- 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_2005_FIg3ab.cellml
<?xml version='1.0'?>
<model cmeta:id="yang_2005_Fig3ab" name="yang_2005_Fig3ab" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="yang_et_al_2005cd.cellml">
<component component_ref="VSMC_relaxation" name="VSMC_relaxation"/>
<component component_ref="Ca2_entry" name="Ca2_entry"/>
<component component_ref="smooth_muscle_contraction" name="smooth_muscle_contraction"/>
</import>
<units name="per_s">
<unit exponent="-1" units="second"/>
</units>
<units name="millivolt">
<unit prefix="milli" units="volt"/>
</units>
<units name="nanomolar">
<unit prefix="nano" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="nm_per_s">
<unit units="nanomolar"/>
<unit units="per_s"/>
</units>
<units name="micromolar">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="per_nM_per_s">
<unit exponent="-1" units="nanomolar"/>
<unit units="per_s"/>
</units>
<units name="per_microM_per_s">
<unit exponent="-1" units="micromolar"/>
<unit units="per_s"/>
</units>
<units name="microM_per_s">
<unit units="micromolar"/>
<unit units="per_s"/>
</units>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
</component>
<component name="sGC_activation">
<variable initial_value="1" name="E_b" public_interface="out" units="dimensionless"/>
<variable initial_value="0" name="E_6c" public_interface="out" units="dimensionless"/>
<variable initial_value="0" name="E_5c" public_interface="out" units="dimensionless"/>
<variable initial_value="2" name="k_1" units="per_nM_per_s"/>
<variable initial_value="100" name="k_m1" units="per_s"/>
<variable initial_value="0.1" name="k_2" units="per_s"/>
<variable initial_value="0.003" name="k_3" units="per_nM_per_s"/>
<variable name="k_4" units="per_s"/>
<variable initial_value="220" name="NO" units="nanomolar"/>
<variable initial_value="3" name="J_no" units="nm_per_s"/>
<variable initial_value="0.01" name="k_dno" units="per_s"/>
<variable initial_value="0.4" name="K_4" public_interface="out" units="per_s"/>
<variable initial_value="0" name="m" public_interface="out" units="dimensionless"/>
<variable name="cGMP" public_interface="in" units="micromolar"/>
<variable name="E0" units="dimensionless"/>
<variable 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 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 initial_value="1.26" name="V_max_sGC" public_interface="out" units="microM_per_s"/>
<variable name="E_5c" public_interface="in" units="dimensionless"/>
<variable initial_value="0" name="cGMP" public_interface="out" units="micromolar"/>
<variable name="V_max_pde" units="microM_per_s"/>
<variable initial_value="2" name="K_m_pde" units="micromolar"/>
<variable initial_value="0.0695" name="k_pde" public_interface="out" units="per_s"/>
<variable name="time" public_interface="in" units="second"/>
<variable name="V_p" public_interface="out" units="microM_per_s"/>
<variable 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>
<connection>
<map_components component_1="smooth_muscle_contraction" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="sGC_activation" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="c_GMP" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="sGC_activation" component_2="c_GMP"/>
<map_variables variable_1="E_5c" variable_2="E_5c"/>
<map_variables variable_1="cGMP" variable_2="cGMP"/>
</connection>
<connection>
<map_components component_1="c_GMP" component_2="VSMC_relaxation"/>
<map_variables variable_1="cGMP" variable_2="cGMP"/>
</connection>
<connection>
<map_components component_1="Ca2_entry" component_2="VSMC_relaxation"/>
<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="smooth_muscle_contraction" component_2="VSMC_relaxation"/>
<map_variables variable_1="R_mlcp" variable_2="R_mlcp"/>
</connection>
<connection>
<map_components component_1="Ca2_entry" component_2="smooth_muscle_contraction"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<!-- Your code goes here-->
</model>
