2.1 Networks: the representation of a system at the basis of systems biology
2.2 Biochemical networks
2.2.1 Metabolic networks
2.2.2 Protein-protein interaction networks
2.2.3 Genetic regulatory networks
2.2.4 Neural networks
2.3 Phylogenetic networks
2.4 Signaling networks
2.5 Ecological networks
2.6 Challenges in computational network biology
3. Network inference for drug discovery
3.1 How network biology helps drug discovery
3.2 Computational methods
3.2.1 Classifier-based methods
3.2.2 Reverse-engineering methods
3.2.3 Integrating static and dynamic data: a promising venue
Part II
4. An introduction to differential and integral calculus
4.1 Derivative of a real function
4.2 Examples of derivatives
4.3 Geometric interpretation of the derivative
4.4 The algebra of derivatives
4.5 Definition of integral
4.6 Relation between integral and derivative
4.7 Methods of integration
4.7.1 Integration by parts
4.7.2 Integration by substitution
4.7.3 Integration by partial fraction decomposition
4.7.4 The reverse chain rule
4.7.5 Using combinations of methods
4.8 Ordinary differential equations
4.8.1 First-order linear equations
4.8.2 Initial value problems
4.9 Partial differential equations
4.10 Discretization of differential equations
4.10.1 The Implicit or Backward Euler Method
4.10.2 The Runge-Kutta Method
4.11 Systems of differential equations
5. Modelling chemical reactions
5.1 Modelling in systems biology
5.2 The different types of mathematical models
5.3 Chemical kinetics: From diagrams to mathematical equations
5.4 Kinetics of chemical reactions
5.4.1 The law of mass action
5.4.2 Example 1: The Lotka-Volterra System
5.4.3 Example 2: The Michaelis-Mentin Reactions
5.5 Conservation laws
5.6 Markov passes
5.7 The master equation
5.7.1 The chemical master equation
5.8 Molecular approach to chemical kinetics
5.8.1 Reactions are collisions
5.8.2 Reaction rate
5.8.3 Zeroth-, first, and second order reactions
5.8.4 Higher-order reactions
5.9 Fundamental hypothesis of stochastic chemical kinetics
5.10 The reaction probability density function
5.11 The stochastic simulation algorithms
5.11.1 Direct method
5.11.2 First Reaction Method
5.11.3 Next Reaction Method
5.12 Spatio-temporal simulation algorithms
5.13 Ordinary differential equation stochastic models: the Langevin equation
5.14 Hybrid algorithms
6. Reaction-diffusion systems
6.1 The physics of reaction-diffusion systems
6.2 Diffusion of non-charged molecules
6.2.1 Intrinsic viscosity and frictional coefficient
6.2.2. Calculated second virial coefficient
6.3 Algorithm and data structures
6.4 Drug release
6.4.1 The Higuchi model
6.4.2 Systems with different geometries
6.4.3 The power-law model
6.5 What drug dissolution is
6.6 The diffusion layer model (Noyes and Whitney)
6.7 The Weibull function in dissolution
6.7.1 Inhomogeneous conditions
6.7.2 Drug dissolution is a stochastic process
6.7.3 The inter-facial barrier model
6.7.4 Compartmental model
Part III
7. Linear Algebra Background
7.1 Matrices
7.1.1 Introduction
7.1.2 Special matrices
7.1.3 Operation on matrices
7.1.4 Transposition and symmetries
7.2 Linear systems
7.2.1 Introduction
7.2.2 Special linear systems
7.2.3 General linear systems
7.2.4 The Gaussian Elimination method
7.2.5 Gaussian elimination for rectangular systems
7.2.6 Consistency of linear systems
7.2.7 Homogeneous linear systems
7.2.8 Nonhomogeneous linear systems
7.3 Least-squares problems
7.4 Permutations and determinants
7.5 Eigenvalue problems
7.5.1 Introduction
7.5.2 Computing the eigenvalues and the eigenvectors
8. Regression
8.1 Regression as a geometric problem
8.1.1 Standard error on regression coefficients
8.2 Regression via maximum-likelihood estimation
8.3 Regression diagnostic
8.4 How to assess the goodness of the model
8.5 Other types of regression
8.6 Case study 1: Regression analysis of sweat secretion volumes in cystic fibrosis patients
8.6.1 The experiments
8.6.2 The multilinear model
8.6.3 Results
8.7 Nonlinear regression
8.8 Case study 2: inference of kinetic rate constants
8.8.1 Parameter space restriction
8.8.2 Variance of the estimated parameters
9. Cardiac electrophysiology
9.1 The bidomain model
9.2 Adaptive algorithms
9.3 Iterative methods for linear systems
9.4 Krylov subspace methods
9.5 Parallel implementation
References
Paola Lecca, Assistant Professor, Faculty of Engineering, Free University of Bozen-Bolzano, Italy
Bruno Carpentieri, Associate Professor, Faculty of Engineering, Free University of Bozen-Balzano, Italy
This introductory guide provides a thorough explanation of the mathematics and algorithms used in standard data analysis techniques within systems biology, biochemistry, and biophysics. Each part of the book covers the mathematical background and practical applications of a given technique. Readers will gain an understanding of the mathematical and algorithmic steps needed to use these software tools appropriately and effectively, as well how to assess their specific circumstance and choose the optimal method and technology. Ideal for students planning for a career in research, early-career researchers, and established scientists undertaking interdiscplinary research.