Compact Kernel Of A Metabolic Flux Balance Solution Space The Concepts Algorithms And Implementation

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Compact Kernel Of A Metabolic Flux Balance Solution Space, The: Concepts, Algorithms And Implementation

Wynand S Verwoerd
Compact Kernel Of A Metabolic Flux Balance Solution Space The Concepts Algorithms And Implementation Book PDF

Author : Wynand S Verwoerd
Publisher : World Scientific
Page : 249 pages
File Size : 43,9 Mb
Release : 2022-09-20
Category : Science
ISBN : 9789811255854

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Compact Kernel Of A Metabolic Flux Balance Solution Space, The: Concepts, Algorithms And Implementation by Wynand S Verwoerd Pdf

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.

The Compact Kernel of a Metabolic Flux Balance Solution Space

Wynand S. Verwoerd
The Compact Kernel of a Metabolic Flux Balance Solution Space Book PDF

Author : Wynand S. Verwoerd
Publisher : Unknown
Page : 0 pages
File Size : 41,6 Mb
Release : 2022
Category : Cell metabolism
ISBN : 9811255849

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The Compact Kernel of a Metabolic Flux Balance Solution Space by Wynand S. Verwoerd Pdf

"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"--

Metabolic Flux Analysis

Jens O. Krömer,Lars K. Nielsen,Lars M. Blank
Metabolic Flux Analysis Book PDF

Author : Jens O. Krömer,Lars K. Nielsen,Lars M. Blank
Publisher : Humana
Page : 0 pages
File Size : 47,8 Mb
Release : 2016-09-17
Category : Science
ISBN : 1493941593

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Metabolic Flux Analysis by Jens O. Krömer,Lars K. Nielsen,Lars M. Blank Pdf

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.

Systems Biology

Bernhard Palsson
Systems Biology Book PDF

Author : Bernhard Palsson
Publisher : Cambridge University Press
Page : 551 pages
File Size : 51,5 Mb
Release : 2015-01-26
Category : Medical
ISBN : 9781107038851

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Systems Biology by Bernhard Palsson Pdf

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

Cellular Automata

Giancarlo Mauri,Samira El Yacoubi,Alberto Dennunzio,Katsuhiro Nishinari,Luca Manzoni
Cellular Automata Book PDF

Author : Giancarlo Mauri,Samira El Yacoubi,Alberto Dennunzio,Katsuhiro Nishinari,Luca Manzoni
Publisher : Springer
Page : 528 pages
File Size : 48,7 Mb
Release : 2018-09-03
Category : Computers
ISBN : 9783319998138

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Cellular Automata by Giancarlo Mauri,Samira El Yacoubi,Alberto Dennunzio,Katsuhiro Nishinari,Luca Manzoni Pdf

This book constitutes the proceedings of the 13th International Conference on Cellular Automata for Research and Industry, ACRI 2018, held in Como, Italy, in September 2018. The 47 full papers presented in this volume were carefully reviewed and selected from 64 submissions. This volume contains invited contributions and accepted papers from the main track and from the three organized workshops. The volume is organized in the following topics: biological systems modeling; simulation and other applications of CA; multi-agent systems; pedestrian and traffic dynamics; synchronization and control; theory and cryptography; asynchronous cellular automata; and crowds, traffic and cellular automata.

A Life Course Perspective on Health Trajectories and Transitions

Claudine Burton-Jeangros,Stéphane Cullati,Amanda Sacker,David Blane
A Life Course Perspective on Health Trajectories and Transitions Book PDF

Author : Claudine Burton-Jeangros,Stéphane Cullati,Amanda Sacker,David Blane
Publisher : Springer
Page : 213 pages
File Size : 43,8 Mb
Release : 2016-10-22
Category : Medical
ISBN : 3319372440

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A Life Course Perspective on Health Trajectories and Transitions by Claudine Burton-Jeangros,Stéphane Cullati,Amanda Sacker,David Blane Pdf

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.

Systems Biology in Practice

Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach
Systems Biology in Practice Book PDF

Author : Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach
Publisher : John Wiley & Sons
Page : 486 pages
File Size : 44,8 Mb
Release : 2008-07-15
Category : Medical
ISBN : 9783527604883

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Systems Biology in Practice by Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach Pdf

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.

Mathematical Modeling in Systems Biology

Brian P. Ingalls
Mathematical Modeling in Systems Biology Book PDF

Author : Brian P. Ingalls
Publisher : MIT Press
Page : 423 pages
File Size : 55,8 Mb
Release : 2022-06-07
Category : Science
ISBN : 9780262545822

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Mathematical Modeling in Systems Biology by Brian P. Ingalls Pdf

An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.

Large Scale Methods to Enumerate Extreme Rays and Elementary Modes (b/w Print)

Marco Terzer
Large Scale Methods to Enumerate Extreme Rays and Elementary Modes b w Print Book PDF

Author : Marco Terzer
Publisher : Lulu.com
Page : 170 pages
File Size : 48,7 Mb
Release : 2009
Category : Electronic
ISBN : 9781445248776

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Large Scale Methods to Enumerate Extreme Rays and Elementary Modes (b/w Print) by Marco Terzer Pdf

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.

MATLAB for Machine Learning

Giuseppe Ciaburro
MATLAB for Machine Learning Book PDF

Author : Giuseppe Ciaburro
Publisher : Packt Publishing Ltd
Page : 374 pages
File Size : 53,8 Mb
Release : 2017-08-28
Category : Computers
ISBN : 9781788399395

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MATLAB for Machine Learning by Giuseppe Ciaburro Pdf

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.

Combinatorics and Computer Science

M. Deza,Reinhardt Euler
Combinatorics and Computer Science Book PDF

Author : M. Deza,Reinhardt Euler
Publisher : Springer Science & Business Media
Page : 436 pages
File Size : 54,6 Mb
Release : 1996-08-07
Category : Computers
ISBN : 3540615768

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Combinatorics and Computer Science by M. Deza,Reinhardt Euler Pdf

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.

High-Performance Modelling and Simulation for Big Data Applications

Joanna Kołodziej,Horacio González-Vélez
High Performance Modelling and Simulation for Big Data Applications Book PDF

Author : Joanna Kołodziej,Horacio González-Vélez
Publisher : Springer
Page : 364 pages
File Size : 42,7 Mb
Release : 2019-03-25
Category : Computers
ISBN : 9783030162726

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High-Performance Modelling and Simulation for Big Data Applications by Joanna Kołodziej,Horacio González-Vélez Pdf

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications.

Handbook of Optimization in Complex Networks

My T. Thai,Panos M. Pardalos
Handbook of Optimization in Complex Networks Book PDF

Author : My T. Thai,Panos M. Pardalos
Publisher : Springer Science & Business Media
Page : 539 pages
File Size : 42,8 Mb
Release : 2011-11-25
Category : Mathematics
ISBN : 9781461408574

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Handbook of Optimization in Complex Networks by My T. Thai,Panos M. Pardalos Pdf

Complex Social Networks is a newly emerging (hot) topic with applications in a variety of domains, such as communication networks, engineering networks, social networks, and biological networks. In the last decade, there has been an explosive growth of research on complex real-world networks, a theme that is becoming pervasive in many disciplines, ranging from mathematics and computer science to the social and biological sciences. Optimization of complex communication networks requires a deep understanding of the interplay between the dynamics of the physical network and the information dynamics within the network. Although there are a few books addressing social networks or complex networks, none of them has specially focused on the optimization perspective of studying these networks. This book provides the basic theory of complex networks with several new mathematical approaches and optimization techniques to design and analyze dynamic complex networks. A wide range of applications and optimization problems derived from research areas such as cellular and molecular chemistry, operations research, brain physiology, epidemiology, and ecology.

Biochar for Environmental Management

Johannes Lehmann,Stephen Joseph
Biochar for Environmental Management Book PDF

Author : Johannes Lehmann,Stephen Joseph
Publisher : Routledge
Page : 449 pages
File Size : 54,6 Mb
Release : 2012-05-16
Category : Business & Economics
ISBN : 9781136571213

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Biochar for Environmental Management by Johannes Lehmann,Stephen Joseph Pdf

Biochar is the carbon-rich product when biomass (such as wood, manure or crop residues) is heated in a closed container with little or no available air. It can be used to improve agriculture and the environment in several ways, and its stability in soil and superior nutrient-retention properties make it an ideal soil amendment to increase crop yields. In addition to this, biochar sequestration, in combination with sustainable biomass production, can be carbon-negative and therefore used to actively remove carbon dioxide from the atmosphere, with major implications for mitigation of climate change. Biochar production can also be combined with bioenergy production through the use of the gases that are given off in the pyrolysis process. This book is the first to synthesize the expanding research literature on this topic. The book's interdisciplinary approach, which covers engineering, environmental sciences, agricultural sciences, economics and policy, is a vital tool at this stage of biochar technology development. This comprehensive overview of current knowledge will be of interest to advanced students, researchers and professionals in a wide range of disciplines.

Control Theory and Systems Biology

Pablo A. Iglesias,Brian P. Ingalls
Control Theory and Systems Biology Book PDF

Author : Pablo A. Iglesias,Brian P. Ingalls
Publisher : MIT Press
Page : 359 pages
File Size : 45,9 Mb
Release : 2010
Category : Biological control systems
ISBN : 9780262013345

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Control Theory and Systems Biology by Pablo A. Iglesias,Brian P. Ingalls Pdf

A survey of how engineering techniques from control and systems theory can be used to help biologists understand the behavior of cellular systems.