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 : 68. 69 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 Simulation Of Dynamic Network States

Author : CTI Reviews
ISBN : 9781490272214
Genre : Education
File Size : 50. 95 MB
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Facts101 is your complete guide to Systems Biology, Simulation of Dynamic Network States. In this book, you will learn topics such as as those in your book plus much more. With key features such as key terms, people and places, Facts101 gives you all the information you need to prepare for your next exam. Our practice tests are specific to the textbook and we have designed tools to make the most of your limited study time.

Systems Biology

Author : Bernhard Palsson
ISBN : 9781107038851
Genre : Medical
File Size : 62. 58 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.

Multiskalenmodellierung Der Progression Von Glioblastomen

Author : Tina Anne Schütz
ISBN : 9783658070755
Genre : Mathematics
File Size : 52. 40 MB
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​Tina Anne Schütz entwickelt und diskutiert ein neues Multiskalenmodell zur Abbildung der frühen Wachstumsphase von Glioblastomen. Um mehrere Skalen abzubilden, koppelt die Autorin ein hybrides Modell auf der mikroskopischen Ebene mit dem Modell eines molekularen Interaktionsnetzwerkes. Durch den Vergleich mit In-vitro-Daten validiert sie das Modell und führt Simulationen durch, um so Rückschlüsse für die Biologie und Medizin zu ziehen. Insbesondere liefert das Modell Hinweise auf neue prognostische Marker für die Progression von Glioblastomen und auf neue Therapieansätze.​

Contextualizing Systems Biology

Author : Martin Döring
ISBN : 9783319171067
Genre : Science
File Size : 77. 90 MB
Format : PDF, Kindle
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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 : 36. 63 MB
Format : PDF
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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.

Kompendium Systembiologie

Author : Andreas Kremling
ISBN : 9783834886071
Genre : Science
File Size : 65. 51 MB
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Das Buch beschreibt die Grundlagen der mathematischen Modellierung zellulärer Systeme. Nach einer Klassifikation von Modellen wird schwerpunktmäßig auf deterministische Modelle eingegangen und für alle relevanten zellulären Prozesse entsprechende Gleichungen angegeben. Anschließend werden eine Reihe von Verfahren zur Modellanalyse vorgestellt. Etwas kürzer werden Verfahren zum Reverse Engineering und zur Analyse von Netzwerkgraphen abgehandelt. Am Ende werden noch Verfahren der Parameteridentifikation besprochen.

Introduction To Systems Biology

Author : Sangdun Choi
ISBN : 9781597455312
Genre : Science
File Size : 62. 64 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.

Modeling In Systems Biology

Author : Ina Koch
ISBN : 1849964742
Genre : Computers
File Size : 88. 12 MB
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The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Systems Biology

Author : Lilia Alberghina
ISBN : 3540742697
Genre : Computers
File Size : 76. 9 MB
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For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.

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