<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : sneyd_model_2002.xml
CREATED : 22nd May 2007
LAST MODIFIED : 22nd May 2007
AUTHOR : Catherine Lloyd
The Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.1 Specification.
DESCRIPTION : This file contains a CellML description of James Sneyd and Jean-Francois Dufuor's 2002 dynamic model of the type-2 inositol triphosphate receptor.
CHANGES:
-->
<model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="sneyd_2002" name="sneyd_dufour_2002_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>A Dynamic Model Of The Type-2 Inositol Triphosphate Receptor</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML model runs in OpenCell and COR. The units have been checked and they are consistent. In the absence of published values for the initial probabilities of each channel state we have used 0.16 for A, I1, I2, and R and 0.01 for O.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
ABSTRACT: The dynamic properties of the inositol (1,4,5)-trisphosphate (IP(3)) receptor are crucial for the control of intracellular Ca(2+), including the generation of Ca(2+) oscillations and waves. However, many models of this receptor do not agree with recent experimental data on the dynamic responses of the receptor. We construct a model of the IP(3) receptor and fit the model to dynamic and steady-state experimental data from type-2 IP(3) receptors. Our results indicate that, (i) Ca(2+) binds to the receptor using saturating, not mass-action, kinetics; (ii) Ca(2+) decreases the rate of IP(3) binding while simultaneously increasing the steady-state sensitivity of the receptor to IP(3); (iii) the rate of Ca(2+)-induced receptor activation increases with Ca(2+) and is faster than Ca(2+)-induced receptor inactivation; and (iv) IP(3) receptors are sequentially activated and inactivated by Ca(2+) even when IP(3) is bound. Our results emphasize that measurement of steady-state properties alone is insufficient to characterize the functional properties of the receptor.
</para>
<para>
The original paper reference is cited below:
</para>
<para>
A dynamic model of the type-2 inositol triphosphate receptor, James Sneyd and Jean-Francois Dufour, 2002, <emphasis>Proceedings of the National Academy of Sciences </emphasis>, 99, 2398-2403. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11842185&dopt=Abstract">PubMed ID: 11842185</ulink>
</para>
<informalfigure float="0" id="fig_simplified_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A simplified diagram of the IPR model</title>
</objectinfo>
<imagedata fileref="sneyd_2002.png"/>
</imageobject>
</mediaobject>
<caption>A simplified diagram of the IPR model, where R represents the free receptor, O is the open state of the channel, A is the activated state of the channel and I1, I2, and S are three inactive states.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="flux">
<unit units="micromolar"/>
<unit units="second" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1"/>
</units>
<units name="second_order_rate_constant">
<unit units="micromolar" exponent="-1"/>
<unit units="second" exponent="-1"/>
</units>
<component name="environment">
<variable units="second" public_interface="out" name="time"/>
</component>
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<variable units="second_order_rate_constant" public_interface="in" name="phi_2"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_2b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_1b"/>
<variable units="first_order_rate_constant" public_interface="in" name="l_2b"/>
<variable units="dimensionless" public_interface="in" name="I_1"/>
<variable units="dimensionless" public_interface="in" name="O"/>
<variable units="micromolar" public_interface="in" name="p"/>
<variable units="second" public_interface="in" name="time"/>
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</bvar>
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<ci> O </ci>
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<ci> I_1 </ci>
</apply>
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<ci> R </ci>
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</apply>
</apply>
</math>
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<component cmeta:id="O" name="O">
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<variable units="second_order_rate_constant" public_interface="in" name="phi_3"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_4"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_4b"/>
<variable units="second_order_rate_constant" public_interface="in" name="phi_2"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_2b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_3b"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="dimensionless" public_interface="in" name="A"/>
<variable units="dimensionless" public_interface="in" name="S"/>
<variable units="micromolar" public_interface="in" name="p"/>
<variable units="second" public_interface="in" name="time"/>
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</bvar>
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<ci> p </ci>
<ci> R </ci>
</apply>
<apply>
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<ci> A </ci>
</apply>
<apply>
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<ci> k_3b </ci>
<ci> S </ci>
</apply>
</apply>
<apply>
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<ci> phi_4 </ci>
<apply>
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<cn cellml:units="micromolar"> 1.0 </cn>
<ci> phi_3 </ci>
</apply>
</apply>
<ci> O </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S" name="S">
<variable units="dimensionless" public_interface="out" name="S"/>
<variable units="dimensionless" public_interface="in" name="I_1"/>
<variable units="dimensionless" public_interface="in" name="I_2"/>
<variable units="dimensionless" public_interface="in" name="O"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="dimensionless" public_interface="in" name="A"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<ci> O </ci>
<ci> A </ci>
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<ci> I_2 </ci>
</apply>
</apply>
</apply>
</math>
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<variable units="first_order_rate_constant" public_interface="in" name="phi_1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_1b"/>
<variable units="first_order_rate_constant" public_interface="in" name="l_2b"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci>time</ci>
</bvar>
<ci> I_1 </ci>
</apply>
<apply>
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<ci> phi_1 </ci>
<ci> R </ci>
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<apply>
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<ci> l_2b </ci>
</apply>
<ci> I_1 </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="I_2" name="I_2">
<variable units="dimensionless" public_interface="out" initial_value="0.16" name="I_2"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_5"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_1b"/>
<variable units="first_order_rate_constant" public_interface="in" name="l_2b"/>
<variable units="dimensionless" public_interface="in" name="A"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<apply>
<diff/>
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<ci>time</ci>
</bvar>
<ci> I_2 </ci>
</apply>
<apply>
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<ci> phi_5 </ci>
<ci> A </ci>
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<apply>
<times/>
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<ci> l_2b </ci>
</apply>
<ci> I_2 </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="A" name="A">
<variable units="dimensionless" public_interface="out" initial_value="0.16" name="A"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_5"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_4"/>
<variable units="first_order_rate_constant" public_interface="in" name="phi_4b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_1b"/>
<variable units="first_order_rate_constant" public_interface="in" name="l_2b"/>
<variable units="dimensionless" public_interface="in" name="I_2"/>
<variable units="dimensionless" public_interface="in" name="O"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<apply>
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<bvar>
<ci>time</ci>
</bvar>
<ci> A </ci>
</apply>
<apply>
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</apply>
<apply>
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<ci> A </ci>
</apply>
<apply>
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<ci> A </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="reaction_rate_constants">
<variable units="first_order_rate_constant" public_interface="out" name="phi_1"/>
<variable units="second_order_rate_constant" public_interface="out" name="phi_2"/>
<variable units="first_order_rate_constant" public_interface="out" name="phi_2b"/>
<variable units="second_order_rate_constant" public_interface="out" name="phi_3"/>
<variable units="first_order_rate_constant" public_interface="out" name="phi_4"/>
<variable units="first_order_rate_constant" public_interface="out" name="phi_4b"/>
<variable units="first_order_rate_constant" public_interface="out" name="phi_5"/>
<variable units="micromolar" public_interface="out" name="p" initial_value="10.0"/>
<variable units="second_order_rate_constant" name="k_1a" initial_value="0.64"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_1b" initial_value="0.04"/>
<variable units="second_order_rate_constant" name="k_2a" initial_value="37.4"/>
<variable units="first_order_rate_constant" name="k_2b" initial_value="1.4"/>
<variable units="second_order_rate_constant" name="k_3a" initial_value="0.11"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_3b" initial_value="29.8"/>
<variable units="second_order_rate_constant" name="k_4a" initial_value="4.0"/>
<variable units="first_order_rate_constant" name="k_4b" initial_value="0.54"/>
<variable units="first_order_rate_constant" name="l_2a" initial_value="1.7"/>
<variable units="first_order_rate_constant" public_interface="out" name="l_2b" initial_value="0.8"/>
<variable units="second_order_rate_constant" name="l_4a" initial_value="1.7"/>
<variable units="second_order_rate_constant" name="l_4b" initial_value="2.5"/>
<variable units="first_order_rate_constant" name="l_6a" initial_value="4707.0"/>
<variable units="first_order_rate_constant" name="l_6b" initial_value="11.4"/>
<variable units="micromolar" name="L_1" initial_value="0.12"/>
<variable units="micromolar" name="L_3" initial_value="0.025"/>
<variable units="micromolar" name="L_5" initial_value="54.7"/>
<variable units="micromolar" name="c" initial_value="1.0"/>
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<apply>
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<apply>
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<apply>
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</apply>
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<apply id="phi_2_calculation">
<eq/>
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<apply>
<divide/>
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<times/>
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<ci> L_3 </ci>
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<ci> c </ci>
</apply>
</apply>
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<plus/>
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<apply>
<times/>
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<apply>
<plus/>
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<apply>
<divide/>
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<ci> L_1 </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
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<apply id="phi_2b_calculation">
<eq/>
<ci> phi_2b </ci>
<apply>
<divide/>
<apply>
<plus/>
<ci> k_2b </ci>
<apply>
<times/>
<ci> l_4b </ci>
<ci> c </ci>
</apply>
</apply>
<apply>
<plus/>
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<apply>
<divide/>
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<ci> L_5 </ci>
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<eq/>
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<apply>
<divide/>
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<times/>
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<ci> L_5 </ci>
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<apply>
<plus/>
<ci> c </ci>
<ci> L_5 </ci>
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</apply>
</apply>
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<eq/>
<ci> phi_4 </ci>
<apply>
<divide/>
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<times/>
<apply>
<plus/>
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<times/>
<ci> k_4a </ci>
<ci> L_5 </ci>
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<ci> l_6a </ci>
</apply>
<ci> c </ci>
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<apply>
<plus/>
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<ci> L_5 </ci>
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</apply>
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<eq/>
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<divide/>
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<times/>
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<plus/>
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<ci> l_6b </ci>
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</apply>
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<ci> L_1 </ci>
</apply>
</apply>
</apply>
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<eq/>
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<ci> L_1 </ci>
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<ci> l_2a </ci>
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<ci> c </ci>
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<ci> c </ci>
<ci> L_1 </ci>
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<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="O"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="I_1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="I_2"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="A"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="reaction_rate_constants" component_1="R"/>
<map_variables variable_2="phi_1" variable_1="phi_1"/>
<map_variables variable_2="phi_2" variable_1="phi_2"/>
<map_variables variable_2="phi_2b" variable_1="phi_2b"/>
<map_variables variable_2="k_1b" variable_1="k_1b"/>
<map_variables variable_2="l_2b" variable_1="l_2b"/>
<map_variables variable_2="p" variable_1="p"/>
</connection>
<connection>
<map_components component_2="reaction_rate_constants" component_1="O"/>
<map_variables variable_2="phi_3" variable_1="phi_3"/>
<map_variables variable_2="phi_2" variable_1="phi_2"/>
<map_variables variable_2="phi_2b" variable_1="phi_2b"/>
<map_variables variable_2="phi_4" variable_1="phi_4"/>
<map_variables variable_2="phi_4b" variable_1="phi_4b"/>
<map_variables variable_2="k_3b" variable_1="k_3b"/>
<map_variables variable_2="p" variable_1="p"/>
</connection>
<connection>
<map_components component_2="reaction_rate_constants" component_1="I_1"/>
<map_variables variable_2="phi_1" variable_1="phi_1"/>
<map_variables variable_2="k_1b" variable_1="k_1b"/>
<map_variables variable_2="l_2b" variable_1="l_2b"/>
</connection>
<connection>
<map_components component_2="reaction_rate_constants" component_1="I_2"/>
<map_variables variable_2="phi_5" variable_1="phi_5"/>
<map_variables variable_2="k_1b" variable_1="k_1b"/>
<map_variables variable_2="l_2b" variable_1="l_2b"/>
</connection>
<connection>
<map_components component_2="reaction_rate_constants" component_1="A"/>
<map_variables variable_2="phi_5" variable_1="phi_5"/>
<map_variables variable_2="phi_4" variable_1="phi_4"/>
<map_variables variable_2="phi_4b" variable_1="phi_4b"/>
<map_variables variable_2="k_1b" variable_1="k_1b"/>
<map_variables variable_2="l_2b" variable_1="l_2b"/>
</connection>
<connection>
<map_components component_2="I_1" component_1="R"/>
<map_variables variable_2="R" variable_1="R"/>
<map_variables variable_2="I_1" variable_1="I_1"/>
</connection>
<connection>
<map_components component_2="O" component_1="R"/>
<map_variables variable_2="R" variable_1="R"/>
<map_variables variable_2="O" variable_1="O"/>
</connection>
<connection>
<map_components component_2="O" component_1="S"/>
<map_variables variable_2="S" variable_1="S"/>
<map_variables variable_2="O" variable_1="O"/>
</connection>
<connection>
<map_components component_2="O" component_1="A"/>
<map_variables variable_2="A" variable_1="A"/>
<map_variables variable_2="O" variable_1="O"/>
</connection>
<connection>
<map_components component_2="I_2" component_1="A"/>
<map_variables variable_2="A" variable_1="A"/>
<map_variables variable_2="I_2" variable_1="I_2"/>
</connection>
<connection>
<map_components component_2="R" component_1="S"/>
<map_variables variable_2="R" variable_1="R"/>
</connection>
<connection>
<map_components component_2="A" component_1="S"/>
<map_variables variable_2="A" variable_1="A"/>
</connection>
<connection>
<map_components component_2="I_1" component_1="S"/>
<map_variables variable_2="I_1" variable_1="I_1"/>
</connection>
<connection>
<map_components component_2="I_2" component_1="S"/>
<map_variables variable_2="I_2" variable_1="I_2"/>
</connection>
<rdf:RDF>
<rdf:Bag rdf:about="rdf:#b865b3df-b00a-4e44-a8ce-886187f7eea9">
<rdf:li>calcium dynamics</rdf:li>
<rdf:li>IP3 receptor</rdf:li>
</rdf:Bag>
<rdf:Seq rdf:about="rdf:#6111cd36-0957-42ed-a020-0a413b58e32e">
<rdf:li rdf:resource="rdf:#292f31fd-3a27-479c-994d-5e112c60017a"/>
<rdf:li rdf:resource="rdf:#600a325c-8a8b-43ac-b8d7-625a5b7d799b"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#67d268c3-19f0-420c-9721-31f6f32f6324">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="#A">
<dcterms:alternative>Active state</dcterms:alternative>
<dc:title>A</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#cef5a763-b1c9-4c6b-8bc9-9daaa5b9e08a">
<dc:title>PNAS</dc:title>
</rdf:Description>
<rdf:Description rdf:about="">
<dc:publisher>The University of Auckland, Auckland Bioengineering Institute</dc:publisher>
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<rdf:value>The new version of this model has been re-coded to remove the reaction element and replace it with a simple MathML description of the model reaction kinetics. This is thought to be truer to the original publication, and information regarding the enzyme kinetics etc will later be added to the metadata through use of an ontology. The model runs in the PCEnv simulator and gives a nice curved output.</rdf:value>
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<dc:title>A dynamic model of the type-2 inositol triphosphate receptor</dc:title>
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<vCard:Orgname>The University of Auckland</vCard:Orgname>
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<vCard:Given>James</vCard:Given>
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<vCard:Given>Jean-Francois</vCard:Given>
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<vCard:FN>Catherine Lloyd</vCard:FN>
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<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
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<vCard:Given>Catherine</vCard:Given>
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<rdf:value>This is the CellML description of Sneyd and Dufour's 2002 dynamic model of type-2 inositol triphosphate receptor. The dynamic properties of this receptor are essential for the control of intracellular calcium, including the generation of calcium oscillations and waves.</rdf:value>
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<dcterms:alternative>Inactive state 1</dcterms:alternative>
<dc:title>I_1</dc:title>
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<dcterms:alternative>Inactive state 2</dcterms:alternative>
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<dc:title>
The Sneyd-Dufour 2002 dynamic model of the type-2 inositol triphosphate receptor.
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<rdf:value>Corrected two of the equations.</rdf:value>
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<dcterms:W3CDTF>2002-02-19</dcterms:W3CDTF>
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