- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2024-10-15 23:30:29+13:00
- Desc:
- Tweaking figure 5 model and simulation experiment to match revised manuscript
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/be4/rawfile/daaa0d50a81d9c1e50ea5139e20555ae6f66f44a/fig5.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>
<!-- Figure 5c-->
<import xlink:href="model.cellml">
<component component_ref="steadystate_model" name="x2m"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="steadystate_model" name="x2p57m"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="steadystate_model" name="x3m"/>
</import>
<import xlink:href="model.cellml">
<component component_ref="steadystate_model" name="x4m"/>
</import>
<component name="alpha">
<variable initial_value="7020" name="alpha_baseline" public_interface="out" units="molecules_per_hour"/>
<variable name="x2" public_interface="out" units="molecules_per_hour"/>
<variable name="x2p57" public_interface="out" units="molecules_per_hour"/>
<variable name="x3" public_interface="out" units="molecules_per_hour"/>
<variable name="x4" public_interface="out" units="molecules_per_hour"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>x2</ci>
<apply>
<times/>
<cn cellml:units="dimenionless">2</cn>
<ci>alpha_baseline</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>x2p57</ci>
<apply>
<times/>
<cn cellml:units="dimenionless">2.57</cn>
<ci>alpha_baseline</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>x3</ci>
<apply>
<times/>
<cn cellml:units="dimenionless">3</cn>
<ci>alpha_baseline</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>x4</ci>
<apply>
<times/>
<cn cellml:units="dimenionless">4</cn>
<ci>alpha_baseline</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="alpha" component_2="x2m"/>
<map_variables variable_1="x2" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="alpha" component_2="x2p57m"/>
<map_variables variable_1="x2p57" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="alpha" component_2="x3m"/>
<map_variables variable_1="x3" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="alpha" component_2="x4m"/>
<map_variables variable_1="x4" variable_2="alpha_baseline"/>
</connection>
<connection>
<map_components component_1="main" component_2="x2m"/>
<map_variables variable_1="reelin_copy_number_x2" variable_2="reelin_copy_number"/>
<map_variables variable_1="AB_copy_number_x2" variable_2="AB_copy_number"/>
<map_variables variable_1="tau" variable_2="tau"/>
</connection>
<connection>
<map_components component_1="main" component_2="x2p57m"/>
<map_variables variable_1="reelin_copy_number_x2p57" variable_2="reelin_copy_number"/>
<map_variables variable_1="AB_copy_number_x2p57" variable_2="AB_copy_number"/>
<map_variables variable_1="tau" variable_2="tau"/>
</connection>
<connection>
<map_components component_1="main" component_2="x3m"/>
<map_variables variable_1="reelin_copy_number_x3" variable_2="reelin_copy_number"/>
<map_variables variable_1="AB_copy_number_x3" variable_2="AB_copy_number"/>
<map_variables variable_1="tau" variable_2="tau"/>
</connection>
<connection>
<map_components component_1="main" component_2="x4m"/>
<map_variables variable_1="reelin_copy_number_x4" variable_2="reelin_copy_number"/>
<map_variables variable_1="AB_copy_number_x4" variable_2="AB_copy_number"/>
<map_variables variable_1="tau" variable_2="tau"/>
</connection>
<component name="main">
<variable initial_value="0" name="t" units="hour"/>
<variable initial_value="79000" name="tau_wildtype" units="molecules_per_hour"/>
<variable initial_value="0.05" name="tau_fraction" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>tau_fraction</ci>
</apply>
<cn cellml:units="dimensionless">1</cn>
</apply>
</math>
<variable name="tau" units="molecules_per_hour"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>tau</ci>
<apply>
<times/>
<ci>tau_wildtype</ci>
<ci>tau_fraction</ci>
</apply>
</apply>
</math>
<variable name="reelin_copy_number_x2" public_interface="in" units="molecules"/>
<variable name="reelin_copy_number_x2p57" public_interface="in" units="molecules"/>
<variable name="reelin_copy_number_x3" public_interface="in" units="molecules"/>
<variable name="reelin_copy_number_x4" public_interface="in" units="molecules"/>
<variable name="AB_copy_number_x2" public_interface="in" units="molecules"/>
<variable name="AB_copy_number_x2p57" public_interface="in" units="molecules"/>
<variable name="AB_copy_number_x3" public_interface="in" units="molecules"/>
<variable name="AB_copy_number_x4" public_interface="in" units="molecules"/>
</component>
</model>
