Download or read book Identification of Dynamic Metabolic Flux Balance Models Based on Parametric Sensitivity Analysis written by Ricardo Martinez Villegas and published by . This book was released on 2016 with total page 103 pages. Available in PDF, EPUB and Kindle. Book excerpt: A dynamic mathematical model that involves a set of physicochemical parameters can describe a dynamic system. Parametric sensitivity analysis studies the effect of changes in these parameters on model outputs of interest. If a system is operated within a region of high sensitivity any small change in the parameter values drastically affect the output. Hence, it is essential to be able to predict this sensitivity when designing, operating or optimizing a system based on the model. Dynamical biological models that describe gene regulation, signalling, and metabolic networks are strongly dependent on a large number of parameters. Most of these models are highly nonlinear and involve a high-dimensional state space. Conventional parametric sensitivity analysis that examines the effect of each parameter independently at one specific moment is generally inaccurate since it ignores correlations between parameters. Thus, it is very important to account for correlations when conducting a parametric sensitivity analysis.
Download or read book Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism written by Kazuyuki Shimizu and published by Bentham Science Publishers. This book was released on 2015-06-04 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: An understanding of biological systems at cellular and molecular levels helps researchers to model cellular behavior in different experimental conditions. This, in turn, can lead to insights about the influence of cell culture environment and the effect of knockout gene research when studying mutations that affect specific metabolic pathways. A systems biology approach, therefore, allows researchers to simulate experimental observations in order to predict outcomes at the cellular level. Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism presents the basic concepts required for a systems biology approach towards cellular modeling. The book is intended as a primer for systems biology and biomedical engineering graduates and researchers. The text introduces readers to concepts related to cellular metabolism and its regulation, (enzymatic regulation and transcriptional regulation) which are also incorporated into a main metabolic model of a cell. The book also has chapters dedicated to identifying and incorporating steady-state and dynamic characteristics when considering a biological model for a computer simulation. Readers will be able to (1) understand the basis of systems analysis towards creating appropriate biological models and simulations, (2) develop useful kinetic models based on cellular transport phenomena and metabolic regulation, (3) understand how to simulate a cell growth phenotype, and analyze it with experimental data.
Download or read book Systems Metabolic Engineering written by Christoph Wittmann and published by Springer Science & Business Media. This book was released on 2012-06-15 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Metabolic Engineering is changing the way microbial cell factories are designed and optimized for industrial production. Integrating systems biology and biotechnology with new concepts from synthetic biology enables the global analysis and engineering of microorganisms and bioprocesses at super efficiency and versatility otherwise not accessible. Without doubt, systems metabolic engineering is a major driver towards bio-based production of chemicals, materials and fuels from renewables and thus one of the core technologies of global green growth. In this book, Christoph Wittmann and Sang-Yup Lee have assembled the world leaders on systems metabolic engineering and cover the full story – from genomes and networks via discovery and design to industrial implementation practises. This book is a comprehensive resource for students and researchers from academia and industry interested in systems metabolic engineering. It provides us with the fundaments to targeted engineering of microbial cells for sustainable bio-production and stimulates those who are interested to enter this exiting research field.
Download or read book Proceedings of the 8th International Conference on Foundations of Computer Aided Process Design written by and published by Elsevier. This book was released on 2014-07-14 with total page 835 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume collects together the presentations at the Eighth International Conference on Foundations of Computer-Aided Process Design, FOCAPD-2014, an event that brings together researchers, educators, and practitioners to identify new challenges and opportunities for process and product design. The chemical industry is currently entering a new phase of rapid evolution. The availability of low-cost feedstocks from natural gas is causing renewed investment in basic chemicals in the OECD, while societal pressures for sustainability and energy security continue to be key drivers in technology development and product selection. This dynamic environment creates opportunities to launch new products and processes and to demonstrate new methodologies for innovation, synthesis and design. FOCAPD-2014 fosters constructive interaction among thought leaders from academia, industry, and government and provides a showcase for the latest research in product and process design. - Focuses exclusively on the fundamentals and applications of computer-aided design for the process industries. - Provides a fully archival and indexed record of the FOCAPD14 conference - Aligns the FOCAPD series with the ESCAPE and PSE series
Download or read book Parametric Sensitivity Analysis of Metabolic Pathways written by Ye Wang and published by . This book was released on 2007 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
Download or read book Systems Biology written by Bernhard Ø. Palsson and published by Cambridge University Press. This book was released on 2006-01-16 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook, devoted to systems biology, describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated website Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results.
Download or read book Understanding the Control of Metabolism written by David Fell and published by . This book was released on 1997 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cybernetic Modeling for Bioreaction Engineering written by Doraiswami Ramkrishna and published by Cambridge University Press. This book was released on 2018-10-18 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: Describes dynamic state of metabolic systems, while paving the way for fully predictive modeling frameworks.
Download or read book Pyomo Optimization Modeling in Python written by William E. Hart and published by Springer Science & Business Media. This book was released on 2012-02-15 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a complete and comprehensive reference/guide to Pyomo (Python Optimization Modeling Objects) for both beginning and advanced modelers, including students at the undergraduate and graduate levels, academic researchers, and practitioners. The text illustrates the breadth of the modeling and analysis capabilities that are supported by the software and support of complex real-world applications. Pyomo is an open source software package for formulating and solving large-scale optimization and operations research problems. The text begins with a tutorial on simple linear and integer programming models. A detailed reference of Pyomo's modeling components is illustrated with extensive examples, including a discussion of how to load data from data sources like spreadsheets and databases. Chapters describing advanced modeling capabilities for nonlinear and stochastic optimization are also included. The Pyomo software provides familiar modeling features within Python, a powerful dynamic programming language that has a very clear, readable syntax and intuitive object orientation. Pyomo includes Python classes for defining sparse sets, parameters, and variables, which can be used to formulate algebraic expressions that define objectives and constraints. Moreover, Pyomo can be used from a command-line interface and within Python's interactive command environment, which makes it easy to create Pyomo models, apply a variety of optimizers, and examine solutions. The software supports a different modeling approach than commercial AML (Algebraic Modeling Languages) tools, and is designed for flexibility, extensibility, portability, and maintainability but also maintains the central ideas in modern AMLs.
Download or read book Computer Applications in Biotechnology 2004 written by Marie-Noelle Pons and published by Elsevier. This book was released on 2005-08-02 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Systems Biology written by Bernhard Ø. Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of computational models of biological functions, and how these models can be used to address key biological questions and enable predictive biology. Developed through extensive classroom use, the book is designed to provide students with a solid conceptual framework and an invaluable set of modeling tools and computational approaches.
Download or read book Exploring Cancer Metabolic Reprogramming through Molecular Imaging written by Franca Podo and published by Frontiers Media SA. This book was released on 2017-07-27 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: The inclusion of oncogene-driven reprogramming of energy metabolism within the list of cancer hallmarks (Hanahan and Weinberg, Cell 2000, 2011) has provided major impetus to further investigate the existence of a much wider metabolic rewiring in cancer cells, which not only includes deregulated cellular bioenergetics, but also encompasses multiple links with a more comprehensive network of altered biochemical pathways. This network is currently held responsible for redirecting carbon and phosphorus fluxes through the biosynthesis of nucleotides, amino acids, lipids and phospholipids and for the production of second messengers essential to cancer cells growth, survival and invasiveness in the hostile tumor environment. The capability to develop such a concerted rewiring of biochemical pathways is a versatile tool adopted by cancer cells to counteract the host defense and eventually resist the attack of anticancer treatments. Integrated efforts elucidating key mechanisms underlying this complex cancer metabolic reprogramming have led to the identification of new signatures of malignancy that are providing a strong foundation for improving cancer diagnosis and monitoring tumor response to therapy using appropriate molecular imaging approaches. In particular, the recent evolution of positron emission tomography (PET), magnetic resonance spectroscopy (MRS), spectroscopic imaging (MRSI), functional MR imaging (fMRI) and optical imaging technologies, combined with complementary cellular imaging approaches, have created new ways to explore and monitor the effects of metabolic reprogramming in cancer at clinical and preclinical levels. Thus, the progress of high-tech engineering and molecular imaging technologies, combined with new generation genomic, proteomic and phosphoproteomic methods, can significantly improve the clinical effectiveness of image-based interventions in cancer and provide novel insights to design and validate new targeted therapies. The Frontiers in Oncology Research Topic “Exploring Cancer Metabolic Reprogramming Through Molecular Imaging” focusses on current achievements, challenges and needs in the application of molecular imaging methods to explore cancer metabolic reprogramming, and evaluate its potential impact on clinical decisions and patient outcome. A series of reviews and perspective articles, along with original research contributions on humans and on preclinical models have been concertedly included in the Topic to build an open forum on perspectives, present needs and future challenges of this cutting-edge research area.
Download or read book Dynamical Modelling Estimation in Wastewater Treatment Processes written by D. Dochain and published by IWA Publishing. This book was released on 2001-12-01 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental quality is becoming an increasing concern in our society. In that context, waste and wastewater treatment, and more specifically biological wastewater treatment processes play an important role. In this book, we concentrate on the mathematical modelling of these processes. The main purpose is to provide the increasing number of professionals who are using models to design, optimise and control wastewater treatment processes with the necessary background for their activities of model building, selection and calibration. The book deals specifically with dynamic models because they allow us to describe the behaviour of treatment plants under the highly dynamic conditions that we want them to operate (e.g. Sequencing Batch Reactors) or we have to operate them (e.g. storm conditions, spills). Further extension is provided to new reactor systems for which partial differential equation descriptions are necessary to account for their distributed parameter nature (e.g. settlers, fixed bed reactors). The model building exercise is introduced as a step-wise activity that, in this book, starts from mass balancing principles. In many cases, different hypotheses and their corresponding models can be proposed for a particular process. It is therefore essential to be able to select from these candidate models in an objective manner. To this end, structure characterisation methods are introduced. Important sections of the book deal with the collection of high quality data using optimal experimental design, parameter estimation techniques for calibration and the on-line use of models in state and parameter estimators. Contents Dynamical Modelling Dynamical Mass Balance Model Building and Analysis Structure Characterisation (SC) Structural Identifiability Practical Identifiability and Optimal Experiment Design for Parameter Estimation (OED/PE) Estimation of Model Parameters Recursive State and Parameter Estimation Glossary Nomenclature
Download or read book Bioreaction Engineering written by K. Schügerl and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 639 pages. Available in PDF, EPUB and Kindle. Book excerpt: Alongside presenting the fundamentals, this book reviews the state of the art of mathematical modeling and control of bioprocesses, while demonstrating the application in various biological systems important to industry. At the same time, the application of different types of models and control strategies are illustrated, taking into account the recent developments in reactor modeling. In addition to modeling and control, the metabolic flux analysis and the metabolic design and their application to bioprocesses are considered.
Download or read book Control Theory and Systems Biology written by Pablo A. Iglesias and published by MIT Press. This book was released on 2010 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: A survey of how engineering techniques from control and systems theory can be used to help biologists understand the behavior of cellular systems.
Download or read book Systems and Synthetic Immunology written by Shailza Singh and published by Springer Nature. This book was released on 2020-04-24 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems and Synthetic Immunology focuses on the similarities between biology and engineering at the systems level, which are important for applying engineering theories to biology problems. With the advent of new genomic techniques, there are numerous systematic investigations underway in the scientific world. This volume highlights techniques that can be used to effectively combine two of the most essential biological fields - Systems Biology and Synthetic Immunology. The respective chapters discuss the role of synthetic immunology in biotechnology, production of biomaterials, and their use in vaccine delivery. Further topics include the importance of cytokines; the use of genomic engineering tools in immunotherapy; immunosensors; nanotherapeutics; and bioinformatics tools in biomedical applications. Given its scope, the book offers readers an up-to-date and comprehensive review of this unique and dynamic field of research.
