- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2025-08-25 22:04:17+12:00
- Desc:
- Adding flattened model to work on the web simulator and the associated files to build the COMBINE archive.
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d5c/rawfile/654d22aca937fbfb98adc11b672b7b404e26a22f/GLUT_ss_oi_flat.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="GLUT2_BG" xmlns="http://www.cellml.org/cellml/1.0#">
<units name="amol">
<unit prefix="atto" units="mole"/>
</units>
<units name="per_s">
<unit exponent="-1" units="second"/>
</units>
<units name="J_per_K_mol">
<unit units="joule"/>
<unit exponent="-1" units="kelvin"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="C_per_mol">
<unit units="coulomb"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="J_per_mol">
<unit units="joule"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="fmol">
<unit prefix="femto" units="mole"/>
</units>
<units name="fF">
<unit prefix="femto" units="farad"/>
</units>
<units name="fC">
<unit prefix="femto" units="coulomb"/>
</units>
<units name="fS">
<unit prefix="femto" units="siemens"/>
</units>
<units name="fA">
<unit prefix="femto" units="ampere"/>
</units>
<units name="pL">
<unit prefix="pico" units="litre"/>
</units>
<units name="mM">
<unit prefix="milli" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="uM">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="fM">
<unit prefix="femto" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="mM_per_s">
<unit units="mM"/>
<unit exponent="-1" units="second"/>
</units>
<units name="uM_per_s">
<unit units="uM"/>
<unit exponent="-1" units="second"/>
</units>
<units name="fM_per_s">
<unit units="fM"/>
<unit exponent="-1" units="second"/>
</units>
<units name="per_s_fM">
<unit exponent="-1" units="second"/>
<unit exponent="-1" units="fM"/>
</units>
<units name="per_fmol">
<unit exponent="-1" units="fmol"/>
</units>
<units name="fmol_per_s">
<unit units="fmol"/>
<unit exponent="-1" units="second"/>
</units>
<component name="GLUT2_BG">
<variable name="t" units="second"/>
<variable name="K_Ai" public_interface="in" units="per_fmol"/>
<variable name="K_Ao" public_interface="in" units="per_fmol"/>
<variable name="K_1" public_interface="in" units="per_fmol"/>
<variable name="K_2" public_interface="in" units="per_fmol"/>
<variable name="K_3" public_interface="in" units="per_fmol"/>
<variable name="K_4" public_interface="in" units="per_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="q_Ai" units="fmol"/>
<variable name="q_Ao" units="fmol"/>
<variable name="lambda" units="dimensionless"/>
<variable name="q_tot" units="fmol"/>
<variable name="v_max" units="fmol_per_s"/>
<variable name="k_m_1" units="dimensionless"/>
<variable name="k_m_2" units="dimensionless"/>
<variable name="k_m_3" units="dimensionless"/>
<variable name="v" units="fmol_per_s"/>
<variable name="v_max_free" units="fmol_per_s"/>
<variable name="v_free" units="fmol_per_s"/>
<variable name="k_m_1_free" units="dimensionless"/>
<variable name="k_m_2_free" units="dimensionless"/>
<variable initial_value="218.96" name="k_m_3_free" units="dimensionless"/>
<variable initial_value="0.1094" name="k_oi_math" units="mM"/>
<variable initial_value="1.609" name="k_io_math" units="mM"/>
<variable initial_value="0.004839" name="v_oi_max" units="mM_per_s"/>
<variable initial_value="0.07117" name="v_io_max" units="mM_per_s"/>
<variable initial_value="1" name="V_E" units="pL"/>
<variable initial_value="6.67" name="GC" units="uM"/>
<variable initial_value="1e-8" name="g_i" units="mM"/>
<variable initial_value="1e-8" name="g_o" units="mM"/>
<variable initial_value="0.09" name="V_i" units="pL"/>
<variable initial_value="0.09" name="V_o" units="pL"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>g_o</ci>
</apply>
<cn cellml:units="mM_per_s">1</cn>
</apply>
<apply>
<eq/>
<ci>q_Ao</ci>
<apply>
<times/>
<ci>g_o</ci>
<ci>V_o</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Ai</ci>
<apply>
<times/>
<ci>g_i</ci>
<ci>V_i</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_tot</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>GC</ci>
<ci>V_E</ci>
<cn cellml:units="fmol">1</cn>
</apply>
<cn cellml:units="amol">1000</cn>
</apply>
</apply>
<apply>
<eq/>
<ci>v_max_free</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v_oi_max</ci>
<ci>V_E</ci>
</apply>
<ci>k_m_1_free</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_m_1_free</ci>
<apply>
<times/>
<ci>k_oi_math</ci>
<ci>V_i</ci>
<ci>K_Ai</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_m_2_free</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v_io_max</ci>
<ci>V_E</ci>
</apply>
<ci>v_max_free</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>lambda</ci>
<apply>
<divide/>
<ci>kappa_r2</ci>
<ci>kappa_r1</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_max</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>q_tot</ci>
<ci>kappa_r2</ci>
<ci>K_3</ci>
</apply>
<apply>
<plus/>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_1</ci>
</apply>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_4</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k_m_1</ci>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_1</ci>
</apply>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_4</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_2</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>lambda</ci>
<ci>K_3</ci>
</apply>
<ci>K_4</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k_m_2</ci>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_1</ci>
</apply>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_4</ci>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<apply>
<times/>
<ci>lambda</ci>
<ci>K_3</ci>
</apply>
<ci>K_1</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k_m_3</ci>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_1</ci>
</apply>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_4</ci>
</apply>
</apply>
<apply>
<times/>
<ci>lambda</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<ci>K_3</ci>
<ci>K_2</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v_max</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_Ao</ci>
<ci>q_Ao</ci>
</apply>
<apply>
<times/>
<ci>K_Ai</ci>
<ci>q_Ai</ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Ao</ci>
<ci>q_Ao</ci>
</apply>
<ci>k_m_1</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Ai</ci>
<ci>q_Ai</ci>
</apply>
<ci>k_m_2</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Ao</ci>
<ci>q_Ao</ci>
<ci>K_Ai</ci>
<ci>q_Ai</ci>
</apply>
<ci>k_m_3</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_free</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v_max_free</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_Ao</ci>
<ci>q_Ao</ci>
</apply>
<apply>
<times/>
<ci>K_Ai</ci>
<ci>q_Ai</ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Ao</ci>
<ci>q_Ao</ci>
</apply>
<ci>k_m_1_free</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Ai</ci>
<ci>q_Ai</ci>
</apply>
<ci>k_m_2_free</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Ao</ci>
<ci>q_Ao</ci>
<ci>K_Ai</ci>
<ci>q_Ai</ci>
</apply>
<ci>k_m_3_free</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="params_BG">
<variable initial_value="8.31" name="R" public_interface="out" units="J_per_K_mol"/>
<variable initial_value="273.15" name="T" public_interface="out" units="kelvin"/>
<variable initial_value="149.65" name="K_Ai" public_interface="out" units="per_fmol"/>
<variable name="q_init_Ai" public_interface="out" units="fmol"/>
<variable initial_value="149.65" name="K_Ao" public_interface="out" units="per_fmol"/>
<variable name="q_init_Ao" public_interface="out" units="fmol"/>
<variable initial_value="33.20" name="K_1" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0017" name="q_init_1" public_interface="out" units="fmol"/>
<variable initial_value="4.25e+03" name="K_2" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0017" name="q_init_2" public_interface="out" units="fmol"/>
<variable initial_value="344.59" name="K_3" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0017" name="q_init_3" public_interface="out" units="fmol"/>
<variable initial_value="1.99" name="K_4" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0017" name="q_init_4" public_interface="out" units="fmol"/>
<variable initial_value="0.36" name="kappa_r1" public_interface="out" units="fmol_per_s"/>
<variable initial_value="0.26" name="kappa_r2" public_interface="out" units="fmol_per_s"/>
<variable initial_value="1.01e+05" name="kappa_r3" public_interface="out" units="fmol_per_s"/>
<variable initial_value="1.01e+04" name="kappa_r4" public_interface="out" units="fmol_per_s"/>
<variable initial_value="0.09" name="V_i" units="pL"/>
<variable initial_value="10" name="g_i" units="mM"/>
<variable initial_value="1e-5" name="g_o" units="mM"/>
<variable initial_value="0.09" name="V_o" public_interface="out" units="pL"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<apply>
<eq/>
<ci>q_init_Ao</ci>
<apply>
<times/>
<ci>g_o</ci>
<ci>V_o</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_init_Ai</ci>
<apply>
<times/>
<ci>g_i</ci>
<ci>V_i</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="params_BG" component_2="GLUT2_BG"/>
<map_variables variable_1="K_Ai" variable_2="K_Ai"/>
<map_variables variable_1="K_Ao" variable_2="K_Ao"/>
<map_variables variable_1="K_1" variable_2="K_1"/>
<map_variables variable_1="K_2" variable_2="K_2"/>
<map_variables variable_1="K_3" variable_2="K_3"/>
<map_variables variable_1="K_4" variable_2="K_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>
