- 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/CellMLV2/GLUT1_BG.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/2.0#" name="GLUT1_BG">
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="params_BG_fit.cellml">
<component component_ref="params_BG" name="params_BG"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="./units.cellml">
<units units_ref="fmol" name="fmol"/>
<units units_ref="J_per_K_mol" name="J_per_K_mol"/>
<units units_ref="fmol_per_s" name="fmol_per_s"/>
<units units_ref="J_per_mol" name="J_per_mol"/>
<units units_ref="per_fmol" name="per_fmol"/>
</import>
<component name="GLUT1_BG">
<variable name="t" units="second"/>
<variable name="R" units="J_per_K_mol" interface="public"/>
<variable name="T" units="kelvin" interface="public"/>
<variable name="K_Ai" units="per_fmol" interface="public"/>
<variable name="q_init_Ai" units="fmol" interface="public"/>
<variable name="K_Ao" units="per_fmol" interface="public"/>
<variable name="q_init_Ao" units="fmol" interface="public"/>
<variable name="K_1" units="per_fmol" interface="public"/>
<variable name="q_init_1" units="fmol" interface="public"/>
<variable name="K_2" units="per_fmol" interface="public"/>
<variable name="q_init_2" units="fmol" interface="public"/>
<variable name="K_3" units="per_fmol" interface="public"/>
<variable name="q_init_3" units="fmol" interface="public"/>
<variable name="K_4" units="per_fmol" interface="public"/>
<variable name="q_init_4" units="fmol" interface="public"/>
<variable name="kappa_r1" units="fmol_per_s" interface="public"/>
<variable name="kappa_r2" units="fmol_per_s" interface="public"/>
<variable name="kappa_r3" units="fmol_per_s" interface="public"/>
<variable name="kappa_r4" units="fmol_per_s" interface="public"/>
<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 name="q_1" units="fmol" initial_value="q_init_1"/>
<variable name="q_2" units="fmol" initial_value="q_init_2"/>
<variable name="q_3" units="fmol" initial_value="q_init_3"/>
<variable name="q_4" units="fmol" initial_value="q_init_4"/>
<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 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>
