- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-09-09 16:29:05+12:00
- Desc:
- Calling new submodules from cellml
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/700/rawfile/a937e7e137dc3338f8fe5c4fa5505ca4cbe7f2dd/BG_M2_composite.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_muscarinic_composite" 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 xlink:href="units_and_constants/units_BG.cellml">
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="fmol" units_ref="fmol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="mM" units_ref="mM"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<import xlink:href="6f9/BG_GiProtein.cellml">
<component component_ref="GiProtein" name="GiProtein"/>
</import>
<import xlink:href="6f7/BG_LRGbinding.cellml">
<component component_ref="LRGbinding" name="LRGbinding"/>
</import>
<component name="muscarinic_parameters">
<variable initial_value="238142" name="kappa_sig1" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="266.437" name="kappa_sig2" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="3304.28" name="kappa_sig3" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="53920.1" name="kappa_sig4" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.00103925" name="kappa_act1" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.69088e-05" name="kappa_act2" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0682376" name="kappa_hyd" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="76.6955" name="kappa_reassoc" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.190462" name="K_L" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0844987" name="K_R" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00948347" name="K_G" public_interface="out" units="per_fmol"/>
<variable initial_value="5.77509" name="K_LR" public_interface="out" units="per_fmol"/>
<variable initial_value="16.2165" name="K_RG" public_interface="out" units="per_fmol"/>
<variable initial_value="17.9264" name="K_LRG" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0164815" name="K_a_GTP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0731915" name="K_beta_gamma" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00880903" name="K_a_GDP" public_interface="out" units="per_fmol"/>
</component>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial conditions-->
<variable name="q_L_init" units="fmol"/>
<variable initial_value="1e-16" name="q_LRG_init" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_init" units="fmol"/>
<variable initial_value="0.00072" name="q_R_init" units="fmol"/>
<variable initial_value="0.00836" name="q_G_init" units="fmol"/>
<variable initial_value="1e-16" name="q_RG_init" units="fmol"/>
<variable initial_value="1e-16" name="q_a_GTP_init" units="fmol"/>
<variable initial_value="1e-16" name="q_beta_gamma_init" units="fmol"/>
<variable initial_value="1e-16" name="q_a_GDP_init" units="fmol"/>
<!-- Iancu: Acetylcholine stimulus = 10uM = 0.38 fmol. then it becomes zero, not 1e-3. opencor struggles, but exporting to matlab works fine!-->
<variable initial_value="0.38" name="q_L_max" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_L_init</ci>
<piecewise>
<piece>
<ci>q_L_max</ci>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">0</cn>
</apply>
<apply>
<leq/>
<ci>time</ci>
<cn cellml:units="second">0.1</cn>
</apply>
</apply>
</piece>
<piece>
<apply>
<times/>
<ci>q_L_max</ci>
<apply>
<minus/>
<cn cellml:units="second">1</cn>
<ci>time</ci>
</apply>
</apply>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">0.1</cn>
</apply>
<apply>
<leq/>
<ci>time</ci>
<cn cellml:units="second">0.99</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="fmol" type="e-notation">1<sep/>-3</cn>
</otherwise>
</piecewise>
</apply>
</math>
<!-- from submodules-->
<variable name="q_R_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_G_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_RG_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_LR_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_LRG_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_a_GTP_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_beta_gamma_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_a_GDP_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_L_mLRGbinding" public_interface="in" units="fmol"/>
<variable name="q_R_mLRGbinding" public_interface="in" units="fmol"/>
<variable name="q_G_mLRGbinding" public_interface="in" units="fmol"/>
<variable name="q_LR_mLRGbinding" public_interface="in" units="fmol"/>
<variable name="q_RG_mLRGbinding" public_interface="in" units="fmol"/>
<variable name="q_LRG_mLRGbinding" public_interface="in" units="fmol"/>
<!-- Global values-->
<variable name="q_L" public_interface="out" units="fmol"/>
<variable name="q_LRG" public_interface="out" units="fmol"/>
<variable name="q_LR" public_interface="out" units="fmol"/>
<variable name="q_R" public_interface="out" units="fmol"/>
<variable name="q_G" public_interface="out" units="fmol"/>
<variable name="q_RG" public_interface="out" units="fmol"/>
<variable name="q_a_GTP" public_interface="out" units="fmol"/>
<variable name="q_beta_gamma" public_interface="out" units="fmol"/>
<variable name="q_a_GDP" public_interface="out" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_L</ci>
<apply>
<plus/>
<ci>q_L_mLRGbinding</ci>
<ci>q_L_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R</ci>
<apply>
<plus/>
<ci>q_R_mLRGbinding</ci>
<ci>q_R_mGiProtein</ci>
<ci>q_R_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_G</ci>
<apply>
<plus/>
<ci>q_G_mLRGbinding</ci>
<ci>q_G_mGiProtein</ci>
<ci>q_G_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR</ci>
<apply>
<plus/>
<ci>q_LR_mLRGbinding</ci>
<ci>q_LR_mGiProtein</ci>
<ci>q_LR_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_RG</ci>
<apply>
<plus/>
<ci>q_RG_mLRGbinding</ci>
<ci>q_RG_mGiProtein</ci>
<ci>q_RG_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LRG</ci>
<apply>
<plus/>
<ci>q_LRG_mLRGbinding</ci>
<ci>q_LRG_mGiProtein</ci>
<ci>q_LRG_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_a_GTP</ci>
<apply>
<plus/>
<ci>q_a_GTP_mGiProtein</ci>
<ci>q_a_GTP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_beta_gamma</ci>
<apply>
<plus/>
<ci>q_beta_gamma_mGiProtein</ci>
<ci>q_beta_gamma_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_a_GDP</ci>
<apply>
<plus/>
<ci>q_a_GDP_mGiProtein</ci>
<ci>q_a_GDP_init</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="LRGbinding"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_L_mLRGbinding" variable_2="q_L"/>
<map_variables variable_1="q_L" variable_2="q_L_global"/>
<map_variables variable_1="q_R_mLRGbinding" variable_2="q_R"/>
<map_variables variable_1="q_R" variable_2="q_R_global"/>
<map_variables variable_1="q_G_mLRGbinding" variable_2="q_G"/>
<map_variables variable_1="q_G" variable_2="q_G_global"/>
<map_variables variable_1="q_LR_mLRGbinding" variable_2="q_LR"/>
<map_variables variable_1="q_LR" variable_2="q_LR_global"/>
<map_variables variable_1="q_RG_mLRGbinding" variable_2="q_RG"/>
<map_variables variable_1="q_RG" variable_2="q_RG_global"/>
<map_variables variable_1="q_LRG_mLRGbinding" variable_2="q_LRG"/>
<map_variables variable_1="q_LRG" variable_2="q_LRG_global"/>
</connection>
<connection>
<map_components component_1="environment" component_2="GiProtein"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_R_mGiProtein" variable_2="q_R"/>
<map_variables variable_1="q_R" variable_2="q_R_global"/>
<map_variables variable_1="q_G_mGiProtein" variable_2="q_G"/>
<map_variables variable_1="q_G" variable_2="q_G_global"/>
<map_variables variable_1="q_RG_mGiProtein" variable_2="q_RG"/>
<map_variables variable_1="q_RG" variable_2="q_RG_global"/>
<map_variables variable_1="q_LR_mGiProtein" variable_2="q_LR"/>
<map_variables variable_1="q_LR" variable_2="q_LR_global"/>
<map_variables variable_1="q_LRG_mGiProtein" variable_2="q_LRG"/>
<map_variables variable_1="q_LRG" variable_2="q_LRG_global"/>
<map_variables variable_1="q_a_GTP_mGiProtein" variable_2="q_a_GTP"/>
<map_variables variable_1="q_a_GTP" variable_2="q_a_GTP_global"/>
<map_variables variable_1="q_beta_gamma_mGiProtein" variable_2="q_beta_gamma"/>
<map_variables variable_1="q_beta_gamma" variable_2="q_beta_gamma_global"/>
<map_variables variable_1="q_a_GDP_mGiProtein" variable_2="q_a_GDP"/>
<map_variables variable_1="q_a_GDP" variable_2="q_a_GDP_global"/>
</connection>
<connection>
<map_components component_1="muscarinic_parameters" component_2="LRGbinding"/>
<map_variables variable_1="kappa_sig1" variable_2="kappa_sig1"/>
<map_variables variable_1="kappa_sig2" variable_2="kappa_sig2"/>
<map_variables variable_1="kappa_sig3" variable_2="kappa_sig3"/>
<map_variables variable_1="kappa_sig4" variable_2="kappa_sig4"/>
<map_variables variable_1="K_L" variable_2="K_L"/>
<map_variables variable_1="K_R" variable_2="K_R"/>
<map_variables variable_1="K_G" variable_2="K_G"/>
<map_variables variable_1="K_LR" variable_2="K_LR"/>
<map_variables variable_1="K_RG" variable_2="K_RG"/>
<map_variables variable_1="K_LRG" variable_2="K_LRG"/>
</connection>
<connection>
<map_components component_1="muscarinic_parameters" component_2="GiProtein"/>
<map_variables variable_1="kappa_act1" variable_2="kappa_act1"/>
<map_variables variable_1="kappa_act2" variable_2="kappa_act2"/>
<map_variables variable_1="kappa_hyd" variable_2="kappa_hyd"/>
<map_variables variable_1="kappa_reassoc" variable_2="kappa_reassoc"/>
<map_variables variable_1="K_LRG" variable_2="K_LRG"/>
<map_variables variable_1="K_R" variable_2="K_R"/>
<map_variables variable_1="K_RG" variable_2="K_RG"/>
<map_variables variable_1="K_G" variable_2="K_G"/>
<map_variables variable_1="K_LR" variable_2="K_LR"/>
<map_variables variable_1="K_a_GTP" variable_2="K_a_GTP"/>
<map_variables variable_1="K_beta_gamma" variable_2="K_beta_gamma"/>
<map_variables variable_1="K_a_GDP" variable_2="K_a_GDP"/>
</connection>
<connection>
<map_components component_1="constants" component_2="LRGbinding"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
<connection>
<map_components component_1="constants" component_2="GiProtein"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
