systems biology simulation of dynamic network states

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Systems Biology Simulation Of Dynamic Network States

Author : Bernhard Ø. Palsson
ISBN : 9781139495424
Genre : Science
File Size : 46. 79 MB
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Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard Ø. Palsson shows how network reconstructions that are based on genomic and bibliomic data, and take the form of established stoichiometric matrices, can be converted into dynamic models using metabolomic and fluxomic data. The Mass Action Stoichiometric Simulation (MASS) procedure can be used for any cellular process for which data is available and allows a scalable step-by-step approach to the practical construction of network models. Specifically, it can treat integrated processes that need explicit accounting of small molecules and protein, which allows simulation at the molecular level. The material has been class-tested by the author at both the undergraduate and graduate level. All computations in the text are available online in MATLAB and MATHEMATICA® workbooks, allowing hands-on practice with the material.

Systems Biology

Author : Bernhard Palsson
ISBN : 9781107038851
Genre : Medical
File Size : 59. 38 MB
Format : PDF
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The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

Bond Graphs For Modelling Control And Fault Diagnosis Of Engineering Systems

Author : Wolfgang Borutzky
ISBN : 9783319474342
Genre : Technology & Engineering
File Size : 84. 97 MB
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This book presents theory and latest application work in Bond Graph methodology with a focus on: • Hybrid dynamical system models, • Model-based fault diagnosis, model-based fault tolerant control, fault prognosis • and also addresses • Open thermodynamic systems with compressible fluid flow, • Distributed parameter models of mechanical subsystems. In addition, the book covers various applications of current interest ranging from motorised wheelchairs, in-vivo surgery robots, walking machines to wind-turbines.The up-to-date presentation has been made possible by experts who are active members of the worldwide bond graph modelling community. This book is the completely revised 2nd edition of the 2011 Springer compilation text titled Bond Graph Modelling of Engineering Systems – Theory, Applications and Software Support. It extends the presentation of theory and applications of graph methodology by new developments and latest research results. Like the first edition, this book addresses readers in academia as well as practitioners in industry and invites experts in related fields to consider the potential and the state-of-the-art of bond graph modelling.

Contextualizing Systems Biology

Author : Martin Döring
ISBN : 9783319171067
Genre : Science
File Size : 84. 75 MB
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This collective monograph aims at contributing to an improved understanding of the epistemic presumptions, sociocultural implications and historically backgrounds of the newly emerging and currently expanding approach of systems biology. In doing so, it offers empirically grounded, valuable and reflexive information about a paradigmatic shift in the biosciences for a wide range of scientists working in the interdisciplinary areas of systems biology, synthetic biology, molecular biology, biology, the philosophy of science, the sociology of science and scientific knowledge, science and technology studies, technology assessment and the like. The authors of this monograph share the theoretical methodological premise that science is a culturally and socially embedded practice which characterizes our culture as a scientific one and at the same time draws its innovative potential from its socio-cultural context. This dialectic relationship lies at the heart of the current development of systems biology which is conceived as a so-called successor of ‘-omics’ research and triggered by high-throughput information technologies. At the same time a need for a holistic conceptualization of complex biological processes emerges. The title Contextualizing Systems Biology suggests that this book analyzes the development and advent of systems biology from different theoretical and methodological perspectives. We investigate a variety of contexts ranging from the analysis of cognitive contexts (such as basic theoretical concepts) to regulative contexts (policies) to the concrete application of a systems biology in the socio-scientific context of a European research project. In empirically analyzing these different and interrelated layers and dimensions of systems biology, the scope of the book goes beyond present attempts to investigate the advent of new approaches in the biological sciences as it frames and assesses systems biology from an interdisciplinary and integrated perspective.

The Physics Of Living Processes

Author : Thomas Andrew Waigh
ISBN : 9781118698273
Genre : Science
File Size : 78. 64 MB
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This full-colour undergraduate textbook, based on a two semestercourse, presents the fundamentals of biological physics,introducing essential modern topics that include cells, polymers,polyelectrolytes, membranes, liquid crystals, phase transitions,self-assembly, photonics, fluid mechanics, motility, chemicalkinetics, enzyme kinetics, systems biology, nerves, physiology, thesenses, and the brain. The comprehensive coverage, featuring in-depth explanations ofrecent rapid developments, demonstrates this to be one of the mostdiverse of modern scientific disciplines. The Physics of Living Processes: A Mesoscopic Approach iscomprised of five principal sections: • Building Blocks • Soft Condensed Matter Techniques in Biology • Experimental Techniques • Systems Biology • Spikes, Brains and the Senses The unique focus is predominantly on the mesoscale —structures on length scales between those of atoms and themacroscopic behaviour of whole organisms. The connections betweenmolecules and their emergent biological phenomena provide a novelintegrated perspective on biological physics, making this animportant text across a variety of scientific disciplines includingbiophysics, physics, physical chemistry, chemical engineering andbioengineering. An extensive set of worked tutorial questions are included,which will equip the reader with a range of new physical tools toapproach problems in the life sciences from medicine,pharmaceutical science and agriculture.

Computational Methods In Systems Biology

Author : Corrado Priami
ISBN : 9783540006053
Genre : Computers
File Size : 54. 13 MB
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Rovereto,December2002 CorradoPriami ProgrammeCommitteeofCMSB 2003 CorradoPriami(Chair),UniversityofTrento(Italy), CharlesAu?ray,CNRS,Villejuif(France), CosimaBaldari,Universit`adiSiena(Italy), AlexanderBockmayr,Universit ́eHenriPoincar ́e(France), LucaCardelli,MicrosoftResearchCambridge(UK), VincentDanos,Universit ́eParisVII(France), PierpaoloDegano,Universitad ` iPisa(Italy), Francois ̧ Fages,INRIA,Rocquencourt(France), DrabløsFinn,NorwegianUniversityofScienceandTechnology,Trondheim(N- way), MonikaHeiner,BrandenburgUniversityofTechnologyatCottbus(Germany), InaKoch,UniversityofAppliedSciencesBerlin,(Germany), JohnE.

Systems Biology In Biotech Pharma

Author : Aleš Prokop
ISBN : 9789400728493
Genre : Medical
File Size : 40. 66 MB
Format : PDF
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The US is currently well ahead of the rest of the world in the development and application of SB and its principles especially as they pertain to basic medical research and development. This lead is largely due to its earlier start in the academic arena. However, there is evidence of rapid development in both the UK/EU and Japan, and the gap is narrowing, particularly in the UK. From an industrial point of view, the Pharmaceutical Industry based in the US and UK can capitalize on these opportunities and gain the benefits of this technology. Many educational institutions (particularly their medical divisions) at present are heavily business-oriented, realize that in this particular industrial environment, that every dollar counts.

Systems Biology

Author : Marvin Cassman
ISBN : 9781402054686
Genre : Mathematics
File Size : 69. 12 MB
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This book explores Systems Biology as the understanding of biological network behaviors, and in particular their dynamic aspects, which requires the utilization of mathematical modeling tightly linked to experiment. A variety of approaches are discussed here: the identification and validation of networks, the creation of appropriate datasets, the development of tools for data acquisition and software development, and the use of modeling and simulation software in close concert with experiment.

Introduction To Systems Biology

Author : Sangdun Choi
ISBN : 9781597455312
Genre : Science
File Size : 30. 40 MB
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This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Stochastic Modelling For Systems Biology

Author : Darren J. Wilkinson
ISBN : 1584885408
Genre : Mathematics
File Size : 50. 74 MB
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Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. The stochastic processes formalism provides a beautiful, elegant, and coherent foundation for chemical kinetics and there is a wealth of associated theory every bit as powerful and elegant as that for conventional continuous deterministic models. The time is right for an introductory text written from this perspective. Stochastic Modelling for Systems Biology presents an accessible introduction to stochastic modelling using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modelling biological systems. He provides a comprehensive understanding of stochastic kinetic modelling of biological networks in the systems biology context. The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications. While emphasizing the necessary probabilistic and stochastic methods, the author takes a practical approach, rooting his theoretical development in discussions of the intended application. Written with self-study in mind, the book includes technical chapters that deal with the difficult problems of inference for stochastic kinetic models from experimental data. Providing enough background information to make the subject accessible to the non-specialist, the book integrates a fairly diverse literature into a single convenient and notationally consistent source.

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