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In general, several mathematical models can be designed in order to describe a biological or medical process and there is no unique criterion which model gives the best description. This book presents several of these models and shows applications of them to different biological and medical problems. The book shows that operations research expertise is necessary in respect to modeling, analysis and optimization of biosystems.
In general, several mathematical models can be designed in order to describe a biological or medical process and there is no unique criterion which model gives the best description. This book presents several of these models and shows applications of them to different biological and medical problems. The book shows that operations research expertise is necessary in respect to modeling, analysis and optimization of biosystems.
Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it mostly focuses on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. Unlike other bioinformatics books which are mostly theoretical, this book provides practical examples for the readers on state-of-the-art open source tools to solve biological problems. Flow charts of experiments, graphical illustrations, and mock data are included for quick reference. Volume I is therefore an ideal companion for students and early stage professionals wishing to master this blooming field.
This volume is an interdisciplinary book which introduces, in a very readable way, state-of-the-art research in the fundamental topics of mathematical modelling of Biosystems. In short, the book offers an overview of mathematical and computational modelling of biosystems including biological phenomena in general. There is also a special introduction to Protein Physics which aims to explain the all-or-none first order phase transitions from native to denatured states.
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.
The volume presents a selection of in-depth studies and state-of-the-art surveys of several challenging topics that are at the forefront of modern applied mathematics, mathematical modeling, and computational science. These three areas represent the foundation upon which the methodology of mathematical modeling and computational experiment is built as a ubiquitous tool in all areas of mathematical applications. This book covers both fundamental and applied research, ranging from studies of elliptic curves over finite fields with their applications to cryptography, to dynamic blocking problems, to random matrix theory with its innovative applications. The book provides the reader with state-of-the-art achievements in the development and application of new theories at the interface of applied mathematics, modeling, and computational science. This book aims at fostering interdisciplinary collaborations required to meet the modern challenges of applied mathematics, modeling, and computational science. At the same time, the contributions combine rigorous mathematical and computational procedures and examples from applications ranging from engineering to life sciences, providing a rich ground for graduate student projects.
Shows the newest developments in the field of multi-parametric model predictive control and optimization and their application for drug delivery systems This book is based on the Modelling, Control and Optimization of Biomedical Systems (MOBILE) project, which was created to derive intelligent computer model-based systems for optimization of biomedical drug delivery systems in the cases of diabetes, anaesthesia, and blood cancer. These systems can ensure reliable and fast calculation of the optimal drug dosage without the need for an online computer—while taking into account the specifics and constraints of the patient model, flexibility to adapt to changing patient characteristics and incorporation of the physician’s performance criteria, and maintaining the safety of the patients. Modelling Optimization and Control of Biomedical Systems covers: mathematical modelling of drug delivery systems; model analysis, parameter estimation, and approximation; optimization and control; sensitivity analysis & model reduction; multi-parametric programming and model predictive control; estimation techniques; physiologically-based patient model; control design for volatile anaesthesia; multiparametric model based approach to intravenous anaesthesia; hybrid model predictive control strategies; Type I Diabetes Mellitus; in vitro and in silico block of the integrated platform for the study of leukaemia; chemotherapy treatment as a process systems application; and more. Introduces readers to the Modelling, Control and Optimization of Biomedical Systems (MOBILE) project Presents in detail the theoretical background, computational tools, and methods that are used in all the different biomedical systems Teaches the theory for multi-parametric mixed-integer programming and explicit optimal control of volatile anaesthesia Provides an overview of the framework for modelling, optimization, and control of biomedical systems This book will appeal to students, researchers, and scientists working on the modelling, control, and optimization of biomedical systems and to those involved in cancer treatment, anaesthsia, and drug delivery systems.
A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
This richly illustrated book presents the objectives of, and the latest techniques for, the identifiability analysis and standard and robust regression analysis of complex dynamical models. The book first provides a definition of complexity in dynamic systems by introducing readers to the concepts of system size, density of interactions, stiff dynamics, and hybrid nature of determination. In turn, it presents the mathematical foundations of and algorithmic procedures for model structural and practical identifiability analysis, multilinear and non-linear regression analysis, and best predictor selection. Although the main fields of application discussed in the book are biochemistry and systems biology, the methodologies described can also be employed in other disciplines such as physics and the environmental sciences. Readers will learn how to deal with problems such as determining the identifiability conditions, searching for an identifiable model, and conducting their own regression analysis and diagnostics without supervision. Featuring a wealth of real-world examples, exercises, and codes in R, the book addresses the needs of doctoral students and researchers in bioinformatics, bioengineering, systems biology, biophysics, biochemistry, the environmental sciences and experimental physics. Readers should be familiar with the fundamentals of probability and statistics (as provided in first-year university courses) and a basic grasp of R.
Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.