
Total Pages : 339 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis Computational Methods in Systems Biology by : Jérôme Feret

Download or read book Computational Methods in Systems Biology written by Jérôme Feret and published by Springer. This book was released on 2017-09-18 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41 regular paper submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verication, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.

'In Silico' Simulation of Biological Processes

Author : Gregory R. Bock
Publisher : John Wiley & Sons
ISBN 13 :
Total Pages : 280 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis 'In Silico' Simulation of Biological Processes by : Gregory R. Bock

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 --

Agent-based Modeling and Simulation

Author : S. Taylor
Publisher : Springer
ISBN 13 : 1137453648
Total Pages : 223 pages
Book Rating : 4.1/5 (374 download)

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Book Synopsis Agent-based Modeling and Simulation by : S. Taylor

Download or read book Agent-based Modeling and Simulation written by S. Taylor and published by Springer. This book was released on 2014-08-27 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: Operational Research (OR) deals with the use of advanced analytical methods to support better decision-making. It is multidisciplinary with strong links to management science, decision science, computer science and many application areas such as engineering, manufacturing, commerce and healthcare. In the study of emergent behaviour in complex adaptive systems, Agent-based Modelling & Simulation (ABMS) is being used in many different domains such as healthcare, energy, evacuation, commerce, manufacturing and defense. This collection of articles presents a convenient introduction to ABMS with papers ranging from contemporary views to representative case studies. The OR Essentials series presents a unique cross-section of high quality research work fundamental to understanding contemporary issues and research across a range of Operational Research (OR) topics. It brings together some of the best research papers from the esteemed Operational Research Society and its associated journals, also published by Palgrave Macmillan.

Modeling and Simulation-Based Systems Engineering Handbook

Author : Daniele Gianni
Publisher : CRC Press
ISBN 13 : 1466571454
Total Pages : 518 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Modeling and Simulation-Based Systems Engineering Handbook by : Daniele Gianni

Download or read book Modeling and Simulation-Based Systems Engineering Handbook written by Daniele Gianni and published by CRC Press. This book was released on 2014-12-02 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: The capability modeling and simulation (M&S) supplies for managing systems complexity and investigating systems behaviors has made it a central activity in the development of new and existing systems. However, a handbook that provides established M&S practices has not been available. Until now. Modeling and Simulation-Based Systems Engineering Handbook details the M&S practices for supporting systems engineering in diverse domains. It discusses how you can identify systems engineering needs and adapt these practices to suit specific application domains, thus avoiding redefining practices from scratch. Although M&S practices are used and embedded within individual disciplines, they are often developed in isolation. However, they address recurring problems common to all disciplines. The editors of this book tackled the challenge by recruiting key representatives from several communities, harmonizing the different perspectives derived from individual backgrounds, and lining them up with the book’s vision. The result is a collection of M&S systems engineering examples that offer an initial means for cross-domain capitalization of the knowledge, methodologies, and technologies developed in several communities. These examples provide the pros and cons of the methods and techniques available, lessons learned, and pitfalls to avoid. As our society moves further in the information era, knowledge and M&S capabilities become key enablers for the engineering of complex systems and systems of systems. Therefore, knowledge and M&S methodologies and technologies become valuable output in an engineering activity, and their cross-domain capitalization is key to further advance the future practices in systems engineering. This book collates information across disciplines to provide you with the tools to more efficiently design and manage complex systems that achieve their goals.

Computational Methods in Systems Biology

Author : Corrado Priami
Publisher : Springer
ISBN 13 : 3540461671
Total Pages : 332 pages
Book Rating : 4.5/5 (44 download)

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Book Synopsis Computational Methods in Systems Biology by : Corrado Priami

Download or read book Computational Methods in Systems Biology written by Corrado Priami and published by Springer. This book was released on 2006-10-11 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2006, held in Trento, Italy, in October 2006. The 22 fully revised papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer sciences, such as language design, concurrency theory, software engineering, and formal methods.