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
Get Book Here
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: 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: 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.
Author: Jérôme Idier
Publisher: John Wiley & Sons
ISBN: 111862369X
Category : Mathematics
Languages : en
Pages : 322
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Book Description
Many scientific, medical or engineering problems raise the issue of recovering some physical quantities from indirect measurements; for instance, detecting or quantifying flaws or cracks within a material from acoustic or electromagnetic measurements at its surface is an essential problem of non-destructive evaluation. The concept of inverse problems precisely originates from the idea of inverting the laws of physics to recover a quantity of interest from measurable data. Unfortunately, most inverse problems are ill-posed, which means that precise and stable solutions are not easy to devise. Regularization is the key concept to solve inverse problems. The goal of this book is to deal with inverse problems and regularized solutions using the Bayesian statistical tools, with a particular view to signal and image estimation. The first three chapters bring the theoretical notions that make it possible to cast inverse problems within a mathematical framework. The next three chapters address the fundamental inverse problem of deconvolution in a comprehensive manner. Chapters 7 and 8 deal with advanced statistical questions linked to image estimation. In the last five chapters, the main tools introduced in the previous chapters are put into a practical context in important applicative areas, such as astronomy or medical imaging.
Author: Marco Terzer
Publisher: Lulu.com
ISBN: 1445248794
Category :
Languages : en
Pages : 170
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Book Description
A major challenge in systems biology is to improve the understanding of complex metabolic networks. Here, we focus on structural analysis since it requires mainly reaction stoichiometries, in contrary to detailed dynamic methods that are often limited by insufficient knowledge on mechanisms and parameters. Thermodynamic reaction constraints and the steady state assumption reduce the solution space for valid reaction fluxes to a convex polyhedral cone. Pathway analysis methods aim at finding a unique generating set for the flux cone---called extreme rays or elementary modes. We describe critical aspects for an efficient implementation of the double description method for large scale application. The efficiency of introduced techniques is demonstrated with large application examples from combinatorics and systems biology.
Author: Giuseppe Ciaburro
Publisher: Packt Publishing Ltd
ISBN: 1788399390
Category : Computers
Languages : en
Pages : 374
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Book Description
Extract patterns and knowledge from your data in easy way using MATLAB About This Book Get your first steps into machine learning with the help of this easy-to-follow guide Learn regression, clustering, classification, predictive analytics, artificial neural networks and more with MATLAB Understand how your data works and identify hidden layers in the data with the power of machine learning. Who This Book Is For This book is for data analysts, data scientists, students, or anyone who is looking to get started with machine learning and want to build efficient data processing and predicting applications. A mathematical and statistical background will really help in following this book well. What You Will Learn Learn the introductory concepts of machine learning. Discover different ways to transform data using SAS XPORT, import and export tools, Explore the different types of regression techniques such as simple & multiple linear regression, ordinary least squares estimation, correlations and how to apply them to your data. Discover the basics of classification methods and how to implement Naive Bayes algorithm and Decision Trees in the Matlab environment. Uncover how to use clustering methods like hierarchical clustering to grouping data using the similarity measures. Know how to perform data fitting, pattern recognition, and clustering analysis with the help of MATLAB Neural Network Toolbox. Learn feature selection and extraction for dimensionality reduction leading to improved performance. In Detail MATLAB is the language of choice for many researchers and mathematics experts for machine learning. This book will help you build a foundation in machine learning using MATLAB for beginners. You'll start by getting your system ready with t he MATLAB environment for machine learning and you'll see how to easily interact with the Matlab workspace. We'll then move on to data cleansing, mining and analyzing various data types in machine learning and you'll see how to display data values on a plot. Next, you'll get to know about the different types of regression techniques and how to apply them to your data using the MATLAB functions. You'll understand the basic concepts of neural networks and perform data fitting, pattern recognition, and clustering analysis. Finally, you'll explore feature selection and extraction techniques for dimensionality reduction for performance improvement. At the end of the book, you will learn to put it all together into real-world cases covering major machine learning algorithms and be comfortable in performing machine learning with MATLAB. Style and approach The book takes a very comprehensive approach to enhance your understanding of machine learning using MATLAB. Sufficient real-world examples and use cases are included in the book to help you grasp the concepts quickly and apply them easily in your day-to-day work.
Author: Edda Klipp
Publisher: John Wiley & Sons
ISBN: 352760488X
Category : Medical
Languages : en
Pages : 486
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Book Description
Presenting the main concepts, this book leads students as well as advanced researchers from different disciplines to an understanding of current ideas in the complex field of comprehensive experimental investigation of biological objects, analysis of data, development of models, simulation, and hypothesis generation. It provides readers with guidance on how a specific complex biological question may be tackled: - How to formulate questions that can be answered - Which experiments to perform - Where to find information in databases and on the Internet - What kinds of models are appropriate - How to use simulation tools - What can be learned from the comparison of experimental data and modeling results - How to make testable predictions. The authors demonstrate how mathematical concepts can illuminate the principles underlying biology at a genetic, molecular, cellular and even organism level, and how to use mathematical tools for analysis and prediction.
Author: M. Deza
Publisher: Springer Science & Business Media
ISBN: 9783540615767
Category : Computers
Languages : en
Pages : 436
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Book Description
This book presents a collection of 33 strictly refereed full papers on combinatorics and computer science; these papers have been selected from the 54 papers accepted for presentation at the joint 8th Franco-Japanese and 4th Franco-Chinese Conference on Combinatorics in Computer Science, CCS '96, held in Brest, France in July 1995. The papers included in the book have been contributed by authors from 10 countries; they are organized in sections entitled graph theory, combinatorial optimization, selected topics, and parallel and distributed computing.
