Location: FCU_guanylylCyclase @ 680764a384e9 / FCU_guanylylCyclase.cellml

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-16 09:58:52+12:00
Desc:
Fix tab/space in RST
Permanent Source URI:
https://staging.physiomeproject.org/workspace/860/rawfile/680764a384e9850b39d5b1521c67ac32a4364b2c/FCU_guanylylCyclase.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="FCU_guanylylCyclase" 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="per_second" units_ref="per_second"/>
        <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>
    <import xlink:href="HaiMurphy/BG_HaiMurphy.cellml">
        <component component_ref="HaiMurphy" name="HaiMurphy"/>
    </import>
    <import xlink:href="cGMP/BG_cGMP.cellml">
        <component component_ref="cGMP" name="cGMP"/>
    </import>
    <import xlink:href="sGC/BG_sGC.cellml">
        <component component_ref="sGC" name="sGC"/>
    </import>
    <component name="BG_parameters">
        <variable initial_value="0.0628586" name="kappa_R_12" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="10.3507" name="kappa_R_34" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="1.13145" name="kappa_R_56" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.031236" name="kappa_R_78" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="192.663" name="kappa_R_1a_cGMP" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.00328297" name="kappa_R_1b_cGMP" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="56591.2" name="kappa_R_2a_cGMP" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.0110353" name="kappa_R_2b_cGMP" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="3.61127e+06" name="kappa_R_1_sGC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.00328297" name="kappa_R_2_sGC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="4.92446" name="kappa_R_3_sGC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.0361127" name="kappa_R_4_sGC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.01" name="kappa_R_DNO_sGC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="1.65213" name="K_A" public_interface="out" units="per_fmol"/>
        <variable initial_value="15.6959" name="K_M" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.105259" name="K_Mp" public_interface="out" units="per_fmol"/>
        <variable initial_value="1.44065" name="K_AM" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.00966114" name="K_AMp" public_interface="out" units="per_fmol"/>
        <variable initial_value="723.915" name="K_Pi" public_interface="out" units="per_fmol"/>
        <variable initial_value="1" name="K_Ca_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="1" name="K_cGMP" public_interface="out" units="per_fmol"/>
        <variable initial_value="17040" name="K_GTP" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.304602" name="K_E5c" public_interface="out" units="per_fmol"/>
        <variable initial_value="17.6706" name="K_PDE" public_interface="out" units="per_fmol"/>
        <variable initial_value="5190.42" name="K_GTP_E5c" public_interface="out" units="per_fmol"/>
        <variable initial_value="35.3412" name="K_cGMP_PDE" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0051282" name="K_GMP" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0276911" name="K_Eb" public_interface="out" units="per_fmol"/>
        <variable initial_value="1" name="K_NO" public_interface="out" units="per_fmol"/>
        <variable initial_value="30.4602" name="K_E6c" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.1" name="K_NO_product" public_interface="out" units="per_fmol"/>
    </component>
    <component name="environment">
        <variable name="t" public_interface="out" units="second"/>
        <variable initial_value="1" name="vol_myo" public_interface="out" units="pL"/>
        <!-- concentrations and molar amounts of GC, PDE, GMP, AM/M (etc) need to be sourced - they are currently guesses.-->
        <variable initial_value="1e-6" name="q_A" public_interface="out" units="fmol"/>
        <variable initial_value="1e-6" name="q_M" public_interface="out" units="fmol"/>
        <variable initial_value="0" name="q_Mp" public_interface="out" units="fmol"/>
        <variable initial_value="0" name="q_AM" public_interface="out" units="fmol"/>
        <variable initial_value="0" name="q_AMp" public_interface="out" units="fmol"/>
        <variable initial_value="15" name="q_Pi" public_interface="out" units="fmol"/>
        <variable initial_value="1e-3" name="q_Ca_i" public_interface="out" units="fmol"/>
        <variable initial_value="1e-6" name="q_cGMP" public_interface="out" units="fmol"/>
        <variable initial_value="0.0005" name="q_GTP" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_E5c" public_interface="out" units="fmol"/>
        <variable initial_value="1e-10" name="q_PDE" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_GTP_E5c" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_cGMP_PDE" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_GMP" public_interface="out" units="fmol"/>
        <variable initial_value="1e-6" name="q_Eb" public_interface="out" units="fmol"/>
        <variable initial_value="0.00836" name="q_NO" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_E6c" public_interface="out" units="fmol"/>
        <variable initial_value="1e-16" name="q_NO_product" public_interface="out" units="fmol"/>
        <!-- HaiMurphy imports-->
        <variable name="v_R_12" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_34" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_56" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_78" public_interface="in" units="fmol_per_sec"/>
        <variable initial_value="1.66" name="n_Cai_SM" public_interface="out" units="dimensionless"/>
        <!-- cGMP imports-->
        <variable name="v_R_1a_cGMP" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_1b_cGMP" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_2a_cGMP" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_2b_cGMP" public_interface="in" units="fmol_per_sec"/>
        <!-- sGC imports-->
        <variable name="v_R_1_sGC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_2_sGC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_3_sGC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_4_sGC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_DNO_sGC" public_interface="in" units="fmol_per_sec"/>
        <!-- constant rate of NO generation, converted from kinetic model J_NO-->
        <variable initial_value="0.000114" name="v_NO_generation" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_A</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_34</ci>
                    </apply>
                    <ci>v_R_78</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_M</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_12</ci>
                    </apply>
                    <ci>v_R_78</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Mp</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_12</ci>
                    <ci>v_R_34</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_AM</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_56</ci>
                    <ci>v_R_78</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_AMp</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_34</ci>
                    <ci>v_R_56</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Pi</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_12</ci>
                    </apply>
                    <ci>v_R_56</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Ca_i</ci>
                </apply>
                <apply>
                    <times/>
                    <ci>n_Cai_SM</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <minus/>
                            <ci>v_R_12</ci>
                        </apply>
                        <ci>v_R_56</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_cGMP</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <minus/>
                        <apply>
                            <minus/>
                            <apply>
                                <plus/>
                                <ci>v_R_12</ci>
                                <ci>v_R_56</ci>
                                <ci>v_R_1b_cGMP</ci>
                            </apply>
                            <ci>v_R_2a_cGMP</ci>
                        </apply>
                        <ci>v_R_2b_cGMP</ci>
                    </apply>
                    <apply>
                        <times/>
                        <cn cellml:units="dimensionless">2</cn>
                        <ci>v_R_4_sGC</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_GTP</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_1a_cGMP</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_E5c</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <plus/>
                        <apply>
                            <minus/>
                            <ci>v_R_1a_cGMP</ci>
                        </apply>
                        <ci>v_R_1b_cGMP</ci>
                        <ci>v_R_2_sGC</ci>
                        <ci>v_R_3_sGC</ci>
                    </apply>
                    <ci>v_R_4_sGC</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_PDE</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_2a_cGMP</ci>
                    </apply>
                    <ci>v_R_2b_cGMP</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_GTP_E5c</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_1a_cGMP</ci>
                    <ci>v_R_1b_cGMP</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_cGMP_PDE</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_2a_cGMP</ci>
                    <ci>v_R_2b_cGMP</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_GMP</ci>
                </apply>
                <ci>v_R_2b_cGMP</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Eb</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_1_sGC</ci>
                    </apply>
                    <ci>v_R_4_sGC</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_NO</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <apply>
                            <plus/>
                            <apply>
                                <minus/>
                                <ci>v_R_1_sGC</ci>
                            </apply>
                            <ci>v_R_4_sGC</ci>
                        </apply>
                        <ci>v_R_DNO_sGC</ci>
                    </apply>
                    <ci>v_NO_generation</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_E6c</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <minus/>
                        <ci>v_R_1_sGC</ci>
                        <ci>v_R_2_sGC</ci>
                    </apply>
                    <ci>v_R_3_sGC</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_NO_product</ci>
                </apply>
                <ci>v_R_DNO_sGC</ci>
            </apply>
        </math>
        <!-- stress calculation: from original HM 
 stress = AM + AMp -->
        <variable name="stress" units="dimensionless"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>stress</ci>
                <apply>
                    <divide/>
                    <apply>
                        <plus/>
                        <ci>q_AM</ci>
                        <ci>q_AMp</ci>
                    </apply>
                    <cn cellml:units="fmol">1</cn>
                </apply>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="environment" component_2="HaiMurphy"/>
        <map_variables variable_1="t" variable_2="time"/>
        <map_variables variable_1="q_A" variable_2="q_A"/>
        <map_variables variable_1="q_M" variable_2="q_M"/>
        <map_variables variable_1="q_Mp" variable_2="q_Mp"/>
        <map_variables variable_1="q_AM" variable_2="q_AM"/>
        <map_variables variable_1="q_AMp" variable_2="q_AMp"/>
        <map_variables variable_1="q_Pi" variable_2="q_Pi"/>
        <map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
        <map_variables variable_1="q_cGMP" variable_2="q_cGMP"/>
        <map_variables variable_1="v_R_12" variable_2="v_R_12"/>
        <map_variables variable_1="v_R_34" variable_2="v_R_34"/>
        <map_variables variable_1="v_R_56" variable_2="v_R_56"/>
        <map_variables variable_1="v_R_78" variable_2="v_R_78"/>
        <map_variables variable_1="n_Cai_SM" variable_2="n_Cai_SM"/>
    </connection>
    <connection>
        <map_components component_1="environment" component_2="cGMP"/>
        <map_variables variable_1="t" variable_2="time"/>
        <map_variables variable_1="q_GTP" variable_2="q_GTP"/>
        <map_variables variable_1="q_E5c" variable_2="q_E5c"/>
        <map_variables variable_1="q_cGMP" variable_2="q_cGMP"/>
        <map_variables variable_1="q_PDE" variable_2="q_PDE"/>
        <map_variables variable_1="q_GTP_E5c" variable_2="q_GTP_E5c"/>
        <map_variables variable_1="q_cGMP_PDE" variable_2="q_cGMP_PDE"/>
        <map_variables variable_1="q_GMP" variable_2="q_GMP"/>
        <map_variables variable_1="v_R_1a_cGMP" variable_2="v_R_1a_cGMP"/>
        <map_variables variable_1="v_R_1b_cGMP" variable_2="v_R_1b_cGMP"/>
        <map_variables variable_1="v_R_2a_cGMP" variable_2="v_R_2a_cGMP"/>
        <map_variables variable_1="v_R_2b_cGMP" variable_2="v_R_2b_cGMP"/>
    </connection>
    <connection>
        <map_components component_1="environment" component_2="sGC"/>
        <map_variables variable_1="t" variable_2="time"/>
        <map_variables variable_1="q_Eb" variable_2="q_Eb"/>
        <map_variables variable_1="q_NO" variable_2="q_NO"/>
        <map_variables variable_1="q_E6c" variable_2="q_E6c"/>
        <map_variables variable_1="q_E5c" variable_2="q_E5c"/>
        <map_variables variable_1="q_cGMP" variable_2="q_cGMP"/>
        <map_variables variable_1="q_NO_product" variable_2="q_NO_product"/>
        <map_variables variable_1="v_R_1_sGC" variable_2="v_R_1_sGC"/>
        <map_variables variable_1="v_R_2_sGC" variable_2="v_R_2_sGC"/>
        <map_variables variable_1="v_R_3_sGC" variable_2="v_R_3_sGC"/>
        <map_variables variable_1="v_R_4_sGC" variable_2="v_R_4_sGC"/>
        <map_variables variable_1="v_R_DNO_sGC" variable_2="v_R_DNO_sGC"/>
    </connection>
    <connection>
        <map_components component_1="BG_parameters" component_2="HaiMurphy"/>
        <map_variables variable_1="kappa_R_12" variable_2="kappa_R_12"/>
        <map_variables variable_1="kappa_R_34" variable_2="kappa_R_34"/>
        <map_variables variable_1="kappa_R_56" variable_2="kappa_R_56"/>
        <map_variables variable_1="kappa_R_78" variable_2="kappa_R_78"/>
        <map_variables variable_1="K_A" variable_2="K_A"/>
        <map_variables variable_1="K_M" variable_2="K_M"/>
        <map_variables variable_1="K_Mp" variable_2="K_Mp"/>
        <map_variables variable_1="K_AM" variable_2="K_AM"/>
        <map_variables variable_1="K_AMp" variable_2="K_AMp"/>
        <map_variables variable_1="K_Pi" variable_2="K_Pi"/>
        <map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
        <map_variables variable_1="K_cGMP" variable_2="K_cGMP"/>
    </connection>
    <connection>
        <map_components component_1="BG_parameters" component_2="cGMP"/>
        <map_variables variable_1="kappa_R_1a_cGMP" variable_2="kappa_R_1a_cGMP"/>
        <map_variables variable_1="kappa_R_1b_cGMP" variable_2="kappa_R_1b_cGMP"/>
        <map_variables variable_1="kappa_R_2a_cGMP" variable_2="kappa_R_2a_cGMP"/>
        <map_variables variable_1="kappa_R_2b_cGMP" variable_2="kappa_R_2b_cGMP"/>
        <map_variables variable_1="K_GTP" variable_2="K_GTP"/>
        <map_variables variable_1="K_E5c" variable_2="K_E5c"/>
        <map_variables variable_1="K_cGMP" variable_2="K_cGMP"/>
        <map_variables variable_1="K_PDE" variable_2="K_PDE"/>
        <map_variables variable_1="K_GTP_E5c" variable_2="K_GTP_E5c"/>
        <map_variables variable_1="K_cGMP_PDE" variable_2="K_cGMP_PDE"/>
        <map_variables variable_1="K_GMP" variable_2="K_GMP"/>
    </connection>
    <connection>
        <map_components component_1="BG_parameters" component_2="sGC"/>
        <map_variables variable_1="kappa_R_1_sGC" variable_2="kappa_R_1_sGC"/>
        <map_variables variable_1="kappa_R_2_sGC" variable_2="kappa_R_2_sGC"/>
        <map_variables variable_1="kappa_R_3_sGC" variable_2="kappa_R_3_sGC"/>
        <map_variables variable_1="kappa_R_4_sGC" variable_2="kappa_R_4_sGC"/>
        <map_variables variable_1="kappa_R_DNO_sGC" variable_2="kappa_R_DNO_sGC"/>
        <map_variables variable_1="K_Eb" variable_2="K_Eb"/>
        <map_variables variable_1="K_NO" variable_2="K_NO"/>
        <map_variables variable_1="K_E6c" variable_2="K_E6c"/>
        <map_variables variable_1="K_E5c" variable_2="K_E5c"/>
        <map_variables variable_1="K_cGMP" variable_2="K_cGMP"/>
        <map_variables variable_1="K_NO_product" variable_2="K_NO_product"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="HaiMurphy"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="cGMP"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="sGC"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
</model>