Mathematical Modeling in Systems Biology: code

Mathematical Modeling in Systems Biology: An Introduction
Brian Ingalls

Code for figures and selected end-of-chapter problems.

	MATLAB	XPPAUT	Python
Chapter 1
Figure 1.7	Collins_toggle_switch.m	Collins_toggle_switch.ode	Collins_toggle_switch.py
Figure 1.9	Hodgkin_Huxley.m	Hodgkin_Huxley.ode	Hodgkin_Huxley.py

Chapter 2
Figure 2.4	exponential_decay.m	------	exponential_decay.py
Figure 2.7	Eulers_method.m	Eulers_method.ode	Eulers_method.py
Figure 2.9	network_example.m	network_example.ode	network_example.py
Figure 2.11	rapid_equilibrium_approximation1.m	rapid_equilibrium_approximation1.ode	rapid_equilibrium_approximation1.py
Figure 2.12	rapid_equilibrium_approximation1.m	rapid_equilibrium_approximation1.ode	rapid_equilibrium_approximation1.py
Figure 2.13	rapid_equilibrium_approximation2.m	rapid_equilibrium_approximation2.ode	rapid_equilibrium_approximation2.py
Figure 2.14	quasi_steady_state_approximation.m	quasi_steady_state_approximation.ode	quasi_steady_state_approximation.py
Problem 2.4.6	problem2_4_6.m	problem2_4_6.ode	problem2_4_6.py

Chapter 3
Figure 3.3	Michaelis_Menten.m	Michaelis_Menten.ode	Michaelis_Menten.py
Figure 3.13	gma_approximations.m	------	gma_approximations.py
Problem 3.7.5	problem3_7_5.m	problem3_7_5.ode	problem3_7_5.py

Chapter 4
Figure 4.2	asymmetric_network.m	asymmetric_network.ode	asymmetric_network.py
Figure 4.3	asymmetric_network.m	asymmetric_network.ode	asymmetric_network.py
Figure 4.4A	asymmetric_network.m	asymmetric_network.ode	asymmetric_network.py
Figure 4.5	asymmetric_network.m	asymmetric_network.ode	asymmetric_network.py
Figure 4.7	symmetric_network.m	symmetric_network.ode	symmetric_network.py
Figure 4.8	symmetric_network.m	symmetric_network.ode	symmetric_network.py
Figure 4.9	symmetric_network.m	symmetric_network.ode	symmetric_network.py
Figure 4.11	potential_wells.m	------	potentialwells.m
Figure 4.13	surface_tangent.m	------	------
Figure 4.15	oscillatory_network.m	oscillatory_network.ode	oscillatory_network.py
Figure 4.16	oscillatory_network.m	oscillatory_network.ode	oscillatory_network.py
Figure 4.17	oscillatory_network.m	oscillatory_network.ode	oscillatory_network.py
Figure 4.18	------	asymmetric_network.ode	asymmetric_network.py
Figure 4.19	symmetric_network.m	symmetric_network.ode	symmetric_network.py
Figure 4.21	------	oscillatory_network.ode	oscillatory_network.py
Figure 4.22	local_sensitivity.m	------	local_sensitivity.py

Chapter 5
Figure 5.10	methionine_model.m	methionine_model.ode	methionine_model.py
Figure 5.11	methionine_model.m	methionine_model.ode	methionine_model.py
Figure 5.12	methionine_model.m	------	methionine_model.py
Problem 5.6.1	problem5_6_1.m	problem5_6_1.ode	problem5_6_1.py
Problem 5.6.2	problem5_6_2.m	problem5_6_2.ode	problem5_6_2.py
Problem 5.6.6	methionine_model.m	methionine_model.ode	methionine_model.py
Problem 5.6.7	arabidopsis_branch.m	arabidopsis_branch.ode	arabidopsis_branch.py

Chapter 6
Figure 6.3	two_component_pathway.m	two_component_pathway.ode	two_component_pathway.py
Figure 6.5	gprotein_pathway.m	gprotein_pathway.ode	gprotein_pathway.py
Figure 6.7	Goldbeter_Koshland_switch.m	------	Goldbeter_Koshland_switch.py
Figure 6.14	chemotaxis.m	chemotaxis.ode	chemotaxis.py
Figure 6.16	apoptosis.m	------	apoptosis.py
Figure 6.18	calcium_oscillations.m	calcium_oscillations.ode	calcium_oscillations.py
Figure 6.19	gprotein_sine_response.m	gprotein_sine_response.ode	gprotein_sine_response.py
Figure 6.20	gprotein_multi_sine_response.m	------	------
Figure 6.21	gprotein_bodeplots.m	------	------
Figure 6.22	resonant_system.m	------	------
Figure 6.23	frequency_filtering.m	------	------
Problem 6.8.8	mapk_pathway.m	mapk_pathway.ode	mapk_pathway.py
Problem 6.8.15	camp_signaling.m	camp_signaling.ode	camp_signaling.py

Chapter 7
Figure 7.7	lac_operon.m	lac_operon.ode	lac_operon.py
Figure 7.11	phage_lambda.m	phage_lambda.ode	phage_lambda.py
Figure 7.13	Collins_toggle_switch.m	Collins_toggle_switch.ode	Collins_toggle_switch.py
Figure 7.14A	Collins_toggle_switch.m	Collins_toggle_switch.ode	Collins_toggle_switch.py
Figure 7.14B	Collins_toggle_switch_induced.m	Collins_toggle_switch.ode	Collins_toggle_switch.py
Figure 7.15	Collins_toggle_switch.m	------	------
Figure 7.17	Goodwin_oscillator.m	Goodwin_oscillator.ode	Goodwin_oscillator.py
Figure 7.19	circadian_rhythm.m	circadian_rhythm.ode	circadian_rhythm.py
Figure 7.21	repressilator.m	repressilator.ode	repressilator.py
Figure 7.23	genetic_relaxation_oscillator.m	genetic_relaxation_oscillator.ode	genetic_relaxation_oscillator.py
Figure 7.25	quorum_sensing.m	------	quorum_sensing.py
Figure 7.28	pulse_generator.m	pulse_generator.ode	pulse_generator.py
Figure 7.30	band_detector.m	------	band_detector.py
Figure 7.31	synchronized_oscillators.m	synchronized_oscillators.ode	synchronized_oscillators.py
Figure 7.38	stochastic_decay.m	stochastic_decay.ode	stochastic_decay.py
Figure 7.40	chemical_master_equation_example.m	------	chemical_master_equation_example.py
Figure 7.41	chemical_master_equation_example.m	------	chemical_master_equation_example.py
Figure 7.45	stochastic_decay_ensemble.m	stochastic_decay.ode	stochastic_decay_ensemble.py
Figure 7.46	stochastic_gene_expression.m	stochastic_gene_expression.ode	stochastic_gene_expression.py
Figure 7.47	stochastic_brusselator.m	stochastic_brusselator.ode	stochastic_brusselator.py
Problem 7.8.15	NF-kB_signaling.m	NF-kB_signaling.ode	nfkb_signaling.py
Problem 7.8.19	synchronized_repressilators.m	synchronized_repressilators.ode	synchronized_repressilators.py
Problem 7.8.20 (a)	population_control.m	population_control.ode	population_control.py
Problem 7.8.20 (b)	predator_prey.m	predator_prey.ode	predator_prey.py
Problem 7.8.26	stochastic_toggle_switch.m	stochastic_toggle_switch.ode	stochastic_toggle_switch.py
Problem 7.8.27	stochastic_Vilar_oscillator.m deterministic_Vilar_oscillator.m	stochastic_Vilar_oscillator.ode deterministic_Vilar_oscillator.ode	stochastic_Vilar_oscillator.py deterministic_Vilar_oscillator.py

Chapter 8
Figure 8.3	passive_membrane.m	passive_membrane.ode	passive_membrane.py
Figure 8.6	Morris_Lecar.m	Morris_Lecar.ode	Morris_Lecar.py
Figure 8.7	Morris_Lecar.m	Morris_Lecar.ode	Morris_Lecar.py
Figure 8.9	Morris_Lecar_synapse.m	Morris_Lecar_synapse.ode	morris_lecar_synapse.py
Figure 8.11	linear_cable_equation.m	------	------
Figure 8.2	nonlinear_cable_equation.m	------	------
Problem 8.6.4	Hodgkin_Huxley.m	Hodgkin_Huxley.ode	Hodgkin_Huxley.py
Problem 8.6.10	morphogen_diffusion.m	------	------
Problem 8.6.11	Turing_pattern.m	------	------

Appendix C
	------	chain1.ode	------
	------	bistable_example1.ode	------
	------	oscillatory_example1.ode	------
	------	gillespie1.ode	------
	chain1.m	------	------
	gillespie.m	------	------