Compact Kernel Of A Metabolic Flux Balance Solution Space, The: Concepts, Algorithms And Implementation PDF Download
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Author: Wynand S Verwoerd
Publisher: World Scientific
ISBN: 9811255857
Category : Science
Languages : en
Pages : 249
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Book Description
This monograph offers a fundamentally new approach to facilitate the study of metabolic networks in cells. It aims to overcome the limitations of either just a single FBA solution, or an overwhelming number of extreme pathways in a realistic network. Instead it focusses on the FBA solution space and describes it in a simplified way by extracting just a bounded subspace: the Solution Space Kernel or SSK. This reduces the relevant number of flux space dimensions by orders of magnitude, and allows its location, size and shape to be characterised. It is a multi-stage process, requiring many new concepts and algorithms for manipulating polytopes in high dimensional spaces.The book introduces and develops these concepts in a pragmatic way that takes into account the difficulties of performing analyses in a flux space with dimensions counting in the hundreds or thousands. It emphasizes the details of implementation in computational code and applications to realistic models are demonstrated. For many cases, the number of constraints and flux variables that fully specify the SSK polytope is only a single or double-digit number. This allows the range of metabolic states accessible to a cell to be further interpreted geometrically in terms of a manageable set of orthogonal diameters and aspect ratios. In addition, explicit representative fluxes, giving the centre and periphery of the solution space kernel, become available for further exploration.
Author: Wynand S Verwoerd
Publisher: World Scientific
ISBN: 9811255857
Category : Science
Languages : en
Pages : 249
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Book Description
This monograph offers a fundamentally new approach to facilitate the study of metabolic networks in cells. It aims to overcome the limitations of either just a single FBA solution, or an overwhelming number of extreme pathways in a realistic network. Instead it focusses on the FBA solution space and describes it in a simplified way by extracting just a bounded subspace: the Solution Space Kernel or SSK. This reduces the relevant number of flux space dimensions by orders of magnitude, and allows its location, size and shape to be characterised. It is a multi-stage process, requiring many new concepts and algorithms for manipulating polytopes in high dimensional spaces.The book introduces and develops these concepts in a pragmatic way that takes into account the difficulties of performing analyses in a flux space with dimensions counting in the hundreds or thousands. It emphasizes the details of implementation in computational code and applications to realistic models are demonstrated. For many cases, the number of constraints and flux variables that fully specify the SSK polytope is only a single or double-digit number. This allows the range of metabolic states accessible to a cell to be further interpreted geometrically in terms of a manageable set of orthogonal diameters and aspect ratios. In addition, explicit representative fluxes, giving the centre and periphery of the solution space kernel, become available for further exploration.
Author: Wynand S. Verwoerd
Publisher:
ISBN: 9789811255847
Category : Cell metabolism
Languages : en
Pages : 0
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Book Description
"This monograph offers a fundamentally new approach to facilitate the study of metabolic networks in cells. It aims to overcome the limitations of either just a single FBA solution, or an overwhelming number of extreme pathways in a realistic network. Instead it focusses on the FBA solution space and describes it in a simplified way by extracting just a bounded subspace: the Solution Space Kernel or SSK. This reduces the relevant number of flux space dimensions by orders of magnitude, and allows its location, size and shape to be characterised. It is a multi-stage process, requiring many new concepts and algorithms for manipulating polytopes in high dimensional spaces. The book introduces and develops these concepts in a pragmatic way that takes into account the difficulties of performing analyses in a flux space with dimensions counting in the hundreds or thousands. It emphasizes the details of implementation in computational code and applications to realistic models are demonstrated. For many cases, the number of constraints and flux variables that fully specify the SSK polytope is only a single or double-digit number. This allows the range of metabolic states accessible to a cell to be further interpreted geometrically in terms of a manageable set of orthogonal diameters and aspect ratios. In addition, explicit representative fluxes, giving the centre and periphery of the solution space kernel, become available for further exploration"--
Author: Jens O. Krömer
Publisher: Humana
ISBN: 9781493941599
Category : Science
Languages : en
Pages : 0
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Book Description
Metabolic Flux Analysis: Methods and Protocols opens up the field of metabolic flux analysis to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. Metabolic flux analysis emerged from the current limitation for the prediction of metabolic fluxes from a measured inventory of the cell. Divided into convenient thematic parts, topics in this essential volume include the fundamental characteristics of the underlying networks, the application of quantitative metabolite data and thermodynamic principles to constrain the solution space for flux balance analysis (FBA), the experimental toolbox to conduct different types of flux analysis experiments, the processing of data from 13C experiments and three chapters that summarize some recent key findings. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Metabolic Flux Analysis: Methods and Protocols presents protocols that cover a range of relevant organisms currently used in the field, providing a solid basis to anybody interested in the field of metabolic flux analysis.
Author: Athel Cornish-Bowden
Publisher: Springer Science & Business Media
ISBN: 9401140723
Category : Medical
Languages : en
Pages : 366
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Book Description
Two decades have passed since the mechanisms of protein synthesis became well enough understood to permit the genetic modification oforganisms. An impressive amount of new knowledge has emerged from the new technology, but much ofthe promise of20years ago has notyet been fulfilled. In biotechnology, efforts to increase the yields of commercially valuable metabolites have been less successful than ex pected, and when they have succeeded it has often been as much from selective breeding as from new methods. The cell is more complicated than what is presented in the classical teaching of biochemistry, it contains more structure than was dreamed of 20 years ago, and the behaviour ofany systemofenzymes is more elaborate than can be explained in terms ofa single supposedly rate-limiting enzyme. Even if classical enzymology and meta bolism may have seemed rather unfashionable during the rise ofmolecular biology, they remain central to any modification ofthe metabolic behaviour oforganisms. As such modification is essential in much ofbiotechnology and drug development, bio technologists can only ignore these topics at their peril.
Author: Edda Klipp
Publisher: John Wiley & Sons
ISBN: 3527336362
Category : Medical
Languages : en
Pages : 504
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Book Description
This advanced textbook is tailored for an introductory course in Systems Biology and is well-suited for biologists as well as engineers and computer scientists. It comes with student-friendly reading lists and a companion website featuring a short exam prep version of the book and educational modeling programs. The text is written in an easily accessible style and includes numerous worked examples and study questions in each chapter. For this edition, a section on medical systems biology has been included.
Author: Bernhard Palsson
Publisher: Cambridge University Press
ISBN: 1107038855
Category : Medical
Languages : en
Pages : 551
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Book Description
The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
Author: Michiel Hazewinkel
Publisher: Springer Science & Business Media
ISBN: 9400903650
Category : Mathematics
Languages : en
Pages : 743
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Book Description
This ENCYCLOPAEDIA OF MATHEMATICS aims to be a reference work for all parts of mathe matics. It is a translation with updates and editorial comments of the Soviet Mathematical Encyclopaedia published by 'Soviet Encyclopaedia Publishing House' in five volumes in 1977-1985. The annotated translation consists of ten volumes including a special index volume. There are three kinds of articles in this ENCYCLOPAEDIA. First of all there are survey-type articles dealing with the various main directions in mathematics (where a rather fine subdivi sion has been used). The main requirement for these articles has been that they should give a reasonably complete up-to-date account of the current state of affairs in these areas and that they should be maximally accessible. On the whole, these articles should be understandable to mathematics students in their first specialization years, to graduates from other mathematical areas and, depending on the specific subject, to specialists in other domains of science, en gineers and teachers of mathematics. These articles treat their material at a fairly general level and aim to give an idea of the kind of problems, techniques and concepts involved in the area in question. They also contain background and motivation rather than precise statements of precise theorems with detailed definitions and technical details on how to carry out proofs and constructions. The second kind of article, of medium length, contains more detailed concrete problems, results and techniques.
Author: Ganesh Sriram
Publisher: Humana
ISBN: 9781493958818
Category : Science
Languages : en
Pages : 0
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Book Description
In Plant Metabolism: Methods and Protocols, expert researchers in the field present the latest methods on quantitative analysis of plant metabolism. The methods focus on measurements, analyses and simulations of molecules, fluxes, and ultimately entire metabolic pathways and networks. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, reagents, or software, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Metabolism: Methods and Protocols seeks to benefit scientists ranging from plant biology, metabolic engineering, and biotechnology.
Author:
Publisher:
ISBN:
Category : Aeronautics
Languages : en
Pages : 1492
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Book Description
Author: Claudine Burton-Jeangros
Publisher: Springer
ISBN: 331920484X
Category : Medical
Languages : en
Pages : 215
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Book Description
This open access book examines health trajectories and health transitions at different stages of the life course, including childhood, adulthood and later life. It provides findings that assess the role of biological and social transitions on health status over time. The essays examine a wide range of health issues, including the consequences of military service on body mass index, childhood obesity and cardiovascular health, socio-economic inequalities in preventive health care use, depression and anxiety during the child rearing period, health trajectories and transitions in people with cystic fibrosis and oral health over the life course. The book addresses theoretical, empirical and methodological issues as well as examines different national contexts, which help to identify factors of vulnerability and potential resources that support resilience available for specific groups and/or populations. Health reflects the ability of individuals to adapt to their social environment. This book analyzes health as a dynamic experience. It examines how different aspects of individual health unfold over time as a result of aging but also in relation to changing socioeconomic conditions. It also offers readers potential insights into public policies that affect the health status of a population.
