The Dynamics of Life (The book + Solutions to exercises + Data sets)
The Dynamics of Life
Modelling biological systems with R
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.
About the Author
Packages
The Book
PDF
EPUB
WEB
English
The book + Solutions to exercises + Data sets
Together 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.
Includes:
Datasets and scripts to exercises
Once 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.
PDF
EPUB
WEB
English
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.
Includes:
Datasets and scripts to exercises
Once 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.
PDF
EPUB
WEB
English
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
- Notes
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