Stochastic Methods For Parameter Estimation And Design Of Experiments In Systems Biology
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Stochastic Methods For Parameter Estimation And Design Of Experiments In Systems Biology
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Author : Andrei Kramer
language : en
Publisher: Logos Verlag Berlin GmbH
Release Date : 2016-02-11
Stochastic Methods For Parameter Estimation And Design Of Experiments In Systems Biology written by Andrei Kramer and has been published by Logos Verlag Berlin GmbH this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-02-11 with Biological systems categories.
Markov Chain Monte Carlo (MCMC) methods are sampling based techniques, which use random numbers to approximate deterministic but unknown values. They can be used to obtain expected values, estimate parameters or to simply inspect the properties of a non-standard, high dimensional probability distribution. Bayesian analysis of model parameters provides the mathematical foundation for parameter estimation using such probabilistic sampling. The strengths of these stochastic methods are their robustness and relative simplicity even for nonlinear problems with dozens of parameters as well as a built-in uncertainty analysis. Because Bayesian model analysis necessarily involves the notion of prior knowledge, the estimation of unidentifiable parameters can be regularised (by priors) in a straight forward way. This work draws the focus on typical cases in systems biology: relative data, nonlinear ordinary differential equation models and few data points. It also investigates the consequences of parameter estimation from steady state data; consequences such as performance benefits. In biology the data is almost exclusively relative, the raw measurements (e.g. western blot intensities) are normalised by control experiments or a reference value within a series and require the model to do the same when comparing its output to the data. Several sampling algorithms are compared in terms of effective sampling speed and necessary adaptations to relative and steady state data are explained.
Stochastic Methods In Experimental Sciences
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Author : Waclaw Kasprzak
language : en
Publisher: World Scientific
Release Date : 1990-08-23
Stochastic Methods In Experimental Sciences written by Waclaw Kasprzak and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 1990-08-23 with categories.
This volume, containing selected papers presented during the COSMEX '89 meeting, provides readers with integrative and innovative articles on many aspects on many aspects of stochastic methods and their applications to experimental sciences. Offering an interdisciplinary presentation on the uses of stochastic methods, this publication discusses the practical applications of stochastic methods to such diverse areas as biology, chemistry, physics, mechanics and engineering. It also discusses computer implementation of theoretically derived algorithms especially for experimental designs.
Computational Methods In Systems Biology
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Author : Olivier Roux
language : en
Publisher: Springer
Release Date : 2015-09-01
Computational Methods In Systems Biology written by Olivier Roux and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-09-01 with Computers categories.
This book constitutes the refereed proceedings of the 13th International Conference on Computational Methods in Systems Biology, CMSB 2015, held in Nantes, France, in September 2015. The 20 full papers and 2 short papers presented were carefully reviewed and selected from 43 full and 4 short paper submissions. The papers cover a wide range of topics in the analysis of biological systems, networks and data such as model checking, stochastic analysis, hybrid systems, circadian clock, time series data, logic programming, and constraints solving ranging from intercellular to multiscale.
Systems Biology For Signaling Networks
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Author : Sangdun Choi
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-08-09
Systems Biology For Signaling Networks written by Sangdun Choi 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 2010-08-09 with Science categories.
System Biology encompasses the knowledge from diverse fields such as Molecular Biology, Immunology, Genetics, Computational Biology, Mathematical Biology, etc. not only to address key questions that are not answerable by individual fields alone, but also to help in our understanding of the complexities of biological systems. Whole genome expression studies have provided us the means of studying the expression of thousands of genes under a particular condition and this technique had been widely used to find out the role of key macromolecules that are involved in biological signaling pathways. However, making sense of the underlying complexity is only possible if we interconnect various signaling pathways into human and computer readable network maps. These maps can then be used to classify and study individual components involved in a particular phenomenon. Apart from transcriptomics, several individual gene studies have resulted in adding to our knowledge of key components that are involved in a signaling pathway. It therefore becomes imperative to take into account of these studies also, while constructing our network maps to highlight the interconnectedness of the entire signaling pathways and the role of that particular individual protein in the pathway. This collection of articles will contain a collection of pioneering work done by scientists working in regulatory signaling networks and the use of large scale gene expression and omics data. The distinctive features of this book would be: Act a single source of information to understand the various components of different signaling network (roadmap of biochemical pathways, the nature of a molecule of interest in a particular pathway, etc.), Serve as a platform to highlight the key findings in this highly volatile and evolving field, and Provide answers to various techniques both related to microarray and cell signaling to the readers.
Systems Biomedicine
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Author : Edison T. Liu
language : en
Publisher: Academic Press
Release Date : 2009-09-17
Systems Biomedicine written by Edison T. Liu and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-09-17 with Science categories.
Systems biology is a critical emerging field that quantifies and annotates the complexity of biological systems in order to construct algorithmic models to predict outcomes from component input. Applications in medicine are revolutionizing our understanding of biological processes and systems. Systems Biomedicine is organized around foundations, computational modeling, network biology, and integrative biology, with the extension of examples from human biology and pharmacology, to focus on the applications of systems approaches to medical problems. An integrative approach to the underlying genomic, proteomic, and computational biology principles provides researchers with guidance in the use of qualitative systems and hypothesis generators. To reflect the highly interdisciplinary nature of the field, careful detail has been extended to ensure explanations of complex mathematical and biological principles are clear with minimum technical jargon. Organized to reflect the important distinguishing characteristics of systems strategies in experimental biology and medicine Provides precise and comprehensive measurement tools for constructing a model of the system and tools for defining complexity as an experimental dependent variable Includes a thorough discussion of the applications of quantitative principles to biomedical problems
Computer Applications In Biotechnology 2004
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Author : Marie-Noelle Pons
language : en
Publisher: Elsevier
Release Date : 2005-08-02
Computer Applications In Biotechnology 2004 written by Marie-Noelle Pons and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-08-02 with Science categories.
Stochastic Approaches For Systems Biology
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Author : Mukhtar Ullah
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-07-12
Stochastic Approaches For Systems Biology written by Mukhtar Ullah 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 2011-07-12 with Mathematics categories.
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.
Handbook Of Statistical Systems Biology
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Author : Michael Stumpf
language : en
Publisher: John Wiley & Sons
Release Date : 2011-09-09
Handbook Of Statistical Systems Biology written by Michael Stumpf 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 2011-09-09 with Science categories.
Systems Biology is now entering a mature phase in which the key issues are characterising uncertainty and stochastic effects in mathematical models of biological systems. The area is moving towards a full statistical analysis and probabilistic reasoning over the inferences that can be made from mathematical models. This handbook presents a comprehensive guide to the discipline for practitioners and educators, in providing a full and detailed treatment of these important and emerging subjects. Leading experts in systems biology and statistics have come together to provide insight in to the major ideas in the field, and in particular methods of specifying and fitting models, and estimating the unknown parameters. This book: Provides a comprehensive account of inference techniques in systems biology. Introduces classical and Bayesian statistical methods for complex systems. Explores networks and graphical modeling as well as a wide range of statistical models for dynamical systems. Discusses various applications for statistical systems biology, such as gene regulation and signal transduction. Features statistical data analysis on numerous technologies, including metabolic and transcriptomic technologies. Presents an in-depth presentation of reverse engineering approaches. Provides colour illustrations to explain key concepts. This handbook will be a key resource for researchers practising systems biology, and those requiring a comprehensive overview of this important field.
Prediction And Optimal Experimental Design In Systems Biology Models
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Author : Fergal P. Casey
language : en
Publisher:
Release Date : 2007
Prediction And Optimal Experimental Design In Systems Biology Models written by Fergal P. Casey and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with categories.
Hybrid Systems Biology
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Author : Oded Maler
language : en
Publisher: Springer
Release Date : 2015-12-24
Hybrid Systems Biology written by Oded Maler and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-12-24 with Computers categories.
This book constitutes the thoroughly refereed post-workshop proceedings of the Second International Workshop on Hybrid Systems Biology, HSB 2013, held as part of the ECAL 2013 event, in Taormina, Italy, in September 2013; and the Third International Workshop on Hybrid Systems Biology, HSB 2014, held as part of CAV 2014, in Vienna, Austria, in July 2014. This volume presents 8 full papers together with 2 invited tutorials/surveys from 21 submissions. The HSB 2013 workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. The scope of the HSB 2014 workshop is the general area of dynamical models in biology with an emphasis on hybrid approaches, which are not restricted to a narrow class of mathematical models, and which take advantage of techniques developed separately in different sub-fields. “br> /div