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Developing bioinformatics computer skills : an introduction to software tools for biological applications
Authors: ---
ISBN: 1565926641 9781565926646 Year: 2001 Publisher: Beijing : Cambridge : O'Reilly,

Algorithms on strings, trees, and sequences
Author:
ISBN: 1107192145 1139811487 0511574932 1139811738 0511969651 1283870797 1139811606 9781139811736 9780511574931 0521585198 9780521585194 9781107192140 9781139811484 9780511969652 9781283870795 9781139811606 Year: 1997 Publisher: Cambridge [England] New York Cambridge University Press

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String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This 1997 book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.


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Networks : an introduction
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ISBN: 9780199206650 0199206651 Year: 2010 Publisher: Oxford : Oxford University Press,

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"The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availability of inexpensive computers have made it possible to gather and analyze network data on a large scale, and the development of a variety of new theoretical tools has allowed us to extract new knowledge from many different kinds of networks. The study of networks is broadly interdisciplinary and important developments have occurred in many fields, including mathematics, physics, computer and information sciences, biology, and the social sciences. This book brings together for the first time the most important breakthroughs in each of these fields and presents them in a coherent fashion, highlighting the strong interconnections between work in different areas. Subjects covered include the measurement and structure of networks in many branches of science, methods for analyzing network data, including methods developed in physics, statistics, and sociology, the fundamentals of graph theory, computer algorithms, and spectral methods, mathematical models of networks, including random graph models and generative models, and theories of dynamical processes taking place on networks"--

Introductory Statistics with R
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ISBN: 0387954759 9780387954752 9786610009749 1280009748 038722632X Year: 2002 Publisher: New York : Springer,

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"This books provides an elementary-level introduction to R, targeting both non-statistician scientists in various fields and students of statistics."--Back cover.

Keywords

Statistics --- R (Computer program language) --- Statistique --- R (Langage de programmation) --- Data processing --- Informatique --- R (Computer program language). --- Data processing. --- Programming --- Mathematical statistics --- #SBIB:303H4 --- 681.3*G3 --- 519.2 --- -R (Computer program language) --- -519.5 --- GNU-S (Computer program language) --- Domain-specific programming languages --- 519.2 Probability. Mathematical statistics --- Probability. Mathematical statistics --- 681.3*G3 Probability and statistics: probabilistic algorithms (including Monte Carlo)random number generation statistical computing statistical software (Mathematics of computing) --- Probability and statistics: probabilistic algorithms (including Monte Carlo)random number generation statistical computing statistical software (Mathematics of computing) --- Statistical analysis --- Statistical data --- Statistical methods --- Statistical science --- Mathematics --- Econometrics --- Informatica in de sociale wetenschappen --- EPUB-LIV-FT SPRINGER-B --- Mathematics. --- Bioinformatics. --- Computational biology. --- Probabilities. --- Statistics. --- Probability Theory and Stochastic Processes. --- Statistics and Computing/Statistics Programs. --- Computer Appl. in Life Sciences. --- 519.5 --- 681.3*G3 Probability and statistics: probabilistic algorithms (including Monte Carlo);random number generation; statistical computing; statistical software (Mathematics of computing) --- Probability and statistics: probabilistic algorithms (including Monte Carlo);random number generation; statistical computing; statistical software (Mathematics of computing) --- Distribution (Probability theory. --- Mathematical statistics. --- Biology --- Statistics . --- Bioinformatics . --- Computational biology . --- Bioinformatics --- Bio-informatics --- Biological informatics --- Information science --- Computational biology --- Systems biology --- Probability --- Statistical inference --- Combinations --- Chance --- Least squares --- Risk --- Statistics - Data processing --- Estadística $xInformática --- R (Lenguaje de programación) --- Estadística matemática

Structured population models in biology and epidemiology
Authors: --- ---
ISBN: 9783540782728 3540782729 3540782737 Year: 2008 Publisher: Berlin : Springer,

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This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

Tutorials in mathematical biosciences IV : evolution and ecology.
Authors: --- ---
ISBN: 9783540743286 9783540238584 9783540254393 9783540291626 3540238581 3540254390 3540291628 3540743286 3540315446 3540314385 3540743316 3540324151 Year: 2008 Volume: 1867 Publisher: Berlin Springer

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This volume introduces some basic mathematical models for cell cycle, proliferation, cancer, and cancer therapy. Chapter 1 gives an overview of the modeling of the cell division cycle. Chapter 2 describes how tumor secretes growth factors to form new blood vessels in its vicinity, which provide it with nutrients it needs in order to grow. Chapter 3 explores the process that enables the tumor to invade the neighboring tissue. Chapter 4 models the interaction between a tumor and the immune system. Chapter 5 is concerned with chemotherapy; it uses concepts from control theory to minimize obstacles arising from drug resistance and from cell cycle dynamics. Finally, Chapter 6 reviews mathematical results for various cancer models.

Keywords

51-7 --- 51:37 --- 51:37 Mathematics-:-Opvoeding en onderwijs --(algemeen) --- Mathematics-:-Opvoeding en onderwijs --(algemeen) --- 51-7 Mathematical studies and methods in other sciences. Scientific mathematics. Actuarial mathematics. Biometrics. Econometrics etc. --- Mathematical studies and methods in other sciences. Scientific mathematics. Actuarial mathematics. Biometrics. Econometrics etc. --- Neurosciences informatiques --- Differential Equations. --- Mathematical Biology in General. --- Ordinary Differential Equations. --- Computational Mathematics and Numerical Analysis. --- Computer Appl. in Life Sciences. --- Models, Neurological --- Nerve Net --- Mathematical Modeling and Industrial Mathematics. --- Muscle Contraction --- Musculoskeletal Physiological Processes --- Musculoskeletal Physiological Phenomena --- Experimental Model --- Experimental Models --- Mathematical Model --- Model, Experimental --- Models (Theoretical) --- Models, Experimental --- Models, Theoretic --- Theoretical Study --- Mathematical Models --- Model (Theoretical) --- Model, Mathematical --- Model, Theoretical --- Studies, Theoretical --- Study, Theoretical --- Theoretical Model --- Theoretical Models --- Theoretical Studies --- Nervous Systems --- System, Nervous --- Systems, Nervous --- Computer mathematics --- Metabolic Phenomenon --- Metabolic Process --- Metabolism Concepts --- Metabolism Phenomena --- Process, Metabolic --- Processes, Metabolic --- Anabolism --- Catabolism --- Metabolic Concepts --- Metabolic Processes --- Concept, Metabolic --- Concept, Metabolism --- Concepts, Metabolic --- Concepts, Metabolism --- Metabolic Concept --- Metabolism Concept --- Phenomena, Metabolic --- Phenomena, Metabolism --- Phenomenon, Metabolic --- Musculoskeletal Physiologic Process --- Musculoskeletal Physiological Concepts --- Musculoskeletal Physiological Phenomenon --- Physiology, Musculoskeletal --- Musculoskeletal Physiologic Processes --- Musculoskeletal Physiological Process --- Musculoskeletal Physiology --- Concept, Musculoskeletal Physiological --- Concepts, Musculoskeletal Physiological --- Musculoskeletal Physiological Concept --- Phenomena, Musculoskeletal Physiological --- Phenomenon, Musculoskeletal Physiological --- Physiologic Process, Musculoskeletal --- Physiologic Processes, Musculoskeletal --- Process, Musculoskeletal Physiologic --- Process, Musculoskeletal Physiological --- Processes, Musculoskeletal Physiologic --- Processes, Musculoskeletal Physiological --- Active Ion Transport --- Facilitated Ion Transport --- Passive Ion Transport --- Antiport --- Ion Cotransport --- Ion Exchange, Intracellular --- Symport --- Uniport --- Cotransport, Ion --- Exchange, Intracellular Ion --- Intracellular Ion Exchange --- Ion Transport, Active --- Ion Transport, Facilitated --- Ion Transport, Passive --- Transport, Active Ion --- Transport, Ion --- Second Messengers --- Intracellular Second Messengers --- Intracellular Second Messenger --- Messenger, Second --- Messengers, Intracellular Second --- Messengers, Second --- Second Messenger --- Second Messenger System --- Second Messenger, Intracellular --- Second Messengers, Intracellular --- System, Second Messenger --- Systems, Second Messenger --- Calcium Puffs --- Calcium Sparks --- Calcium Spikes --- Calcium Oscillations --- Calcium Waves --- Calcium Oscillation --- Calcium Puff --- Calcium Signalings --- Calcium Spark --- Calcium Spike --- Calcium Wave --- Oscillation, Calcium --- Oscillations, Calcium --- Puff, Calcium --- Puffs, Calcium --- Signaling, Calcium --- Signalings, Calcium --- Spark, Calcium --- Sparks, Calcium --- Spike, Calcium --- Spikes, Calcium --- Wave, Calcium --- Waves, Calcium --- Muscular Contraction --- Inotropism --- Contraction, Muscle --- Contraction, Muscular --- Contractions, Muscle --- Contractions, Muscular --- Inotropisms --- Muscle Contractions --- Muscular Contractions --- Calculus of Variations and Optimal Control; Optimization. --- Physiological, Cellular and Medical Topics. --- Cell Cycle --- Processes, Cell Growth --- Cell Division Cycle --- Cell Cycles --- Cell Division Cycles --- Cycle, Cell --- Cycle, Cell Division --- Cycles, Cell --- Cycles, Cell Division --- Division Cycle, Cell --- Division Cycles, Cell --- Cell Multiplication --- Cell Number Growth --- Cell Growth in Number --- Cellular Proliferation --- Growth, Cell Number --- Multiplication, Cell --- Number Growth, Cell --- Proliferation, Cell --- Proliferation, Cellular --- Mathematics. --- Cell biology. --- Mathematical models. --- Biomathematics. --- Mathematical and Computational Biology. --- Cell Biology. --- Differential equations. --- Partial differential equations. --- Calculus of variations. --- Partial Differential Equations. --- Bioinformatics. --- Computational biology. --- Neurobiology. --- Computer mathematics. --- Ecology --- Evolution (Biology) --- Phylogeny --- Population genetics --- Animal phylogeny --- Animals --- Phylogenetics --- Phylogeny (Zoology) --- Biology --- Mathematical models --- Mathematical studies and methods in other sciences. Scientific mathematics. Actuarial mathematics. Biometrics. Econometrics etc --- Math --- Science --- Mathematics --- Models, Mathematical --- Simulation methods --- Cell biology --- Cellular biology --- Cells --- Cytologists --- Neurosciences --- Discrete mathematics --- Electronic data processing --- Partial differential equations --- 517.91 Differential equations --- Differential equations --- Bioinformatics --- Bio-informatics --- Biological informatics --- Information science --- Computational biology --- Systems biology --- Data processing --- Isoperimetrical problems --- Variations, Calculus of --- Maxima and minima --- Cellular signal transduction. --- Calcium --- Physiological effect. --- Computational neuroscience. --- Differential equations, partial. --- Mathematical optimization. --- Physiology --- Computer science --- Data processing. --- Cytology. --- Animal physiology --- Anatomy --- Optimization (Mathematics) --- Optimization techniques --- Optimization theory --- Systems optimization --- Mathematical analysis --- Operations research --- System analysis --- Cell proliferation. --- Cell cycle. --- Cancer cells. --- Pathology, Cellular --- Mitotic cycle --- Nuclear cycle (Cytology) --- Biological rhythms --- Cell renewal --- Cellular proliferation --- Cell cycle --- Cell division --- Cell populations --- Growth --- Neural circuitry --- Auditory pathways. --- Cellular signal transduction --- Physiological transport --- Physiological effect --- Metabolism --- Bioinformatics . --- Computational biology . --- Calcium - Physiological effect.

Interactive and Dynamic Graphics for Data Analysis : with R and GGobi
Authors: --- ---
ISBN: 9780387717616 0387717617 9786611067069 1281067067 0387717625 Year: 2007 Publisher: New York : Springer Verlag,

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This richly illustrated book describes the use of interactive and dynamic graphics as part of multidimensional data analysis. Chapters include clustering, supervised classification, and working with missing values. A variety of plots and interaction methods are used in each analysis, often starting with brushing linked low-dimensional views and working up to manual manipulation of tours of several variables. The role of graphical methods is shown at each step of the analysis, not only in the early exploratory phase, but in the later stages, too, when comparing and evaluating models. All examples are based on freely available software: GGobi for interactive graphics and R for static graphics, modeling, and programming. The printed book is augmented by a wealth of material on the web, encouraging readers follow the examples themselves. The web site has all the data and code necessary to reproduce the analyses in the book, along with movies demonstrating the examples. The book may be used as a text in a class on statistical graphics or exploratory data analysis, for example, or as a guide for the independent learner. Each chapter ends with a set of exercises. The authors are both Fellows of the American Statistical Association, past chairs of the Section on Statistical Graphics, and co-authors of the GGobi software. Dianne Cook is Professor of Statistics at Iowa State University. Deborah Swayne is a member of the Statistics Research Department at AT&T Labs.

Keywords

Programming --- Artificial intelligence. Robotics. Simulation. Graphics --- Mathematical statistics --- Statistics --- Visualization --- Computer graphics --- R (Computer program language) --- Statistique --- Visualisation --- Infographie --- R (Langage de programmation) --- Graphic methods --- Congresses --- Méthodes graphiques --- Congrès --- Computer graphics. --- Graphic methods. --- Mathematical statistics -- Graphic methods. --- R (Computer program language). --- Statistics -- Graphic methods. --- Statistics --Graphic methods. --- Visualization -- Congresses. --- Visualization --Congresses. --- Mathematics --- Physical Sciences & Mathematics --- Mathematical Statistics --- -Visualization --- -R (Computer program language) --- 006.6 --- GNU-S (Computer program language) --- Domain-specific programming languages --- Imagery (Psychology) --- Imagination --- Visual perception --- Statistical analysis --- Statistical data --- Statistical methods --- Statistical science --- Econometrics --- Automatic drafting --- Graphic data processing --- Graphics, Computer --- Computer art --- Graphic arts --- Electronic data processing --- Engineering graphics --- Image processing --- Graphics --- Graphs --- Geometrical drawing --- Least squares --- Mechanical drawing --- Digital techniques --- Diagrams, Statistical --- Statistical diagrams --- Mathematical statistics. --- Data mining. --- Bioinformatics. --- Visualization. --- Statistical Theory and Methods. --- Statistics and Computing/Statistics Programs. --- Data Mining and Knowledge Discovery. --- Curve fitting --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Algorithmic knowledge discovery --- Factual data analysis --- KDD (Information retrieval) --- Knowledge discovery in data --- Knowledge discovery in databases --- Mining, Data --- Database searching --- Statistical inference --- Statistics, Mathematical --- Probabilities --- Sampling (Statistics) --- Data processing --- Statistics . --- Mathematics. --- Math --- Science

Geometric numerical integration : structure-preserving algorithms for ordinary differential equations
Authors: --- ---
ISBN: 3540430032 366205020X 3662050188 Year: 2002 Publisher: Berlin : Springer,

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The subject of this book is numerical methods that preserve geometric properties of the flow of a differential equation: symplectic integrators for Hamiltonian systems, symmetric integrators for reversible systems, methods preserving first integrals and numerical methods on manifolds, including Lie group methods and integrators for constrained mechanical systems, and methods for problems with highly oscillatory solutions. A complete theory of symplectic and symmetric Runge-Kutta, composition, splitting, multistep and various specially designed integrators is presented, and their construction and practical merits are discussed. The long-time behaviour of the numerical solutions is studied using a backward error analysis (modified equations) combined with KAM theory and related perturbation theories. The book is illustrated by many figures, it treats applications from physics and astronomy and contains many numerical experiments and comparisons of different approaches.

Keywords

519.62 --- 681.3*G17 --- Numerical methods for solution of ordinary differential equations --- Ordinary differential equations: boundary value problems; convergence and stability; error analysis; initial value problems; multistep methods; single step methods; stiff equations (Numerical analysis) --- Differential equations --- Hamiltonian systems. --- Numerical integration. --- Numerical solutions. --- 681.3*G17 Ordinary differential equations: boundary value problems; convergence and stability; error analysis; initial value problems; multistep methods; single step methods; stiff equations (Numerical analysis) --- 519.62 Numerical methods for solution of ordinary differential equations --- Hamiltonian systems --- Numerical integration --- Integration, Numerical --- Mechanical quadrature --- Quadrature, Mechanical --- Definite integrals --- Interpolation --- Numerical analysis --- Hamiltonian dynamical systems --- Systems, Hamiltonian --- Differentiable dynamical systems --- 517.91 Differential equations --- Numerical solutions --- 517.91 --- Dynamique différentiable. --- Systèmes hamiltoniens. --- Differentiable dynamical systems. --- Numerical analysis. --- Mathematical analysis. --- Analysis (Mathematics). --- Mathematical physics. --- Physics. --- Biomathematics. --- Numerical Analysis. --- Analysis. --- Theoretical, Mathematical and Computational Physics. --- Mathematical Methods in Physics. --- Numerical and Computational Physics, Simulation. --- Mathematical and Computational Biology. --- Biology --- Mathematics --- Natural philosophy --- Philosophy, Natural --- Physical sciences --- Dynamics --- Physical mathematics --- Physics --- 517.1 Mathematical analysis --- Mathematical analysis --- Numerical solutions&delete& --- Systèmes hamiltoniens --- Integration numerique --- Analyse numerique --- Equations differentielles

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