Logical Modeling Of Cellular Processes From Software Development To Network Dynamics
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| Author | : Matteo Barberis |
| Publisher | : Frontiers Media SA |
| Total Pages | : 340 |
| Release | : 2019-08-16 |
| Genre | : |
| ISBN | : 2889459837 |
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 | : Krastan B. Blagoev |
| Publisher | : Springer Nature |
| Total Pages | : 265 |
| Release | : 2022-09-08 |
| Genre | : Science |
| ISBN | : 3030986063 |
This is a graduate-level introduction to quantitative concepts and methods in the science of living systems. It relies on a systems approach for understanding the physical principles operating in biology. Physical phenomena are treated at the appropriate spatio-temporal scale and phenomenological equations are used in order to reflect the system of interest. Biological details enter to the degree necessary for understanding specific processes, but in many cases the approach is not reductionist. This is in line with the approach taken by physics to many other complex systems. The book bridges the gap between graduate students’ general physics courses and research papers published in professional journals. It gives students the foundations needed for independent research in biological physics and for working in collaborations aimed at quantitative biology and biomedical research. Also included are modern mathematical and theoretical physics methods, giving the student a broad knowledge of tools that can shed light on the sophisticated mechanisms brought forth by evolution in biological systems. The content covers many aspects that have been the focus of active research over the past twenty years, reflecting the authors' experience as leading researchers and teachers in this field.
| Author | : Werner Dubitzky |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 249 |
| Release | : 2011-01-07 |
| Genre | : Science |
| ISBN | : 1441979646 |
This book is intended as a communication platform to bridge the cultural, conceptual, and technological gap among the key systems biology disciplines of biology, mathematics, and information technology. To support this goal, contributors were asked to adopts an approach that appeals to audiences from different backgrounds.
| Author | : Andrei Voronkov |
| Publisher | : Springer |
| Total Pages | : 455 |
| Release | : 2013-04-05 |
| Genre | : Mathematics |
| ISBN | : 3642376517 |
This Festschrift volume, published in memory of Harald Ganzinger, contains 17 papers from colleagues all over the world and covers all the fields to which Harald Ganzinger dedicated his work during his academic career. The volume begins with a complete account of Harald Ganzinger's work and then turns its focus to the research of his former colleagues, students, and friends who pay tribute to him through their writing. Their individual papers span a broad range of topics, including programming language semantics, analysis and verification, first-order and higher-order theorem proving, unification theory, non-classical logics, reasoning modulo theories, and applications of automated reasoning in biology.
| Author | : Olivier Roux |
| Publisher | : Springer |
| Total Pages | : 302 |
| Release | : 2015-09-01 |
| Genre | : Computers |
| ISBN | : 3319234013 |
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.
| Author | : Sangdun Choi |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 900 |
| Release | : 2010-08-09 |
| Genre | : Science |
| ISBN | : 1441957979 |
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.
| Author | : Pietro Liò |
| Publisher | : Springer |
| Total Pages | : 471 |
| Release | : 2019-06-11 |
| Genre | : Computers |
| ISBN | : 303017297X |
This book presents outstanding contributions in an exciting, new and multidisciplinary research area: the application of formal, automated reasoning techniques to analyse complex models in systems biology and systems medicine. Automated reasoning is a field of computer science devoted to the development of algorithms that yield trustworthy answers, providing a basis of sound logical reasoning. For example, in the semiconductor industry formal verification is instrumental to ensuring that chip designs are free of defects (or “bugs”). Over the past 15 years, systems biology and systems medicine have been introduced in an attempt to understand the enormous complexity of life from a computational point of view. This has generated a wealth of new knowledge in the form of computational models, whose staggering complexity makes manual analysis methods infeasible. Sound, trusted, and automated means of analysing the models are thus required in order to be able to trust their conclusions. Above all, this is crucial to engineering safe biomedical devices and to reducing our reliance on wet-lab experiments and clinical trials, which will in turn produce lower economic and societal costs. Some examples of the questions addressed here include: Can we automatically adjust medications for patients with multiple chronic conditions? Can we verify that an artificial pancreas system delivers insulin in a way that ensures Type 1 diabetic patients never suffer from hyperglycaemia or hypoglycaemia? And lastly, can we predict what kind of mutations a cancer cell is likely to undergo? This book brings together leading researchers from a number of highly interdisciplinary areas, including: · Parameter inference from time series · Model selection · Network structure identification · Machine learning · Systems medicine · Hypothesis generation from experimental data · Systems biology, systems medicine, and digital pathology · Verification of biomedical devices “This book presents a comprehensive spectrum of model-focused analysis techniques for biological systems ...an essential resource for tracking the developments of a fast moving field that promises to revolutionize biology and medicine by the automated analysis of models and data.”Prof Luca Cardelli FRS, University of Oxford
| Author | : Jinhu Lü |
| Publisher | : Springer Nature |
| Total Pages | : 464 |
| Release | : 2020-12-06 |
| Genre | : Science |
| ISBN | : 981159144X |
This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.
| Author | : Daniel Machado |
| Publisher | : Frontiers Media SA |
| Total Pages | : 117 |
| Release | : 2016-01-21 |
| Genre | : Biology (General) |
| ISBN | : 2889197549 |
Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.
| Author | : |
| Publisher | : |
| Total Pages | : 946 |
| Release | : 2008 |
| Genre | : Dissertations, Academic |
| ISBN | : |
