GitHub - ModelDBRepository/229640: Respiratory control model with brainstem CPG and sensory feedback (Diekman, Thomas, and Wilson 2017)

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Respiratory control model with brainstem CPG and sensory feedback (Diekman, Thomas, and Wilson 2017)

modeldb.science/229640

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
data_figure10		data_figure10
data_figure14		data_figure14
data_figure4		data_figure4
arrow.m		arrow.m
closed-loop model equations.pdf		closed-loop model equations.pdf
closedloop.m		closedloop.m
closedloopM.m		closedloopM.m
closedloop_clampgtonic.m		closedloop_clampgtonic.m
closedloop_hstatic.m		closedloop_hstatic.m
closedloop_tauh.m		closedloop_tauh.m
events_figure13.m		events_figure13.m
events_figure5.m		events_figure5.m
fastsubsystem.m		fastsubsystem.m
fig1.png		fig1.png
fig2.png		fig2.png
generate_figure10_bifurcation_curves.ode		generate_figure10_bifurcation_curves.ode
generate_figure4_bifurcation_curves.ode		generate_figure4_bifurcation_curves.ode
openloop.m		openloop.m
openloopM.m		openloopM.m
openloop_tauh.m		openloop_tauh.m
readme.html		readme.html
reproduce_figure1.m		reproduce_figure1.m
reproduce_figure10.m		reproduce_figure10.m
reproduce_figure12.m		reproduce_figure12.m
reproduce_figure13.m		reproduce_figure13.m
reproduce_figure14.m		reproduce_figure14.m
reproduce_figure15.m		reproduce_figure15.m
reproduce_figure2.m		reproduce_figure2.m
reproduce_figure3.m		reproduce_figure3.m
reproduce_figure4.m		reproduce_figure4.m
reproduce_figure5.m		reproduce_figure5.m
reproduce_figure6.m		reproduce_figure6.m
reproduce_figure7.m		reproduce_figure7.m
reproduce_figure8.m		reproduce_figure8.m
reproduce_figure9.m		reproduce_figure9.m
reproduce_figureA1.m		reproduce_figureA1.m
rotateXLabels.m		rotateXLabels.m
runsims_figure14.m		runsims_figure14.m

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<b>README file for code associated with the paper "Eupnea, Tachypnea, and Autoresuscitation
in a Closed-Loop Respiratory Control Model" </b>

Diekman CO, Thomas PJ, and Wilson CG (2017). <i>Journal of Neurophysiology</i> doi: 10.1152/jn.00170.2017

This folder contains MATLAB and XPPAUT code for reproducing the figures in the paper.
Estimated runtimes are for a standard laptop/desktop personal computer.

Figure 1: 'reproduce_figure1.m' runs simulations and plots the figure shown below. Runtime: minutes

Figure 2: 'reproduce_figure2.m' runs simulations and plots the figure shown below. Runtime: minutes

Figure 3: 'reproduce_figure3.m' runs simulations and plots the figure. Runtime: hours

Figure 4: 'reproduce_figure4.m' runs simulations, reads in pre-computed bifurcation curves,
and plots the figure. Runtime: minutes
To generate the bifurcation curves, use XPPAUT and follow the instructions in 'generate_figure4_bifurcation_curves.ode'.

Figure 5: 'reproduce_figure5.m' runs simulations and plots the figure. Runtime: hours

Figure 6: 'reproduce_figure6.m' runs simulations and plots the figure. Runtime: minutes

Figure 7: 'reproduce_figure8.m' runs simulations and plots the figure. Runtime: hours

Figure 8: 'reproduce_figure9.m' runs simulations and plots the figure. Runtime: hours

Figure 9: 'reproduce_figure10.m' runs simulations and plots the figure. Runtime: minutes

Figure 10: 'reproduce_figure10.m' runs simulations, reads in pre-computed bifurcation curves,
and plots the figure. Runtime: minutes
To generate the bifurcation curves, use XPPAUT and follow the instructions in 'generate_figure10_bifurcation_curves.ode'.

Figure 11: No code provided since this figure displays experimental rather than computational data.

Figure 12: 'reproduce_figure12.m' runs simulations and plots the figure. Note that the estimated
location of the boundary limit cycle is sensitive to numerical precision and round-off error.
If the figure looks different on your machine you may need to adjust the gtonic clamp duration
"breakDur" to find values that lead to recovery (for panels A and C) and failure (panels B and D).
Runtime: minutes

Figure 13: 'reproduce_figure13.m' runs simulations and plots the figure. This figure involves
simulating one period near the unstable boundary limit cycle to compute Floquet multipliers,
and so is very sensitive to numerical precision and round-off error. Use 'reproduce_figure12.m'
to find the breakDur values that put you close to the boundary limit cycle. For the breakDur value
that leads to recovery in Figure 13, save the state variables "inits3" and then set those as
"initsR" for Figure 13. Likewise set "initsF" in 'reproduce_figure13.m' to the state variables
in "inits3" of 'reproduce_figure12.m' corresponding to the breakDur that leads to failure.
Runtime: minutes

Figure 14: 'reproduce_figure14.m' reads in pre-computed data files and plots the figure. Runtime: seconds.
To run the simulations that produce the data files, use 'runsims_figure14.m'. Runtime: days

Figure 15: 'reproduce_figure15.m' runs simulations and plots the figure. Similar to Figure 12,
you may need to adjust "breakDur". Runtime: minutes

Figure A1: 'reproduce_figure7.m' runs simulations and plots the figure. Runtime: minutes

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