Location: BG_PLB @ 9b3da81dfeeb / BG_PKA.cellml
- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-29 16:45:32+12:00
- Desc:
- Adding stoich matrices
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6d1/rawfile/9b3da81dfeebecdabd68d179e63fef79d8a8a395/BG_PKA.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_PKA" 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"/>
</component>
<component name="PKA">
<variable name="time" public_interface="in" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- PKA parameters-->
<variable initial_value="308157" name="kappa_aI" units="fmol_per_sec"/>
<variable initial_value="4.21426e+07" name="kappa_bI" units="fmol_per_sec"/>
<variable initial_value="9.63258e-12" name="kappa_dI" units="fmol_per_sec"/>
<variable initial_value="0.0157933" name="kappa_iI" units="fmol_per_sec"/>
<variable initial_value="308157" name="kappa_aII" units="fmol_per_sec"/>
<variable initial_value="4.21426e+07" name="kappa_bII" units="fmol_per_sec"/>
<variable initial_value="9.63258e-12" name="kappa_dII" units="fmol_per_sec"/>
<variable initial_value="0.0157933" name="kappa_iII" units="fmol_per_sec"/>
<variable initial_value="4.45869e-21" name="K_cAMP" units="per_fmol"/>
<variable initial_value="6.22149e-14" name="K_PKI" units="per_fmol"/>
<variable initial_value="0.0796295" name="K_RCI" units="per_fmol"/>
<variable initial_value="0.0032451" name="K_ARCI" units="per_fmol"/>
<variable initial_value="2.3729e-05" name="K_A2RCI" units="per_fmol"/>
<variable initial_value="5088.64" name="K_CI" units="per_fmol"/>
<variable initial_value="2.04012e+10" name="K_A2RI" units="per_fmol"/>
<variable initial_value="63317.9" name="K_PKACI_PKI" units="per_fmol"/>
<variable initial_value="0.0796295" name="K_RCII" units="per_fmol"/>
<variable initial_value="0.0032451" name="K_ARCII" units="per_fmol"/>
<variable initial_value="2.3729e-05" name="K_A2RCII" units="per_fmol"/>
<variable initial_value="5088.64" name="K_CII" units="per_fmol"/>
<variable initial_value="2.04012e+10" name="K_A2RII" units="per_fmol"/>
<variable initial_value="63317.9" name="K_PKACII_PKI" units="per_fmol"/>
<variable initial_value="3.212E-02" name="q_cAMP" units="fmol"/>
<variable initial_value="6.840E-03" name="q_PKI" units="fmol"/>
<variable initial_value="2.242E-02" name="q_RCI" units="fmol"/>
<variable initial_value="3.800E-15" name="q_ARCI" units="fmol"/>
<variable initial_value="3.800E-15" name="q_A2RCI" units="fmol"/>
<variable initial_value="3.800E-15" name="q_CI" units="fmol"/>
<variable initial_value="3.800E-15" name="q_A2RI" units="fmol"/>
<variable initial_value="3.800E-15" name="q_PKACI_PKI" units="fmol"/>
<variable initial_value="9.500E-04" name="q_RCII" units="fmol"/>
<variable initial_value="3.800E-15" name="q_ARCII" units="fmol"/>
<variable initial_value="3.800E-15" name="q_A2RCII" units="fmol"/>
<variable initial_value="3.800E-15" name="q_CII" units="fmol"/>
<variable initial_value="3.800E-15" name="q_A2RII" units="fmol"/>
<variable initial_value="3.800E-15" name="q_PKACII_PKI" units="fmol"/>
<variable name="vaI" units="fmol_per_sec"/>
<variable name="vbI" units="fmol_per_sec"/>
<variable name="vdI" units="fmol_per_sec"/>
<variable name="viI" units="fmol_per_sec"/>
<variable name="vaII" units="fmol_per_sec"/>
<variable name="vbII" units="fmol_per_sec"/>
<variable name="vdII" units="fmol_per_sec"/>
<variable name="viII" units="fmol_per_sec"/>
<variable name="mu_cAMP" units="J_per_mol"/>
<variable name="mu_PKI" units="J_per_mol"/>
<variable name="mu_RCI" units="J_per_mol"/>
<variable name="mu_ARCI" units="J_per_mol"/>
<variable name="mu_A2RCI" units="J_per_mol"/>
<variable name="mu_CI" units="J_per_mol"/>
<variable name="mu_A2RI" units="J_per_mol"/>
<variable name="mu_PKACI_PKI" units="J_per_mol"/>
<variable name="mu_RCII" units="J_per_mol"/>
<variable name="mu_ARCII" units="J_per_mol"/>
<variable name="mu_A2RCII" units="J_per_mol"/>
<variable name="mu_CII" units="J_per_mol"/>
<variable name="mu_A2RII" units="J_per_mol"/>
<variable name="mu_PKACII_PKI" units="J_per_mol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PKI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PKI</ci>
<ci>q_PKI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_RCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_RCI</ci>
<ci>q_RCI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_ARCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ARCI</ci>
<ci>q_ARCI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_A2RCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_A2RCI</ci>
<ci>q_A2RCI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_CI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_CI</ci>
<ci>q_CI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_A2RI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_A2RI</ci>
<ci>q_A2RI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PKACI_PKI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PKACI_PKI</ci>
<ci>q_PKACI_PKI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_RCII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_RCII</ci>
<ci>q_RCII</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_ARCII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ARCII</ci>
<ci>q_ARCII</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_A2RCII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_A2RCII</ci>
<ci>q_A2RCII</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_CII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_CII</ci>
<ci>q_CII</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_A2RII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_A2RII</ci>
<ci>q_A2RII</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PKACII_PKI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PKACII_PKI</ci>
<ci>q_PKACII_PKI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vaI</ci>
<apply>
<times/>
<ci>kappa_aI</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_RCI</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_ARCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vbI</ci>
<apply>
<times/>
<ci>kappa_bI</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_ARCI</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_A2RCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vdI</ci>
<apply>
<times/>
<ci>kappa_dI</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_A2RCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_A2RI</ci>
<ci>mu_CI</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>viI</ci>
<apply>
<times/>
<ci>kappa_iI</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_CI</ci>
<ci>mu_PKI</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PKACI_PKI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vaII</ci>
<apply>
<times/>
<ci>kappa_aII</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_RCII</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_ARCII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vbII</ci>
<apply>
<times/>
<ci>kappa_bII</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_ARCII</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_A2RCII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vdII</ci>
<apply>
<times/>
<ci>kappa_dII</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_A2RCII</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_A2RII</ci>
<ci>mu_CII</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>viII</ci>
<apply>
<times/>
<ci>kappa_iII</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_CII</ci>
<ci>mu_PKI</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PKACII_PKI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_cAMP</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>vaI</ci>
</apply>
<ci>vbI</ci>
</apply>
<ci>vaII</ci>
</apply>
<ci>vbII</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PKI</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>viI</ci>
</apply>
<ci>viII</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_RCI</ci>
</apply>
<apply>
<minus/>
<ci>vaI</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_ARCI</ci>
</apply>
<apply>
<minus/>
<ci>vaI</ci>
<ci>vbI</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_A2RCI</ci>
</apply>
<apply>
<minus/>
<ci>vbI</ci>
<ci>vdI</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_CI</ci>
</apply>
<apply>
<minus/>
<ci>vdI</ci>
<ci>viI</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_A2RI</ci>
</apply>
<ci>vdI</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PKACI_PKI</ci>
</apply>
<ci>viI</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_RCII</ci>
</apply>
<apply>
<minus/>
<ci>vaII</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_ARCII</ci>
</apply>
<apply>
<minus/>
<ci>vaII</ci>
<ci>vbII</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_A2RCII</ci>
</apply>
<apply>
<minus/>
<ci>vbII</ci>
<ci>vdII</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_CII</ci>
</apply>
<apply>
<minus/>
<ci>vdII</ci>
<ci>viII</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_A2RII</ci>
</apply>
<ci>vdII</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PKACII_PKI</ci>
</apply>
<ci>viII</ci>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="PKA"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="constants" component_2="PKA"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>