Matlab Simulators from SYSTEMS BIOLOGY: Simulation of Dynamic Network States

PART I: Simulation of Dynamic States

Chapter 3

Section 3.4 Example 3.4 ODE Example 3.4 Sim

Chapter 4

Section 4.2 Example 4.2 ODE Example 4.2 Sim

Section 4.3 Example 4.3 ODE Example 4.3 Sim

Section 4.4 Example 4.4 ODE Example 4.4 Sim

Section 4.5 Example 4.5 ODE Example 4.5 Sim

PART III: Metabolism

Chapter 10 Glycolysis Simulator

Chapter 11 Glycolysis PPP Simulator

Chapter 12 Glycolysis PPP AMP Salvage Simulator

To use

Place all three files (ODE, Sim, and Model) into one folder. The ODE .m file contains the differential equations for simulation. The model .mat file contains all the information on the parameters for the model. The Sim .m file is the script that loads the two and runs the ODE solver. Perturbations and changes are typically made in the Sim .m file.