- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-11-26 14:26:35+13:00
- Desc:
- Updating Knames
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/707/rawfile/88369d2f746a0234b3ff860cfe8cca2efe643f28/BG_LRGbinding_M2.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_LRGbinding_M2" 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="mM" units_ref="mM"/>
<units name="fmol" units_ref="fmol"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="microm3" units_ref="microm3"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="fA" units_ref="fA"/>
<units name="per_second" units_ref="per_second"/>
<units name="millivolt" units_ref="millivolt"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<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="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>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial values-->
<variable name="q_L_M2_init" units="fmol"/>
<variable initial_value="0.00072162" name="q_R_M2_init" units="fmol"/>
<variable initial_value="0.00836" name="q_Gi_init" units="fmol"/>
<variable initial_value="1e-18" name="q_LR_M2_init" units="fmol"/>
<variable initial_value="1e-18" name="q_R_M2Gi_init" units="fmol"/>
<variable initial_value="1e-18" name="q_LR_M2Gi_init" units="fmol"/>
<!-- stimulus-->
<variable initial_value="3.1" name="stimSt" units="second"/>
<variable initial_value="0.5e1" name="stimDur" units="second"/>
<variable initial_value="0.3e1" name="tR" units="second"/>
<variable initial_value="1e-7" name="stimMag" units="fmol"/>
<variable initial_value="1e-8" name="stimHolding" units="fmol"/>
<variable name="m" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>m</ci>
<apply>
<divide/>
<ci>stimMag</ci>
<ci>tR</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_L_M2_init</ci>
<piecewise>
<piece>
<apply>
<plus/>
<ci>stimHolding</ci>
<apply>
<times/>
<ci>m</ci>
<apply>
<plus/>
<apply>
<minus/>
<ci>time</ci>
<ci>stimSt</ci>
</apply>
<ci>tR</ci>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<lt/>
<ci>time</ci>
<ci>stimSt</ci>
</apply>
<apply>
<gt/>
<ci>time</ci>
<apply>
<minus/>
<ci>stimSt</ci>
<ci>tR</ci>
</apply>
</apply>
</apply>
</piece>
<piece>
<apply>
<plus/>
<ci>stimMag</ci>
<ci>stimHolding</ci>
</apply>
<apply>
<and/>
<apply>
<geq/>
<ci>time</ci>
<ci>stimSt</ci>
</apply>
<apply>
<lt/>
<ci>time</ci>
<apply>
<plus/>
<ci>stimSt</ci>
<ci>stimDur</ci>
</apply>
</apply>
</apply>
</piece>
<piece>
<apply>
<plus/>
<ci>stimHolding</ci>
<apply>
<times/>
<apply>
<minus/>
<ci>m</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>time</ci>
<ci>stimSt</ci>
</apply>
<ci>tR</ci>
</apply>
<ci>stimDur</ci>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<lt/>
<ci>time</ci>
<apply>
<plus/>
<ci>stimSt</ci>
<ci>tR</ci>
<ci>stimDur</ci>
</apply>
</apply>
<apply>
<geq/>
<ci>time</ci>
<apply>
<plus/>
<ci>stimSt</ci>
<ci>stimDur</ci>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<ci>stimHolding</ci>
</otherwise>
</piecewise>
</apply>
</math>
<!-- Global value-->
<variable name="q_L_M2" public_interface="out" units="fmol"/>
<variable name="q_R_M2" public_interface="out" units="fmol"/>
<variable name="q_Gi" public_interface="out" units="fmol"/>
<variable name="q_LR_M2" public_interface="out" units="fmol"/>
<variable name="q_R_M2Gi" public_interface="out" units="fmol"/>
<variable name="q_LR_M2Gi" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="q_L_M2_mLRGbinding_M2" public_interface="in" units="fmol"/>
<variable name="q_R_M2_mLRGbinding_M2" public_interface="in" units="fmol"/>
<variable name="q_Gi_mLRGbinding_M2" public_interface="in" units="fmol"/>
<variable name="q_LR_M2_mLRGbinding_M2" public_interface="in" units="fmol"/>
<variable name="q_R_M2Gi_mLRGbinding_M2" public_interface="in" units="fmol"/>
<variable name="q_LR_M2Gi_mLRGbinding_M2" public_interface="in" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_L_M2</ci>
<apply>
<plus/>
<ci>q_L_M2_mLRGbinding_M2</ci>
<ci>q_L_M2_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R_M2</ci>
<apply>
<plus/>
<ci>q_R_M2_mLRGbinding_M2</ci>
<ci>q_R_M2_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Gi</ci>
<apply>
<plus/>
<ci>q_Gi_mLRGbinding_M2</ci>
<ci>q_Gi_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_M2</ci>
<apply>
<plus/>
<ci>q_LR_M2_mLRGbinding_M2</ci>
<ci>q_LR_M2_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R_M2Gi</ci>
<apply>
<plus/>
<ci>q_R_M2Gi_mLRGbinding_M2</ci>
<ci>q_R_M2Gi_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_M2Gi</ci>
<apply>
<plus/>
<ci>q_LR_M2Gi_mLRGbinding_M2</ci>
<ci>q_LR_M2Gi_init</ci>
</apply>
</apply>
</math>
<!-- mass conservation checks -->
<variable name="L_T" units="fmol"/>
<variable name="R_T" units="fmol"/>
<variable name="Gi_T" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>L_T</ci>
<apply>
<plus/>
<ci>q_L_M2</ci>
<ci>q_LR_M2</ci>
<ci>q_LR_M2Gi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>R_T</ci>
<apply>
<plus/>
<ci>q_R_M2</ci>
<ci>q_LR_M2</ci>
<ci>q_R_M2Gi</ci>
<ci>q_LR_M2Gi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Gi_T</ci>
<apply>
<plus/>
<ci>q_Gi</ci>
<ci>q_R_M2Gi</ci>
<ci>q_LR_M2Gi</ci>
</apply>
</apply>
</math>
</component>
<component name="LRGbinding_M2_parameters">
<variable initial_value="18188.9" name="kappa_R_C_M2" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="626.532" name="kappa_R_R_M2" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="13018.6" name="kappa_R_L_M2" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0767207" name="K_L_M2" public_interface="out" units="per_fmol"/>
<variable initial_value="0.846069" name="K_R_M2" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0549123" name="K_Gi" public_interface="out" units="per_fmol"/>
<variable initial_value="24.5623" name="K_LR_M2" public_interface="out" units="per_fmol"/>
<variable initial_value="47.9464" name="K_R_M2Gi" public_interface="out" units="per_fmol"/>
<variable initial_value="106.329" name="K_LR_M2Gi" public_interface="out" units="per_fmol"/>
</component>
<component name="LRGbinding_M2">
<variable name="time" public_interface="in" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- parameters-->
<variable name="kappa_R_C_M2" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_R_M2" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_L_M2" public_interface="in" units="fmol_per_sec"/>
<variable name="K_L_M2" public_interface="in" units="per_fmol"/>
<variable name="K_R_M2" public_interface="in" units="per_fmol"/>
<variable name="K_Gi" public_interface="in" units="per_fmol"/>
<variable name="K_LR_M2" public_interface="in" units="per_fmol"/>
<variable name="K_R_M2Gi" public_interface="in" units="per_fmol"/>
<variable name="K_LR_M2Gi" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_L_M2_global" public_interface="in" units="fmol"/>
<variable name="q_R_M2_global" public_interface="in" units="fmol"/>
<variable name="q_Gi_global" public_interface="in" units="fmol"/>
<variable name="q_LR_M2_global" public_interface="in" units="fmol"/>
<variable name="q_R_M2Gi_global" public_interface="in" units="fmol"/>
<variable name="q_LR_M2Gi_global" public_interface="in" units="fmol"/>
<!-- Output to global environment-->
<variable initial_value="1e-16" name="q_L_M2" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_R_M2" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Gi" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_M2" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_R_M2Gi" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_M2Gi" public_interface="out" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_L_M2" units="J_per_mol"/>
<variable name="mu_R_M2" units="J_per_mol"/>
<variable name="mu_Gi" units="J_per_mol"/>
<variable name="mu_LR_M2" units="J_per_mol"/>
<variable name="mu_R_M2Gi" units="J_per_mol"/>
<variable name="mu_LR_M2Gi" units="J_per_mol"/>
<variable name="v_R_C_M2" units="fmol_per_sec"/>
<variable name="v_R_R_M2" units="fmol_per_sec"/>
<variable name="v_R_L_M2" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_L_M2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_L_M2</ci>
<ci>q_L_M2_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_M2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_M2</ci>
<ci>q_R_M2_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Gi</ci>
<ci>q_Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_M2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_M2</ci>
<ci>q_LR_M2_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_M2Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_M2Gi</ci>
<ci>q_R_M2Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_M2Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_M2Gi</ci>
<ci>q_LR_M2Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_C_M2</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_R_C_M2</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_M2</ci>
<ci>mu_Gi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_R_M2Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_R_M2</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_R_R_M2</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_LR_M2</ci>
<ci>mu_Gi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR_M2Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_L_M2</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_R_L_M2</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_M2</ci>
<ci>mu_L_M2</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR_M2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_L_M2</ci>
</apply>
<apply>
<minus/>
<ci>v_R_L_M2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_M2</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v_R_C_M2</ci>
</apply>
<ci>v_R_L_M2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Gi</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v_R_C_M2</ci>
</apply>
<ci>v_R_R_M2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_M2</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_R_M2</ci>
</apply>
<ci>v_R_L_M2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_M2Gi</ci>
</apply>
<ci>v_R_C_M2</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_M2Gi</ci>
</apply>
<ci>v_R_R_M2</ci>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="LRGbinding_M2"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_L_M2_mLRGbinding_M2" variable_2="q_L_M2"/>
<map_variables variable_1="q_L_M2" variable_2="q_L_M2_global"/>
<map_variables variable_1="q_R_M2_mLRGbinding_M2" variable_2="q_R_M2"/>
<map_variables variable_1="q_R_M2" variable_2="q_R_M2_global"/>
<map_variables variable_1="q_Gi_mLRGbinding_M2" variable_2="q_Gi"/>
<map_variables variable_1="q_Gi" variable_2="q_Gi_global"/>
<map_variables variable_1="q_LR_M2_mLRGbinding_M2" variable_2="q_LR_M2"/>
<map_variables variable_1="q_LR_M2" variable_2="q_LR_M2_global"/>
<map_variables variable_1="q_R_M2Gi_mLRGbinding_M2" variable_2="q_R_M2Gi"/>
<map_variables variable_1="q_R_M2Gi" variable_2="q_R_M2Gi_global"/>
<map_variables variable_1="q_LR_M2Gi_mLRGbinding_M2" variable_2="q_LR_M2Gi"/>
<map_variables variable_1="q_LR_M2Gi" variable_2="q_LR_M2Gi_global"/>
</connection>
<connection>
<map_components component_1="LRGbinding_M2" component_2="LRGbinding_M2_parameters"/>
<map_variables variable_1="kappa_R_C_M2" variable_2="kappa_R_C_M2"/>
<map_variables variable_1="kappa_R_R_M2" variable_2="kappa_R_R_M2"/>
<map_variables variable_1="kappa_R_L_M2" variable_2="kappa_R_L_M2"/>
<map_variables variable_1="K_L_M2" variable_2="K_L_M2"/>
<map_variables variable_1="K_R_M2" variable_2="K_R_M2"/>
<map_variables variable_1="K_Gi" variable_2="K_Gi"/>
<map_variables variable_1="K_LR_M2" variable_2="K_LR_M2"/>
<map_variables variable_1="K_R_M2Gi" variable_2="K_R_M2Gi"/>
<map_variables variable_1="K_LR_M2Gi" variable_2="K_LR_M2Gi"/>
</connection>
<connection>
<map_components component_1="constants" component_2="LRGbinding_M2"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
