- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2024-09-30 16:24:03+13:00
- Desc:
- rename alpha_initial to alpha_baseline
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/be4/rawfile/f18b8851776399963e1272fcbf193b22c35a6c39/figs-1-4.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="my_model" 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">
<!-- (4 eqn model for Alzheimer calculation) -->
<units name="molecules">
<unit units="dimensionless"/>
</units>
<units name="hour">
<unit multiplier="3600" units="second"/>
</units>
<units name="per_hour">
<unit exponent="-1" units="hour"/>
</units>
<units name="molecules_per_hour">
<unit units="molecules"/>
<unit units="per_hour"/>
</units>
<units name="per_molecules_per_hour">
<unit exponent="-1" units="molecules"/>
<unit units="per_hour"/>
</units>
<units name="per_hour2">
<unit exponent="-2" units="hour"/>
</units>
<units name="per_hour4">
<unit exponent="-4" units="hour"/>
</units>
<units name="micrometer">
<unit prefix="micro" units="meter"/>
</units>
<units name="micrometer_cubed">
<unit exponent="3" units="micrometer"/>
</units>
<units name="nM">
<unit exponent="-1" units="micrometer_cubed"/>
</units>
<!-- Geometry is constant for all figures-->
<import xlink:href="parameters.cellml">
<component component_ref="cell_geometry" name="geometry"/>
</import>
<!-- Figure 1-->
<import xlink:href="parameters.cellml">
<component component_ref="LR_neurons" name="fig1p"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="main" name="fig1m"/>
</import>
<connection>
<map_components component_1="geometry" component_2="fig1m"/>
<map_variables variable_1="volume" variable_2="volume"/>
<map_variables variable_1="A_N" variable_2="A_N"/>
</connection>
<connection>
<map_components component_1="fig1p" component_2="fig1m"/>
<map_variables variable_1="beta" variable_2="beta"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="tau" variable_2="tau"/>
<map_variables variable_1="rho" variable_2="rho"/>
<map_variables variable_1="delta" variable_2="delta"/>
<map_variables variable_1="eta" variable_2="eta"/>
<map_variables variable_1="kappa" variable_2="kappa"/>
<map_variables variable_1="G_tot" variable_2="G_tot"/>
<map_variables variable_1="alpha_infection" variable_2="alpha_infection"/>
<map_variables variable_1="alpha_baseline" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="main" component_2="fig1m"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="period_1" variable_2="period_1"/>
<map_variables variable_1="period_2" variable_2="period_2"/>
<map_variables variable_1="AB_conc_fig1" variable_2="AB_conc"/>
<map_variables variable_1="Reelin_conc_fig1" variable_2="Reelin_conc"/>
<map_variables variable_1="ABR_conc_fig1" variable_2="ABR_conc"/>
<map_variables variable_1="GSK3Bp_norm_fig1" variable_2="GSK3Bp_norm"/>
</connection>
<!-- Figure 2-->
<import xlink:href="parameters.cellml">
<component component_ref="Re_plus_alECLII_neurons" name="fig2p"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="main" name="fig2m"/>
</import>
<connection>
<map_components component_1="geometry" component_2="fig2m"/>
<map_variables variable_1="volume" variable_2="volume"/>
<map_variables variable_1="A_N" variable_2="A_N"/>
</connection>
<connection>
<map_components component_1="fig2p" component_2="fig2m"/>
<map_variables variable_1="beta" variable_2="beta"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="tau" variable_2="tau"/>
<map_variables variable_1="rho" variable_2="rho"/>
<map_variables variable_1="delta" variable_2="delta"/>
<map_variables variable_1="eta" variable_2="eta"/>
<map_variables variable_1="kappa" variable_2="kappa"/>
<map_variables variable_1="G_tot" variable_2="G_tot"/>
<map_variables variable_1="alpha_infection" variable_2="alpha_infection"/>
<map_variables variable_1="alpha_baseline" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="main" component_2="fig2m"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="period_1" variable_2="period_1"/>
<map_variables variable_1="period_2" variable_2="period_2"/>
<map_variables variable_1="AB_conc_fig2" variable_2="AB_conc"/>
<map_variables variable_1="Reelin_conc_fig2" variable_2="Reelin_conc"/>
<map_variables variable_1="ABR_conc_fig2" variable_2="ABR_conc"/>
<map_variables variable_1="GSK3Bp_norm_fig2" variable_2="GSK3Bp_norm"/>
</connection>
<!-- Figure 3-->
<import xlink:href="parameters.cellml">
<component component_ref="Re_plus_alECLII_neurons" name="fig3p"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="main" name="fig3m"/>
</import>
<connection>
<map_components component_1="geometry" component_2="fig3m"/>
<map_variables variable_1="volume" variable_2="volume"/>
<map_variables variable_1="A_N" variable_2="A_N"/>
</connection>
<component name="COLBOS_reelin">
<variable initial_value="0.0000001" name="gamma" public_interface="out" units="per_molecules_per_hour"/>
</component>
<connection>
<map_components component_1="COLBOS_reelin" component_2="fig3m"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
</connection>
<connection>
<map_components component_1="fig3p" component_2="fig3m"/>
<map_variables variable_1="beta" variable_2="beta"/>
<map_variables variable_1="tau" variable_2="tau"/>
<map_variables variable_1="rho" variable_2="rho"/>
<map_variables variable_1="delta" variable_2="delta"/>
<map_variables variable_1="eta" variable_2="eta"/>
<map_variables variable_1="kappa" variable_2="kappa"/>
<map_variables variable_1="G_tot" variable_2="G_tot"/>
<map_variables variable_1="alpha_infection" variable_2="alpha_infection"/>
<map_variables variable_1="alpha_baseline" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="main" component_2="fig3m"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="period_1" variable_2="period_1"/>
<map_variables variable_1="period_2" variable_2="period_2"/>
<map_variables variable_1="AB_conc_fig3" variable_2="AB_conc"/>
<map_variables variable_1="Reelin_conc_fig3" variable_2="Reelin_conc"/>
<map_variables variable_1="ABR_conc_fig3" variable_2="ABR_conc"/>
<map_variables variable_1="GSK3Bp_norm_fig3" variable_2="GSK3Bp_norm"/>
</connection>
<!-- Figure 4-->
<import xlink:href="parameters.cellml">
<component component_ref="Re_plus_alECLII_neurons" name="fig4p"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="main" name="fig4m"/>
</import>
<connection>
<map_components component_1="geometry" component_2="fig4m"/>
<map_variables variable_1="volume" variable_2="volume"/>
<map_variables variable_1="A_N" variable_2="A_N"/>
</connection>
<component name="ApoEe4_e4">
<variable initial_value="0.2" name="rho" public_interface="out" units="per_molecules_per_hour"/>
</component>
<connection>
<map_components component_1="ApoEe4_e4" component_2="fig4m"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="fig4p" component_2="fig4m"/>
<map_variables variable_1="beta" variable_2="beta"/>
<map_variables variable_1="tau" variable_2="tau"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="delta" variable_2="delta"/>
<map_variables variable_1="eta" variable_2="eta"/>
<map_variables variable_1="kappa" variable_2="kappa"/>
<map_variables variable_1="G_tot" variable_2="G_tot"/>
<map_variables variable_1="alpha_infection" variable_2="alpha_infection"/>
<map_variables variable_1="alpha_baseline" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="main" component_2="fig4m"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="period_1" variable_2="period_1"/>
<map_variables variable_1="period_2" variable_2="period_2"/>
<map_variables variable_1="AB_conc_fig4" variable_2="AB_conc"/>
<map_variables variable_1="Reelin_conc_fig4" variable_2="Reelin_conc"/>
<map_variables variable_1="ABR_conc_fig4" variable_2="ABR_conc"/>
<map_variables variable_1="GSK3Bp_norm_fig4" variable_2="GSK3Bp_norm"/>
</connection>
<component name="main">
<variable initial_value="0" name="t" units="hour"/>
<variable initial_value="50" name="period_1" public_interface="out" units="hour"/>
<variable initial_value="170" name="period_2" public_interface="out" units="hour"/>
<!-- Figure 1 outputs-->
<variable name="AB_conc_fig1" public_interface="in" units="nM"/>
<variable name="Reelin_conc_fig1" public_interface="in" units="nM"/>
<variable name="ABR_conc_fig1" public_interface="in" units="nM"/>
<variable name="GSK3Bp_norm_fig1" public_interface="in" units="molecules"/>
<!-- Figure 2 outputs-->
<variable name="AB_conc_fig2" public_interface="in" units="nM"/>
<variable name="Reelin_conc_fig2" public_interface="in" units="nM"/>
<variable name="ABR_conc_fig2" public_interface="in" units="nM"/>
<variable name="GSK3Bp_norm_fig2" public_interface="in" units="molecules"/>
<!-- Figure 3 outputs-->
<variable name="AB_conc_fig3" public_interface="in" units="nM"/>
<variable name="Reelin_conc_fig3" public_interface="in" units="nM"/>
<variable name="ABR_conc_fig3" public_interface="in" units="nM"/>
<variable name="GSK3Bp_norm_fig3" public_interface="in" units="molecules"/>
<!-- Figure 3 outputs-->
<variable name="AB_conc_fig4" public_interface="in" units="nM"/>
<variable name="Reelin_conc_fig4" public_interface="in" units="nM"/>
<variable name="ABR_conc_fig4" public_interface="in" units="nM"/>
<variable name="GSK3Bp_norm_fig4" public_interface="in" units="molecules"/>
</component>
</model>
