- Author:
- Leyla <noroozbabaee@gmail.com>
- Date:
- 2021-10-11 15:58:15+13:00
- Desc:
- The final version of Imtiaz model ready for curation.
- Permanent Source URI:
- https://models.fieldml.org/workspace/763/rawfile/d42ef5a082ba250a7078b4a897abdf19ce5ff033/Experiment/IP3_Imtiaz_2002.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="my_model" 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#">
<units name="minute">
<unit multiplier="60" units="second"/>
</units>
<units name="per_minute">
<unit exponent="-1" units="minute"/>
</units>
<units name="conductance_units">
<unit prefix="milli" units="siemens"/>
</units>
<units name="millifarads">
<unit prefix="milli" units="farad"/>
</units>
<units name="voltage_units">
<unit prefix="milli" units="volt"/>
</units>
<units name="current_units">
<!-- micro-amp-->
<unit units="voltage_units"/>
<unit units="conductance_units"/>
</units>
<units name="micromolar">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="micromolar_per_minute">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
<unit exponent="-1" units="minute"/>
</units>
<units name="per_micromolar">
<unit units="litre"/>
<unit exponent="-1" prefix="micro" units="mole"/>
</units>
<units name="per_millimolar">
<unit units="litre"/>
<unit exponent="-1" prefix="milli" units="mole"/>
</units>
<units name="time_units">
<unit units="minute"/>
</units>
<component name="Time">
<variable cmeta:id="time" name="time" private_interface="out" public_interface="out" units="time_units"/>
</component>
<component name="vin">
<!-- var time: time_units {pub: in};-->
<variable initial_value="3.4" name="v0" units="micromolar_per_minute"/>
<variable initial_value="3.4" name="v1" units="per_minute"/>
<!--3.4 discripency in units
var v1: micromolar_per_minute {init: 3.4};-->
<variable name="p_ip3" private_interface="out" public_interface="in" units="micromolar"/>
<variable name="vin" public_interface="out" units="micromolar_per_minute"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>vin</ci>
<apply>
<plus/>
<ci>v0</ci>
<apply>
<times/>
<ci>p_ip3</ci>
<ci>v1</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v2">
<!-- var time: time_units{pub: in};-->
<variable name="z" private_interface="out" public_interface="in" units="micromolar"/>
<variable initial_value="1" name="k2" units="micromolar"/>
<variable initial_value="50" name="vm2" units="micromolar_per_minute"/>
<variable initial_value="2" name="n" units="dimensionless"/>
<variable name="v2" public_interface="out" units="micromolar_per_minute"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v2</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>vm2</ci>
<apply>
<power/>
<ci>z</ci>
<ci>n</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>k2</ci>
<ci>n</ci>
</apply>
<apply>
<power/>
<ci>z</ci>
<ci>n</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v3">
<!-- var time: time_units {pub: in}; -->
<variable name="z" private_interface="out" public_interface="in" units="micromolar"/>
<variable name="p_ip3" private_interface="out" public_interface="in" units="micromolar"/>
<variable name="y" private_interface="out" public_interface="in" units="micromolar"/>
<variable initial_value="650" name="vm3" units="micromolar_per_minute"/>
<variable initial_value="4" name="w" units="dimensionless"/>
<variable initial_value="2" name="m" units="dimensionless"/>
<variable initial_value="4" name="o" units="dimensionless"/>
<variable initial_value="0.9" name="ka" units="micromolar"/>
<variable initial_value="2" name="kr" units="micromolar"/>
<variable initial_value="0.65" name="kp" units="micromolar"/>
<variable name="v3" public_interface="out" units="micromolar_per_minute"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v3</ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>vm3</ci>
<apply>
<power/>
<ci>z</ci>
<ci>w</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>ka</ci>
<ci>w</ci>
</apply>
<apply>
<power/>
<ci>z</ci>
<ci>w</ci>
</apply>
</apply>
</apply>
<apply>
<power/>
<ci>y</ci>
<ci>m</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>kr</ci>
<ci>m</ci>
</apply>
<apply>
<power/>
<ci>y</ci>
<ci>m</ci>
</apply>
</apply>
</apply>
<apply>
<power/>
<ci>p_ip3</ci>
<ci>o</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>kp</ci>
<ci>o</ci>
</apply>
<apply>
<power/>
<ci>p_ip3</ci>
<ci>o</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="ca">
<variable name="time" private_interface="out" public_interface="in" units="time_units"/>
<variable name="vin" private_interface="in" public_interface="out" units="micromolar_per_minute"/>
<variable name="v2" private_interface="in" public_interface="out" units="micromolar_per_minute"/>
<variable name="v3" private_interface="in" public_interface="out" units="micromolar_per_minute"/>
<variable initial_value="1" name="kf" units="per_minute"/>
<variable initial_value="10" name="k" units="per_minute"/>
<variable initial_value="0.475" name="z_init" units="micromolar"/>
<variable initial_value="4.439" name="y_init" units="micromolar"/>
<variable initial_value="z_init" name="z" public_interface="out" units="micromolar"/>
<variable initial_value="y_init" name="y" public_interface="out" units="micromolar"/>
<variable name="p_ip3" private_interface="out" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>z</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<ci>vin</ci>
<ci>v2</ci>
</apply>
<ci>v3</ci>
<apply>
<times/>
<ci>kf</ci>
<ci>y</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k</ci>
<ci>z</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>y</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v2</ci>
<ci>v3</ci>
</apply>
<apply>
<times/>
<ci>kf</ci>
<ci>y</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="g_ca">
<!-- var time: time_units {pub: in};-->
<variable initial_value="4" name="g_m_ca" units="conductance_units"/>
<variable initial_value="1.4" name="kca" units="micromolar"/>
<variable initial_value="4" name="q" units="dimensionless"/>
<variable name="z" private_interface="out" public_interface="in" units="micromolar"/>
<variable name="g_ca" public_interface="out" units="conductance_units"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>g_ca</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>g_m_ca</ci>
<apply>
<power/>
<ci>z</ci>
<ci>q</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>kca</ci>
<ci>q</ci>
</apply>
<apply>
<power/>
<ci>z</ci>
<ci>q</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="vm">
<variable name="time" private_interface="out" public_interface="in" units="time_units"/>
<variable initial_value="1.12" name="g_i" units="conductance_units"/>
<variable name="g_ca" private_interface="in" public_interface="out" units="conductance_units"/>
<variable name="z" private_interface="out" public_interface="in" units="micromolar"/>
<variable initial_value="-67.2" name="Ei" units="voltage_units"/>
<variable initial_value="-20.0" name="Eca" units="voltage_units"/>
<variable initial_value="1.7" name="cm" units="millifarads"/>
<variable initial_value="-65.09" name="vm_init" units="voltage_units"/>
<variable initial_value="vm_init" name="vm" public_interface="out" units="voltage_units"/>
<variable name="I_i" public_interface="out" units="current_units"/>
<variable name="I_ca" public_interface="out" units="current_units"/>
<variable name="I_stim" units="current_units"/>
<variable initial_value="0" name="I_clamp0" units="current_units"/>
<variable initial_value="-15" name="I_clamp1" units="current_units"/>
<variable initial_value="22" name="I_clamp2" units="current_units"/>
<variable initial_value="13" name="t_1" units="time_units"/>
<variable initial_value="26" name="t_2" units="time_units"/>
<variable initial_value="26" name="t_3" units="time_units"/>
<variable initial_value="39" name="t_4" units="time_units"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>I_stim</ci>
<piecewise>
<piece>
<ci>I_clamp0</ci>
<apply>
<leq/>
<ci>time</ci>
<ci>t_1</ci>
</apply>
</piece>
<piece>
<ci>I_clamp1</ci>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<ci>t_1</ci>
</apply>
<apply>
<leq/>
<ci>time</ci>
<ci>t_2</ci>
</apply>
</apply>
</piece>
<piece>
<ci>I_clamp2</ci>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<ci>t_3</ci>
</apply>
<apply>
<leq/>
<ci>time</ci>
<ci>t_4</ci>
</apply>
</apply>
</piece>
<otherwise>
<ci>I_clamp0</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>I_i</ci>
<apply>
<times/>
<ci>g_i</ci>
<apply>
<minus/>
<ci>vm</ci>
<ci>Ei</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>I_ca</ci>
<apply>
<times/>
<ci>g_ca</ci>
<apply>
<minus/>
<ci>vm</ci>
<ci>Eca</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>vm</ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<ci>I_i</ci>
<ci>I_ca</ci>
</apply>
<ci>I_stim</ci>
</apply>
</apply>
<ci>cm</ci>
</apply>
<cn cellml:units="dimensionless">60</cn>
<cn cellml:units="dimensionless">1</cn>
</apply>
</apply>
</math>
</component>
<component name="pv">
<variable initial_value="0.8" name="p_mv" units="micromolar_per_minute"/>
<variable initial_value="-58" name="kv" units="voltage_units"/>
<variable initial_value="8" name="r" units="dimensionless"/>
<variable name="vm" private_interface="out" public_interface="in" units="voltage_units"/>
<variable name="pv" public_interface="out" units="micromolar_per_minute"/>
<variable name="pv1" public_interface="out" units="micromolar_per_minute"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>pv1</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>p_mv</ci>
<apply>
<power/>
<ci>vm</ci>
<ci>r</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>kv</ci>
<ci>r</ci>
</apply>
<apply>
<power/>
<ci>vm</ci>
<ci>r</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pv</ci>
<apply>
<times/>
<ci>p_mv</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<apply>
<power/>
<ci>vm</ci>
<ci>r</ci>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>kv</ci>
<ci>r</ci>
</apply>
<apply>
<power/>
<ci>vm</ci>
<ci>r</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="p_ip3">
<variable name="time" private_interface="out" public_interface="in" units="time_units"/>
<variable name="pv" private_interface="in" public_interface="out" units="micromolar_per_minute"/>
<variable name="vm" private_interface="out" public_interface="in" units="voltage_units"/>
<!-- does not follow unit consictancy-->
<variable initial_value="0.95" name="b_ip3" units="micromolar_per_minute"/>
<variable initial_value="0.9" name="eps_ip3" units="per_minute"/>
<variable initial_value="2.0" name="vm4" units="micromolar_per_minute"/>
<variable initial_value="0.5" name="k4" units="micromolar"/>
<variable initial_value="4.0" name="u" units="dimensionless"/>
<variable initial_value="0.397" name="p_ip3_init" public_interface="out" units="micromolar"/>
<variable initial_value="p_ip3_init" name="p_ip3" public_interface="out" units="micromolar"/>
<variable name="p_ip3_p2" public_interface="out" units="micromolar_per_minute"/>
<variable name="p_ip3_p3" public_interface="out" units="micromolar_per_minute"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>p_ip3_p2</ci>
<apply>
<times/>
<apply>
<minus/>
<ci>eps_ip3</ci>
</apply>
<ci>p_ip3</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>p_ip3_p3</ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<minus/>
<ci>vm4</ci>
</apply>
<apply>
<power/>
<ci>p_ip3</ci>
<ci>u</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>k4</ci>
<ci>u</ci>
</apply>
<apply>
<power/>
<ci>p_ip3</ci>
<ci>u</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>p_ip3</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>b_ip3</ci>
<apply>
<times/>
<ci>eps_ip3</ci>
<ci>p_ip3</ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>vm4</ci>
<apply>
<power/>
<ci>p_ip3</ci>
<ci>u</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>k4</ci>
<ci>u</ci>
</apply>
<apply>
<power/>
<ci>p_ip3</ci>
<ci>u</ci>
</apply>
</apply>
</apply>
</apply>
<ci>pv</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="ca" component_2="vin"/>
<map_variables variable_1="vin" variable_2="vin"/>
<map_variables variable_1="p_ip3" variable_2="p_ip3"/>
</connection>
<connection>
<map_components component_1="ca" component_2="v2"/>
<map_variables variable_1="v2" variable_2="v2"/>
<map_variables variable_1="z" variable_2="z"/>
</connection>
<connection>
<map_components component_1="ca" component_2="v3"/>
<map_variables variable_1="v3" variable_2="v3"/>
<map_variables variable_1="z" variable_2="z"/>
<map_variables variable_1="y" variable_2="y"/>
</connection>
<connection>
<map_components component_1="vm" component_2="ca"/>
<map_variables variable_1="z" variable_2="z"/>
</connection>
<connection>
<map_components component_1="Time" component_2="vm"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="vm" component_2="pv"/>
<map_variables variable_1="vm" variable_2="vm"/>
</connection>
<connection>
<map_components component_1="Time" component_2="ca"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="g_ca" component_2="ca"/>
<map_variables variable_1="z" variable_2="z"/>
</connection>
<connection>
<map_components component_1="g_ca" component_2="vm"/>
<map_variables variable_1="g_ca" variable_2="g_ca"/>
</connection>
<connection>
<map_components component_1="Time" component_2="p_ip3"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="pv" component_2="p_ip3"/>
<map_variables variable_1="pv" variable_2="pv"/>
</connection>
<connection>
<map_components component_1="v3" component_2="p_ip3"/>
<map_variables variable_1="p_ip3" variable_2="p_ip3"/>
</connection>
<connection>
<map_components component_1="vm" component_2="p_ip3"/>
<map_variables variable_1="vm" variable_2="vm"/>
</connection>
<connection>
<map_components component_1="ca" component_2="p_ip3"/>
<map_variables variable_1="p_ip3" variable_2="p_ip3"/>
</connection>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="ca">
<component_ref component="vin"/>
<component_ref component="v2"/>
<component_ref component="v3"/>
</component_ref>
<component_ref component="vm">
<component_ref component="g_ca"/>
</component_ref>
<component_ref component="p_ip3">
<component_ref component="pv"/>
</component_ref>
</group>
</model>
