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Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology

Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology
  • Author : Paola Lecca,Ian Laurenzi,Ferenc Jordan
  • Publisher :Unknown
  • Release Date :2013-04-09
  • Total pages :390
  • ISBN : 9781908818218
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Summary : Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics. Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples Presents recently developed discrete stochastic formalisms for modelling biological systems and processes Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics

Synthetic Biology - a Primer (revised Edition)

Synthetic Biology - a Primer (revised Edition)
  • Author : Paul S. FREEMONT,Richard I. KITNEY
  • Publisher :Unknown
  • Release Date :2015-08-24
  • Total pages :196
  • ISBN : 9781783268801
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Summary :

Identifiability and Regression Analysis of Biological Systems Models

Identifiability and Regression Analysis of Biological Systems Models
  • Author : Paola Lecca
  • Publisher :Unknown
  • Release Date :2020-03-05
  • Total pages :82
  • ISBN : 9783030412555
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Summary : 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.

Theoretical Physics for Biological Systems

Theoretical Physics for Biological Systems
  • Author : Paola Lecca,Angela Re
  • Publisher :Unknown
  • Release Date :2019-01-30
  • Total pages :146
  • ISBN : 9781351374323
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Summary : Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.

Stochastic Modelling for Systems Biology, Third Edition

Stochastic Modelling for Systems Biology, Third Edition
  • Author : Darren J. Wilkinson
  • Publisher :Unknown
  • Release Date :2018-12-07
  • Total pages :384
  • ISBN : 9781351000901
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Summary : Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Dynamic Systems Biology Modeling and Simulation

Dynamic Systems Biology Modeling and Simulation
  • Author : Joseph DiStefano III
  • Publisher :Unknown
  • Release Date :2015-01-10
  • Total pages :884
  • ISBN : 9780124104938
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Summary : Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author’s own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics; PLUS ....... The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of “math modeling” with life sciences. Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization. Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models. A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course. Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content. The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: [email protected]

Introduction to Modeling and Simulation with MATLAB® and Python

Introduction to Modeling and Simulation with MATLAB® and Python
  • Author : Steven I. Gordon,Brian Guilfoos
  • Publisher :Unknown
  • Release Date :2017-07-12
  • Total pages :192
  • ISBN : 9781498773881
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Summary : Introduction to Modeling and Simulation with MATLAB and Python is intended for students and professionals in science, social science, and engineering that wish to learn the principles of computer modeling, as well as basic programming skills. The book content focuses on meeting a set of basic modeling and simulation competencies that were developed as part of several National Science Foundation grants. Even though computer science students are much more expert programmers, they are not often given the opportunity to see how those skills are being applied to solve complex science and engineering problems and may also not be aware of the libraries used by scientists to create those models. The book interleaves chapters on modeling concepts and related exercises with programming concepts and exercises. The authors start with an introduction to modeling and its importance to current practices in the sciences and engineering. They introduce each of the programming environments and the syntax used to represent variables and compute mathematical equations and functions. As students gain more programming expertise, the authors return to modeling concepts, providing starting code for a variety of exercises where students add additional code to solve the problem and provide an analysis of the outcomes. In this way, the book builds both modeling and programming expertise with a "just-in-time" approach so that by the end of the book, students can take on relatively simple modeling example on their own. Each chapter is supplemented with references to additional reading, tutorials, and exercises that guide students to additional help and allows them to practice both their programming and analytical modeling skills. In addition, each of the programming related chapters is divided into two parts – one for MATLAB and one for Python. In these chapters, the authors also refer to additional online tutorials that students can use if they are having difficulty with any of the topics. The book culminates with a set of final project exercise suggestions that incorporate both the modeling and programming skills provided in the rest of the volume. Those projects could be undertaken by individuals or small groups of students. The companion website at http://www.intromodeling.com provides updates to instructions when there are substantial changes in software versions, as well as electronic copies of exercises and the related code. The website also offers a space where people can suggest additional projects they are willing to share as well as comments on the existing projects and exercises throughout the book. Solutions and lecture notes will also be available for qualifying instructors.

Stochastic Modelling of Reaction-Diffusion Processes

Stochastic Modelling of Reaction-Diffusion Processes
  • Author : Radek Erban,S. Jonathan Chapman
  • Publisher :Unknown
  • Release Date :2019-12-31
  • Total pages :318
  • ISBN : 9781108498128
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Summary : Practical introduction for advanced undergraduate or beginning graduate students of applied mathematics, developed at the University of Oxford.

Foundations of Theoretical Approaches in Systems Biology

Foundations of Theoretical Approaches in Systems Biology
  • Author : Alberto Marin-Sanguino,Julio Vera,Rui Alves
  • Publisher :Unknown
  • Release Date :2019-01-11
  • Total pages :229
  • ISBN : 9782889456833
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Summary : If biology in the 20th century was characterized by an explosion of new technologies and experimental methods, that of the 21st has seen an equally exuberant proliferation of mathematical and computational methods that attempt to systematize and explain the abundance of available data. As we live through the consolidation of a new paradigm where experimental data goes hand in hand with computational analysis, we contemplate the challenge of fusing these two aspects of the new biology into a consistent theoretical framework. Whether systems biology will survive as a field or be washed away by the tides of future fads will ultimately depend on its success to achieve this type of synthesis. The famous quote attributed to Kurt Lewin comes to mind: "there is nothing more practical than a good theory". This book presents a wide assortment of articles on systems biology in an attempt to capture the variety of current methods in systems biology and show how they can help to find answers to the challenges of modern biology.

Computational Systems Biology

Computational Systems Biology
  • Author : Andres Kriete,Roland Eils
  • Publisher :Unknown
  • Release Date :2013-11-26
  • Total pages :548
  • ISBN : 9780124059382
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Summary : This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

Control Theory and Systems Biology

Control Theory and Systems Biology
  • Author : Pablo A. Iglesias,Brian P. Ingalls
  • Publisher :Unknown
  • Release Date :2010
  • Total pages :345
  • ISBN : 9780262013345
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Summary : A survey of how engineering techniques from control and systems theory can be used tohelp biologists understand the behavior of cellular systems.

Protein Folding in Silico

Protein Folding in Silico
  • Author : Irena Roterman-Konieczna
  • Publisher :Unknown
  • Release Date :2012-10-04
  • Total pages :240
  • ISBN : 9781908818256
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Summary : Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory

Allergens and Respiratory Pollutants

Allergens and Respiratory Pollutants
  • Author : Marc A. Williams
  • Publisher :Unknown
  • Release Date :2011-07-18
  • Total pages :312
  • ISBN : 9781908818065
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Summary : Allergens and respiratory pollutants is a collection of 12 authoritative papers that draws upon the collective expertise of world leaders in the fields of innate immunity, immunotoxicology and pulmonary biology. The book critically explores the biological and immunological mechanisms that contribute to immune dysfunction on exposure to allergens and the susceptibility to infectious disease on exposure to ambient pollutants. The clinical relevance of exposure to ambient airborne xenobiotics is critically discussed and collectively, this book provides an educational forum that links the health effects of environmental exposures, immune dysfunction and inflammatory airways disease. Discusses recent advances in our understanding of cell-mediated innate immune mechanisms that occur during allergic inflammation and provides important timely coverage of diseases of concern and how such diseases are influenced by a dysfunctional immune system Provides useful information on linking environmental 'danger signals' that provoke immune dysfunction and exacerbation of existing disease Draws upon the collective expertise of an international college of leaders in the field, but also provides chapters that provide essential reference material

Annotating New Genes

Annotating New Genes
  • Author : Shizuka Uchida
  • Publisher :Unknown
  • Release Date :2012-08-06
  • Total pages :196
  • ISBN : 9781908818126
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Summary : In recent years, a number of academic and commercial software packages and databases have been developed for the analysis and screening of biological data; however, the usability of these data is compromised by so-called novel genes to which no biological function is assigned. Annotating new genes outlines an approach to the analysis of evolutionary-conserved, heart-enriched genes with unknown functions, offering a step-by-step description of the procedure from screening to validation. The book begins by offering an introduction to the databases and software available, before moving on to cover programming guidelines, including a specific case study on the use of C-It for in silico screening. The second half of the book offers a step-by-step guide to experimental validation concepts and procedures, as well as an overview of additional potential applications of this approach in the field of stem cells and tissue regeneration, before a concluding chapter summarises the concepts and theories presented. Focuses not only on screening but also on biological validations Provides details of databases and software (web interface) products for biologists with minimal computation skills Offers a step-by-step outline of the procedure involved

Computer-Aided Vaccine Design

Computer-Aided Vaccine Design
  • Author : Joo Chuan Tong,Shoba Ranganathan
  • Publisher :Unknown
  • Release Date :2013-07-31
  • Total pages :164
  • ISBN : 9781908818416
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Summary : Computational pre-screening of antigens is now routinely applied to the discovery of vaccine candidates. Computer-aided vaccine design is a comprehensive introduction to this exciting field of study. The book is intended to be a textbook for researchers and for courses in bioinformatics, as well as a laboratory reference guide. It is written mainly for biologists who want to understand the current methods of computer-aided vaccine design. The contents are designed to help biologists appreciate the underlying concepts and algorithms used, as well as limitations of the methods and strategies for their use. Chapters include: MHC and T cell responses; Immunoglobulins and B cell responses; Scientific publications and databases; Database design; Computational T cell vaccine design; Computational B cell vaccine design; infectious disease informatics; Vaccine safety and quality assessments; and Vaccine adjuvant informatics. Essential reading for any biologist who wants to understand methods of computer-aided vaccine design Description of available data sources and publicly available software, with detailed analysis of strengths and weaknesses Theoretical concepts and practical examples of database design and development for a virtual screening campaign

Orphan Drugs

Orphan Drugs
  • Author : Elizabeth Hernberg-Ståhl,Miroslav Reljanović
  • Publisher :Unknown
  • Release Date :2013-11-15
  • Total pages :334
  • ISBN : 9781908818393
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Summary : This authoritative and comprehensive book makes the reader familiar with the processes of bringing orphan drugs to the global market. There are between 5,000 and 7,000 rare diseases and the number of patients suffering from them is estimated to be more than 50 million in the US and Europe. Before the orphan drug legislation enacted in the US in 1983, there was a limited interest from industry to develop treatment for very small patient groups. One of the difficulties is, of course, that similar levels of investment are needed from a pharmaceutical company to bring a drug to the market for both small and large patient groups. The journey from application of an orphan drug designation to a reimbursed market- approved drug is long and many obstacles occur during the journey. After reading the book, readers will: Understand who the players/stakeholders are in the rare orphan disease field and their specific needs and concerns: patients and patient organizations, researchers and treating physicians within the field, industry, regulatory and reimbursement bodies* Understand the strong partnership between the different players and the various initiatives to improve and increase access to treatment for patients; minimizing the gap between numbers of known diseases, orphan designations, approved drugs and paid drugs. The book also provides short practical case stories from patients and researchers, as well as representatives from industry and authorities on the challenges they came across in developing orphan drugs or getting access to orphan drugs. A comprehensive overview of strategy, key activities and considerations of how to bring an orphan drug from concept to the market and make it available to patients A source of updated information, news and trends for those who are already active in this fast-evolving field Covers the global definitions and the criteria for getting an orphan drug designation in, for example, the US and Europe

Bioinformatics for Biomedical Science and Clinical Applications

Bioinformatics for Biomedical Science and Clinical Applications
  • Author : K-H Liang
  • Publisher :Unknown
  • Release Date :2013-07-31
  • Total pages :170
  • ISBN : 9781908818232
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Summary : Contemporary biomedical and clinical research is undergoing constant development thanks to the rapid advancement of various high throughput technologies at the DNA, RNA and protein levels. These technologies can generate vast amounts of raw data, making bioinformatics methodologies essential in their use for basic biomedical and clinical applications. Bioinformatics for biomedical science and clinical applications demonstrates what these cutting-edge technologies can do and examines how to design an appropriate study, including how to deal with data and address specific clinical questions. The first two chapters consider Bioinformatics and analysis of the human genome. The subsequent three chapters cover the introduction of Transcriptomics, Proteomics and Systems biomedical science. The remaining chapters move on to critical developments, clinical information and conclude with domain knowledge and adaptivity. A coherent presentation of concepts, methodologies and practical tools that systematically lead to significant discoveries in the biomedical and clinical area Real examples of cutting edge discoveries The introduction of study types and technologies for all the DNA, RNA and protein levels

Practical Leadership for Biopharmaceutical Executives

Practical Leadership for Biopharmaceutical Executives
  • Author : Jane Y Chin
  • Publisher :Unknown
  • Release Date :2011-05-05
  • Total pages :216
  • ISBN : 9781908818027
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Summary : The biohealthcare executive in upper-middle management confronts leadership challenges unique to their industry: they manage highly specialized knowledge workers and innovators, compete at the speed of technology, work in a highly regulated environment where "free speech" often does not apply due to patient safety and privacy concerns, and increasingly are leading virtual teams who may be located in different parts of the world. Practical leadership for biopharmaceutical executives is a guide that strips away the theory and meets head-on the practical leadership challenges these executives face on a daily basis, and provides these "innovator leaders" with the tools to lead effectively in the face of technological complexity. Focuses on personal leadership, where the executive has an opportunity to manage his/her own effectiveness as a leader and manager, and engage with their own career development and method of contribution within their chosen industry Discusses particularly the unique leadership challenges in biohealthcare: an industry that is at once highly innovative and emotive. Biohealthcare companies are often viewed with suspicion by the consumers who question corporate motives, and product marketing and sales practices. The effective biohealthcare leaders are well aware of these emotive features, and embody ethics through action - not just lip service Includes real life examples, including a series of both phone-based and email-based interviews of executives

Outsourcing Biopharma R&D to India

Outsourcing Biopharma R&D to India
  • Author : P R Chowdhury
  • Publisher :Unknown
  • Release Date :2011-05-05
  • Total pages :130
  • ISBN : 9781908818010
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Summary : The trend of outsourcing to India for research and development is catching on fast. Over the last decade, worldwide pharmaceutical and biotechnology companies have made India their choice for a research destination. Initially R&D was inclined more towards developing products for the Indian market within the country. This led to several multinational companies opening up production plants in India, primarily due to the globalization of the Indian economy and offshoring jobs to India. Alongside, several global pharma-biotech majors ascertained large market requirements within the country and capitalized on the advantage of serving Indian customers. Strategies were devised to optimize operational expenses with the setting up of on-site R&D to develop products for local requirements. In view of this, this book seeks to explore various nuances of the outsourcing sector with respect to biopharma in India. Constitutes the first ever comprehensive insight on the Indian biopharma sector Provides a perspective based on practical hands-on legal experience Simply structured, clearly presented and free from excessive legal jargon

Gene therapy

Gene therapy
  • Author : Surendra Nimesh
  • Publisher :Unknown
  • Release Date :2013-10-31
  • Total pages :380
  • ISBN : 9781908818645
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Summary : Gene therapy is emerging as a new class of therapeutics for the treatment of inherited and acquired diseases. However, poor cellular uptake and instability of DNA in the physiological milieu limits its therapeutic potential, hence a vector which can protect and efficiently transport DNA to the target cells must be developed. Nanotechnology-based non-viral vectors have been proposed as potential candidates. Various polymeric nanoparticles have been shown to be suitable, with high cellular uptake efficiencies and reduced cytotoxicity. These delivery vectors form condensed complexes with DNA which result in shielding against enzymatic degradation and enhanced cellular targeting. Advantages including easy manipulatibility, high stability, low cost and high payload, mean that nanoparticles from various polymers have been exploited. Gene therapy gives a systematic account of the many aspects of nanotechnology mediated gene therapy, from the preparation of nanoparticles to physicochemical characterization, and follows with applications in in vitro and in vivo models. This book emphasizes the various aspects of nanotechnology-based gene therapy, with initial chapters detailing the tools and techniques available for preparation and in vitro and in vivo characterization of nanoparticles. Later chapters provide exhaustive details on polymeric systems employed for gene therapy. Provides an overview of nanotechnology applications in gene therapy, from preparation of nanoparticles to in vitro and in vivo studies Details the tools and techniques available for preparation, characterization and in vitro and in vivo study of nanoparticles Details the limitations of nanoparticle-mediated gene therapy and proposes ways in which they may be overcome

Human Papillomavirus Infections

Human Papillomavirus Infections
  • Author : Fernando Cobo
  • Publisher :Unknown
  • Release Date :2012-07-27
  • Total pages :168
  • ISBN : 9781908818171
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Summary : Human papillomavirus (HPV) is one of the most common causes of sexually transmitted diseases worldwide, both in men and women. Human papillomavirus infections provides the scientific background needed to understand the natural history and pathogenesis of HPV infection and offers discussion of its clinical features, diagnosis, treatment and prevention. The book begins with chapters covering the epidemiology, virology, history and transmission of the infection, as well as its pathogenesis and clinical features. Following a discussion of the relationship between HPV and cancer, chapters in the second half of the book look at diagnosis, testing and treatment. The book concludes with detailed coverage of the prevention of HPV through worldwide vaccination programmes. Covers all the important issues relating to both male and female HPV infection Provides overview of the current knowledge about epidemiology, basic virology, pathogenesis and diagnosis methods Explores the relationship between HPV and cancer