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Logical Modeling Of Biological Systems

Logical Modeling of Biological Systems PDF
Author: Luis Fariñas del Cerro
Publisher: John Wiley & Sons
Release: 2014-08-08
ISBN: 1119015219
Size: 24.20 MB
Format: PDF, ePub, Docs
Category : Science
Languages : en
Pages : 410
View: 5464

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Logical Modeling Of Biological Systems

by Luis Fariñas del Cerro, Logical Modeling Of Biological Systems Books available in PDF, EPUB, Mobi Format. Download Logical Modeling Of Biological Systems books, Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language. This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming. It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.



Logical Modeling Of Biological Systems

Logical Modeling of Biological Systems PDF
Author: Katsumi Inoue
Publisher:
Release: 2014
ISBN: 9781119005223
Size: 55.27 MB
Format: PDF, Kindle
Category : Biological systems
Languages : en
Pages : 429
View: 6889

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Logical Modeling Of Biological Systems

by Katsumi Inoue, Logical Modeling Of Biological Systems Books available in PDF, EPUB, Mobi Format. Download Logical Modeling Of Biological Systems books, Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expr.



Logical Modeling Of Cellular Processes From Software Development To Network Dynamics

Logical Modeling of Cellular Processes  From Software Development to Network Dynamics PDF
Author: Matteo Barberis
Publisher: Frontiers Media SA
Release: 2019-08-16
ISBN: 2889459837
Size: 20.72 MB
Format: PDF, Mobi
Category :
Languages : en
Pages :
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Logical Modeling Of Cellular Processes From Software Development To Network Dynamics

by Matteo Barberis, Logical Modeling Of Cellular Processes From Software Development To Network Dynamics Books available in PDF, EPUB, Mobi Format. Download Logical Modeling Of Cellular Processes From Software Development To Network Dynamics books, Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.



The Dynamics Of Biological Systems

The Dynamics of Biological Systems PDF
Author: Arianna Bianchi
Publisher: Springer Nature
Release: 2019-10-02
ISBN: 3030225836
Size: 27.52 MB
Format: PDF, ePub
Category : Mathematics
Languages : en
Pages : 267
View: 5898

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The Dynamics Of Biological Systems

by Arianna Bianchi, The Dynamics Of Biological Systems Books available in PDF, EPUB, Mobi Format. Download The Dynamics Of Biological Systems books, The book presents nine mini-courses from a summer school, Dynamics of Biological Systems, held at the University of Alberta in 2016, as part of the prestigious seminar series: Séminaire de Mathématiques Supérieures (SMS). It includes new and significant contributions in the field of Dynamical Systems and their applications in Biology, Ecology, and Medicine. The chapters of this book cover a wide range of mathematical methods and biological applications. They - explain the process of mathematical modelling of biological systems with many examples, - introduce advanced methods from dynamical systems theory, - present many examples of the use of mathematical modelling to gain biological insight - discuss innovative methods for the analysis of biological processes, - contain extensive lists of references, which allow interested readers to continue the research on their own. Integrating the theory of dynamical systems with biological modelling, the book will appeal to researchers and graduate students in Applied Mathematics and Life Sciences.



Modeling In Systems Biology

Modeling in Systems Biology PDF
Author: Ina Koch
Publisher: Springer
Release: 2012-12-03
ISBN: 9781447125983
Size: 74.84 MB
Format: PDF, Mobi
Category : Computers
Languages : en
Pages : 364
View: 7524

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Modeling In Systems Biology

by Ina Koch, Modeling In Systems Biology Books available in PDF, EPUB, Mobi Format. Download Modeling In Systems Biology books, The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.



Logical Interaction Networks In Biology Theory And Application

Logical Interaction Networks in Biology  Theory and Application PDF
Author: Kathrin Ballerstein
Publisher: Cuvillier Verlag
Release: 2012-10-01
ISBN: 3736941951
Size: 13.40 MB
Format: PDF, Kindle
Category : Mathematics
Languages : en
Pages : 238
View: 5397

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Logical Interaction Networks In Biology Theory And Application

by Kathrin Ballerstein, Logical Interaction Networks In Biology Theory And Application Books available in PDF, EPUB, Mobi Format. Download Logical Interaction Networks In Biology Theory And Application books, This thesis deals with a general modeling framework for large-scale biological systems which is, on the one hand, applied to various practical instances, and on the other hand, strictly formalized and mathematically analyzed with respect to its complexity and structure. For the biological application initially an overview of existing analytic methods for biological systems is presented, and the proposed modeling framework is classified in this context. The framework is based on logical implication formulas. It allows for the verification of a biological model, the prediction of its response to prescribed stimuli, as well as the identification of possible intervention strategies for diseases or failure modes. This basic model is afterwards extended into two directions: First, timing information of reactions in the biological unit are incorporated. This generalization additionally enables to detect possible unknown timing information or inconsistencies that arise due to modeling errors. Besides this, it provides a method to consistently integrate the logical models of related biological units into one model. Second, the purely binary basic framework is enhanced by including a fine discretization of a biological component's activity level. This permits to express different effects depending on different levels of activity of one component, and therefore the predictions of the model become more sophisticated. On the mathematical side the logical framework and its extensions are derived and formalized. The basic model evolves to a special type of satisfiability problem (SAT) whose complexity is classified to be generally hard but mathematically easy subclasses are identified. The correspondence between SAT and integer programming is exploited and the underlying polyhedra are analyzed. Interestingly, the SAT problem allows for a wider class of polynomially solvable problems than its integer programming equivalent. Nevertheless, the computational results provided proof that the integer programming approach is computationally feasible. The basic SAT problem can additionally be translated into a bipartite digraph for which algorithms are adapted, and their practical use is discussed. Furthermore, for a special class of biological units a duality framework based on linear programming duality is derived, which completes the theory of such biological units. The dynamic extension of the basic framework yields a related SAT problem that contains the original one as a special case, and is thus hard to solve as well. The focus for this extension is on the analysis of maximally feasible and minimally infeasible solutions of the extended SAT problem. Therefore, it is necessary to optimize over the set of solutions of the SAT problem which suggests to employ the equivalent integer programming approach. To enumerate all maximally feasible and minimally infeasible solutions the Joint Generation algorithm is utilized. To this end, a monotone reformulation of the extended SAT problem is derived that preserves the maximally feasible and minimally infeasible solutions, and at the same time significantly reduces the size of the description. In certain very restrictive cases the resulting integer optimization problems are even computationally tractable. Finally, the minimally infeasible solutions are completely characterized by means of graph structures in the original digraph, and an alternative method for computing all minimally infeasible solutions via polyhedral projection is obtained. The discrete extension of the logical framework leads to a generalization of the SAT problem, the so called interval satisfiability problem. In this setting the variables are integer valued and associated intervals provide the set of values for which the expression becomes TRUE. To computationally determine feasible solutions, this problem is transformed to a system of polynomials which can be checked for feasibility by means of Hilbert's Nullstellensatz. Moreover, the general interval satisfiability problem is analyzed with respect to complexity and satisfiability. Concerning the computational complexity, it is shown to be generally hard even if assuming certain restrictions for the formulas. Concerning the satisfiability behavior the well known threshold phenomenon of classical random SAT, which has been observed for interval satisfiability, is examined and lower bounds on specific thresholds are identified.



Integration Of Omics Approaches And Systems Biology For Clinical Applications

Integration of Omics Approaches and Systems Biology for Clinical Applications PDF
Author: Antonia Vlahou
Publisher: John Wiley & Sons
Release: 2018-02-21
ISBN: 1119181143
Size: 73.31 MB
Format: PDF, ePub, Docs
Category : Science
Languages : en
Pages : 384
View: 6252

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Integration Of Omics Approaches And Systems Biology For Clinical Applications

by Antonia Vlahou, Integration Of Omics Approaches And Systems Biology For Clinical Applications Books available in PDF, EPUB, Mobi Format. Download Integration Of Omics Approaches And Systems Biology For Clinical Applications books, Introduces readers to the state of the art of omics platforms and all aspects of omics approaches for clinical applications This book presents different high throughput omics platforms used to analyze tissue, plasma, and urine. The reader is introduced to state of the art analytical approaches (sample preparation and instrumentation) related to proteomics, peptidomics, transcriptomics, and metabolomics. In addition, the book highlights innovative approaches using bioinformatics, urine miRNAs, and MALDI tissue imaging in the context of clinical applications. Particular emphasis is put on integration of data generated from these different platforms in order to uncover the molecular landscape of diseases. The relevance of each approach to the clinical setting is explained and future applications for patient monitoring or treatment are discussed. Integration of omics Approaches and Systems Biology for Clinical Applications presents an overview of state of the art omics techniques. These methods are employed in order to obtain the comprehensive molecular profile of biological specimens. In addition, computational tools are used for organizing and integrating these multi-source data towards developing molecular models that reflect the pathophysiology of diseases. Investigation of chronic kidney disease (CKD) and bladder cancer are used as test cases. These represent multi-factorial, highly heterogeneous diseases, and are among the most significant health issues in developed countries with a rapidly aging population. The book presents novel insights on CKD and bladder cancer obtained by omics data integration as an example of the application of systems biology in the clinical setting. Describes a range of state of the art omics analytical platforms Covers all aspects of the systems biology approach—from sample preparation to data integration and bioinformatics analysis Contains specific examples of omics methods applied in the investigation of human diseases (Chronic Kidney Disease, Bladder Cancer) Integration of omics Approaches and Systems Biology for Clinical Applications will appeal to a wide spectrum of scientists including biologists, biotechnologists, biochemists, biophysicists, and bioinformaticians working on the different molecular platforms. It is also an excellent text for students interested in these fields.



Computational Systems Biology

Computational Systems Biology PDF
Author: Andres Kriete
Publisher: Academic Press
Release: 2013-11-26
ISBN: 0124059384
Size: 67.32 MB
Format: PDF
Category : Computers
Languages : en
Pages : 548
View: 6911

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Computational Systems Biology

by Andres Kriete, Computational Systems Biology Books available in PDF, EPUB, Mobi Format. Download Computational Systems Biology books, This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.



Modeling In Systems Biology

Modeling in Systems Biology PDF
Author: Ina Koch
Publisher: Springer Science & Business Media
Release: 2010-10-21
ISBN: 9781849964746
Size: 53.86 MB
Format: PDF, ePub, Docs
Category : Computers
Languages : en
Pages : 364
View: 304

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Modeling In Systems Biology

by Ina Koch, Modeling In Systems Biology Books available in PDF, EPUB, Mobi Format. Download Modeling In Systems Biology books, The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.



Computer Modeling Of Complex Biological Systems

Computer Modeling of Complex Biological Systems PDF
Author: S. Sitharama Iyengar
Publisher: CRC Press
Release: 1984-01-13
ISBN:
Size: 16.14 MB
Format: PDF, ePub, Mobi
Category : Medical
Languages : en
Pages : 142
View: 7445

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Computer Modeling Of Complex Biological Systems

by S. Sitharama Iyengar, Computer Modeling Of Complex Biological Systems Books available in PDF, EPUB, Mobi Format. Download Computer Modeling Of Complex Biological Systems books, :Computer modeling of biological systems, a process of building new sets of conceptualizations, theories, and implementations is cov-ered in depth. The emphasis is on how computer modeling encom-passes three distinct areas of science (computer science, biology, and medicine) for building a framework for investigating the behavior of a complex biological system. Simulation and modeling are dis-cussed because these two factors provide the methodology for the design, development, experimentation, analysis, and evaluation of a experiment under study. Because of their high degree of modular-ity and collective complexity, computer systems such as analog, digital, or hybrid are reviewed. This presentation of computer mod-eling of biological systems delves into the study of data represen-tation (or data structures) and their transformation into an empirical model via a software program.