- Author:
- AnandR <a.rampadarath@auckland.ac.nz>
- Date:
- 2018-12-18 16:37:00+13:00
- Desc:
- Extracted cellML model from the original paper.
Annotated the model using SemGen
- Permanent Source URI:
- http://models.cellml.org/workspace/562/rawfile/d244a015b9a673a14de122e4dcfbe0cf0f7667e2/yang_et_al_2005.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="yang_et_al_2005" cmeta:id="yang_et_al_2005">
<units name="per_microM_per_s">
<unit exponent="-1.0" units="micromolar" />
<unit units="per_s" />
</units>
<units name="micromolar">
<unit exponent="-1.0" units="litre" />
<unit prefix="micro" units="mole" />
</units>
<units name="per_s">
<unit exponent="-1.0" units="second" />
</units>
<units name="millivolt">
<unit prefix="milli" units="volt" />
</units>
<units name="per_nM_per_s">
<unit exponent="-1.0" units="nanomolar" />
<unit units="per_s" />
</units>
<units name="microM_per_s">
<unit units="micromolar" />
<unit units="per_s" />
</units>
<units name="nanomolar">
<unit prefix="nano" units="mole" />
<unit exponent="-1.0" units="litre" />
</units>
<units name="nm_per_s">
<unit units="per_s" />
<unit units="nanomolar" />
</units>
<component name="environment">
<variable cmeta:id="environment.time" name="time" public_interface="out" units="second" />
</component>
<component name="sGC_activation">
<variable cmeta:id="sGC_activation.E_b" initial_value="1" name="E_b" public_interface="out" units="dimensionless" />
<variable cmeta:id="sGC_activation.E_6c" initial_value="0" name="E_6c" public_interface="out" units="dimensionless" />
<variable cmeta:id="sGC_activation.E_5c" initial_value="0" name="E_5c" public_interface="out" units="dimensionless" />
<variable cmeta:id="sGC_activation.k_1" initial_value="2" name="k_1" units="per_nM_per_s" />
<variable cmeta:id="sGC_activation.k_m1" initial_value="100" name="k_m1" units="per_s" />
<variable cmeta:id="sGC_activation.k_2" initial_value="0.1" name="k_2" units="per_s" />
<variable cmeta:id="sGC_activation.k_3" initial_value="0.003" name="k_3" units="per_nM_per_s" />
<variable cmeta:id="sGC_activation.k_4" name="k_4" units="per_s" />
<variable cmeta:id="sGC_activation.NO" initial_value="220" name="NO" units="nanomolar" />
<variable cmeta:id="sGC_activation.J_no" initial_value="3" name="J_no" units="nm_per_s" />
<variable cmeta:id="sGC_activation.k_dno" initial_value="0.01" name="k_dno" units="per_s" />
<variable cmeta:id="sGC_activation.K_4" initial_value="0.011" name="K_4" public_interface="out" units="per_s" />
<variable cmeta:id="sGC_activation.m" initial_value="2" name="m" public_interface="out" units="dimensionless" />
<variable cmeta:id="sGC_activation.cGMP" name="cGMP" public_interface="in" units="micromolar" />
<variable cmeta:id="sGC_activation.E0" name="E0" units="dimensionless" />
<variable cmeta:id="sGC_activation.time" name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>E_b</ci>
</apply>
<apply>
<plus />
<apply>
<times />
<apply>
<minus />
<ci>k_1</ci>
</apply>
<ci>E_b</ci>
<ci>NO</ci>
</apply>
<apply>
<times />
<ci>k_m1</ci>
<ci>E_6c</ci>
</apply>
<apply>
<times />
<ci>k_4</ci>
<ci>E_5c</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>E_6c</ci>
</apply>
<apply>
<minus />
<apply>
<minus />
<apply>
<minus />
<apply>
<times />
<ci>k_1</ci>
<ci>E_b</ci>
<ci>NO</ci>
</apply>
<apply>
<times />
<ci>k_m1</ci>
<ci>E_6c</ci>
</apply>
</apply>
<apply>
<times />
<ci>k_2</ci>
<ci>E_6c</ci>
</apply>
</apply>
<apply>
<times />
<ci>k_3</ci>
<ci>E_6c</ci>
<ci>NO</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>E_5c</ci>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>k_3</ci>
<ci>E_6c</ci>
<ci>NO</ci>
</apply>
<apply>
<times />
<ci>k_2</ci>
<ci>E_6c</ci>
</apply>
</apply>
<apply>
<times />
<ci>k_4</ci>
<ci>E_5c</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>k_4</ci>
<apply>
<times />
<ci>K_4</ci>
<apply>
<power />
<apply>
<divide />
<ci>cGMP</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="micromolar">1</cn>
</apply>
<ci>m</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>NO</ci>
</apply>
<apply>
<minus />
<ci>J_no</ci>
<apply>
<times />
<ci>k_dno</ci>
<ci>NO</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>E0</ci>
<apply>
<plus />
<ci>E_b</ci>
<ci>E_6c</ci>
<ci>E_5c</ci>
</apply>
</apply>
</math>
</component>
<component name="c_GMP">
<variable cmeta:id="c_GMP.V_max_sGC" initial_value="0.8520" name="V_max_sGC" public_interface="out" units="microM_per_s" />
<variable cmeta:id="c_GMP.E_5c" name="E_5c" public_interface="in" units="dimensionless" />
<variable cmeta:id="c_GMP.cGMP" initial_value="0" name="cGMP" public_interface="out" units="micromolar" />
<variable cmeta:id="c_GMP.V_max_pde" name="V_max_pde" units="microM_per_s" />
<variable cmeta:id="c_GMP.K_m_pde" initial_value="2" name="K_m_pde" units="micromolar" />
<variable cmeta:id="c_GMP.k_pde" initial_value="0.0195" name="k_pde" public_interface="out" units="per_s" />
<variable cmeta:id="c_GMP.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="c_GMP.V_p" name="V_p" public_interface="out" units="microM_per_s" />
<variable cmeta:id="c_GMP.V_d" name="V_d" public_interface="out" units="microM_per_s" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>cGMP</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>V_max_sGC</ci>
<ci>E_5c</ci>
</apply>
<apply>
<divide />
<apply>
<times />
<ci>cGMP</ci>
<ci>V_max_pde</ci>
</apply>
<apply>
<plus />
<ci>K_m_pde</ci>
<ci>cGMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>V_max_pde</ci>
<apply>
<times />
<ci>k_pde</ci>
<ci>cGMP</ci>
</apply>
</apply>
<apply>
<eq />
<ci>V_p</ci>
<apply>
<times />
<ci>V_max_sGC</ci>
<ci>E_5c</ci>
</apply>
</apply>
<apply>
<eq />
<ci>V_d</ci>
<apply>
<divide />
<apply>
<times />
<ci>cGMP</ci>
<ci>V_max_pde</ci>
</apply>
<apply>
<plus />
<ci>K_m_pde</ci>
<ci>cGMP</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="VSMC_relaxation">
<variable cmeta:id="VSMC_relaxation.R_cGMP" name="R_cGMP" public_interface="out" units="dimensionless" />
<variable cmeta:id="VSMC_relaxation.R_NO" name="R_NO" public_interface="out" units="dimensionless" />
<variable cmeta:id="VSMC_relaxation.R_mlcp" name="R_mlcp" public_interface="out" units="dimensionless" />
<variable cmeta:id="VSMC_relaxation.cGMP" name="cGMP" public_interface="in" units="micromolar" />
<variable cmeta:id="VSMC_relaxation.n_H" initial_value="2" name="n_H" units="dimensionless" />
<variable cmeta:id="VSMC_relaxation.n_NO" initial_value="1" name="n_NO" units="dimensionless" />
<variable cmeta:id="VSMC_relaxation.n_mlcp" initial_value="2" name="n_mlcp" units="dimensionless" />
<variable cmeta:id="VSMC_relaxation.K_m_nh" initial_value="0.55" name="K_m_nh" units="micromolar" />
<variable cmeta:id="VSMC_relaxation.K_m_NO" initial_value="200" name="K_m_NO" units="nanomolar" />
<variable cmeta:id="VSMC_relaxation.K_m_mlcp" initial_value="5.5" name="K_m_mlcp" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>R_cGMP</ci>
<apply>
<divide />
<apply>
<power />
<ci>cGMP</ci>
<ci>n_H</ci>
</apply>
<apply>
<plus />
<apply>
<power />
<ci>cGMP</ci>
<ci>n_H</ci>
</apply>
<apply>
<power />
<ci>K_m_nh</ci>
<ci>n_H</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>R_NO</ci>
<apply>
<divide />
<apply>
<power />
<apply>
<divide />
<ci>cGMP</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="micromolar">1</cn>
</apply>
<ci>n_NO</ci>
</apply>
<apply>
<plus />
<apply>
<power />
<apply>
<divide />
<ci>cGMP</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="micromolar">1</cn>
</apply>
<ci>n_NO</ci>
</apply>
<apply>
<power />
<apply>
<divide />
<ci>K_m_NO</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="nanomolar">1</cn>
</apply>
<ci>n_NO</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>R_mlcp</ci>
<apply>
<divide />
<apply>
<power />
<ci>cGMP</ci>
<ci>n_mlcp</ci>
</apply>
<apply>
<plus />
<apply>
<power />
<ci>cGMP</ci>
<ci>n_mlcp</ci>
</apply>
<apply>
<power />
<ci>K_m_mlcp</ci>
<ci>n_mlcp</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Ca2_entry">
<variable cmeta:id="Ca2_entry.P_0" name="P_0" units="dimensionless" />
<variable cmeta:id="Ca2_entry.V_m" initial_value="40" name="V_m" units="millivolt" />
<variable cmeta:id="Ca2_entry.v_half" name="v_half" units="millivolt" />
<variable cmeta:id="Ca2_entry.S_KCa" initial_value="30.8" name="S_KCa" units="millivolt" />
<variable cmeta:id="Ca2_entry.V_ca" initial_value="-53.7" name="V_ca" units="millivolt" />
<variable cmeta:id="Ca2_entry.Ca_i" initial_value="1" name="Ca_i" public_interface="out" units="micromolar" />
<variable cmeta:id="Ca2_entry.V_cGMP" initial_value="66.9" name="V_cGMP" units="millivolt" />
<variable cmeta:id="Ca2_entry.R_cGMP" name="R_cGMP" public_interface="in" units="dimensionless" />
<variable cmeta:id="Ca2_entry.V_NO" initial_value="100" name="V_NO" units="millivolt" />
<variable cmeta:id="Ca2_entry.R_NO" name="R_NO" public_interface="in" units="dimensionless" />
<variable cmeta:id="Ca2_entry.V_b" initial_value="283.7" name="V_b" units="millivolt" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>P_0</ci>
<apply>
<divide />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<apply>
<exp />
<apply>
<divide />
<apply>
<minus />
<apply>
<minus />
<ci>V_m</ci>
<ci>v_half</ci>
</apply>
</apply>
<ci>S_KCa</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>v_half</ci>
<apply>
<minus />
<apply>
<minus />
<apply>
<minus />
<apply>
<times />
<ci>V_ca</ci>
<apply>
<log />
<apply>
<divide />
<ci>Ca_i</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="micromolar">1</cn>
</apply>
</apply>
</apply>
<apply>
<times />
<ci>V_cGMP</ci>
<ci>R_cGMP</ci>
</apply>
</apply>
<apply>
<times />
<ci>V_NO</ci>
<ci>R_NO</ci>
</apply>
</apply>
<ci>V_b</ci>
</apply>
</apply>
</math>
</component>
<component name="smooth_muscle_contraction">
<variable cmeta:id="smooth_muscle_contraction.AM" initial_value="0" name="AM" public_interface="out" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.AMp" initial_value="0" name="AMp" public_interface="out" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.Mp" initial_value="0" name="Mp" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.M" initial_value="1" name="M" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.R_mlcp" name="R_mlcp" public_interface="in" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.k_mlcp" name="k_mlcp" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.kb_mlcp" initial_value="0.0086" name="kb_mlcp" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.kc_mlcp" initial_value="0.0327" name="kc_mlcp" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.k_mlck" name="k_mlck" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.k_mlck_bar" initial_value="1180" name="k_mlck_bar" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.K3" initial_value="1.8" name="K3" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.K4" initial_value="0.1" name="K4" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.K7" initial_value="0.045" name="K7" units="per_s" />
<variable cmeta:id="smooth_muscle_contraction.gamma" initial_value="1.66" name="gamma" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.theta_ca" name="theta_ca" units="dimensionless" />
<variable cmeta:id="smooth_muscle_contraction.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="smooth_muscle_contraction.Ca_i" name="Ca_i" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>M</ci>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>k_mlcp</ci>
<ci>Mp</ci>
</apply>
<apply>
<times />
<ci>K7</ci>
<ci>AM</ci>
</apply>
</apply>
<apply>
<times />
<ci>k_mlck</ci>
<ci>M</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Mp</ci>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>k_mlck</ci>
<ci>M</ci>
</apply>
<apply>
<times />
<ci>K4</ci>
<ci>AMp</ci>
</apply>
</apply>
<apply>
<times />
<apply>
<plus />
<ci>k_mlcp</ci>
<ci>K3</ci>
</apply>
<ci>Mp</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>AMp</ci>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>k_mlck</ci>
<ci>AM</ci>
</apply>
<apply>
<times />
<ci>K3</ci>
<ci>Mp</ci>
</apply>
</apply>
<apply>
<times />
<apply>
<plus />
<ci>k_mlcp</ci>
<ci>K4</ci>
</apply>
<ci>AMp</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>AM</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k_mlcp</ci>
<ci>AMp</ci>
</apply>
<apply>
<times />
<apply>
<plus />
<ci>K7</ci>
<ci>k_mlck</ci>
</apply>
<ci>AM</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>k_mlcp</ci>
<apply>
<plus />
<ci>kb_mlcp</ci>
<apply>
<times />
<ci>kc_mlcp</ci>
<ci>R_mlcp</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>theta_ca</ci>
<apply>
<divide />
<ci>gamma</ci>
<apply>
<plus />
<apply>
<divide />
<ci>k_mlck</ci>
<ci>k_mlcp</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>k_mlck</ci>
<apply>
<times />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_s">1</cn>
<ci>k_mlck_bar</ci>
<apply>
<power />
<apply>
<divide />
<ci>Ca_i</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="micromolar">1</cn>
</apply>
<ci>gamma</ci>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="Ca2_entry" component_2="smooth_muscle_contraction" />
<map_variables variable_1="Ca_i" variable_2="Ca_i" />
</connection>
<connection>
<map_components component_1="c_GMP" component_2="sGC_activation" />
<map_variables variable_1="cGMP" variable_2="cGMP" />
</connection>
<connection>
<map_components component_1="environment" component_2="c_GMP" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="sGC_activation" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="VSMC_relaxation" component_2="Ca2_entry" />
<map_variables variable_1="R_cGMP" variable_2="R_cGMP" />
<map_variables variable_1="R_NO" variable_2="R_NO" />
</connection>
<connection>
<map_components component_1="sGC_activation" component_2="c_GMP" />
<map_variables variable_1="E_5c" variable_2="E_5c" />
</connection>
<connection>
<map_components component_1="environment" component_2="smooth_muscle_contraction" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="VSMC_relaxation" component_2="smooth_muscle_contraction" />
<map_variables variable_1="R_mlcp" variable_2="R_mlcp" />
</connection>
<connection>
<map_components component_1="c_GMP" component_2="VSMC_relaxation" />
<map_variables variable_1="cGMP" variable_2="cGMP" />
</connection>
<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
<rdf:Description rdf:about="#VSMC_relaxation.R_mlcp">
<dcterms:description>Mlcp regulatory effect</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#sGC_activation.NO">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_0">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of>
<rdf:Description rdf:about="#entity_1">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/cl/CL:0000359" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:16480" />
</rdf:Description>
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