Systems Biology: Simulation of Dynamic Network States
Systems Biology: Simulation of Dynamic Network States

Author: Bernhard Ø. Palsson

Publisher: Cambridge University Press

Published: 2011-05-26

Total Pages: 333

ISBN-13: 1139495429

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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
Systems Biology

Author: Bernhard Palsson

Publisher:

Published: 2011

Total Pages: 317

ISBN-13: 9781139113052

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Master the process of building MASS models with real examples and hands-on practice.

Systems Biology
Systems Biology

Author: Bernhard Ø. Palsson

Publisher: Cambridge University Press

Published: 2006-01-16

Total Pages: 287

ISBN-13: 1139448943

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Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook, devoted to systems biology, describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated website Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results.

Systems Biology
Systems Biology

Author: Bernhard Palsson

Publisher: Cambridge University Press

Published: 2015-01-26

Total Pages: 551

ISBN-13: 1107038855

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The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

Systems Biology
Systems Biology

Author: Bernhard Ø. Palsson

Publisher: Cambridge University Press

Published: 2015-01-26

Total Pages: 551

ISBN-13: 1316239942

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Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of computational models of biological functions, and how these models can be used to address key biological questions and enable predictive biology. Developed through extensive classroom use, the book is designed to provide students with a solid conceptual framework and an invaluable set of modeling tools and computational approaches.

Systems Biology
Systems Biology

Author: Mariano Bizzarri

Publisher: Springer Nature

Published: 2024-01-08

Total Pages: 261

ISBN-13: 1071635778

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This second edition volume expands on the previous edition with discussions of the latest advancements and methods used by scientists to study systems biology. The chapters in this book are organized into four parts. Part One looks at models in systems biology and parameters identification such as short peptide analysis, metastasis models, and metabolomics. Part Two covers computational methods in the study of organisms, and cancer non-linear dynamics. Part Three discusses critical transition states across Waddington’s like landscapes such as understanding cell differentiation through single-cell approaches and modeling mammary organogenesis from biological first principles. Part Four talks about specific fields of investigation including inborn errors of metabolism, system biology approach in epithelial-mesenchymal transition, and an approach to understanding how COVID-19 spreads in the population. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Systems Biology, Second Edition is a valuable tool for any researcher looking to learn more about this important and developing field.

Computational Systems Biology in Medicine and Biotechnology
Computational Systems Biology in Medicine and Biotechnology

Author: Sonia Cortassa

Publisher: Springer Nature

Published: 2022-05-23

Total Pages: 494

ISBN-13: 1071618318

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This volume addresses the latest state-of-the-art systems biology-oriented approaches that--driven by big data and bioinformatics--are utilized by Computational Systems Biology, an interdisciplinary field that bridges experimental tools with computational tools to tackle complex questions at the frontiers of knowledge in medicine and biotechnology. The chapters in this book are organized into six parts: systems biology of the genome, epigenome, and redox proteome; metabolic networks; aging and longevity; systems biology of diseases; spatiotemporal patterns of rhythms, morphogenesis, and complex dynamics; and genome scale metabolic modeling in biotechnology. In every chapter, readers will find varied methodological approaches applied at different levels, from molecular, cellular, organ to organisms, genome to phenome, and health and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; criteria utilized for applying specific methodologies; lists of the necessary materials, reagents, software, databases, algorithms, mathematical models, and dedicated analytical procedures; step-by-step, readily reproducible laboratory, bioinformatics, and computational protocols all delivered in didactic and clear style and abundantly illustrated with express case studies and tutorials; and tips on troubleshooting and advice for achieving reproducibility while avoiding mistakes and misinterpretations. The overarching goal driving this volume is to excite the expert and stimulate the newcomer to the field of Computational Systems Biology. Cutting-edge and authoritative, Computational Systems Biology in Medicine and Biotechnology: Methods and Protocols is a valuable resource for pre- and post-graduate students in medicine and biotechnology, and in diverse areas ranging from microbiology to cellular and organismal biology, as well as computational and experimental biologists, and researchers interested in utilizing comprehensive systems biology oriented methods.

Bond Graphs for Modelling, Control and Fault Diagnosis of Engineering Systems
Bond Graphs for Modelling, Control and Fault Diagnosis of Engineering Systems

Author: Wolfgang Borutzky

Publisher: Springer

Published: 2016-12-31

Total Pages: 680

ISBN-13: 3319474340

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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
Contextualizing Systems Biology

Author: Martin Döring

Publisher: Springer

Published: 2015-12-18

Total Pages: 325

ISBN-13: 3319171062

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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
The Physics of Living Processes

Author: Thomas Andrew Waigh

Publisher: John Wiley & Sons

Published: 2014-10-20

Total Pages: 617

ISBN-13: 1118449940

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This full-colour undergraduate textbook, based on a two semester course, 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, chemical kinetics, enzyme kinetics, systems biology, nerves, physiology, the senses, and the brain. The comprehensive coverage, featuring in-depth explanations of recent rapid developments, demonstrates this to be one of the most diverse of modern scientific disciplines. The Physics of Living Processes: A Mesoscopic Approach is comprised 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 the macroscopic behaviour of whole organisms. The connections between molecules and their emergent biological phenomena provide a novel integrated perspective on biological physics, making this an important text across a variety of scientific disciplines including biophysics, physics, physical chemistry, chemical engineering and bioengineering. An extensive set of worked tutorial questions are included, which will equip the reader with a range of new physical tools to approach problems in the life sciences from medicine, pharmaceutical science and agriculture.