- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-12-21 17:24:56+13:00
- Desc:
- Adding another reaction to represent negative feedback of activated species on itself
- Permanent Source URI:
- http://models.cellml.org/workspace/7e8/rawfile/92b9be68073862b6b2ffe10eaf4683c3fb8df96a/kraeutler_TOY_composite.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="toy_normalised_hill_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">
<units name="mM">
<unit prefix="milli" units="mole"/>
</units>
<import xlink:href="kraetler_functions.cellml">
<component component_ref="f_module" name="f_A_module"/>
</import>
<import xlink:href="kraetler_functions.cellml">
<component component_ref="f_module" name="f_B_module"/>
</import>
<import xlink:href="kraetler_functions.cellml">
<component component_ref="f_module" name="f_C_module"/>
</import>
<import xlink:href="kraetler_functions.cellml">
<component component_ref="f_module" name="f_D_module"/>
</import>
<import xlink:href="kraetler_functions.cellml">
<component component_ref="f_module" name="f_E_module"/>
</import>
<component name="env">
<!-- guess everything is dimensionless, except Ymax has same units as chemical species A-->
<variable name="time" units="second"/>
<variable name="A" public_interface="out" units="mM"/>
<variable name="B" public_interface="out" units="mM"/>
<variable initial_value="0" name="C" public_interface="out" units="mM"/>
<variable initial_value="0" name="D" public_interface="out" units="mM"/>
<variable initial_value="0" name="E" public_interface="out" units="mM"/>
<variable initial_value="1" name="tau" units="second"/>
<variable initial_value="1" name="Ymax" public_interface="out" units="mM"/>
<variable initial_value="0.5" name="EC50" public_interface="out" units="dimensionless"/>
<variable initial_value="1" name="W" public_interface="out" units="dimensionless"/>
<variable initial_value="1.4" name="n" public_interface="out" units="dimensionless"/>
<variable name="beta_A" public_interface="in" units="dimensionless"/>
<variable name="K_A" public_interface="in" units="dimensionless"/>
<variable name="f_act_A" public_interface="in" units="dimensionless"/>
<variable name="f_act_B" public_interface="in" units="dimensionless"/>
<variable name="f_act_C" public_interface="in" units="dimensionless"/>
<variable name="f_act_D" public_interface="in" units="dimensionless"/>
<variable name="f_act_E" public_interface="in" units="dimensionless"/>
<variable name="f_inh_D" public_interface="in" units="dimensionless"/>
<variable name="OR_C" units="dimensionless"/>
<!-- stimuli A and B-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>A</ci>
<piecewise>
<piece>
<cn cellml:units="mM">1</cn>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">10</cn>
</apply>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">30</cn>
</apply>
</apply>
</piece>
<piece>
<cn cellml:units="mM">1</cn>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">90</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM">0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>B</ci>
<piecewise>
<piece>
<cn cellml:units="mM">1</cn>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">50</cn>
</apply>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">70</cn>
</apply>
</apply>
</piece>
<piece>
<cn cellml:units="mM">1</cn>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">90</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM">0</cn>
</otherwise>
</piecewise>
</apply>
<!-- ode(A,time) = (W*Ymax-A)/tau;
ode(B,time) = (W*Ymax-B)/tau;-->
<apply>
<eq/>
<ci>OR_C</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>f_act_A</ci>
<ci>f_act_E</ci>
</apply>
<apply>
<times/>
<ci>f_act_A</ci>
<ci>f_act_E</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>C</ci>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<times/>
<ci>OR_C</ci>
<ci>Ymax</ci>
</apply>
<ci>C</ci>
</apply>
<ci>tau</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>D</ci>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<times/>
<ci>f_act_B</ci>
<ci>Ymax</ci>
</apply>
<ci>D</ci>
</apply>
<ci>tau</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>E</ci>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<times/>
<ci>f_act_C</ci>
<ci>f_inh_D</ci>
<ci>Ymax</ci>
</apply>
<ci>E</ci>
</apply>
<ci>tau</ci>
</apply>
</apply>
</math>
<variable initial_value="0" name="D_test" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>D_test</ci>
</apply>
<apply>
<divide/>
<ci>f_act_D</ci>
<ci>tau</ci>
</apply>
</apply>
</math>
<variable name="prod_fAfE" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>prod_fAfE</ci>
<apply>
<times/>
<ci>f_act_A</ci>
<ci>f_act_E</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="env" component_2="f_A_module"/>
<map_variables variable_1="W" variable_2="W"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="EC50" variable_2="EC50"/>
<map_variables variable_1="A" variable_2="X"/>
<map_variables variable_1="f_act_A" variable_2="f_act"/>
<map_variables variable_1="K_A" variable_2="K"/>
<map_variables variable_1="beta_A" variable_2="beta"/>
</connection>
<connection>
<map_components component_1="env" component_2="f_B_module"/>
<map_variables variable_1="W" variable_2="W"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="EC50" variable_2="EC50"/>
<map_variables variable_1="B" variable_2="X"/>
<map_variables variable_1="f_act_B" variable_2="f_act"/>
</connection>
<connection>
<map_components component_1="env" component_2="f_C_module"/>
<map_variables variable_1="W" variable_2="W"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="EC50" variable_2="EC50"/>
<map_variables variable_1="C" variable_2="X"/>
<map_variables variable_1="f_act_C" variable_2="f_act"/>
</connection>
<connection>
<map_components component_1="env" component_2="f_D_module"/>
<map_variables variable_1="W" variable_2="W"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="EC50" variable_2="EC50"/>
<map_variables variable_1="D" variable_2="X"/>
<map_variables variable_1="f_act_D" variable_2="f_act"/>
<map_variables variable_1="f_inh_D" variable_2="f_inhib"/>
</connection>
<connection>
<map_components component_1="env" component_2="f_E_module"/>
<map_variables variable_1="W" variable_2="W"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="EC50" variable_2="EC50"/>
<map_variables variable_1="E" variable_2="X"/>
<map_variables variable_1="f_act_E" variable_2="f_act"/>
</connection>
</model>
