Stochastic Models For In Silico Event Based Biological Network Simulation
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Stochastic Models For In Silico Event Based Biological Network Simulation
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Author : Preetam Ghosh
language : en
Publisher: ProQuest
Release Date : 2007
Stochastic Models For In Silico Event Based Biological Network Simulation written by Preetam Ghosh and has been published by ProQuest this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Bioinformatics categories.
The multi-scale biological system model is a new research direction to capture the dynamic measurements of complex biological systems. The current statistical thermodynamic models can not scale to this challenge due to the explosion of state-spaces of the system, where a biological organ may have billions of cells, each with millions of molecule types and each type may have a few million molecules. We seek to propose a phenomenological theory that will require a smaller number of state variables to address this multi-scaling problem. Discrete Markov statistical process is used to understand the system dynamics in the networking community for a long time. In this dissertation, we focus more specifically on a composite system by combining the state variables in the time-space domain as events, and determine the immediate dynamics between the events by using statistical analysis or simulation methods. In our approach the space-time behavior of the cell dynamics is captured by discrete state variables, where an event is a combined process of a large number of state transitions between a set of state variables. The execution time of these state transitions to manifest the event outcome is a random variable called event-holding time. The underlying assumption is that it will be possible to segregate the complete system state-space into a disjoint set of independent events and events can be executed simultaneously without any interaction once the execution conditions are satisfied (removal of resource bottleneck, collision). In this dissertation, we present the event-time models for some biological functions that will be incorporated in the discrete-event based stochastic simulator. In particular, we present analytical models for the molecular transport event in cells considering charged/non-charged macromolecules. We show, that molecular transport event completion time can be approximated by an exponential distribution. Next we present stochastic models for biochemical reactions in the cell (that can be extended to reactions occurring in the cell cytoplasm, membrane or nucleus). We show that the reaction completion time follows an exponential distribution when one of the reactant molecules enter the cell one at a time, whereas, it follows a gamma distribution when a batch of the reactant molecules enter the cell. We also present stochastic models for the protein-DNA binding and protein-ligand docking events and show that both these events have an exponentially distributed event completion time. We also validate each of the models presented in the dissertation with experimental findings reported in the literature. Finally, we present a markov chain based stochastic biochemical system simulator which can give us the dynamics of more complex events and can be used to improve the scalability of the discrete-event based stochastic simulator. We propose to successfully demonstrate this technique by modeling the complete dynamics of one Salmonella cell.
Stochastic Modelling For Systems Biology Third Edition
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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2018-12-07
Stochastic Modelling For Systems Biology Third Edition 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 2018-12-07 with Mathematics categories.
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.
Stochastic Modelling For Systems Biology Second Edition
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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2011-11-09
Stochastic Modelling For Systems Biology Second Edition 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 2011-11-09 with Mathematics categories.
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. Re-written to reflect this modern perspective, this second edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. Keeping with the spirit of the first edition, 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. New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more modular way An ancillary website provides links, resources, errata, and up-to-date information on installation and use of the associated R package More background material on the theory of Markov processes and stochastic differential equations, providing more substance for mathematically inclined readers Discussion of some of the more advanced concepts relating to stochastic kinetic models, such as random time change representations, Kolmogorov equations, Fokker-Planck equations and the linear noise approximation Simple modelling of "extrinsic" and "intrinsic" noise An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional mathematical detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.
Transactions On Computational Systems Biology Viii
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Author : Corrado Priami
language : en
Publisher: Springer
Release Date : 2007-10-28
Transactions On Computational Systems Biology Viii written by Corrado Priami and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-10-28 with Computers categories.
The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences. It supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. The six papers selected for this special issue cover a broad range of topics.
Computational Science And Its Applications Iccsa 2006
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Author : Marina Gavrilova
language : en
Publisher: Springer Science & Business Media
Release Date : 2006
Computational Science And Its Applications Iccsa 2006 written by Marina Gavrilova 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 2006 with Computers categories.
The five-volume set LNCS 3980-3984 constitutes the refereed proceedings of the International Conference on Computational Science and Its Applications, ICCSA 2006, held in Glasgow, UK in May 2006.The five volumes present a total of 664 papers selected from over 2300 submissions. The papers present a wealth of original research results in the field of computational science, from foundational issues in computer science and mathematics to advanced applications in virtually all sciences making use of computational techniques. The topics of the refereed papers are structured according to the five major conference themes: computational methods, algorithms and applications high performance technical computing and networks advanced and emerging applications geometric modelling, graphics and visualization information systems and information technologies.Moreover, submissions from 31 Workshops and technical sessions in the areas, such as information security, mobile communication, grid computing, modeling, optimization, computational geometry, virtual reality, symbolic computations, molecular structures, Web systems and intelligence, spatial analysis, bioinformatics and geocomputations, contribute to this publication.
Endothelial Signaling In Vascular Dysfunction And Disease
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Author : Shampa Chatterjee
language : en
Publisher: Academic Press
Release Date : 2021-01-20
Endothelial Signaling In Vascular Dysfunction And Disease written by Shampa Chatterjee and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-01-20 with Science categories.
Endothelial Signaling in Vascular Dysfunction and Disease: From Bench to Bedside provides a detailed understanding of the endothelium, its activation and their link to some common clinical disorders. In addition, the book covers earlier discoveries, including those from the last and 19th centuries. It is split into five sections that cover the vascular tree as an integrative structure, the endothelium in inflammation, endothelial signaling, activation and toxicity with chemotherapy, radiation induced endothelial dysfunction and vascular disease, and therapies in combating vascular diseases. Each section is discussed with a translational approach in order to make the content truly applicable. This book is a valuable source for basic researchers, clinicians in the fields of Oncology, Cardiovascular Medicine and Radiology, and members of the biomedical field who are conducting studies related to the endothelium and vascular disease. Discusses the most relevant discoveries in endothelial biology and their link to manifestations of clinical disease Presents history and diagrams in each section to highlight the original biological discovery and its link of clinical manifestations of vascular disease Includes recent findings on the relationship between endothelial signaling, chemotherapy and radiation induced endothelial dysfunction
Deterministic Versus Stochastic Modelling In Biochemistry And Systems Biology
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Author : Paola Lecca
language : en
Publisher: Elsevier
Release Date : 2013-04-09
Deterministic Versus Stochastic Modelling In Biochemistry And Systems Biology written by Paola Lecca and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-04-09 with Mathematics categories.
Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics. Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples Presents recently developed discrete stochastic formalisms for modelling biological systems and processes Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics
In Silico Simulation Of Biological Processes
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Author : Gregory R. Bock
language : en
Publisher: John Wiley & Sons
Release Date : 2003-07-07
In Silico Simulation Of Biological Processes written by Gregory R. Bock and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-07-07 with Science categories.
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.
Complex Sciences
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Author : Jie Zhou
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-06-26
Complex Sciences written by Jie Zhou 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 2009-06-26 with Computers categories.
I was invited to join the Organizing Committee of the First International Conference on Complex Sciences: Theory and Applications (Complex 2009) as its ninth member. At that moment, eight distinguished colleagues, General Co-chairs Eugene Stanley and Gaoxi Xiao, Technical Co-chairs János Kertész and Bing-Hong Wang, Local Co-chairs Hengshan Wang and Hong-An Che, Publicity Team Shi Xiao and Yubo Wang, had spent hundreds of hours pushing the conference half way to its birth. Ever since then, I have been amazed to see hundreds of papers flooding in, reviewed and commented on by the TPC members. Finally, more than 200 contributions were - lected for the proceedings currently in your hands. They include about 200 papers from the main conference (selected from more than 320 submissions) and about 33 papers from the five collated workshops: Complexity Theory of Art and Music (COART) Causality in Complex Systems (ComplexCCS) Complex Engineering Networks (ComplexEN) Modeling and Analysis of Human Dynamics (MANDYN) Social Physics and its Applications (SPA) Complex sciences are expanding their colonies at such a dazzling speed that it - comes literally impossible for any conference to cover all the frontiers.
Tertiary Lymphoid Organs Tlos Powerhouses Of Disease Immunity
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Author : Changjun Yin
language : en
Publisher: Frontiers Media SA
Release Date : 2017-05-22
Tertiary Lymphoid Organs Tlos Powerhouses Of Disease Immunity written by Changjun Yin and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-05-22 with Electronic book categories.
The immune system employs TLOs to elicit highly localized and forceful responses to unresolvable peripheral tissue inflammation. Current data indicate that TLOs are protective but they may also lead to collateral tissue injury and serve as nesting places to generate autoreactive lymphocytes. A better comprehension of these powerhouses of disease immunity will likely facilitate development to unprecedented and specific therapies to fight chronic inflammatory diseases.