The Dynamics of Life
Modelling biological systems with R
Understanding the dynamics of biological systems is becoming indispensable knowledge for biologists. The Dynamics of Life will help you to get a grasp of the fundamentals, and it will show you how to use and develop these aspects with the programming language R.
About
About the Book
Most biological systems are complex. To understand them, we must link and integrate the biological mechanisms that we learn from reductionist science into mathematical model describing how the systems work. This book is developed as a tutorial that will help you to understand and perform this process.
It will show you why you should understand dynamic processes by discussing examples of biological systems ranging from enzyme dynamics to ecology and epidemiology. It will introduce you to the fundamental questions about the dynamics of systems by discussing equilibrium and stability, and the emergence of bistable switches and complex patterns, and you will learn how to measure the parameters of dynamic systems. You will not only understand the theoretical basis of these aspects, but learn to program them with R, a software package that is becoming the standard in academic research.
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All packages include the ebook in the following formats: PDF, EPUB, and Web
The Book
Minimum price
Suggested price$25.00$15.00
The book + Solutions to exercises + Data sets
Minimum price
Suggested price$30.00Together with the book I supply possible solutions (R-code) for all of the exercises and text files of the data used in the chapter on parameter estimation and in the exercises.
$20.00
- Datasets and scripts to exercisesOnce the attachments are unzipped, you'll be able to access each dataset used in the book as a text file, and scripts for the exercises within the text and in the appendix as .R-files.
This book is also available in the following packages:
Solutions to exercises and datasets
The book plus scripts for all of the exercises and the datasets as text files, so in a format that can be read by R.
- Datasets and scripts to exercisesOnce the attachments are unzipped, you'll be able to access each dataset used in the book as a text file, and scripts for the exercises within the text and in the appendix as .R-files.
- Minimum price
- $20.00
- Suggested price
- $30.00
- Datasets and scripts to exercises
Author
About the Author
Jacob C. Koella
Jacob Koella is a professor of evolutionary biology and parasitology at the University of Neuchatel in Switzerland.
With the equivalent of Master's degree in mechanical engineering (specialising in systems dynamics), a Phd in evolutionary ecology and several years experience working on the epidemiology of malaria in Tanzania, he conducts a considerable part of his research on mathematical theory combining the epidemiology and evolutionary ecology of parasites.
He teaches courses on mathematical modelling, parasitology and evolutionary ecology at the University of Neuchatel and at the ETH Zurich.
Contents
Table of Contents
Introduction
The basics of dynamic models
- Modelling is book-keeping
- Book-keeping in continuous time
- A general model: the bathtub
- Models with several variables: an oscillator
- Summary
A first model of biological dynamics
- Enzyme dynamics
- Summary
Steady states and stability of dynamic systems
- One equation
- More than one equation
- A second example: stability of enzyme kinetics
- Periodic forcing
- Summary
Spatial dynamics: synchronisation and pattern formation
- Synchronisation of a predator-prey system
- Pattern formation
- Summary
Bistability and catastrophe
- Development of Xenopus oocytes
- Bistability in bacterial infections
- Spruce-budworm dynamics
- Summary
Estimation of parameters
- Parameters of logistic growth
- Parameters of a flu epidemic
- Pitfalls
- Summary
- Data sets
Appendix 1: Using R
- Installing R and an R interface
- Getting started: R as a calculator
- What if we want to store the results of our calculations?
- Object types
- Vectors
- Matrices
- Data frames
- Control structures
- Functions
- Simple plots
Appendix 2: Exercises
- Basics of dynamics models
- First models of biological systems
- Equilibrium and stability
- Spatial dynamics
- Bistability
- Parameter estimation
- Appendix 1: Using R
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