Simulation Algorithms For Computational Systems Biology
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Simulation Algorithms For Computational Systems Biology
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Author : Luca Marchetti
language : en
Publisher: Springer
Release Date : 2017-09-27
Simulation Algorithms For Computational Systems Biology written by Luca Marchetti and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-27 with Computers categories.
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.
A Guide To Numerical Modelling In Systems Biology
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Author : Peter Deuflhard
language : en
Publisher: Springer
Release Date : 2015-07-06
A Guide To Numerical Modelling In Systems Biology written by Peter Deuflhard and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-06 with Mathematics categories.
This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks and identification of model parameters by means of comparisons with real data. Throughout the text, the strengths and weaknesses of numerical algorithms with respect to various systems biological issues are discussed. Web addresses for downloading the corresponding software are also included.
Biological Modeling And Simulation
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Author : Russell Schwartz
language : en
Publisher: MIT Press
Release Date : 2008-07-25
Biological Modeling And Simulation written by Russell Schwartz and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-07-25 with Science categories.
A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Stochastic Modelling For Systems Biology
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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2006-04-18
Stochastic Modelling For Systems Biology written by Darren J. Wilkinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-04-18 with Mathematics categories.
Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. The stochastic processes formalism provides a beautiful, elegant, and coherent foundation for chemical kinetics and there is a wealth of associated theory every bit as powerful and elegant as that for conventional continuous deterministic models. The time is right for an introductory text written from this perspective. Stochastic Modelling for Systems Biology presents an accessible introduction to stochastic modelling using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modelling biological systems. He provides a comprehensive understanding of stochastic kinetic modelling of biological networks in the systems biology context. The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications. While emphasizing the necessary probabilistic and stochastic methods, the author takes a practical approach, rooting his theoretical development in discussions of the intended application. Written with self-study in mind, the book includes technical chapters that deal with the difficult problems of inference for stochastic kinetic models from experimental data. Providing enough background information to make the subject accessible to the non-specialist, the book integrates a fairly diverse literature into a single convenient and notationally consistent source.
Analysis Of Biological Systems
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Author : Corrado Priami
language : en
Publisher: World Scientific
Release Date : 2015-01-29
Analysis Of Biological Systems written by Corrado Priami and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-01-29 with Science categories.
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.
Transactions On Computational Systems Biology Xi
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Author : Corrado Priami
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-09-07
Transactions On Computational Systems Biology Xi written by Corrado Priami and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-09-07 with Computers categories.
This issue on Computational Models for Cell Processes is based on a workshop that took place in Turku, Finland, May 2008. The papers span a mix of approaches to systems biology, ranging from quantitative techniques to computing paradigms inspired by biology.
Problem Solving Handbook In Computational Biology And Bioinformatics
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Author : Lenwood S. Heath
language : en
Publisher: Springer
Release Date : 2014-08-15
Problem Solving Handbook In Computational Biology And Bioinformatics written by Lenwood S. Heath and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-08-15 with Computers categories.
Bioinformatics is growing by leaps and bounds; theories/algorithms/statistical techniques are constantly evolving. Nevertheless, a core body of algorithmic ideas have emerged and researchers are beginning to adopt a "problem solving" approach to bioinformatics, wherein they use solutions to well-abstracted problems as building blocks to solve larger scope problems. Problem Solving Handbook for Computational Biology and Bioinformatics is an edited volume contributed by world renowned leaders in this field. This comprehensive handbook with problem solving emphasis, covers all relevant areas of computational biology and bioinformatics. Web resources and related themes are highlighted at every opportunity in this central easy-to-read reference. Designed for advanced-level students, researchers and professors in computer science and bioengineering as a reference or secondary text, this handbook is also suitable for professionals working in this industry.
Formal Methods For Computational Systems Biology
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Author : Marco Bernardo
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-05-20
Formal Methods For Computational Systems Biology written by Marco Bernardo and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-05-20 with Computers categories.
This book presents a set of 14 papers accompanying the lectures of leading researchers given at the 8th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008, held in Bertinoro, Italy in June 2008. SFM 2008 was devoted to formal techniques for computational systems biology and covered several aspects of the field, including computational models, calculi and logics for biological systems, and verification and simulation methods. The first part of this volume comprises nine papers based on regular lectures, the second part of this volume comprises five papers based on talks given by people involved in the Italian BISCA research project on Bio-Inspired Systems and Calculi with Applications.
Computational Systems Biology Of Cancer
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Author : Emmanuel Barillot
language : en
Publisher: CRC Press
Release Date : 2012-08-25
Computational Systems Biology Of Cancer written by Emmanuel Barillot and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-08-25 with Science categories.
The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models—integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencing. Offering promising insights on how to defeat cancer, the emerging field of systems biology captures the complexity of biological phenomena using mathematical and computational tools. Novel Approaches to Fighting Cancer Drawn from the authors’ decade-long work in the cancer computational systems biology laboratory at Institut Curie (Paris, France), Computational Systems Biology of Cancer explains how to apply computational systems biology approaches to cancer research. The authors provide proven techniques and tools for cancer bioinformatics and systems biology research. Effectively Use Algorithmic Methods and Bioinformatics Tools in Real Biological Applications Suitable for readers in both the computational and life sciences, this self-contained guide assumes very limited background in biology, mathematics, and computer science. It explores how computational systems biology can help fight cancer in three essential aspects: Categorising tumours Finding new targets Designing improved and tailored therapeutic strategies Each chapter introduces a problem, presents applicable concepts and state-of-the-art methods, describes existing tools, illustrates applications using real cases, lists publically available data and software, and includes references to further reading. Some chapters also contain exercises. Figures from the text and scripts/data for reproducing a breast cancer data analysis are available at www.cancer-systems-biology.net.
Automatic Algorithm Selection For Complex Simulation Problems
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Author : Roland Ewald
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-11-20
Automatic Algorithm Selection For Complex Simulation Problems written by Roland Ewald and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-11-20 with Computers categories.
To select the most suitable simulation algorithm for a given task is often difficult. This is due to intricate interactions between model features, implementation details, and runtime environment, which may strongly affect the overall performance. An automated selection of simulation algorithms supports users in setting up simulation experiments without demanding expert knowledge on simulation. Roland Ewald analyzes and discusses existing approaches to solve the algorithm selection problem in the context of simulation. He introduces a framework for automatic simulation algorithm selection and describes its integration into the open-source modelling and simulation framework James II. Its selection mechanisms are able to cope with three situations: no prior knowledge is available, the impact of problem features on simulator performance is unknown, and a relationship between problem features and algorithm performance can be established empirically. The author concludes with an experimental evaluation of the developed methods.