- Author:
- schdemp <sdem348@aucklanduni.ac.nz>
- Date:
- 2022-06-16 18:11:58-04:00
- Desc:
- Change parameter file names and subsequent loading name strings
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/8a2/rawfile/6c4ba7884bad10ef792565cfc3d30eb9fec6748c/sten2020_NVC_main.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="sten2020_NVC_main" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<!--import modules-->
<import xlink:href="sten2020_neuron_pyramidal.cellml">
<component component_ref="pyramidal" name="pyramidal"/>
</import>
<import xlink:href="sten2020_neuron_GABAergicNPY.cellml">
<component component_ref="gabaNPY" name="gabaNPY"/>
</import>
<import xlink:href="sten2020_neuron_GABAergicNO.cellml">
<component component_ref="gabaNO" name="gabaNO"/>
</import>
<!--import units-->
<import xlink:href="sten2020_units.cellml">
<units name="per_sec" units_ref="per_sec"/>
</import>
<!--import parameters. Change this document to run different model cases!-->
<import xlink:href="sten2020_parameters_Fig5and6_Ana.cellml">
<component component_ref="parameters" name="parameters"/>
</import>
<!-- build environment time and neuronal stimulation-->
<component name="environment">
<variable initial_value="0" name="t" public_interface="out" units="second"/>
<variable name="Sig" public_interface="out" units="dimensionless"/>
<variable name="tstart" public_interface="in" units="second"/>
<variable name="tend" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Sig</ci>
<piecewise>
<piece>
<cn cellml:units="dimensionless">1.0</cn>
<apply>
<and/>
<apply>
<gt/>
<ci>t</ci>
<ci>tstart</ci>
</apply>
<apply>
<lt/>
<ci>t</ci>
<ci>tend</ci>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<component name="NVCUnit">
<!--environment time, signal, and initiate activity-->
<variable name="t" private_interface="out" public_interface="in" units="second"/>
<variable name="Sig" public_interface="in" units="dimensionless"/>
<variable initial_value="0" name="N_Pyr" private_interface="out" units="dimensionless"/>
<variable initial_value="0" name="N_NPY" private_interface="out" units="dimensionless"/>
<variable initial_value="0" name="N_NO" private_interface="out" units="dimensionless"/>
<!--rate constants for neuron interactions-->
<variable name="k_pf1" public_interface="in" units="per_sec"/>
<variable name="k_pf2" public_interface="in" units="per_sec"/>
<variable name="k_in1" public_interface="in" units="per_sec"/>
<variable name="k_in2" public_interface="in" units="per_sec"/>
<variable name="k_inf1" public_interface="in" units="per_sec"/>
<variable name="k_inf2" public_interface="in" units="per_sec"/>
<variable name="k_u_NO" public_interface="in" units="per_sec"/>
<variable name="k_u_NPY" public_interface="in" units="per_sec"/>
<variable name="k_u_Pyr" public_interface="in" units="per_sec"/>
<variable name="E_Pyr" units="dimensionless"/>
<variable name="E_NPY" units="dimensionless"/>
<variable name="E_NO" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>E_Pyr</ci>
<piecewise>
<piece>
<ci>N_Pyr</ci>
<apply>
<gt/>
<ci>N_Pyr</ci>
<cn cellml:units="dimensionless">0</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">0.0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>E_NPY</ci>
<piecewise>
<piece>
<ci>N_NPY</ci>
<apply>
<gt/>
<ci>N_NPY</ci>
<cn cellml:units="dimensionless">0</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">0.0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>E_NO</ci>
<piecewise>
<piece>
<ci>N_NO</ci>
<apply>
<gt/>
<ci>N_NO</ci>
<cn cellml:units="dimensionless">0</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
<!-- imported rate constants for export to each neuronal pathway-->
<variable name="k_Ca" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="initCA_NO" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initNO" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initNO_vsm" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initCA_NPY" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initNPY" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initNPY_vsm" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initCA_Pyr" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initAA" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initPGE2" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="initPGE2_vsm" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="sink_N_NO" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_N_NPY" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_N_Pyr" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_Ca_NO" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_Ca_NPY" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_Ca_Pyr" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="k_PL" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="k_COX" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="k_PGE2" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_PGE2" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="k_NOS" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="k_NO" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="sink_NO" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="k_NPY" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="V_max" private_interface="out" public_interface="in" units="per_sec"/>
<variable name="K_M" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="sink_NPY" private_interface="out" public_interface="in" units="per_sec"/>
<!-- grab the output activities from other modules-->
<variable name="Ca_NPY" private_interface="in" units="dimensionless"/>
<variable name="Ca_Pyr" private_interface="in" units="dimensionless"/>
<variable name="Ca_NO" private_interface="in" units="dimensionless"/>
<variable name="PGE_2vsm" private_interface="in" units="dimensionless"/>
<variable name="NPY_vsm" private_interface="in" units="dimensionless"/>
<variable name="NO_vsm" private_interface="in" units="dimensionless"/>
<variable name="AA" private_interface="in" units="dimensionless"/>
<variable name="PGE_2" private_interface="in" units="dimensionless"/>
<variable name="NO" private_interface="in" units="dimensionless"/>
<variable name="NPY" private_interface="in" units="dimensionless"/>
<!--calculate S, and Dilation-->
<variable name="k_y1" public_interface="in" units="dimensionless"/>
<variable name="k_y2" public_interface="in" units="dimensionless"/>
<variable name="k_y3" public_interface="in" units="dimensionless"/>
<variable name="initS_o" public_interface="in" units="dimensionless"/>
<variable name="D" public_interface="out" units="dimensionless"/>
<variable name="S_t" public_interface="out" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>S_t</ci>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>k_y1</ci>
<ci>NO_vsm</ci>
</apply>
<apply>
<times/>
<ci>k_y2</ci>
<ci>PGE_2vsm</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_y3</ci>
<ci>NPY_vsm</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>D</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">100</cn>
<apply>
<minus/>
<ci>S_t</ci>
<ci>initS_o</ci>
</apply>
</apply>
<ci>initS_o</ci>
</apply>
</apply>
<!--set neuron ode's-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>N_Pyr</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_u_Pyr</ci>
<ci>Sig</ci>
</apply>
<apply>
<times/>
<ci>k_inf1</ci>
<ci>E_NO</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_inf2</ci>
<ci>E_NPY</ci>
</apply>
</apply>
<apply>
<times/>
<ci>sink_N_Pyr</ci>
<ci>N_Pyr</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>N_NPY</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>k_u_NPY</ci>
<ci>Sig</ci>
</apply>
<apply>
<times/>
<ci>k_pf2</ci>
<ci>E_Pyr</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_in2</ci>
<ci>E_NO</ci>
</apply>
</apply>
<apply>
<times/>
<ci>sink_N_NPY</ci>
<ci>N_NPY</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>N_NO</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>k_u_NO</ci>
<ci>Sig</ci>
</apply>
<apply>
<times/>
<ci>k_pf1</ci>
<ci>E_Pyr</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_in1</ci>
<ci>E_NPY</ci>
</apply>
</apply>
<apply>
<times/>
<ci>sink_N_NO</ci>
<ci>N_NO</ci>
</apply>
</apply>
</apply>
</math>
</component>
<!-- necessary maps between all variables and respective modules-->
<connection>
<map_components component_1="parameters" component_2="environment"/>
<map_variables variable_1="tstart" variable_2="tstart"/>
<map_variables variable_1="tend" variable_2="tend"/>
</connection>
<connection>
<map_components component_1="environment" component_2="NVCUnit"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="Sig" variable_2="Sig"/>
</connection>
<connection>
<map_components component_1="parameters" component_2="NVCUnit"/>
<map_variables variable_1="k_Ca" variable_2="k_Ca"/>
<map_variables variable_1="k_pf1" variable_2="k_pf1"/>
<map_variables variable_1="k_pf2" variable_2="k_pf2"/>
<map_variables variable_1="k_in1" variable_2="k_in1"/>
<map_variables variable_1="k_in2" variable_2="k_in2"/>
<map_variables variable_1="k_inf1" variable_2="k_inf1"/>
<map_variables variable_1="k_inf2" variable_2="k_inf2"/>
<map_variables variable_1="sink_N_NO" variable_2="sink_N_NO"/>
<map_variables variable_1="sink_N_NPY" variable_2="sink_N_NPY"/>
<map_variables variable_1="sink_N_Pyr" variable_2="sink_N_Pyr"/>
<map_variables variable_1="sink_Ca_NO" variable_2="sink_Ca_NO"/>
<map_variables variable_1="sink_Ca_NPY" variable_2="sink_Ca_NPY"/>
<map_variables variable_1="sink_Ca_Pyr" variable_2="sink_Ca_Pyr"/>
<map_variables variable_1="k_PL" variable_2="k_PL"/>
<map_variables variable_1="k_COX" variable_2="k_COX"/>
<map_variables variable_1="k_PGE2" variable_2="k_PGE2"/>
<map_variables variable_1="sink_PGE2" variable_2="sink_PGE2"/>
<map_variables variable_1="k_NOS" variable_2="k_NOS"/>
<map_variables variable_1="k_NO" variable_2="k_NO"/>
<map_variables variable_1="sink_NO" variable_2="sink_NO"/>
<map_variables variable_1="k_NPY" variable_2="k_NPY"/>
<map_variables variable_1="V_max" variable_2="V_max"/>
<map_variables variable_1="K_M" variable_2="K_M"/>
<map_variables variable_1="sink_NPY" variable_2="sink_NPY"/>
<map_variables variable_1="k_y1" variable_2="k_y1"/>
<map_variables variable_1="k_y2" variable_2="k_y2"/>
<map_variables variable_1="k_y3" variable_2="k_y3"/>
<map_variables variable_1="k_u_NO" variable_2="k_u_NO"/>
<map_variables variable_1="k_u_NPY" variable_2="k_u_NPY"/>
<map_variables variable_1="k_u_Pyr" variable_2="k_u_Pyr"/>
<map_variables variable_1="initCA_NO" variable_2="initCA_NO"/>
<map_variables variable_1="initNO" variable_2="initNO"/>
<map_variables variable_1="initNO_vsm" variable_2="initNO_vsm"/>
<map_variables variable_1="initCA_NPY" variable_2="initCA_NPY"/>
<map_variables variable_1="initNPY" variable_2="initNPY"/>
<map_variables variable_1="initNPY_vsm" variable_2="initNPY_vsm"/>
<map_variables variable_1="initCA_Pyr" variable_2="initCA_Pyr"/>
<map_variables variable_1="initAA" variable_2="initAA"/>
<map_variables variable_1="initPGE2" variable_2="initPGE2"/>
<map_variables variable_1="initPGE2_vsm" variable_2="initPGE2_vsm"/>
<map_variables variable_1="initS_o" variable_2="initS_o"/>
</connection>
<connection>
<map_components component_1="NVCUnit" component_2="pyramidal"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="initCA_Pyr" variable_2="initCA_Pyr"/>
<map_variables variable_1="initAA" variable_2="initAA"/>
<map_variables variable_1="initPGE2" variable_2="initPGE2"/>
<map_variables variable_1="initPGE2_vsm" variable_2="initPGE2_vsm"/>
<map_variables variable_1="N_Pyr" variable_2="N_Pyr"/>
<map_variables variable_1="k_Ca" variable_2="k_Ca"/>
<map_variables variable_1="sink_Ca_Pyr" variable_2="sink_Ca_Pyr"/>
<map_variables variable_1="k_PL" variable_2="k_PL"/>
<map_variables variable_1="k_COX" variable_2="k_COX"/>
<map_variables variable_1="k_PGE2" variable_2="k_PGE2"/>
<map_variables variable_1="sink_PGE2" variable_2="sink_PGE2"/>
<map_variables variable_1="PGE_2vsm" variable_2="PGE_2vsm"/>
<map_variables variable_1="Ca_Pyr" variable_2="Ca_Pyr"/>
<map_variables variable_1="AA" variable_2="AA"/>
<map_variables variable_1="PGE_2" variable_2="PGE_2"/>
</connection>
<connection>
<map_components component_1="NVCUnit" component_2="gabaNPY"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="initCA_NPY" variable_2="initCA_NPY"/>
<map_variables variable_1="initNPY" variable_2="initNPY"/>
<map_variables variable_1="initNPY_vsm" variable_2="initNPY_vsm"/>
<map_variables variable_1="N_NPY" variable_2="N_NPY"/>
<map_variables variable_1="k_Ca" variable_2="k_Ca"/>
<map_variables variable_1="sink_Ca_NPY" variable_2="sink_Ca_NPY"/>
<map_variables variable_1="k_NPY" variable_2="k_NPY"/>
<map_variables variable_1="V_max" variable_2="V_max"/>
<map_variables variable_1="K_M" variable_2="K_M"/>
<map_variables variable_1="sink_NPY" variable_2="sink_NPY"/>
<map_variables variable_1="NPY" variable_2="NPY"/>
<map_variables variable_1="NPY_vsm" variable_2="NPY_vsm"/>
<map_variables variable_1="Ca_NPY" variable_2="Ca_NPY"/>
</connection>
<connection>
<map_components component_1="NVCUnit" component_2="gabaNO"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="initCA_NO" variable_2="initCA_NO"/>
<map_variables variable_1="initNO" variable_2="initNO"/>
<map_variables variable_1="initNO_vsm" variable_2="initNO_vsm"/>
<map_variables variable_1="N_NO" variable_2="N_NO"/>
<map_variables variable_1="k_Ca" variable_2="k_Ca"/>
<map_variables variable_1="sink_Ca_NO" variable_2="sink_Ca_NO"/>
<map_variables variable_1="k_NOS" variable_2="k_NOS"/>
<map_variables variable_1="k_NO" variable_2="k_NO"/>
<map_variables variable_1="sink_NO" variable_2="sink_NO"/>
<map_variables variable_1="NO" variable_2="NO"/>
<map_variables variable_1="NO_vsm" variable_2="NO_vsm"/>
<map_variables variable_1="Ca_NO" variable_2="Ca_NO"/>
</connection>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="NVCUnit">
<component_ref component="pyramidal"/>
<component_ref component="gabaNPY"/>
<component_ref component="gabaNO"/>
</component_ref>
</group>
</model>
