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 : 20. 43 MB
Format : PDF
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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 : 83. 39 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 : 43. 33 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.

Contextualizing Systems Biology

Author : Martin Döring
ISBN : 9783319171067
Genre : Science
File Size : 61. 54 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 : 9781118449943
Genre : Science
File Size : 79. 37 MB
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Biomechanics Of Cells And Tissues

Author : Paola Lecca
ISBN : 9789400758902
Genre : Technology & Engineering
File Size : 79. 53 MB
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The application of methodological approaches and mathematical formalisms proper to Physics and Engineering to investigate and describe biological processes and design biological structures has led to the development of many disciplines in the context of computational biology and biotechnology. The best known applicative domain is tissue engineering and its branches. Recent domains of interest are in the field of biophysics, e.g.: multiscale mechanics of biological membranes and films and filaments; multiscale mechanics of adhesion; biomolecular motors and force generation. Modern hypotheses, models, and tools are currently emerging and resulting from the convergence of the methods and phylosophycal apporaches of the different research areas and disciplines. All these emerging approaches share the purpose of disentangling the complexity of organisms, tissues, and cells and mimiking the function of living systems. The contributions presented in this book are current research highlights of six challenging and representative applicative domains of phyisical, engineering, and computational approaches in medicine and biology, i.e tissue engineering, modelling of molecular structures, cell mechanics and cell adhesión processes, cancer physics, and physico-chemical processes of metabolic interactions. Each chapter presents a compendium or a review of the original results achieved by authors in the last years. Furthermore, the book also wants to pinpoint the questions that are still open and that could propel the future research.

Introduction To Systems Biology

Author : Sangdun Choi
ISBN : 9781597455312
Genre : Science
File Size : 48. 94 MB
Format : PDF, ePub
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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.

Computational Methods In Systems Biology

Author : Corrado Priami
ISBN : 9783540006053
Genre : Computers
File Size : 88. 1 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.

Modeling In Systems Biology

Author : Ina Koch
ISBN : 1849964742
Genre : Computers
File Size : 65. 98 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.

Computing And Combinatorics

Author : Lusheng Wang
ISBN : 9783540280613
Genre : Computers
File Size : 65. 88 MB
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The refereed proceedings of the 11th Annual International Computing and Combinatorics Conference, COCOON 2005, held in Kunming, China in August 2005. The 96 revised full papers presented together with abstracts of 3 invited talks were carefully reviewed and selected from 353 submissions. The papers cover most aspects of theoretical computer science and combinatorics related to computing and are organized in topical sections on bioinformatics, networks, string algorithms, scheduling, complexity, steiner trees, graph drawing and layout design, quantum computing, randomized algorithms, geometry, codes, finance, facility location, graph theory, graph algorithms.

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