Download or read book Chemical Master Equation for Large Biological Networks written by Don Kulasiri and published by Springer Nature. This book was released on 2021-09-12 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights the theory and practical applications of the chemical master equation (CME) approach for very large biochemical networks, which provides a powerful general framework for model building in a variety of biological networks. The aim of the book is to not only highlight advanced numerical solution methods for the CME, but also reveal their potential by means of practical examples. The case studies presented are mainly from biology; however, the applications from novel methods are discussed comprehensively, underlining the interdisciplinary approach in simulation and the potential of the chemical master equation approach for modelling bionetworks. The book is a valuable guide for researchers, graduate students, and professionals alike.
Download or read book Stochastic Processes written by Don Kulasiri and published by BoD – Books on Demand. This book was released on 2024-07-31 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Stochastic Reactive Distributed Robotic Systems written by Gregory Mermoud and published by Springer. This book was released on 2013-10-01 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph presents the development of novel model-based methodologies for engineering self-organized and self-assembled systems. The work bridges the gap between statistical mechanics and control theory by tackling a number of challenges for a class of distributed systems involving a specific type of constitutive components, namely referred to as Smart Minimal Particles. The results described in the volume are expected to lead to more robust, dependable, and inexpensive distributed systems such as those endowed with complex and advanced sensing, actuation, computation, and communication capabilities.
Download or read book Analysis and Numerics of the Chemical Master Equation written by Vikram Sunkara and published by . This book was released on 2013 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is well known that many realistic mathematical models of biological and chemical systems, such as enzyme cascades and gene regulatory networks, need to include stochasticity. These systems can be described as Markov processes and are modelled using the Chemical Master Equation (CME). The CME is a differential difference equation (continuous in time and discrete in the state space) for the probability of a certain state at a given time. The state space is the population count of species in the system. A successful method for computing the CME is the Finite State Projection Method (FSP). The purpose of this literature is to provide methods to help enhance the computation speed of the CME. We introduce an extension to the FSP method called the Optimal Finite State Projection method (OFSP). The OFSP method keeps the support of the approximation close to the smallest theoretical size, which in turn reduces the computation complexity and increases speed-up. We then introduce the Parallel Finite State Projection method (PFSP), a method to distribute the computation of the CME over multiple cores, to allow the computation of systems with a large CME support. Finally, a method for estimating the support a priori is introduced, called the Gated One Reaction Domain Expansion (GORDE). GORDE is the first domain selection method in the CME literature which can guarantee that the support proposed by the method will give the desired FSP approximation error.
Download or read book Systems Biology written by Bernhard Ø. Palsson and published by Cambridge University Press. This book was released on 2006-01-16 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook, devoted to systems biology, describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated website Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results.
Download or read book Encyclopedia of Systems Biology written by Werner Dubitzky and published by Springer. This book was released on 2013-08-17 with total page 2367 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology refers to the quantitative analysis of the dynamic interactions among several components of a biological system and aims to understand the behavior of the system as a whole. Systems biology involves the development and application of systems theory concepts for the study of complex biological systems through iteration over mathematical modeling, computational simulation and biological experimentation. Systems biology could be viewed as a tool to increase our understanding of biological systems, to develop more directed experiments, and to allow accurate predictions. The Encyclopedia of Systems Biology is conceived as a comprehensive reference work covering all aspects of systems biology, in particular the investigation of living matter involving a tight coupling of biological experimentation, mathematical modeling and computational analysis and simulation. The main goal of the Encyclopedia is to provide a complete reference of established knowledge in systems biology – a ‘one-stop shop’ for someone seeking information on key concepts of systems biology. As a result, the Encyclopedia comprises a broad range of topics relevant in the context of systems biology. The audience targeted by the Encyclopedia includes researchers, developers, teachers, students and practitioners who are interested or working in the field of systems biology. Keeping in mind the varying needs of the potential readership, we have structured and presented the content in a way that is accessible to readers from wide range of backgrounds. In contrast to encyclopedic online resources, which often rely on the general public to author their content, a key consideration in the development of the Encyclopedia of Systems Biology was to have subject matter experts define the concepts and subjects of systems biology.
Download or read book Formal Methods in Systems Biology written by Jasmin Fisher and published by Springer. This book was released on 2008-06-05 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thisvolumecontainstheproceedingsofthe?rstinternationalmeetingonFormal Methods in Systems Biology, held at Microsoft Research, Cambridge, UK, June 4–5, 2008. While there are several venues that cover computational methods in systems biology,there is to date no single conference that brings together the application of the range of formal methods in biology. Therefore, convening such a meeting could prove extremely productive. The purpose of this meeting was to identify techniques for the speci?cation, development and veri?cation of biological m- els.Italsofocusedonthedesignoftoolstoexecuteandanalyzebiologicalmodels in ways that can signi?cantly advance our understanding of biological systems. As a forum for this discussion we invited key scientists in the area of formal methods to this unique meeting. Although this was a one-o? meeting, we are exploring the possibility of this forming the ?rst of what might become an annual conference. Presentations at the meeting were by invitation only; future meetings are expected to operate on a submission and review basis. The Steering Committee and additional referees reviewed the invited papers. Each submission was evaluated by at least two referees. The volume includes nine invited contributions. Formal Methods in Systems Biology 2008 was made possible by the cont- bution and dedication ofmany people. First of all,we wouldlike to thank allthe authors who submitted papers. Secondly, we would like to thank our additional invited speakers and participants. We would also like to thank the members of the Steering Committee for their valuable comments. Finally, we ackno- edge the help of the administrative and technical sta? at the MicrosoftResearch Cambridge lab.
Download or read book Stochastic Modelling for Systems Biology written by Darren J. Wilkinson and published by CRC Press. This book was released on 2006-04-18 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Stochastic Approaches for Systems Biology written by Mukhtar Ullah and published by Springer Science & Business Media. This book was released on 2011-07-12 with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook focuses on stochastic analysis in systems biology containing both the theory and application. While the authors provide a review of probability and random variables, subsequent notions of biochemical reaction systems and the relevant concepts of probability theory are introduced side by side. This leads to an intuitive and easy-to-follow presentation of stochastic framework for modeling subcellular biochemical systems. In particular, the authors make an effort to show how the notion of propensity, the chemical master equation and the stochastic simulation algorithm arise as consequences of the Markov property. The text contains many illustrations, examples and exercises to illustrate the ideas and methods that are introduced. Matlab code is also provided where appropriate. Additionally, the cell cycle is introduced as a more complex case study. Senior undergraduate and graduate students in mathematics and physics as well as researchers working in the area of systems biology, bioinformatics and related areas will find this text useful.
Download or read book Theoretical Physics for Biological Systems written by Paola Lecca and published by CRC Press. This book was released on 2019-01-30 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.
Download or read book Biomolecular Feedback Systems written by Domitilla Del Vecchio and published by Princeton University Press. This book was released on 2014-10-26 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu
Download or read book Inexact Methods for the Chemical Master Equation with Constant Or Time varying Propensities and Application to Parameter Inference written by Khanh Ngoc Dinh and published by . This book was released on 2018 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex reaction networks arise in molecular biology and many other different fields of science such as ecology and social study. A familiar approach to modeling such problems is to find their master equation. In systems biology, the equation is called the chemical master equation (CME), and solving the CME is a difficult task, because of the curse of dimensionality. The goal of this dissertation is to alleviate this curse via the use of the finite state projection (FSP), in both cases where the CME matrix is constant (if the reaction rates are time-independent) or time-varying (if the reaction rates change over time). The work includes a theoretical characterization of the FSP truncation technique by showing that it can be put in the framework of inexact Krylov methods that relax matrix-vector products and compute them expediently by trading accuracy for speed. We also examine practical applications of our work in delay CME and parameter inference through local and global optimization schemes.
Download or read book Emerging Research in the Analysis and Modeling of Gene Regulatory Networks written by Ivanov, Ivan V. and published by IGI Global. This book was released on 2016-06-06 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: While technological advancements have been critical in allowing researchers to obtain more and better quality data about cellular processes and signals, the design and practical application of computational models of genomic regulation continues to be a challenge. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation. Exploring both theoretical and practical topics, this publication is an essential reference source for students, professionals, and researchers working in the fields of genomics, molecular biology, bioinformatics, and drug development.
Download or read book Models and Algorithms for Biomolecules and Molecular Networks written by Bhaskar DasGupta and published by John Wiley & Sons. This book was released on 2016-01-26 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: By providing expositions to modeling principles, theories, computational solutions, and open problems, this reference presents a full scope on relevant biological phenomena, modeling frameworks, technical challenges, and algorithms. Up-to-date developments of structures of biomolecules, systems biology, advanced models, and algorithms Sampling techniques for estimating evolutionary rates and generating molecular structures Accurate computation of probability landscape of stochastic networks, solving discrete chemical master equations End-of-chapter exercises
Download or read book Network Bioscience 2nd Edition written by Marco Pellegrini and published by Frontiers Media SA. This book was released on 2020-03-27 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Network science has accelerated a deep and successful trend in research that influences a range of disciplines like mathematics, graph theory, physics, statistics, data science and computer science (just to name a few) and adapts the relevant techniques and insights to address relevant but disparate social, biological, technological questions. We are now in an era of 'big biological data' supported by cost-effective high-throughput genomic, transcriptomic, proteomic, metabolomic data collection techniques that allow one to take snapshots of the cells' molecular profiles in a systematic fashion. Moreover recently, also phenotypic data, data on diseases, symptoms, patients, etc. are being collected at nation-wide level thus giving us another source of highly related (causal) 'big data'. This wealth of data is usually modeled as networks (aka binary relations, graphs or webs) of interactions, (including protein-protein, metabolic, signaling and transcription-regulatory interactions). The network model is a key view point leading to the uncovering of mesoscale phenomena, thus providing an essential bridge between the observable phenotypes and 'omics' underlying mechanisms. Moreover, network analysis is a powerful 'hypothesis generation' tool guiding the scientific cycle of 'data gathering', 'data interpretation, 'hypothesis generation' and 'hypothesis testing'. A major challenge in contemporary research is the synthesis of deep insights coming from network science with the wealth of data (often noisy, contradictory, incomplete and difficult to replicate) so to answer meaningful biological questions, in a quantifiable way using static and dynamic properties of biological networks.
Download or read book Modeling and Analysis of Bio molecular Networks written by Jinhu Lü and published by Springer Nature. This book was released on 2020-12-06 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.
Download or read book Computational Methods in Systems Biology written by Muffy Calder and published by Springer Science & Business Media. This book was released on 2007-09-05 with total page 257 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 2007, held in Edinburgh, Scotland, September 2007. The 16 revised full papers presented present a variety of techniques from computer science, such as language design, concurrency theory, software engineering, and formal methods, for biologists, physicists, and mathematicians interested in the systems-level understanding of cellular processes.
