Logical Modeling Of Biological Systems

Author : Luis Fariñas del Cerro,Katsumi Inoue
Publisher : John Wiley & Sons
Page : 410 pages
File Size : 47,7 Mb
Release : 2014-08-08
Category : Science
ISBN : 9781119015215

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Logical Modeling of Biological Systems by Luis Fariñas del Cerro,Katsumi Inoue Pdf

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.

Author : Matteo Barberis,Tomáš Helikar
Publisher : Frontiers Media SA
Page : 340 pages
File Size : 53,9 Mb
Release : 2019-08-16
Category : Electronic
ISBN : 9782889459834

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Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by Matteo Barberis,Tomáš Helikar Pdf

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.

Author : Cedric Lhoussaine,Elisabeth Remy
Publisher : John Wiley & Sons
Page : 404 pages
File Size : 51,5 Mb
Release : 2023-07-31
Category : Computers
ISBN : 9781394229079

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Symbolic Approaches to Modeling and Analysis of Biological Systems by Cedric Lhoussaine,Elisabeth Remy Pdf

Systems Biology is an approach to biology that involves understanding the complexity of interactions among biological entities within a systemic whole. The goal is to understand the emergence of physiological or functional properties. Symbolic Approaches to Modeling and Analysis of Biological Systems presents contributions of formal methods from computer science for modeling the dynamics of biological systems. It deals more specifically with symbolic methods, i.e. methods that can establish the qualitative properties of models. This book presents different approaches related to semantics, language, modeling and their link with data, and allows us to examine the fundamental problems and challenges that biological systems are facing. The first part of the book presents works that rely on various available data to build models, while the second part gathers contributions surrounding issues of semantics and formal methods.

Author : Arianna Bianchi,Thomas Hillen,Mark A. Lewis,Yingfei Yi
Publisher : Springer Nature
Page : 267 pages
File Size : 54,6 Mb
Release : 2019-10-02
Category : Mathematics
ISBN : 9783030225834

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The Dynamics of Biological Systems by Arianna Bianchi,Thomas Hillen,Mark A. Lewis,Yingfei Yi Pdf

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.

Author : Cedric Lhoussaine,Elisabeth Remy
Publisher : John Wiley & Sons
Page : 404 pages
File Size : 49,7 Mb
Release : 2023-08-29
Category : Computers
ISBN : 9781789450293

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Symbolic Approaches to Modeling and Analysis of Biological Systems by Cedric Lhoussaine,Elisabeth Remy Pdf

Author : Alberto Marin-Sanguino,Julio Vera,Rui Alves
Publisher : Frontiers Media SA
Page : 216 pages
File Size : 51,5 Mb
Release : 2019-01-11
Category : Electronic
ISBN : 9782889456833

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Foundations of Theoretical Approaches in Systems Biology by Alberto Marin-Sanguino,Julio Vera,Rui Alves Pdf

If biology in the 20th century was characterized by an explosion of new technologies and experimental methods, that of the 21st has seen an equally exuberant proliferation of mathematical and computational methods that attempt to systematize and explain the abundance of available data. As we live through the consolidation of a new paradigm where experimental data goes hand in hand with computational analysis, we contemplate the challenge of fusing these two aspects of the new biology into a consistent theoretical framework. Whether systems biology will survive as a field or be washed away by the tides of future fads will ultimately depend on its success to achieve this type of synthesis. The famous quote attributed to Kurt Lewin comes to mind: "there is nothing more practical than a good theory". This book presents a wide assortment of articles on systems biology in an attempt to capture the variety of current methods in systems biology and show how they can help to find answers to the challenges of modern biology.

Author : Harvey J. Gold
Publisher : John Wiley & Sons
Page : 392 pages
File Size : 49,5 Mb
Release : 1977
Category : Biological models
ISBN : UCAL:B4285115

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Mathematical Modeling of Biological Systems by Harvey J. Gold Pdf

The modeling process - an overview. Dimension and similarity. Probability models. Dynamic processes. Interacting dynamic processes. Feedback control and stability of biological systems. Curve fiting: estimating the parameters. Computing.

Author : Stilianos Louca
Publisher : Stilianos Louca
Page : 545 pages
File Size : 50,6 Mb
Release : 2023-06-07
Category : Mathematics
ISBN : 8210379456XXX

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Dynamical Modeling of Biological Systems by Stilianos Louca Pdf

This book introduces concepts and practical tools for dynamical mathematical modeling of biological systems. Dynamical models describe the behavior of a system over time as a result of internal feedback loops and external forcing, based on mathematically formulated dynamical laws, similarly to how Newton's laws describe the movement of celestial bodies. Dynamical models are increasingly popular in biology, as they tend to be more powerful than static regression models. This book is meant for undergraduate and graduate students in physics, applied mathematics and data science with an interest in biology, as well as students in biology with a strong interest in mathematical methods. The book covers deterministic models (for example differential equations), stochastic models (for example Markov chains and autoregressive models) and model-independent aspects of time series analysis. Plenty of examples and exercises are included, often taken or inspired from the scientific literature, and covering a broad range of topics such as neuroscience, cell biology, genetics, evolution, ecology, microbiology, physiology, epidemiology and conservation. The book delivers generic modeling techniques used across a wide range of situations in biology, and hence readers from other scientific disciplines will find that much of the material is also applicable in their own field. Proofs of most mathematical statements are included for the interested reader, but are not essential for a practical understanding of the material. The book introduces the popular scientific programming language MATLAB as a tool for simulating models, fitting models to data, and visualizing data and model predictions. The material taught is current as of MATLAB version 2022b. The material is taught in a sufficiently general way that also permits the use of alternative programming languages.

Author : Antonia Vlahou,Fulvio Magni,Harald Mischak,Jerome Zoidakis
Publisher : John Wiley & Sons
Page : 386 pages
File Size : 45,9 Mb
Release : 2018-02-21
Category : Science
ISBN : 9781119181149

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Integration of Omics Approaches and Systems Biology for Clinical Applications by Antonia Vlahou,Fulvio Magni,Harald Mischak,Jerome Zoidakis Pdf

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.

Author : James W. Haefner
Publisher : Springer Science & Business Media
Page : 486 pages
File Size : 49,7 Mb
Release : 2012-12-06
Category : Science
ISBN : 9781461541196

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Modeling Biological Systems by James W. Haefner Pdf

This book is intended as a text for a first course on creating and analyzing computer simulation models of biological systems. The expected audience for this book are students wishing to use dynamic models to interpret real data mueh as they would use standard statistical techniques. It is meant to provide both the essential principles as well as the details and equa tions applicable to a few particular systems and subdisciplines. Biological systems, however, encompass a vast, diverse array of topics and problems. This book discusses only a select number of these that I have found to be useful and interesting to biologists just beginning their appreciation of computer simulation. The examples chosen span classical mathematical models of well-studied systems to state-of-the-art topics such as cellular automata and artificial life. I have stressed the relationship between the models and the biology over mathematical analysis in order to give the reader a sense that mathematical models really are useful to biologists. In this light, I have sought examples that address fundamental and, I think, interesting biological questions. Almost all of the models are directly COIIl pared to quantitative data to provide at least a partial demonstration that some biological models can accurately predict.

Author : Mohd Saberi Mohamad,Miguel P. Rocha,Florentino Fdez-Riverola,Francisco J. Domínguez Mayo,Juan F. De Paz
Publisher : Springer
Page : 224 pages
File Size : 49,9 Mb
Release : 2016-05-31
Category : Technology & Engineering
ISBN : 9783319401263

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10th International Conference on Practical Applications of Computational Biology & Bioinformatics by Mohd Saberi Mohamad,Miguel P. Rocha,Florentino Fdez-Riverola,Francisco J. Domínguez Mayo,Juan F. De Paz Pdf

Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘16 hopes to contribute to this effort promoting this fruitful interaction. PACBB'16 technical program included 21 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly promote the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work being developed by each of the participants.

Author : Andreas Kremling
Publisher : CRC Press
Page : 379 pages
File Size : 50,8 Mb
Release : 2013-11-12
Category : Mathematics
ISBN : 9781466567900

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Systems Biology by Andreas Kremling Pdf

Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are sy

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 52,6 Mb
Release : 2007
Category : Electronic
ISBN : OCLC:1132263186

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Mathematical Modeling of Biological Systems by Anonim Pdf

Author : Fred Brauer,Christopher Kribs
Publisher : CRC Press
Page : 482 pages
File Size : 52,9 Mb
Release : 2015-12-23
Category : Mathematics
ISBN : 9781498774048

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Dynamical Systems for Biological Modeling by Fred Brauer,Christopher Kribs Pdf

Dynamical Systems for Biological Modeling: An Introduction prepares both biology and mathematics students with the understanding and techniques necessary to undertake basic modeling of biological systems. It achieves this through the development and analysis of dynamical systems.The approach emphasizes qualitative ideas rather than explicit computa

Author : Andres Kriete,Roland Eils
Publisher : Academic Press
Page : 548 pages
File Size : 51,7 Mb
Release : 2013-11-26
Category : Computers
ISBN : 9780124059382

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Computational Systems Biology by Andres Kriete,Roland Eils Pdf

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.