Location: Activation of the Liver Glycogen Phosphorylase by Ca2+ Oscillations: a Theoretical Study @ a6763c2156d8 / gall_2000b_take2.cellml.xml

Author:
Hanne Nielsen <hnie010@aucklanduni.ac.nz>
Date:
2011-08-18 14:16:39+12:00
Desc:
Added new cellML files for a and b. a now reproduces results but b oscillates differently. Added session files without SVG image. To be added.
Permanent Source URI:
https://models.physiomeproject.org/workspace/35d/rawfile/a6763c2156d8fe15df576a800053176fcd3450d8/gall_2000b_take2.cellml.xml

<?xml version="1.0" encoding="utf-8"?>
<!--
This CellML file was generated on 8/16/2011 at 10:48:09 at AM using:

COR (0.9.31.1409)
Copyright 2002-2011 Dr Alan Garny
http://cor.physiol.ox.ac.uk/ - cor@physiol.ox.ac.uk

CellML 1.0 was used to generate this model
http://www.cellml.org/
-->
<model name="gall_2000b" cmeta:id="gall_2000b" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
   <units name="minute">
      <unit units="second" multiplier="60"/>
   </units>
   <units name="per_minute">
      <unit units="minute" exponent="-1"/>
   </units>
   <units name="millimole">
      <unit units="mole" prefix="milli"/>
   </units>
   <units name="micromole">
      <unit units="mole" prefix="micro"/>
   </units>
   <units name="micromolar">
      <unit units="micromole"/>
      <unit units="litre" exponent="-1"/>
   </units>
   <units name="micromolar_per_minute">
      <unit units="micromolar"/>
      <unit units="minute" exponent="-1"/>
   </units>
   <units name="millimolar">
      <unit units="millimole"/>
      <unit units="litre" exponent="-1"/>
   </units>
   <component name="environment">
      <variable name="time" units="minute" initial_value="0" public_interface="out"/>
   </component>
   <component name="Z">
      <variable name="Z" units="dimensionless" initial_value="0.000179" public_interface="out"/>
      <variable name="V_in" units="dimensionless" public_interface="in"/>
      <variable name="V_2i" units="dimensionless" public_interface="in"/>
      <variable name="V_3i" units="dimensionless" public_interface="in"/>
      <variable name="k_f" units="per_minute" initial_value="0.7"/>
      <variable name="Y" units="dimensionless" public_interface="in"/>
      <variable name="k" units="per_minute" initial_value="10"/>
      <variable name="time" units="minute" public_interface="in"/>
      <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>V_in</ci>
                     <ci>V_2i</ci>
                  </apply>
                  <ci>V_3i</ci>
                  <apply>
                     <times/>
                     <ci>k_f</ci>
                     <ci>Y</ci>
                  </apply>
               </apply>
               <apply>
                  <times/>
                  <ci>k</ci>
                  <ci>Z</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="Y">
      <variable name="Y" units="dimensionless" initial_value="0.00122" public_interface="out"/>
      <variable name="V_2i" units="dimensionless" public_interface="in"/>
      <variable name="V_3i" units="dimensionless" public_interface="in"/>
      <variable name="k_f" units="per_minute" initial_value="0.7"/>
      <variable name="time" units="minute" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Y</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <minus/>
                  <ci>V_2i</ci>
                  <ci>V_3i</ci>
               </apply>
               <apply>
                  <times/>
                  <ci>k_f</ci>
                  <ci>Y</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="V_in">
      <variable name="V_in" units="dimensionless" public_interface="out"/>
      <variable name="v_0" units="micromolar_per_minute" initial_value="1"/>
      <variable name="v_1" units="micromolar_per_minute" initial_value="5.7"/>
      <variable name="beta" units="dimensionless" initial_value="0.3"/>
      <variable name="time" units="minute" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>V_in</ci>
            <apply>
               <plus/>
               <ci>v_0</ci>
               <apply>
                  <times/>
                  <ci>v_1</ci>
                  <ci>beta</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="V_2i">
      <variable name="V_2i" units="dimensionless" public_interface="out"/>
      <variable name="v_M2i" units="micromolar_per_minute" initial_value="30"/>
      <variable name="Z" units="dimensionless" public_interface="in"/>
      <variable name="n" units="dimensionless" initial_value="2" public_interface="out"/>
      <variable name="K_2i" units="micromolar" initial_value="0.5"/>
      <variable name="time" units="minute" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>V_2i</ci>
            <apply>
               <divide/>
               <apply>
                  <times/>
                  <ci>v_M2i</ci>
                  <apply>
                     <power/>
                     <ci>Z</ci>
                     <ci>n</ci>
                  </apply>
               </apply>
               <apply>
                  <plus/>
                  <apply>
                     <power/>
                     <ci>K_2i</ci>
                     <ci>n</ci>
                  </apply>
                  <apply>
                     <power/>
                     <ci>Z</ci>
                     <ci>n</ci>
                  </apply>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="V_3i">
      <variable name="V_3i" units="dimensionless" public_interface="out"/>
      <variable name="v_M3i" units="micromolar_per_minute" initial_value="325"/>
      <variable name="Z" units="dimensionless" public_interface="in"/>
      <variable name="p" units="dimensionless" initial_value="4"/>
      <variable name="Y" units="dimensionless" public_interface="in"/>
      <variable name="m" units="dimensionless" initial_value="4"/>
      <variable name="n" units="dimensionless" public_interface="in"/>
      <variable name="K_Ri" units="micromolar" initial_value="1.7"/>
      <variable name="K_Ai" units="micromolar" initial_value="0.46"/>
      <variable name="time" units="minute" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>V_3i</ci>
            <apply>
               <times/>
               <ci>v_M3i</ci>
               <apply>
                  <times/>
                  <apply>
                     <plus/>
                     <apply>
                        <divide/>
                        <apply>
                           <power/>
                           <ci>Y</ci>
                           <ci>m</ci>
                        </apply>
                        <apply>
                           <power/>
                           <ci>K_Ri</ci>
                           <ci>m</ci>
                        </apply>
                     </apply>
                     <apply>
                        <power/>
                        <ci>Y</ci>
                        <ci>n</ci>
                     </apply>
                  </apply>
                  <apply>
                     <divide/>
                     <apply>
                        <power/>
                        <ci>Z</ci>
                        <ci>p</ci>
                     </apply>
                     <apply>
                        <plus/>
                        <apply>
                           <power/>
                           <ci>K_Ai</ci>
                           <ci>p</ci>
                        </apply>
                        <apply>
                           <power/>
                           <ci>Z</ci>
                           <ci>p</ci>
                        </apply>
                     </apply>
                  </apply>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <connection>
      <map_components component_1="Z" component_2="environment"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   <connection>
      <map_components component_1="Y" component_2="environment"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   <connection>
      <map_components component_1="V_in" component_2="environment"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   <connection>
      <map_components component_1="V_2i" component_2="environment"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   <connection>
      <map_components component_1="V_3i" component_2="environment"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   <connection>
      <map_components component_1="V_3i" component_2="V_2i"/>
      <map_variables variable_1="n" variable_2="n"/>
   </connection>
   <connection>
      <map_components component_1="V_3i" component_2="Y"/>
      <map_variables variable_1="Y" variable_2="Y"/>
      <map_variables variable_1="V_3i" variable_2="V_3i"/>
   </connection>
   <connection>
      <map_components component_1="V_2i" component_2="Y"/>
      <map_variables variable_1="V_2i" variable_2="V_2i"/>
   </connection>
   <connection>
      <map_components component_1="V_3i" component_2="Z"/>
      <map_variables variable_1="Z" variable_2="Z"/>
      <map_variables variable_1="V_3i" variable_2="V_3i"/>
   </connection>
   <connection>
      <map_components component_1="V_2i" component_2="Z"/>
      <map_variables variable_1="Z" variable_2="Z"/>
      <map_variables variable_1="V_2i" variable_2="V_2i"/>
   </connection>
   <connection>
      <map_components component_1="V_in" component_2="Z"/>
      <map_variables variable_1="V_in" variable_2="V_in"/>
   </connection>
   <connection>
      <map_components component_1="Y" component_2="Z"/>
      <map_variables variable_1="Y" variable_2="Y"/>
   </connection>
</model>