Location: BG_LRGbinding_M2 @ 88369d2f746a / BG_LRGbinding_M2.cellml

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>