Download or read book Modeling Complex Cellular Systems written by Sascha Schäuble and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Modeling Cellular Systems written by Frederik Graw and published by Springer. This book was released on 2017-05-08 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: This contributed volume comprises research articles and reviews on topics connected to the mathematical modeling of cellular systems. These contributions cover signaling pathways, stochastic effects, cell motility and mechanics, pattern formation processes, as well as multi-scale approaches. All authors attended the workshop on "Modeling Cellular Systems" which took place in Heidelberg in October 2014. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.
Download or read book Cellular Automata and Complex Systems Methods for Modeling Biological Phenomena written by Bilotta, Eleonora and published by IGI Global. This book was released on 2010-06-30 with total page 502 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The theme of this book is the use of Cellular Automatas (CAs) to model biological systems, describing 2-D CAs to create populations of "life-like agents" with their own genomes"--Provided by publisher.
Download or read book Modeling Complex Systems written by Nino Boccara and published by Springer Science & Business Media. This book was released on 2010-09-09 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book illustrates how models of complex systems are built up and provides indispensable mathematical tools for studying their dynamics. This second edition includes more recent research results and many new and improved worked out examples and exercises.
Download or read book The Role of Model Integration in Complex Systems Modelling written by Manish I. Patel and published by Springer Science & Business Media. This book was released on 2010-09-08 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: Model integration – the process by which different modelling efforts can be brought together to simulate the target system – is a core technology in the field of Systems Biology. In the work presented here model integration was addressed directly taking cancer systems as an example. An in-depth literature review was carried out to survey the model forms and types currently being utilised. This was used to formalise the main challenges that model integration poses, namely that of paradigm (the formalism on which a model is based), focus (the real-world system the model represents) and scale. A two-tier model integration strategy, including a knowledge-driven approach to address model semantics, was developed to tackle these challenges. In the first step a novel description of models at the level of behaviour, rather than the precise mathematical or computational basis of the model, is developed by distilling a set of abstract classes and properties. These can accurately describe model behaviour and hence describe focus in a way that can be integrated with behavioural descriptions of other models. In the second step this behaviour is decomposed into an agent-based system by translating the models into local interaction rules. The book provides a detailed and highly integrated presentation of the method, encompassing both its novel theoretical and practical aspects, which will enable the reader to practically apply it to their model integration needs in academic research and professional settings. The text is self-supporting. It also includes an in-depth current bibliography to relevant research papers and literature. The review of the current state of the art in tumour modelling provides added value.
Download or read book Simulating Complex Systems by Cellular Automata written by Alfons G. Hoekstra and published by Springer. This book was released on 2010-06-03 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deeply rooted in fundamental research in Mathematics and Computer Science, Cellular Automata (CA) are recognized as an intuitive modeling paradigm for Complex Systems. Already very basic CA, with extremely simple micro dynamics such as the Game of Life, show an almost endless display of complex emergent behavior. Conversely, CA can also be designed to produce a desired emergent behavior, using either theoretical methodologies or evolutionary techniques. Meanwhile, beyond the original realm of applications - Physics, Computer Science, and Mathematics – CA have also become work horses in very different disciplines such as epidemiology, immunology, sociology, and finance. In this context of fast and impressive progress, spurred further by the enormous attraction these topics have on students, this book emerges as a welcome overview of the field for its practitioners, as well as a good starting point for detailed study on the graduate and post-graduate level. The book contains three parts, two major parts on theory and applications, and a smaller part on software. The theory part contains fundamental chapters on how to design and/or apply CA for many different areas. In the applications part a number of representative examples of really using CA in a broad range of disciplines is provided - this part will give the reader a good idea of the real strength of this kind of modeling as well as the incentive to apply CA in their own field of study. Finally, we included a smaller section on software, to highlight the important work that has been done to create high quality problem solving environments that allow to quickly and relatively easily implement a CA model and run simulations, both on the desktop and if needed, on High Performance Computing infrastructures.
Download or read book The Regulation of Cellular Systems written by Reinhart Heinrich and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is no doubt that nowadays, biology benefits greatly from mathematics. In particular, cellular biology is, besides population dynamics, a field where tech niques of mathematical modeling are widely used. This is reflected by the large number of journal articles and congress proceedings published every year on the dynamics of complex cellular processes. This applies, among others, to metabolic control analysis, where the number of articles on theoretical fundamentals and experimental applications has increased for about 15 years. Surprisingly, mono graphs and textbooks dealing with the modeling of metabolic systems are still exceptionally rare. We think that now time is ripe to fill this gap. This monograph covers various aspects of the mathematical description of enzymatic systems, such as stoichiometric analysis, enzyme kinetics, dynamical simulation, metabolic control analysis, and evolutionary optimization. We believe that, at present, these are the main approaches by which metabolic systems can be analyzed in mathematical terms. Although stoichiometric analysis and enzyme kinetics are classical fields tracing back to the beginning of our century, there are intriguing recent developments such as detection of elementary biochemical syn thesis routes and rate laws for the situation of metabolic channeling, which we have considered worth being included. Evolutionary optimization of metabolic systems is a rather new field with promising prospects. Its goal is to elucidate the structure and functions of these systems from an evolutionary viewpoint.
Download or read book E Cell System written by Satya Nanda Vel Arjunan and published by Springer Science & Business Media. This book was released on 2013-05-13 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interdisciplinary field of molecular systems biology aims to understand the behavior and mechanisms of biological processes composed of individual molecular components. As we gain more qualitative and quantitative information of complex intracellular processes, biochemical modeling and simulation become indispensable not only to uncover the molecular mechanisms of the processes, but to perform useful predictions. To this end, the E‐Cell System, a multi‐algorithm, multi‐timescale object‐oriented simulation platform, can be used to construct predictive virtual biological systems. Gene regulatory and biochemical networks that constitute a sub‐ or a whole cellular system can be constructed using the E‐Cell System to perform qualitative and quantitative analyses. The purpose of E‐Cell System: Basic Concepts and Applications is to provide a comprehensive guide for the E‐Cell System version 3 in terms of the software features and its usage. While the publicly available E‐Cell Simulation Environment version 3 User's Manual provides the technical details of model building and scripting, it does not describe some of the underlying concepts of the E‐Cell System. The first part of the book addresses this issue by providing the basic concepts of modeling and simulation with the E‐Cell System.
Download or read book Collective Behavior In Systems Biology written by Assaf Steinschneider and published by Academic Press. This book was released on 2019-09-04 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: Collective Behavior In Systems Biology: A Primer on Modeling Infrastructure offers a survey of established and emerging methods for quantifying process behavior in cellular systems. It introduces and applies mathematics and related abstract methods to processes in biological systems - why they are used, how they work, and what they mean. Emphasizing differential equations in an interdisciplinary approach, this book discusses infrastructure for kinetic modeling, technological system and control theories, optimization, and process behavior in cellular networks. The knowledge that the reader gains will be valuable for entering and keeping up with a rapidly developing discipline. Introduces basics of mathematical and abstract methods for understanding, predicting, and modifying collective behavior in cellular systems Targets biomedical professionals as well as computational specialists who are willing to take advantage of novel high-throughput data acquisition technologies
Download or read book Cellular Automata and Modeling of Complex Physical Systems written by Paul Manneville and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cellular automata are fully discrete dynamical systems with dynamical variables defined at the nodes of a lattice and taking values in a finite set. Application of a local transition rule at each lattice site generates the dynamics. The interpretation of systems with a large number of degrees of freedom in terms of lattice gases has received considerable attention recently due to the many applications of this approach, e.g. for simulating fluid flows under nearly realistic conditions, for modeling complex microscopic natural phenomena such as diffusion-reaction or catalysis, and for analysis of pattern-forming systems. The discussion in this book covers aspects of cellular automata theory related to general problems of information theory and statistical physics, lattice gas theory, direct applications, problems arising in the modeling of microscopic physical processes, complex macroscopic behavior (mostly in connection with turbulence), and the design of special-purpose computers.
Download or read book Systems Biology written by Andreas Kremling and published by CRC Press. This book was released on 2013-11-12 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Function and Regulation of Cellular Systems written by Andreas Deutsch and published by Birkhäuser. This book was released on 2012-12-06 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current biological research demands the extensive use of sophisticated mathematical methods and computer-aided analysis of experiments and data. This highly interdisciplinary volume focuses on structural, dynamical and functional aspects of cellular systems and presents corresponding experiments and mathematical models. The book may serve as an introduction for biologists, mathematicians and physicists to key questions in cellular systems which can be studied with mathematical models. Recent model approaches are presented with applications in cellular metabolism, intra- and intercellular signaling, cellular mechanics, network dynamics and pattern formation. In addition, applied issues such as tumor cell growth, dynamics of the immune system and biotechnology are included.
Download or read book Cellular Automaton Modeling of Biological Pattern Formation written by Andreas Deutsch and published by Springer Science & Business Media. This book was released on 2007-12-26 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on a challenging application field of cellular automata: pattern formation in biological systems, such as the growth of microorganisms, dynamics of cellular tissue and tumors, and formation of pigment cell patterns. These phenomena, resulting from complex cellular interactions, cannot be deduced solely from experimental analysis, but can be more easily examined using mathematical models, in particular, cellular automaton models. While there are various books treating cellular automaton modeling, this interdisciplinary work is the first one covering biological applications. The book is aimed at researchers, practitioners, and students in applied mathematics, mathematical biology, computational physics, bioengineering, and computer science interested in a cellular automaton approach to biological modeling.
Download or read book Fundamentals of Systems Biology written by Markus W. Covert and published by CRC Press. This book was released on 2017-10-19 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: For decades biology has focused on decoding cellular processes one gene at a time, but many of the most pressing biological questions, as well as diseases such as cancer and heart disease, are related to complex systems involving the interaction of hundreds, or even thousands, of gene products and other factors. How do we begin to understand this complexity? Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models introduces students to methods they can use to tackle complex systems head-on, carefully walking them through studies that comprise the foundation and frontier of systems biology. The first section of the book focuses on bringing students quickly up to speed with a variety of modeling methods in the context of a synthetic biological circuit. This innovative approach builds intuition about the strengths and weaknesses of each method and becomes critical in the book’s second half, where much more complicated network models are addressed—including transcriptional, signaling, metabolic, and even integrated multi-network models. The approach makes the work much more accessible to novices (undergraduates, medical students, and biologists new to mathematical modeling) while still having much to offer experienced modelers--whether their interests are microbes, organs, whole organisms, diseases, synthetic biology, or just about any field that investigates living systems.
Download or read book A Systems Theoretic Approach to Systems and Synthetic Biology II Analysis and Design of Cellular Systems written by Vishwesh V. Kulkarni and published by Springer. This book was released on 2014-07-03 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume II contains chapters contributed by leading researchers in the field of systems and synthetic biology that concern modeling physiological processes and bottom-up constructions of scalable biological systems. The modeling problems include characterisation and synthesis of memory, understanding how homoeostasis is maintained in the face of shocks and relatively gradual perturbations, understanding the functioning and robustness of biological clocks such as those at the core of circadian rhythms, and understanding how the cell cycles can be regulated, among others. Some of the bottom-up construction problems investigated in Volume II are as follows: How should biomacromolecules, platforms, and scalable architectures be chosen and synthesised in order to build programmable de novo biological systems? What are the types of constrained optimisation problems encountered in this process and how can these be solved efficiently? As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.
Download or read book Structured Biological Modelling written by Michael Kraus and published by CRC Press. This book was released on 1995-07-31 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structured Biological Modelling presents a straightforward introduction for computer-aided analysis, mathematical modelling, and simulation of cell biological systems. This unique guide brings together the physiological, structural, molecular biological, and theoretical aspects of the signal transduction network that regulates growth and proliferation in normal and tumor cells. It provides comprehensive survey of functional and theoretical features of intracellular signal processing and introduces the concept of cellular self-organization. Exemplified by oscillatory calcium waves, strategies for the design of computer experiments are presented that can assist or even substitute for time-consuming biological experiments. The presented minimal model for proliferation-associated signal transduction clearly shows the alterations of the cellular signal network involved in neoplastic growth. This book will be useful to cell and molecular biologists, oncologists, physiologists, theoretical biologists, computer scientists, and all other researchers and students studying functional aspects of cellular signaling.
Download or read book Immune system modeling and analysis written by Ramit Mehr and published by Frontiers Media SA. This book was released on 2015-04-22 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rapid development of new methods for immunological data collection – from multicolor flow cytometry, through single-cell imaging, to deep sequencing – presents us now, for the first time, with the ability to analyze and compare large amounts of immunological data in health, aging and disease. The exponential growth of these datasets, however, challenges the theoretical immunology community to develop methods for data organization and analysis. Furthermore, the need to test hypotheses regarding immune function, and generate predictions regarding the outcomes of medical interventions, necessitates the development of mathematical and computational models covering processes on multiple scales, from the genetic and molecular to the cellular and system scales. The last few decades have seen the development of methods for presentation and analysis of clonal repertoires (those of T and B lymphocytes) and phenotypic (surface-marker based) repertoires of all lymphocyte types, and for modeling the intricate network of molecular and cellular interactions within the immune systems. This e-Book, which has first appeared as a ‘Frontiers in Immunology’ research topic, provides a comprehensive, online, open access snapshot of the current state of the art on immune system modeling and analysis.
