Author: Don Kulasiri Publisher: Springer Nature ISBN: 9811653518 Category : Science Languages : en Pages : 231
Book Description
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.
Author: Gregory Mermoud Publisher: Springer ISBN: 3319026097 Category : Technology & Engineering Languages : en Pages : 213
Book Description
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.
Author: Jasmin Fisher Publisher: Springer ISBN: 3540684131 Category : Computers Languages : en Pages : 146
Book Description
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.
Author: Daniel A. Beard Publisher: Cambridge University Press ISBN: 1139470078 Category : Technology & Engineering Languages : en Pages :
Book Description
Chemical Biophysics provides an engineering-based approach to biochemical system analysis for graduate-level courses on systems biology, computational bioengineering and molecular biophysics. It is the first textbook to apply rigorous physical chemistry principles to mathematical and computational modeling of biochemical systems for an interdisciplinary audience. The book is structured to show the student the basic biophysical concepts before applying this theory to computational modeling and analysis, building up to advanced topics and research. Topics explored include the kinetics of nonequilibrium open biological systems, enzyme mediated reactions, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems. End-of-chapter exercises range from confidence-building calculations to computational simulation projects.
Author: Bernhard Ø. Palsson Publisher: Cambridge University Press ISBN: 1139448943 Category : Science Languages : en Pages : 287
Book Description
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.
Author: Mukhtar Ullah Publisher: Springer Science & Business Media ISBN: 1461404789 Category : Mathematics Languages : en Pages : 319
Book Description
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.
Author: Darren J. Wilkinson Publisher: CRC Press ISBN: 1351000896 Category : Mathematics Languages : en Pages : 366
Book Description
Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.
Author: Ivanov, Ivan V. Publisher: IGI Global ISBN: 1522503544 Category : Medical Languages : en Pages : 437
Book Description
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.
Author: Bhaskar DasGupta Publisher: John Wiley & Sons ISBN: 1119162262 Category : Science Languages : en Pages : 264
Book Description
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
Author: Don Kulasiri
Author: Don Kulasiri
Author: Gregory Mermoud
Author: Jasmin Fisher
Author: Daniel A. Beard
Author: Bernhard Ø. Palsson
Author: Mukhtar Ullah
Author: Darren J. Wilkinson
Author: Ivanov, Ivan V.
Author: Bhaskar DasGupta