Location: NVC @ 8e9f1939f29a / coupling / s-test.cellml
- Author:
- Soroush Safaei <ssaf006@aucklanduni.ac.nz>
- Date:
- 2019-03-14 13:40:39+13:00
- Desc:
- restructuring
- Permanent Source URI:
- http://models.cellml.org/workspace/4bd/rawfile/8e9f1939f29abbc0acf4eda45d6836503466f20d/coupling/s-test.cellml
<?xml version='1.0'?>
<model name="my_model" 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">
<!-- Set the maximum step of CVODE solver to length of stimulus for anything to work-->
<import xlink:href="Units.cellml">
<units name="mM" units_ref="mM"/>
<units name="per_s" units_ref="per_s"/>
<units name="mM_per_s" units_ref="mM_per_s"/>
<units name="per_mM" units_ref="per_mM"/>
<units name="per_mM_s" units_ref="per_mM_s"/>
<units name="per_mM2_s" units_ref="per_mM2_s"/>
</import>
<component name="main">
<variable name="t" units="second"/>
<variable name="stim" units="dimensionless"/>
<variable name="y" units="dimensionless"/>
<variable initial_value="5.5452" name="q_oHb" units="mM"/>
<variable initial_value="14.4548" name="q_dHb" units="mM"/>
<variable initial_value="0.7976" name="q_O_2" units="mM"/>
<variable initial_value="6.8492" name="q_glucose" units="mM"/>
<variable name="k_flow" public_interface="out" units="per_s"/>
<variable initial_value="10" name="q_G_body" units="mM"/>
<variable initial_value="10" name="q_O_2_body" units="mM"/>
<variable initial_value="10" name="q_oHb_body" units="mM"/>
<variable initial_value="10" name="q_dHb_body" units="mM"/>
<variable name="v_basal" units="mM_per_s"/>
<variable name="v_stim" units="mM_per_s"/>
<variable initial_value="0" name="q_inputDelay" units="mM"/>
<variable initial_value="0" name="q_Glu" units="mM"/>
<!-- var q_NO: mM {pub: in};-->
<variable initial_value="0" name="q_Ca_Astro" units="mM"/>
<variable initial_value="0" name="q_AA" units="mM"/>
<variable initial_value="0" name="q_HETE" units="mM"/>
<variable initial_value="0" name="q_S1_HETE" units="mM"/>
<variable initial_value="0" name="q_S2_HETE" units="mM"/>
<variable initial_value="0" name="q_S3_HETE" units="mM"/>
<variable initial_value="0" name="q_PG" units="mM"/>
<variable initial_value="0" name="q_S1_PG" units="mM"/>
<variable initial_value="0" name="q_S2_PG" units="mM"/>
<variable initial_value="0" name="q_S3_PG" units="mM"/>
<variable initial_value="0" name="q_EET" units="mM"/>
<variable initial_value="0" name="q_S1_EET" units="mM"/>
<variable initial_value="0" name="q_S2_EET" units="mM"/>
<variable initial_value="0" name="q_S3_EET" units="mM"/>
<variable initial_value="13.5595" name="q_PL" units="mM"/>
<variable initial_value="0" name="q_Ca_Neuro" units="mM"/>
<variable initial_value="0" name="q_NO" units="mM"/>
<variable initial_value="0" name="q_cGMP" units="mM"/>
<variable initial_value="0" name="q_S1_cGMP" units="mM"/>
<variable initial_value="0" name="q_S2_cGMP" units="mM"/>
<variable initial_value="0" name="q_S3_cGMP" units="mM"/>
<variable name="k_Stimulating" units="per_s"/>
<variable name="k_Inhibiting" units="per_s"/>
<variable name="Act" units="per_s"/>
<!-- Parameters-->
<variable initial_value="22.2302" name="k_metabolic" units="per_s"/>
<variable initial_value="107.8534" name="k_neurotrans" units="per_s"/>
<variable initial_value="0.78" name="k_sink_Input" units="per_s"/>
<variable initial_value="1.3363" name="k_sink_Glu" units="per_s"/>
<variable initial_value="2.0010" name="v_Ca_Abas" units="mM_per_s"/>
<variable initial_value="0.57" name="k_2" units="per_s"/>
<variable initial_value="1.3874" name="k_4" units="per_mM_s"/>
<variable initial_value="1.2939" name="k_5" units="mM_per_s"/>
<variable initial_value="0.3842" name="k_6" units="per_s"/>
<variable initial_value="1.6024" name="k_7" units="mM_per_s"/>
<variable initial_value="1.3788" name="k_8" units="dimensionless"/>
<variable initial_value="1.8126" name="k_9" units="dimensionless"/>
<variable initial_value="0.8928" name="k_12" units="per_s"/>
<variable initial_value="1.0079" name="k_13" units="per_s"/>
<variable initial_value="0.6329" name="k_14" units="per_s"/>
<variable initial_value="7.9729" name="k_15" units="per_s"/>
<variable initial_value="27.7012" name="k_16" units="per_s"/>
<variable initial_value="7.8795" name="k_17" units="per_s"/>
<variable initial_value="0.7128" name="k_18" units="per_s"/>
<variable initial_value="1.4195" name="k_19" units="per_s"/>
<variable initial_value="1.1314" name="k_20" units="per_s"/>
<variable initial_value="1.3786" name="km_1" units="mM"/>
<variable initial_value="1.9805" name="km_2" units="mM"/>
<variable initial_value="0.9936" name="k_sink_A" units="per_s"/>
<variable initial_value="0.59" name="k_sink_H" units="per_s"/>
<variable initial_value="23.9486" name="k_sink_P" units="per_s"/>
<variable initial_value="1.2129" name="k_sink_E" units="per_s"/>
<variable initial_value="3.7830" name="v_Ca_Nbas" units="mM_per_s"/>
<variable initial_value="6.4958" name="k_3" units="per_s"/>
<variable initial_value="0.1335" name="k_10" units="per_s"/>
<variable initial_value="1.5409" name="k_11" units="per_s"/>
<variable initial_value="6.3028" name="k_21" units="per_s"/>
<variable initial_value="1.8901" name="k_22" units="per_s"/>
<variable initial_value="2.0495" name="k_23" units="per_s"/>
<variable initial_value="3.1130" name="k_NO_sink" units="per_s"/>
<variable initial_value="2.4021" name="k_sink_N" units="per_s"/>
<variable initial_value="18.1459" name="k_sink_C" units="per_s"/>
<variable initial_value="19.7612" name="b_1" units="per_mM_s"/>
<variable initial_value="0.2549" name="b_2" units="per_mM_s"/>
<variable initial_value="14.2989" name="b_3" units="per_mM_s"/>
<variable initial_value="2.8037" name="b_4" units="per_mM_s"/>
<variable initial_value="198.8573" name="k_1_f" units="per_s"/>
<variable initial_value="50.9727" name="k_1_b" units="per_mM_s"/>
<variable initial_value="4.1354" name="k_basal" units="per_mM_s"/>
<variable initial_value="2.2892" name="k_flow_basal" units="per_s"/>
<variable initial_value="10.5475" name="proportion_1" units="dimensionless"/>
<variable initial_value="3.6952" name="proportion_2" units="dimensionless"/>
<variable initial_value="100.5114" name="k_y" units="dimensionless"/>
<!-- Stimulus-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>stim</ci>
<piecewise>
<piece>
<cn cellml:units="mM">1</cn>
<apply>
<and/>
<apply>
<gt/>
<ci>t</ci>
<cn cellml:units="second">0.5</cn>
</apply>
<apply>
<lt/>
<ci>t</ci>
<cn cellml:units="second">1</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM">0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_inputDelay</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_metabolic</ci>
<ci>stim</ci>
</apply>
<apply>
<times/>
<ci>q_inputDelay</ci>
<ci>k_sink_Input</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Glu</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_neurotrans</ci>
<ci>stim</ci>
</apply>
<apply>
<times/>
<ci>q_Glu</ci>
<ci>k_sink_Glu</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>y</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k_y</ci>
<ci>q_oHb</ci>
</apply>
<ci>q_dHb</ci>
</apply>
</apply>
<!-- Neuron-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Ca_Neuro</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_3</ci>
<ci>q_Glu</ci>
</apply>
<apply>
<times/>
<ci>q_Ca_Neuro</ci>
<ci>k_sink_N</ci>
</apply>
</apply>
<ci>v_Ca_Nbas</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NO</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_10</ci>
<ci>q_Ca_Neuro</ci>
</apply>
<apply>
<times/>
<ci>k_NO_sink</ci>
<ci>q_NO</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_cGMP</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_23</ci>
<ci>q_S3_cGMP</ci>
</apply>
<apply>
<times/>
<ci>k_sink_C</ci>
<ci>q_cGMP</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S1_cGMP</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_11</ci>
<ci>q_NO</ci>
</apply>
<apply>
<times/>
<ci>k_21</ci>
<ci>q_S1_cGMP</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S2_cGMP</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_21</ci>
<ci>q_S1_cGMP</ci>
</apply>
<apply>
<times/>
<ci>k_22</ci>
<ci>q_S2_cGMP</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S3_cGMP</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_22</ci>
<ci>q_S2_cGMP</ci>
</apply>
<apply>
<times/>
<ci>k_23</ci>
<ci>q_S3_cGMP</ci>
</apply>
</apply>
</apply>
<!-- Astrocyte-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Ca_Astro</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_2</ci>
<ci>q_Glu</ci>
</apply>
<apply>
<times/>
<ci>q_Ca_Astro</ci>
<ci>k_sink_A</ci>
</apply>
</apply>
<ci>v_Ca_Abas</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_AA</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>q_PL</ci>
<ci>q_Ca_Astro</ci>
<ci>k_4</ci>
</apply>
<apply>
<plus/>
<apply>
<divide/>
<apply>
<times/>
<ci>k_5</ci>
<ci>q_AA</ci>
</apply>
<apply>
<plus/>
<ci>km_1</ci>
<apply>
<times/>
<ci>k_8</ci>
<ci>q_NO</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k_6</ci>
<ci>q_AA</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>k_7</ci>
<ci>q_AA</ci>
</apply>
<apply>
<plus/>
<ci>km_2</ci>
<apply>
<times/>
<ci>k_9</ci>
<ci>q_NO</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S1_HETE</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>k_5</ci>
<ci>q_AA</ci>
</apply>
<apply>
<plus/>
<ci>km_1</ci>
<apply>
<times/>
<ci>k_8</ci>
<ci>q_NO</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k_12</ci>
<ci>q_S1_HETE</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S2_HETE</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_12</ci>
<ci>q_S1_HETE</ci>
</apply>
<apply>
<times/>
<ci>k_13</ci>
<ci>q_S2_HETE</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S3_HETE</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_13</ci>
<ci>q_S2_HETE</ci>
</apply>
<apply>
<times/>
<ci>k_14</ci>
<ci>q_S3_HETE</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_HETE</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_14</ci>
<ci>q_S3_HETE</ci>
</apply>
<apply>
<times/>
<ci>q_HETE</ci>
<ci>k_sink_H</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S1_PG</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_6</ci>
<ci>q_AA</ci>
</apply>
<apply>
<times/>
<ci>k_15</ci>
<ci>q_S1_PG</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S2_PG</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_15</ci>
<ci>q_S1_PG</ci>
</apply>
<apply>
<times/>
<ci>k_16</ci>
<ci>q_S2_PG</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S3_PG</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_16</ci>
<ci>q_S2_PG</ci>
</apply>
<apply>
<times/>
<ci>k_17</ci>
<ci>q_S3_PG</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_PG</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_17</ci>
<ci>q_S3_PG</ci>
</apply>
<apply>
<times/>
<ci>q_PG</ci>
<ci>k_sink_P</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S1_EET</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>k_7</ci>
<ci>q_AA</ci>
</apply>
<apply>
<plus/>
<ci>km_2</ci>
<apply>
<times/>
<ci>k_9</ci>
<ci>q_NO</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k_18</ci>
<ci>q_S1_EET</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S2_EET</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_18</ci>
<ci>q_S1_EET</ci>
</apply>
<apply>
<times/>
<ci>k_19</ci>
<ci>q_S2_EET</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_S3_EET</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_19</ci>
<ci>q_S2_EET</ci>
</apply>
<apply>
<times/>
<ci>k_20</ci>
<ci>q_S3_EET</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_EET</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_20</ci>
<ci>q_S3_EET</ci>
</apply>
<apply>
<times/>
<ci>q_EET</ci>
<ci>k_sink_E</ci>
</apply>
</apply>
</apply>
<!-- Blood-->
<apply>
<eq/>
<ci>k_Stimulating</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>b_1</ci>
<ci>q_cGMP</ci>
</apply>
<apply>
<times/>
<ci>b_2</ci>
<ci>q_PG</ci>
</apply>
<apply>
<times/>
<ci>b_3</ci>
<ci>q_EET</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k_Inhibiting</ci>
<apply>
<times/>
<ci>b_4</ci>
<ci>q_HETE</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Act</ci>
<apply>
<minus/>
<ci>k_Stimulating</ci>
<ci>k_Inhibiting</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_flow</ci>
<apply>
<plus/>
<ci>k_flow_basal</ci>
<ci>Act</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_basal</ci>
<apply>
<times/>
<ci>k_basal</ci>
<apply>
<power/>
<ci>q_O_2</ci>
<ci>proportion_1</ci>
</apply>
<ci>q_glucose</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_stim</ci>
<apply>
<times/>
<ci>q_inputDelay</ci>
<apply>
<power/>
<ci>q_O_2</ci>
<ci>proportion_2</ci>
</apply>
<ci>q_glucose</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_oHb</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_1_b</ci>
<ci>q_dHb</ci>
<ci>q_O_2</ci>
</apply>
<apply>
<times/>
<ci>k_1_f</ci>
<ci>q_oHb</ci>
</apply>
</apply>
<apply>
<times/>
<ci>q_oHb_body</ci>
<ci>k_flow</ci>
</apply>
</apply>
<apply>
<times/>
<ci>q_oHb</ci>
<ci>k_flow</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_dHb</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_1_f</ci>
<ci>q_oHb</ci>
</apply>
<apply>
<times/>
<ci>k_1_b</ci>
<ci>q_dHb</ci>
<ci>q_O_2</ci>
</apply>
</apply>
<apply>
<times/>
<ci>q_dHb_body</ci>
<ci>k_flow</ci>
</apply>
</apply>
<apply>
<times/>
<ci>q_dHb</ci>
<ci>k_flow</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_O_2</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_1_f</ci>
<ci>q_oHb</ci>
</apply>
<apply>
<times/>
<ci>k_1_b</ci>
<ci>q_dHb</ci>
<ci>q_O_2</ci>
</apply>
</apply>
<apply>
<times/>
<ci>v_basal</ci>
<ci>proportion_1</ci>
</apply>
</apply>
<apply>
<times/>
<ci>v_stim</ci>
<ci>proportion_2</ci>
</apply>
</apply>
<apply>
<times/>
<ci>q_O_2_body</ci>
<ci>k_flow</ci>
</apply>
</apply>
<apply>
<times/>
<ci>q_O_2</ci>
<ci>k_flow</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_glucose</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<ci>q_G_body</ci>
<ci>k_flow</ci>
</apply>
<apply>
<times/>
<ci>q_glucose</ci>
<ci>k_flow</ci>
</apply>
</apply>
<ci>v_basal</ci>
</apply>
<ci>v_stim</ci>
</apply>
</apply>
</math>
</component>
</model>