Location: BG_GiProtein @ 2f73520c8f49 / BG_GiProtein.cellml

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2021-09-09 16:13:01+12:00
Desc:
Readding files
Permanent Source URI:
https://models.physiomeproject.org/workspace/6f9/rawfile/2f73520c8f4936be8a3f5b6e9425fe6042245549/BG_GiProtein.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_GiProtein" 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>
    <component name="environment">
        <variable name="time" public_interface="out" units="second"/>
        <variable initial_value="1e-6" name="q_LRG_init" units="fmol"/>
        <variable initial_value="1.697e-06" name="q_LR_init" units="fmol"/>
        <variable initial_value="0.000219725" name="q_R_init" units="fmol"/>
        <variable initial_value="0.145305" name="q_G_init" units="fmol"/>
        <variable initial_value="1e-6" name="q_RG_init" units="fmol"/>
        <variable initial_value="0.0009519" name="q_a_GTP_init" units="fmol"/>
        <variable initial_value="0.00097622" name="q_beta_gamma_init" units="fmol"/>
        <variable initial_value="2.44948e-05" name="q_a_GDP_init" units="fmol"/>
        <!-- Global value-->
        <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_LR" public_interface="out" units="fmol"/>
        <variable name="q_LRG" 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"/>
        <!-- From submodule-->
        <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"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>q_R</ci>
                <apply>
                    <plus/>
                    <ci>q_R_mGiProtein</ci>
                    <ci>q_R_init</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>q_G</ci>
                <apply>
                    <plus/>
                    <ci>q_G_mGiProtein</ci>
                    <ci>q_G_init</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>q_RG</ci>
                <apply>
                    <plus/>
                    <ci>q_RG_mGiProtein</ci>
                    <ci>q_RG_init</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>q_LR</ci>
                <apply>
                    <plus/>
                    <ci>q_LR_mGiProtein</ci>
                    <ci>q_LR_init</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>q_LRG</ci>
                <apply>
                    <plus/>
                    <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>
    <component name="GiProtein_parameters">
        <variable initial_value="0.0262364" name="kappa_act1" units="fmol_per_sec"/>
        <variable initial_value="0.00712165" name="kappa_act2" units="fmol_per_sec"/>
        <variable initial_value="0.0166591" name="kappa_hyd" units="fmol_per_sec"/>
        <variable initial_value="6992.75" name="kappa_reassoc" units="fmol_per_sec"/>
        <variable initial_value="8.00405e-06" name="K_R" units="per_fmol"/>
        <variable initial_value="5.03013e-06" name="K_G" units="per_fmol"/>
        <variable initial_value="2.76998" name="K_RG" units="per_fmol"/>
        <variable initial_value="2.94872e-05" name="K_LR" units="per_fmol"/>
        <variable initial_value="0.204094" name="K_LRG" units="per_fmol"/>
        <variable initial_value="1.39598" name="K_a_GTP" units="per_fmol"/>
        <variable initial_value="0.0837972" name="K_beta_gamma" units="per_fmol"/>
        <variable initial_value="0.00174498" name="K_a_GDP" units="per_fmol"/>
    </component>
    <component name="GiProtein">
        <variable name="time" public_interface="in" units="second"/>
        <!-- Physical parameters-->
        <variable name="R" public_interface="in" units="J_per_K_per_mol"/>
        <variable name="T" public_interface="in" units="kelvin"/>
        <!-- BG parameters-->
        <variable name="kappa_act1" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_act2" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_hyd" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_reassoc" public_interface="in" units="fmol_per_sec"/>
        <variable name="K_LRG" public_interface="in" units="per_fmol"/>
        <variable name="K_R" public_interface="in" units="per_fmol"/>
        <variable name="K_G" public_interface="in" units="per_fmol"/>
        <variable name="K_LR" public_interface="in" units="per_fmol"/>
        <variable name="K_RG" public_interface="in" units="per_fmol"/>
        <variable name="K_a_GTP" public_interface="in" units="per_fmol"/>
        <variable name="K_beta_gamma" public_interface="in" units="per_fmol"/>
        <variable name="K_a_GDP" public_interface="in" units="per_fmol"/>
        <!-- Input from global environment-->
        <variable name="q_R_global" public_interface="in" units="fmol"/>
        <variable name="q_G_global" public_interface="in" units="fmol"/>
        <variable name="q_RG_global" public_interface="in" units="fmol"/>
        <variable name="q_LR_global" public_interface="in" units="fmol"/>
        <variable name="q_LRG_global" public_interface="in" units="fmol"/>
        <variable name="q_a_GTP_global" public_interface="in" units="fmol"/>
        <variable name="q_beta_gamma_global" public_interface="in" units="fmol"/>
        <variable name="q_a_GDP_global" public_interface="in" units="fmol"/>
        <!-- Output to global environment-->
        <variable initial_value="1e-16" name="q_R" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_G" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_RG" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_LR" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_LRG" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_a_GTP" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_beta_gamma" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_a_GDP" public_interface="out" units="fmol"/>
        <!-- Bond variables-->
        <variable name="vact1" units="fmol_per_sec"/>
        <variable name="vact2" units="fmol_per_sec"/>
        <variable name="vhyd" units="fmol_per_sec"/>
        <variable name="vreassoc" units="fmol_per_sec"/>
        <variable name="mu_R" units="J_per_mol"/>
        <variable name="mu_G" units="J_per_mol"/>
        <variable name="mu_RG" units="J_per_mol"/>
        <variable name="mu_LR" units="J_per_mol"/>
        <variable name="mu_LRG" units="J_per_mol"/>
        <variable name="mu_a_GTP" units="J_per_mol"/>
        <variable name="mu_beta_gamma" units="J_per_mol"/>
        <variable name="mu_a_GDP" units="J_per_mol"/>
        <!-- Constitutive equations-->
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_R</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_R</ci>
                            <ci>q_R_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_G</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_G</ci>
                            <ci>q_G_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_RG</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_RG</ci>
                            <ci>q_RG_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_LR</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_LR</ci>
                            <ci>q_LR_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_LRG</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_LRG</ci>
                            <ci>q_LRG_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_a_GTP</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_a_GTP</ci>
                            <ci>q_a_GTP_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_beta_gamma</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_beta_gamma</ci>
                            <ci>q_beta_gamma_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_a_GDP</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_a_GDP</ci>
                            <ci>q_a_GDP_global</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vact1</ci>
                <apply>
                    <times/>
                    <ci>kappa_act1</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_RG</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_a_GTP</ci>
                                    <ci>mu_beta_gamma</ci>
                                    <ci>mu_R</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vact2</ci>
                <apply>
                    <times/>
                    <ci>kappa_act2</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_LRG</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_a_GTP</ci>
                                    <ci>mu_beta_gamma</ci>
                                    <ci>mu_LR</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vhyd</ci>
                <apply>
                    <times/>
                    <ci>kappa_hyd</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_a_GTP</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_a_GDP</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vreassoc</ci>
                <apply>
                    <times/>
                    <ci>kappa_reassoc</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_a_GDP</ci>
                                    <ci>mu_beta_gamma</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_G</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_R</ci>
                </apply>
                <ci>vact1</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_RG</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vact1</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_G</ci>
                </apply>
                <ci>vreassoc</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_LR</ci>
                </apply>
                <ci>vact2</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_LRG</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vact2</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_a_GTP</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <plus/>
                        <ci>vact1</ci>
                        <ci>vact2</ci>
                    </apply>
                    <ci>vhyd</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_beta_gamma</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <plus/>
                        <ci>vact1</ci>
                        <ci>vact2</ci>
                    </apply>
                    <ci>vreassoc</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_a_GDP</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vhyd</ci>
                    <ci>vreassoc</ci>
                </apply>
            </apply>
        </math>
    </component>
    <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="GiProtein_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="GiProtein"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
</model>