- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-09-10 11:17:45+12:00
- Desc:
- updating cellml files
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/674/rawfile/0638ad8cc521adabcc15a354e05ada60d639dc9d/BG_cAMP.cellml
<?xml version='1.0' encoding='UTF-8'?>
<!-- BG model of cAMP, based on saucerman2003, v1
20may21 initialising file
24may21: basal reaction with AC.
given Km and kcat for kinetic versions of enzyme reaction, recreate BG parameters by setting k1+ = 1, k2+ = 0, K_E = 1 to be able to solve for K_S, K_C, kappa1 and kappa2
See Pan thesis section 4.2
21 Jul 21: constraint of cAMP to 5AMP using gibbs free energy from literature-->
<model name="BG_cAMP" 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"/>
<!-- initial conditions-->
<variable initial_value="189.99905570" name="q_ATP_init" units="fmol"/>
<variable initial_value="0.0006143333" name="q_AC_init" units="fmol"/>
<variable initial_value="0.0314042742" name="q_cAMP_init" units="fmol"/>
<variable initial_value="0.000614333" name="q_AC_ATP_init" units="fmol"/>
<variable initial_value="0.0000126667" name="q_FSK_init" units="fmol"/>
<variable initial_value="0.0000126667" name="q_FSK_AC_init" units="fmol"/>
<variable initial_value="0.0000126667" name="q_FSK_AC_ATP_init" units="fmol"/>
<variable initial_value="0.00031730" name="q_GsT_init" units="fmol"/>
<variable initial_value="0.00031730" name="q_GsT_AC_init" units="fmol"/>
<variable initial_value="0.00031730" name="q_GsT_AC_ATP_init" units="fmol"/>
<variable initial_value="0.0007171258" name="q_PDE_init" units="fmol"/>
<variable initial_value="1e-13" name="q_PDEinh_init" units="fmol"/>
<variable initial_value="0.0007171258" name="q_PDE_cAMP_init" units="fmol"/>
<variable initial_value="3.80E-06" name="q_IBMX_init" units="fmol"/>
<variable initial_value="1e-18" name="q_five_AMP_init" units="fmol"/>
<!-- Global value-->
<variable name="q_ATP" public_interface="out" units="fmol"/>
<variable name="q_cAMP" public_interface="out" units="fmol"/>
<variable name="q_AC" public_interface="out" units="fmol"/>
<variable name="q_AC_ATP" public_interface="out" units="fmol"/>
<variable name="q_GsT_AC" public_interface="out" units="fmol"/>
<variable name="q_GsT_AC_ATP" public_interface="out" units="fmol"/>
<variable name="q_FSK_AC" public_interface="out" units="fmol"/>
<variable name="q_FSK_AC_ATP" public_interface="out" units="fmol"/>
<variable name="q_PDE" public_interface="out" units="fmol"/>
<variable name="q_PDE_cAMP" public_interface="out" units="fmol"/>
<variable name="q_five_AMP" public_interface="out" units="fmol"/>
<variable name="q_IBMX" public_interface="out" units="fmol"/>
<variable name="q_PDEinh" public_interface="out" units="fmol"/>
<variable name="q_GsT" public_interface="out" units="fmol"/>
<variable name="q_FSK" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="q_ATP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_cAMP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_AC_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_AC_ATP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_GsT_AC_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_GsT_AC_ATP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_FSK_AC_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_FSK_AC_ATP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_PDE_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_PDE_cAMP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_five_AMP_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_IBMX_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_PDEinh_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_GsT_mcAMP" public_interface="in" units="fmol"/>
<variable name="q_FSK_mcAMP" public_interface="in" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_ATP</ci>
<apply>
<plus/>
<ci>q_ATP_mcAMP</ci>
<ci>q_ATP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_cAMP</ci>
<apply>
<plus/>
<ci>q_cAMP_mcAMP</ci>
<ci>q_cAMP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_AC</ci>
<apply>
<plus/>
<ci>q_AC_mcAMP</ci>
<ci>q_AC_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_AC_ATP</ci>
<apply>
<plus/>
<ci>q_AC_ATP_mcAMP</ci>
<ci>q_AC_ATP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_GsT_AC</ci>
<apply>
<plus/>
<ci>q_GsT_AC_mcAMP</ci>
<ci>q_GsT_AC_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_GsT_AC_ATP</ci>
<apply>
<plus/>
<ci>q_GsT_AC_ATP_mcAMP</ci>
<ci>q_GsT_AC_ATP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_FSK_AC</ci>
<apply>
<plus/>
<ci>q_FSK_AC_mcAMP</ci>
<ci>q_FSK_AC_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_FSK_AC_ATP</ci>
<apply>
<plus/>
<ci>q_FSK_AC_ATP_mcAMP</ci>
<ci>q_FSK_AC_ATP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_PDE</ci>
<apply>
<plus/>
<ci>q_PDE_mcAMP</ci>
<ci>q_PDE_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_PDE_cAMP</ci>
<apply>
<plus/>
<ci>q_PDE_cAMP_mcAMP</ci>
<ci>q_PDE_cAMP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_five_AMP</ci>
<apply>
<plus/>
<ci>q_five_AMP_mcAMP</ci>
<ci>q_five_AMP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_IBMX</ci>
<apply>
<plus/>
<ci>q_IBMX_mcAMP</ci>
<ci>q_IBMX_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_PDEinh</ci>
<apply>
<plus/>
<ci>q_PDEinh_mcAMP</ci>
<ci>q_PDEinh_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_GsT</ci>
<apply>
<plus/>
<ci>q_GsT_mcAMP</ci>
<ci>q_GsT_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_FSK</ci>
<apply>
<plus/>
<ci>q_FSK_mcAMP</ci>
<ci>q_FSK_init</ci>
</apply>
</apply>
</math>
</component>
<component name="cAMP_parameters">
<variable initial_value="1.44613e+06" name="kappa_1a" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.000301939" name="kappa_1b" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="94062" name="kappa_2a" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0253818" name="kappa_2b" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.7132e+08" name="kappa_3a" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="3.15488e-17" name="kappa_3b" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="316229" name="kappa_4a" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.21627" name="kappa_4b" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="204.342" name="kappa_5" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="761.387" name="kappa_6" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="219620" name="kappa_7" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.35306e-05" name="K_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="2.35306e-05" name="K_cAMP" public_interface="out" units="per_fmol"/>
<variable initial_value="23.0954" name="K_AC" public_interface="out" units="per_fmol"/>
<variable initial_value="19.2554" name="K_AC_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="38.18" name="K_GsT_AC" public_interface="out" units="per_fmol"/>
<variable initial_value="9.73504" name="K_GsT_AC_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.132364" name="K_FSK_AC" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0921422" name="K_FSK_AC_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="113.566" name="K_PDE" public_interface="out" units="per_fmol"/>
<variable initial_value="0.119504" name="K_PDE_cAMP" public_interface="out" units="per_fmol"/>
<variable initial_value="2.35306e-05" name="K_five_AMP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00121382" name="K_IBMX" public_interface="out" units="per_fmol"/>
<variable initial_value="142.26" name="K_PDEinh" public_interface="out" units="per_fmol"/>
<variable initial_value="0.120142" name="K_GsT" public_interface="out" units="per_fmol"/>
<variable initial_value="3.78646e-06" name="K_FSK" public_interface="out" units="per_fmol"/>
</component>
<component name="cAMP">
<variable name="time" public_interface="in" units="second"/>
<!-- Physical parameters-->
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- Bond graph parameters, found using pinv of kinetic parameters-->
<variable name="kappa_1a" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_1b" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_2a" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_2b" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_3a" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_3b" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_4a" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_4b" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_5" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_6" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_7" public_interface="in" units="fmol_per_sec"/>
<variable name="K_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_cAMP" public_interface="in" units="per_fmol"/>
<variable name="K_AC" public_interface="in" units="per_fmol"/>
<variable name="K_AC_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_GsT_AC" public_interface="in" units="per_fmol"/>
<variable name="K_GsT_AC_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_FSK_AC" public_interface="in" units="per_fmol"/>
<variable name="K_FSK_AC_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_PDE" public_interface="in" units="per_fmol"/>
<variable name="K_PDE_cAMP" public_interface="in" units="per_fmol"/>
<variable name="K_five_AMP" public_interface="in" units="per_fmol"/>
<variable name="K_IBMX" public_interface="in" units="per_fmol"/>
<variable name="K_PDEinh" public_interface="in" units="per_fmol"/>
<variable name="K_GsT" public_interface="in" units="per_fmol"/>
<variable name="K_FSK" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_ATP_global" public_interface="in" units="fmol"/>
<variable name="q_cAMP_global" public_interface="in" units="fmol"/>
<variable name="q_AC_global" public_interface="in" units="fmol"/>
<variable name="q_AC_ATP_global" public_interface="in" units="fmol"/>
<variable name="q_GsT_AC_global" public_interface="in" units="fmol"/>
<variable name="q_GsT_AC_ATP_global" public_interface="in" units="fmol"/>
<variable name="q_FSK_AC_global" public_interface="in" units="fmol"/>
<variable name="q_FSK_AC_ATP_global" public_interface="in" units="fmol"/>
<variable name="q_PDE_global" public_interface="in" units="fmol"/>
<variable name="q_PDE_cAMP_global" public_interface="in" units="fmol"/>
<variable name="q_five_AMP_global" public_interface="in" units="fmol"/>
<variable name="q_IBMX_global" public_interface="in" units="fmol"/>
<variable name="q_PDEinh_global" public_interface="in" units="fmol"/>
<variable name="q_GsT_global" public_interface="in" units="fmol"/>
<variable name="q_FSK_global" public_interface="in" units="fmol"/>
<!-- Output to global environment-->
<variable initial_value="1e-16" name="q_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_cAMP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_AC" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_AC_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_GsT_AC" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_GsT_AC_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_FSK_AC" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_FSK_AC_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_PDE" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_PDE_cAMP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_five_AMP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_IBMX" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_PDEinh" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_GsT" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_FSK" public_interface="out" units="fmol"/>
<!-- Bond variables-->
<variable name="v1a" units="fmol_per_sec"/>
<variable name="v1b" units="fmol_per_sec"/>
<variable name="v2a" units="fmol_per_sec"/>
<variable name="v2b" units="fmol_per_sec"/>
<variable name="v3a" units="fmol_per_sec"/>
<variable name="v3b" units="fmol_per_sec"/>
<variable name="v4a" units="fmol_per_sec"/>
<variable name="v4b" units="fmol_per_sec"/>
<variable name="v5" units="fmol_per_sec"/>
<variable name="v6" units="fmol_per_sec"/>
<variable name="v7" units="fmol_per_sec"/>
<variable name="mu_ATP" units="J_per_mol"/>
<variable name="mu_AC" units="J_per_mol"/>
<variable name="mu_cAMP" units="J_per_mol"/>
<variable name="mu_AC_ATP" units="J_per_mol"/>
<variable name="mu_FSK" units="J_per_mol"/>
<variable name="mu_FSK_AC" units="J_per_mol"/>
<variable name="mu_FSK_AC_ATP" units="J_per_mol"/>
<variable name="mu_GsT" units="J_per_mol"/>
<variable name="mu_GsT_AC" units="J_per_mol"/>
<variable name="mu_GsT_AC_ATP" units="J_per_mol"/>
<variable name="mu_PDE" units="J_per_mol"/>
<variable name="mu_PDEinh" units="J_per_mol"/>
<variable name="mu_PDE_cAMP" units="J_per_mol"/>
<variable name="mu_IBMX" units="J_per_mol"/>
<variable name="mu_five_AMP" units="J_per_mol"/>
<!-- Concentrations - for plotting-->
<variable name="c_ATP" units="uM"/>
<variable name="c_cAMP" units="uM"/>
<variable name="c_FSK" units="uM"/>
<variable name="c_GsT" units="uM"/>
<variable name="c_PDE" units="uM"/>
<variable name="c_IBMX" units="uM"/>
<variable name="c_five_AMP" units="uM"/>
<variable name="c_AC" units="uM"/>
<variable name="c_AC_ATP" units="uM"/>
<variable name="c_GsT_AC_ATP" units="uM"/>
<variable name="c_GsT_AC" units="uM"/>
<variable initial_value="38.0" name="vol" units="pL"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>c_ATP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_ATP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_cAMP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_cAMP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_FSK</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_FSK</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_IBMX</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_IBMX</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_GsT</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_GsT</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_PDE</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_PDE</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_five_AMP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_five_AMP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_AC</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_AC</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_AC_ATP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_AC_ATP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_GsT_AC_ATP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_GsT_AC_ATP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_GsT_AC</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_GsT_AC</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<!-- Constitutive equations-->
<apply>
<eq/>
<ci>mu_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ATP</ci>
<ci>q_ATP_global</ci>
</apply>
</apply>
</apply>
</apply>
<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_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AC</ci>
<ci>q_AC_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AC_ATP</ci>
<ci>q_AC_ATP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GsT_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GsT_AC</ci>
<ci>q_GsT_AC_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GsT_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GsT_AC_ATP</ci>
<ci>q_GsT_AC_ATP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_FSK_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_FSK_AC</ci>
<ci>q_FSK_AC_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_FSK_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_FSK_AC_ATP</ci>
<ci>q_FSK_AC_ATP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PDE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDE</ci>
<ci>q_PDE_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PDE_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDE_cAMP</ci>
<ci>q_PDE_cAMP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_five_AMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_five_AMP</ci>
<ci>q_five_AMP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_IBMX</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_IBMX</ci>
<ci>q_IBMX_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PDEinh</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDEinh</ci>
<ci>q_PDEinh_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GsT</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GsT</ci>
<ci>q_GsT_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_FSK</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_FSK</ci>
<ci>q_FSK_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v1a</ci>
<apply>
<times/>
<ci>kappa_1a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AC</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v1b</ci>
<apply>
<times/>
<ci>kappa_1b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AC</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v2a</ci>
<apply>
<times/>
<ci>kappa_2a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_GsT_AC</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GsT_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v2b</ci>
<apply>
<times/>
<ci>kappa_2b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GsT_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_GsT_AC</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v3a</ci>
<apply>
<times/>
<ci>kappa_3a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_FSK_AC</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_FSK_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v3b</ci>
<apply>
<times/>
<ci>kappa_3b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_FSK_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_FSK_AC</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v4a</ci>
<apply>
<times/>
<ci>kappa_4a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_PDE</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PDE_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v4b</ci>
<apply>
<times/>
<ci>kappa_4b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PDE_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_PDE</ci>
<ci>mu_five_AMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v5</ci>
<apply>
<times/>
<ci>kappa_5</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_PDE</ci>
<ci>mu_IBMX</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PDEinh</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v6</ci>
<apply>
<times/>
<ci>kappa_6</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AC</ci>
<ci>mu_GsT</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GsT_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v7</ci>
<apply>
<times/>
<ci>kappa_7</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_FSK</ci>
<ci>mu_AC</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_FSK_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
<!-- velocity in uM_per_sec-->
<variable name="v1b_kinetic" units="uM_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v1b_kinetic</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v1b</ci>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_ATP</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>v1a</ci>
</apply>
<ci>v3a</ci>
</apply>
<ci>v2a</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_AC</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>v1b</ci>
<ci>v1a</ci>
</apply>
<ci>v6</ci>
</apply>
<ci>v7</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_AC_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v1a</ci>
<ci>v1b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_cAMP</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v1b</ci>
<ci>v3b</ci>
<ci>v2b</ci>
</apply>
<ci>v4a</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_FSK</ci>
</apply>
<apply>
<minus/>
<ci>v7</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_FSK_AC</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v7</ci>
<ci>v3b</ci>
</apply>
<ci>v3a</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_FSK_AC_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v3a</ci>
<ci>v3b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_GsT</ci>
</apply>
<apply>
<minus/>
<ci>v6</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_GsT_AC</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v6</ci>
<ci>v2a</ci>
</apply>
<ci>v2b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_GsT_AC_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v2a</ci>
<ci>v2b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PDE_cAMP</ci>
</apply>
<apply>
<minus/>
<ci>v4a</ci>
<ci>v4b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PDE</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v4b</ci>
<ci>v4a</ci>
</apply>
<ci>v5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_IBMX</ci>
</apply>
<apply>
<minus/>
<ci>v5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PDEinh</ci>
</apply>
<ci>v5</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_five_AMP</ci>
</apply>
<ci>v4b</ci>
</apply>
</math>
<!-- calculate velocity wrt changing concentration rate-->
<variable name="PDE_ACT_4a" units="mM_per_sec"/>
<variable name="PDE_ACT_4ab" units="mM_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>PDE_ACT_4a</ci>
<apply>
<divide/>
<ci>v4a</ci>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>PDE_ACT_4ab</ci>
<apply>
<divide/>
<apply>
<minus/>
<ci>v4a</ci>
<ci>v4b</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="cAMP"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_ATP_mcAMP" variable_2="q_ATP"/>
<map_variables variable_1="q_ATP" variable_2="q_ATP_global"/>
<map_variables variable_1="q_cAMP_mcAMP" variable_2="q_cAMP"/>
<map_variables variable_1="q_cAMP" variable_2="q_cAMP_global"/>
<map_variables variable_1="q_AC_mcAMP" variable_2="q_AC"/>
<map_variables variable_1="q_AC" variable_2="q_AC_global"/>
<map_variables variable_1="q_AC_ATP_mcAMP" variable_2="q_AC_ATP"/>
<map_variables variable_1="q_AC_ATP" variable_2="q_AC_ATP_global"/>
<map_variables variable_1="q_GsT_AC_mcAMP" variable_2="q_GsT_AC"/>
<map_variables variable_1="q_GsT_AC" variable_2="q_GsT_AC_global"/>
<map_variables variable_1="q_GsT_AC_ATP_mcAMP" variable_2="q_GsT_AC_ATP"/>
<map_variables variable_1="q_GsT_AC_ATP" variable_2="q_GsT_AC_ATP_global"/>
<map_variables variable_1="q_FSK_AC_mcAMP" variable_2="q_FSK_AC"/>
<map_variables variable_1="q_FSK_AC" variable_2="q_FSK_AC_global"/>
<map_variables variable_1="q_FSK_AC_ATP_mcAMP" variable_2="q_FSK_AC_ATP"/>
<map_variables variable_1="q_FSK_AC_ATP" variable_2="q_FSK_AC_ATP_global"/>
<map_variables variable_1="q_PDE_mcAMP" variable_2="q_PDE"/>
<map_variables variable_1="q_PDE" variable_2="q_PDE_global"/>
<map_variables variable_1="q_PDE_cAMP_mcAMP" variable_2="q_PDE_cAMP"/>
<map_variables variable_1="q_PDE_cAMP" variable_2="q_PDE_cAMP_global"/>
<map_variables variable_1="q_five_AMP_mcAMP" variable_2="q_five_AMP"/>
<map_variables variable_1="q_five_AMP" variable_2="q_five_AMP_global"/>
<map_variables variable_1="q_IBMX_mcAMP" variable_2="q_IBMX"/>
<map_variables variable_1="q_IBMX" variable_2="q_IBMX_global"/>
<map_variables variable_1="q_PDEinh_mcAMP" variable_2="q_PDEinh"/>
<map_variables variable_1="q_PDEinh" variable_2="q_PDEinh_global"/>
<map_variables variable_1="q_GsT_mcAMP" variable_2="q_GsT"/>
<map_variables variable_1="q_GsT" variable_2="q_GsT_global"/>
<map_variables variable_1="q_FSK_mcAMP" variable_2="q_FSK"/>
<map_variables variable_1="q_FSK" variable_2="q_FSK_global"/>
</connection>
<connection>
<map_components component_1="cAMP_parameters" component_2="cAMP"/>
<map_variables variable_1="kappa_1a" variable_2="kappa_1a"/>
<map_variables variable_1="kappa_1b" variable_2="kappa_1b"/>
<map_variables variable_1="kappa_2a" variable_2="kappa_2a"/>
<map_variables variable_1="kappa_2b" variable_2="kappa_2b"/>
<map_variables variable_1="kappa_3a" variable_2="kappa_3a"/>
<map_variables variable_1="kappa_3b" variable_2="kappa_3b"/>
<map_variables variable_1="kappa_4a" variable_2="kappa_4a"/>
<map_variables variable_1="kappa_4b" variable_2="kappa_4b"/>
<map_variables variable_1="kappa_5" variable_2="kappa_5"/>
<map_variables variable_1="kappa_6" variable_2="kappa_6"/>
<map_variables variable_1="kappa_7" variable_2="kappa_7"/>
<map_variables variable_1="K_ATP" variable_2="K_ATP"/>
<map_variables variable_1="K_cAMP" variable_2="K_cAMP"/>
<map_variables variable_1="K_AC" variable_2="K_AC"/>
<map_variables variable_1="K_AC_ATP" variable_2="K_AC_ATP"/>
<map_variables variable_1="K_GsT_AC" variable_2="K_GsT_AC"/>
<map_variables variable_1="K_GsT_AC_ATP" variable_2="K_GsT_AC_ATP"/>
<map_variables variable_1="K_FSK_AC" variable_2="K_FSK_AC"/>
<map_variables variable_1="K_FSK_AC_ATP" variable_2="K_FSK_AC_ATP"/>
<map_variables variable_1="K_PDE" variable_2="K_PDE"/>
<map_variables variable_1="K_PDE_cAMP" variable_2="K_PDE_cAMP"/>
<map_variables variable_1="K_five_AMP" variable_2="K_five_AMP"/>
<map_variables variable_1="K_IBMX" variable_2="K_IBMX"/>
<map_variables variable_1="K_PDEinh" variable_2="K_PDEinh"/>
<map_variables variable_1="K_GsT" variable_2="K_GsT"/>
<map_variables variable_1="K_FSK" variable_2="K_FSK"/>
</connection>
<connection>
<map_components component_1="constants" component_2="cAMP"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
