Location: BG_Inhib1 @ 21e434d1a778 / BG_PKA.cellml

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2021-08-04 16:31:51+12:00
Desc:
Finding BG parameters from kinetic, version 1 (incomplete)
Permanent Source URI:
https://models.cellml.org/workspace/6d6/rawfile/21e434d1a778b748dbd26e9e8ad894d2fe47c825/BG_PKA.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_PKA" 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"/>
    </component>
    <component name="PKA">
        <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"/>
        <!-- PKA parameters-->
        <variable initial_value="308157" name="kappa_aI" units="fmol_per_sec"/>
        <variable initial_value="4.21426e+07" name="kappa_bI" units="fmol_per_sec"/>
        <variable initial_value="9.63258e-12" name="kappa_dI" units="fmol_per_sec"/>
        <variable initial_value="0.0157933" name="kappa_iI" units="fmol_per_sec"/>
        <variable initial_value="308157" name="kappa_aII" units="fmol_per_sec"/>
        <variable initial_value="4.21426e+07" name="kappa_bII" units="fmol_per_sec"/>
        <variable initial_value="9.63258e-12" name="kappa_dII" units="fmol_per_sec"/>
        <variable initial_value="0.0157933" name="kappa_iII" units="fmol_per_sec"/>
        <variable initial_value="4.45869e-21" name="K_cAMP" units="per_fmol"/>
        <variable initial_value="6.22149e-14" name="K_PKI" units="per_fmol"/>
        <variable initial_value="0.0796295" name="K_RCI" units="per_fmol"/>
        <variable initial_value="0.0032451" name="K_ARCI" units="per_fmol"/>
        <variable initial_value="2.3729e-05" name="K_A2RCI" units="per_fmol"/>
        <variable initial_value="5088.64" name="K_CI" units="per_fmol"/>
        <variable initial_value="2.04012e+10" name="K_A2RI" units="per_fmol"/>
        <variable initial_value="63317.9" name="K_PKACI_PKI" units="per_fmol"/>
        <variable initial_value="0.0796295" name="K_RCII" units="per_fmol"/>
        <variable initial_value="0.0032451" name="K_ARCII" units="per_fmol"/>
        <variable initial_value="2.3729e-05" name="K_A2RCII" units="per_fmol"/>
        <variable initial_value="5088.64" name="K_CII" units="per_fmol"/>
        <variable initial_value="2.04012e+10" name="K_A2RII" units="per_fmol"/>
        <variable initial_value="63317.9" name="K_PKACII_PKI" units="per_fmol"/>
        <variable initial_value="3.212E-02" name="q_cAMP" units="fmol"/>
        <variable initial_value="6.840E-03" name="q_PKI" units="fmol"/>
        <variable initial_value="2.242E-02" name="q_RCI" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_ARCI" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_A2RCI" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_CI" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_A2RI" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_PKACI_PKI" units="fmol"/>
        <variable initial_value="9.500E-04" name="q_RCII" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_ARCII" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_A2RCII" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_CII" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_A2RII" units="fmol"/>
        <variable initial_value="3.800E-15" name="q_PKACII_PKI" units="fmol"/>
        <variable name="vaI" units="fmol_per_sec"/>
        <variable name="vbI" units="fmol_per_sec"/>
        <variable name="vdI" units="fmol_per_sec"/>
        <variable name="viI" units="fmol_per_sec"/>
        <variable name="vaII" units="fmol_per_sec"/>
        <variable name="vbII" units="fmol_per_sec"/>
        <variable name="vdII" units="fmol_per_sec"/>
        <variable name="viII" units="fmol_per_sec"/>
        <variable name="mu_cAMP" units="J_per_mol"/>
        <variable name="mu_PKI" units="J_per_mol"/>
        <variable name="mu_RCI" units="J_per_mol"/>
        <variable name="mu_ARCI" units="J_per_mol"/>
        <variable name="mu_A2RCI" units="J_per_mol"/>
        <variable name="mu_CI" units="J_per_mol"/>
        <variable name="mu_A2RI" units="J_per_mol"/>
        <variable name="mu_PKACI_PKI" units="J_per_mol"/>
        <variable name="mu_RCII" units="J_per_mol"/>
        <variable name="mu_ARCII" units="J_per_mol"/>
        <variable name="mu_A2RCII" units="J_per_mol"/>
        <variable name="mu_CII" units="J_per_mol"/>
        <variable name="mu_A2RII" units="J_per_mol"/>
        <variable name="mu_PKACII_PKI" units="J_per_mol"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_cAMP</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_cAMP</ci>
                            <ci>q_cAMP</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_PKI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_PKI</ci>
                            <ci>q_PKI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_RCI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_RCI</ci>
                            <ci>q_RCI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_ARCI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_ARCI</ci>
                            <ci>q_ARCI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_A2RCI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_A2RCI</ci>
                            <ci>q_A2RCI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_CI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_CI</ci>
                            <ci>q_CI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_A2RI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_A2RI</ci>
                            <ci>q_A2RI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_PKACI_PKI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_PKACI_PKI</ci>
                            <ci>q_PKACI_PKI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_RCII</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_RCII</ci>
                            <ci>q_RCII</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_ARCII</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_ARCII</ci>
                            <ci>q_ARCII</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_A2RCII</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_A2RCII</ci>
                            <ci>q_A2RCII</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_CII</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_CII</ci>
                            <ci>q_CII</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_A2RII</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_A2RII</ci>
                            <ci>q_A2RII</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_PKACII_PKI</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_PKACII_PKI</ci>
                            <ci>q_PKACII_PKI</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vaI</ci>
                <apply>
                    <times/>
                    <ci>kappa_aI</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_RCI</ci>
                                    <ci>mu_cAMP</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_ARCI</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vbI</ci>
                <apply>
                    <times/>
                    <ci>kappa_bI</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_ARCI</ci>
                                    <ci>mu_cAMP</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_A2RCI</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vdI</ci>
                <apply>
                    <times/>
                    <ci>kappa_dI</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_A2RCI</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_A2RI</ci>
                                    <ci>mu_CI</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>viI</ci>
                <apply>
                    <times/>
                    <ci>kappa_iI</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_CI</ci>
                                    <ci>mu_PKI</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_PKACI_PKI</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vaII</ci>
                <apply>
                    <times/>
                    <ci>kappa_aII</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_RCII</ci>
                                    <ci>mu_cAMP</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_ARCII</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vbII</ci>
                <apply>
                    <times/>
                    <ci>kappa_bII</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_ARCII</ci>
                                    <ci>mu_cAMP</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_A2RCII</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>vdII</ci>
                <apply>
                    <times/>
                    <ci>kappa_dII</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_A2RCII</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_A2RII</ci>
                                    <ci>mu_CII</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>viII</ci>
                <apply>
                    <times/>
                    <ci>kappa_iII</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_CII</ci>
                                    <ci>mu_PKI</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_PKACII_PKI</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_cAMP</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <minus/>
                        <apply>
                            <minus/>
                            <apply>
                                <minus/>
                                <ci>vaI</ci>
                            </apply>
                            <ci>vbI</ci>
                        </apply>
                        <ci>vaII</ci>
                    </apply>
                    <ci>vbII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_PKI</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <minus/>
                        <ci>viI</ci>
                    </apply>
                    <ci>viII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_RCI</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vaI</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_ARCI</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vaI</ci>
                    <ci>vbI</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_A2RCI</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vbI</ci>
                    <ci>vdI</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_CI</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vdI</ci>
                    <ci>viI</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_A2RI</ci>
                </apply>
                <ci>vdI</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_PKACI_PKI</ci>
                </apply>
                <ci>viI</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_RCII</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vaII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_ARCII</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vaII</ci>
                    <ci>vbII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_A2RCII</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vbII</ci>
                    <ci>vdII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_CII</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>vdII</ci>
                    <ci>viII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_A2RII</ci>
                </apply>
                <ci>vdII</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_PKACII_PKI</ci>
                </apply>
                <ci>viII</ci>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="environment" component_2="PKA"/>
        <map_variables variable_1="time" variable_2="time"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="PKA"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
</model>