- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-26 14:35:03+13:00
- Desc:
- modifying rdf files
- Permanent Source URI:
- https://models.cellml.org/workspace/7f1/rawfile/4d6408caaf3e7b1b86d33d53d26105360ef95347/wilkins_sneyd_1998/model/wilkins_sneyd_1998.rdf
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:semsim="http://www.bhi.washington.edu/SemSim#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_flux.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_pump.k_gamma">
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<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA:275020"/>
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</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/chebi/CHEBI:29108"/>
</rdf:Description>
</bqbiol:isPropertyOf>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>Michaelis-Menten constant of endoplasmic reticulum calcium pumps</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="./wilkins_sneyd_1998.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of intracellular calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_flux.k1">
<bqbiol:isPropertyOf rdf:resource="./wilkins_sneyd_1998.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>Michaelis-Menten constant for activation of IP3 receptors by calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_pump.c">
<bqbiol:isPropertyOf rdf:resource="./wilkins_sneyd_1998.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of intracellular calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_concentration.Dc">
<dcterms:description>calcium diffusion coefficient</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_flux.mu_p">
<dcterms:description>fraction of IP3 receptors with bound IP3</dcterms:description>
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<bqbiol:is rdf:resource="https://identifiers.org/chebi/CHEBI:16595"/>
</rdf:Description>
</bqbiol:isPropertyOf>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#environment.time">
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</rdf:Description>
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<dcterms:description>calcium flux when all IP3 receptors are open and activated</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_pump.gamma">
<dcterms:description>maximum pumping rate of endoplasmic reticulum calcium pumps</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_flux.h">
<dcterms:description>fraction of IP3 receptors that have not been inactivated by calcium</dcterms:description>
</rdf:Description>
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</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
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</rdf:Description>
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<dcterms:description>fraction of activated IP3 receptors at zero calcium</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux through IP3 receptor</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux through IP3 receptor</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>Michaelis-Menten constant for inactivation of IP3 receptors by calcium</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux out of the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#wilkins_1998"
bqmodel:isDescribedBy="9631570"
semsim:modelName="wilkins_sneyd_1998">
<semsim:modelName>wilkins_1998</semsim:modelName>
<semsim:unknown>Wilkins and Sneyd's 1998 mathematical model of intercellular spiral waves of calcium.</semsim:unknown>
<semsim:hasCellMLdocumentation><documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Intercellular spiral waves of calcium</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 model contains partial differentials and as such can not currently be solved by existing CellML tools.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>ABSTRACT: Intercellular calcium waves have been observed in a large number of cell types, and are known to result from a variety of stimuli, including mechanical or hormonal stimulation. Recently, spiral intercellular waves of calcium have been observed in slices of hippocampal tissue. We use an existing model to study the properties of spiral intercellular calcium waves. Although intercellular spiral waves are well known in the context of cardiac muscle, due to the small value of the calcium diffusion coefficient intercellular calcium waves have fundamentally different properties. We show that homogenisation techniques give a good estimate for the plane wave speed, but do not describe spiral behaviour well. Using an expression for the effective diffusion coefficient we estimate the intercellular calcium permeability in liver. For the bistable equation, we derive an analytic estimate for the value of the intercellular permeability at which wave propagation fails. In the calcium wave model, we show numerically that the spiral period is first a decreasing, then an increasing, function of the intercellular permeability. We hypothesise that this is because the curvature of the spiral core is unimportant at low permeability, the period being approximately set instead by the speed of a plane wave along a line of coupled cells in one dimension.</para>
<para>The original paper reference is cited below:</para>
<para>
Intercellular Spiral Waves of Calcium, Matthew Wilkins and James Sneyd, 1998,
<emphasis>Journal of Theoretical Biology</emphasis>
, 191, 299-308.
<ulink url="http://www.ncbi.nlm.nih.gov/pubmed/9631570">PubMed ID: 9631570</ulink>
</para>
<informalfigure float="0" id="fig_cell_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction diagram</title>
</objectinfo>
<imagedata fileref="wilkins_1998.png" />
</imageobject>
<caption>Schematic diagram showing the transmembrane calcium fluxes which are described by the mathematical model.</caption>
</mediaobject>
</informalfigure>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
</rdf:Description>
<rdf:Description rdf:about="./wilkins_sneyd_1998.cellml#calcium_flux.tau_h">
<dcterms:description>time constant for inactivation of IP3 receptors</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>Michaelis-Menten constant for IP3 binding to receptor</dcterms:description>
</rdf:Description>
</rdf:RDF>
