Location: SLC transporters @ d36dca3e6ed8 / Facilitated transporter / GLUT1_BG.cellml

Author:
Weiwei Ai <wai484@aucklanduni.ac.nz>
Date:
2024-04-08 18:20:16+12:00
Desc:
clean up; correct the cell volume to 0.09 pL; remove the param convertion equations in cellml; use python to do the conversion;
Permanent Source URI:
http://models.cellml.org/workspace/b65/rawfile/d36dca3e6ed80f08a478e14a9be7695786950d7e/Facilitated transporter/GLUT1_BG.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="GLUT1_BG" 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.cellml">
        <units name="fmol" units_ref="fmol"/>
        <units name="J_per_K_mol" units_ref="J_per_K_mol"/>
        <units name="fmol_per_s" units_ref="fmol_per_s"/>
        <units name="J_per_mol" units_ref="J_per_mol"/>
        <units name="per_fmol" units_ref="per_fmol"/>
    </import>
    <import xlink:href="params_BG.cellml">
        <component component_ref="params_BG" name="params_BG"/>
    </import>
    <component name="GLUT1_BG">
        <variable name="t" units="second"/>
        <variable name="R" public_interface="in" units="J_per_K_mol"/>
        <variable name="T" public_interface="in" units="kelvin"/>
        <variable name="K_Ai" public_interface="in" units="per_fmol"/>
        <variable name="q_init_Ai" public_interface="in" units="fmol"/>
        <variable name="K_Ao" public_interface="in" units="per_fmol"/>
        <variable name="q_init_Ao" public_interface="in" units="fmol"/>
        <variable name="K_1" public_interface="in" units="per_fmol"/>
        <variable name="q_init_1" public_interface="in" units="fmol"/>
        <variable name="K_2" public_interface="in" units="per_fmol"/>
        <variable name="q_init_2" public_interface="in" units="fmol"/>
        <variable name="K_3" public_interface="in" units="per_fmol"/>
        <variable name="q_init_3" public_interface="in" units="fmol"/>
        <variable name="K_4" public_interface="in" units="per_fmol"/>
        <variable name="q_init_4" public_interface="in" units="fmol"/>
        <variable name="kappa_r1" public_interface="in" units="fmol_per_s"/>
        <variable name="kappa_r2" public_interface="in" units="fmol_per_s"/>
        <variable name="kappa_r3" public_interface="in" units="fmol_per_s"/>
        <variable name="kappa_r4" public_interface="in" units="fmol_per_s"/>
        <variable name="mu_Ai" units="J_per_mol"/>
        <variable name="v_Ai" units="fmol_per_s"/>
        <variable name="mu_Ao" units="J_per_mol"/>
        <variable name="v_Ao" units="fmol_per_s"/>
        <variable name="mu_1" units="J_per_mol"/>
        <variable name="v_1" units="fmol_per_s"/>
        <variable name="mu_2" units="J_per_mol"/>
        <variable name="v_2" units="fmol_per_s"/>
        <variable name="mu_3" units="J_per_mol"/>
        <variable name="v_3" units="fmol_per_s"/>
        <variable name="mu_4" units="J_per_mol"/>
        <variable name="v_4" units="fmol_per_s"/>
        <variable name="A_f_r1" units="J_per_mol"/>
        <variable name="v_r1" units="fmol_per_s"/>
        <variable name="A_r_r1" units="J_per_mol"/>
        <variable name="A_f_r2" units="J_per_mol"/>
        <variable name="v_r2" units="fmol_per_s"/>
        <variable name="A_r_r2" units="J_per_mol"/>
        <variable name="A_f_r3" units="J_per_mol"/>
        <variable name="v_r3" units="fmol_per_s"/>
        <variable name="A_r_r3" units="J_per_mol"/>
        <variable name="A_f_r4" units="J_per_mol"/>
        <variable name="v_r4" units="fmol_per_s"/>
        <variable name="A_r_r4" units="J_per_mol"/>
        <variable name="q_Ai" units="fmol"/>
        <variable name="q_Ao" units="fmol"/>
        <variable initial_value="q_init_1" name="q_1" units="fmol"/>
        <variable initial_value="q_init_2" name="q_2" units="fmol"/>
        <variable initial_value="q_init_3" name="q_3" units="fmol"/>
        <variable initial_value="q_init_4" name="q_4" units="fmol"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_Ai</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Ai</ci>
                            <ci>q_Ai</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>q_Ai</ci>
                <ci>q_init_Ai</ci>
            </apply>
            <!--  ode(q_Ai,t) = v_Ai;-->
            <apply>
                <eq/>
                <ci>mu_Ao</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Ao</ci>
                            <ci>q_Ao</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>q_Ao</ci>
                <ci>q_init_Ao</ci>
            </apply>
            <!--  ode(q_Ao,t) = v_Ao;-->
            <apply>
                <eq/>
                <ci>mu_1</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_1</ci>
                            <ci>q_1</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_1</ci>
                </apply>
                <ci>v_1</ci>
            </apply>
            <apply>
                <eq/>
                <ci>mu_2</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_2</ci>
                            <ci>q_2</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_2</ci>
                </apply>
                <ci>v_2</ci>
            </apply>
            <apply>
                <eq/>
                <ci>mu_3</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_3</ci>
                            <ci>q_3</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_3</ci>
                </apply>
                <ci>v_3</ci>
            </apply>
            <apply>
                <eq/>
                <ci>mu_4</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_4</ci>
                            <ci>q_4</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_4</ci>
                </apply>
                <ci>v_4</ci>
            </apply>
            <apply>
                <eq/>
                <ci>v_r1</ci>
                <apply>
                    <times/>
                    <ci>kappa_r1</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_f_r1</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_r_r1</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_r2</ci>
                <apply>
                    <times/>
                    <ci>kappa_r2</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_f_r2</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_r_r2</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_r3</ci>
                <apply>
                    <times/>
                    <ci>kappa_r3</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_f_r3</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_r_r3</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_r4</ci>
                <apply>
                    <times/>
                    <ci>kappa_r4</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_f_r4</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>A_r_r4</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Ai</ci>
                <ci>v_r4</ci>
            </apply>
            <apply>
                <eq/>
                <ci>v_Ao</ci>
                <apply>
                    <minus/>
                    <ci>v_r3</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_1</ci>
                <apply>
                    <minus/>
                    <ci>v_r1</ci>
                    <ci>v_r3</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_2</ci>
                <apply>
                    <minus/>
                    <ci>v_r3</ci>
                    <ci>v_r2</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_3</ci>
                <apply>
                    <minus/>
                    <ci>v_r2</ci>
                    <ci>v_r4</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_4</ci>
                <apply>
                    <minus/>
                    <ci>v_r4</ci>
                    <ci>v_r1</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>A_f_r1</ci>
                <ci>mu_4</ci>
            </apply>
            <apply>
                <eq/>
                <ci>A_r_r1</ci>
                <ci>mu_1</ci>
            </apply>
            <apply>
                <eq/>
                <ci>A_f_r2</ci>
                <ci>mu_2</ci>
            </apply>
            <apply>
                <eq/>
                <ci>A_r_r2</ci>
                <ci>mu_3</ci>
            </apply>
            <apply>
                <eq/>
                <ci>A_f_r3</ci>
                <apply>
                    <plus/>
                    <ci>mu_Ao</ci>
                    <ci>mu_1</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>A_r_r3</ci>
                <ci>mu_2</ci>
            </apply>
            <apply>
                <eq/>
                <ci>A_f_r4</ci>
                <ci>mu_3</ci>
            </apply>
            <apply>
                <eq/>
                <ci>A_r_r4</ci>
                <apply>
                    <plus/>
                    <ci>mu_Ai</ci>
                    <ci>mu_4</ci>
                </apply>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="params_BG" component_2="GLUT1_BG"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="K_Ai" variable_2="K_Ai"/>
        <map_variables variable_1="q_init_Ai" variable_2="q_init_Ai"/>
        <map_variables variable_1="K_Ao" variable_2="K_Ao"/>
        <map_variables variable_1="q_init_Ao" variable_2="q_init_Ao"/>
        <map_variables variable_1="K_1" variable_2="K_1"/>
        <map_variables variable_1="q_init_1" variable_2="q_init_1"/>
        <map_variables variable_1="K_2" variable_2="K_2"/>
        <map_variables variable_1="q_init_2" variable_2="q_init_2"/>
        <map_variables variable_1="K_3" variable_2="K_3"/>
        <map_variables variable_1="q_init_3" variable_2="q_init_3"/>
        <map_variables variable_1="K_4" variable_2="K_4"/>
        <map_variables variable_1="q_init_4" variable_2="q_init_4"/>
        <map_variables variable_1="kappa_r1" variable_2="kappa_r1"/>
        <map_variables variable_1="kappa_r2" variable_2="kappa_r2"/>
        <map_variables variable_1="kappa_r3" variable_2="kappa_r3"/>
        <map_variables variable_1="kappa_r4" variable_2="kappa_r4"/>
    </connection>
</model>