259786.omex
title: Respiratory central pattern generator including Kolliker-Fuse nucleus (Wittman et al 2019)
abstract: We present three highly reduced conductance-based models for the core of the respiratory CPG. All successfully simulate respiratory outputs across eupnoeic and vagotomized conditions and show that loss of inhibition to the pontine Kolliker-Fuse nucleus reproduces the key respiratory alterations associated with Rett syndrome.
description: This directory contains model files and scripts which were used to explore the model presented in the research article: Wittman, S. , Abdala, A. P. and Rubin, J. E. (2019), Reduced computational modelling of Kolliker-Fuse contributions to breathing patterns in Rett syndrome. J Physiol, 597:2651-2672. doi:[10.1113/JP277592](http://doi.org/10.1113/JP277592) The model files (with extensions .ode and .set) are designed to be used with the free software package XPPAUT. The software and associated documentation can be obtained here: <http://www.math.pitt.edu/~bard/xpp/xpp.html> The folders "3p", "4p-e", and "4p-r" each refer to one of the models discussed in the article. Each folder contains a single .ode file, which contains the main equations for that model. Each folder also contains several .set files, which correspond to various regimes (i.e. parameter settings) discussed in the article. The models and regimes can be explored in XPPAUT by first loading an .ode file, then using the "Read set" command to read various .set files. The main features of interest for each model can be explored in XPPAUT. The folder "Matlab scripts" contains scripts used to run model files in XPPAUT over iterations of parameters, and to track and plot the results. The scripts include "traj\_plotter\_many.m", which was used to generate voltage-time plots for multiple figures; "orbit\_tracker.m", which was used to generate the orbit panels in Figures 6 and 7; "rett\_figure\_script.m", which was used to generate the inhibition-period plots in Figure 5; and "set\_bar\_graphs.m", which was used to generate the bar graphs in Figure 9. All of these scripts rely on functions from Rob Clewley's XPP-Python interface (see XPPAUT documentation site). Clewley's scripts are included by permission; a more recent version of them is available at his github that may or may not be compatible with our scripts: <https://github.com/robclewley/xpp-matlab> Our scripts are mainly included for transparency, and theref…
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created: 2019-10-07
modified: 2019-10-15

Realistic Network
identifier: http://modeldb.science/ModelList

Rhythmic network

Brainstem
identifier: http://modeldb.science/ModelList

Respiratory CPG

I Na,p
identifier: http://modeldb.science/ModelList

Glutamate
identifier: http://modeldb.science/ModelList

Gaba
identifier: http://modeldb.science/ModelList

Glycine
identifier: http://modeldb.science/ModelList

AMPA
identifier: http://modeldb.science/ModelList

GabaA
identifier: http://modeldb.science/ModelList

Glycine
identifier: http://modeldb.science/ModelList

Respiratory control
identifier: http://modeldb.science/ModelList

Rhythm generation

Samuel Wittman

Jonathan Rubin

Sense Lab at Yale University
identifier: https://senselab.med.yale.edu/
account name: https://senselab.med.yale.edu/

Jonathan R. Karr
identifier: http://identifiers.org/orcid:0000-0002-2605-5080
account name: https://orcid.org/0000-0002-2605-5080

modeldb:259786
identifier: https://identifiers.org/modeldb:259786

00019
identifier: http://identifiers.org/doi:10.1113/JP277592
label: Samuel Wittman, Ana Paula Abdala & Jonathan E. Rubin. Reduced computational modelling of Kölliker-Fuse contributions to breathing patterns in Rett syndrome. The Journal of Physiology 597, 10: 2651-2672 (2019).