- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-26 14:35:03+13:00
- Desc:
- modifying rdf files
- Permanent Source URI:
- http://models.cellml.org/workspace/7f1/rawfile/4d6408caaf3e7b1b86d33d53d26105360ef95347/fink_slepchenko_moraru_watras_schaff_loew_2000/model/fink_slepchenko_moraru_watras_schaff_loew_2000.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="fink_slepchenko_moraru_watras_schaff_loew_2000" cmeta:id="fink_slepchenko_moraru_watras_schaff_loew_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Calcium Waves in Differentiated Neuroblastoma Cells</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>This model is a lumped parameter ODE model produced by taking the original PDE model and stripping out all spatial variation; this gives a spatially homogeneous model which doesn't take into account diffusion.</para>
<para>This model validates with the validation service from the CellML API with no errors or warnings, and has been successfully simulated with the CellML Integration Service using the IDA and CVODE Adams-Moulton order 1-12 integrators. Due to the change to a lumped parameter formulation, the results of this model are not expected to be comparable to the published paper, nor to any biological reality, and so the results have not been checked against any other source.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Intracellular calcium dynamics are frequently the subject of theoretical mathematical models (
<ulink url="${HTML_EXMPL_IP3_CA2+_MODEL}">De Young and Keizer, 1992</ulink>
,
<ulink url="${HTML_EXMPL_LI_MODEL}">Li and Rinzel, 1994</ulink>
,
<ulink url="${HTML_EXMPL_KEIZER_MODEL}">Keizer and Levine, 1996</ulink>
,
<ulink url="${HTML_EXMPL_JRW_MODEL}">Jafri-Rice-Winslow, 1998</ulink>
, and
<ulink url="${HTML_EXMPL_SNYDER_MODEL}">Snyder et al., 2000</ulink>
are just a few examples of calcium dynamic models that have been coded up into CellML). The physical and chemical laws of calcium waves and oscillations can be expressed in terms of differential equations describing reaction kinetics, fluxes through membranes, and diffusion.
</para>
<para>
In this study, Charles C. Fink
<emphasis>et al</emphasis>
. produce an image-based model of a intracellular calcium wave in differentiated neuroblastoma cells (see
<xref linkend="fig_cell_diagram" />
below). One important conclusion from their analysis is that neuronal morphology plays a key role in controlling and shaping the inositol-1,4,5-triphosphate (IP
<subscript>3</subscript>
) dynamics that underlie the calcium wave. The model is comprised of several components including:
<itemizedlist>
<listitem>
<para>
<emphasis role="bold">
IP
<subscript>3</subscript>
dynamics
</emphasis>
-
which account for IP
<subscript>3</subscript>
synthesis at the plasma membrane, diffusion into the cytosol, and its degradation.
</para>
</listitem>
<listitem>
<para>
<emphasis role="bold">Calcium dynamics</emphasis>
-
which calculate the changing intracellular calcium concentration.
</para>
</listitem>
<listitem>
<para>
<emphasis role="bold">Channel kinetics</emphasis>
-
to describe calcium release from the endoplasmic reticulum (ER) into the cytosol through an IP
<subscript>3</subscript>
-sensitive channel.
</para>
</listitem>
<listitem>
<para>
<emphasis role="bold">SERCA pump kinetics</emphasis>
-
to describe calcium uptake into the ER via the sarcoplasmic endoplasmic reticulum ATPase (SERCA) pumps.
</para>
</listitem>
<listitem>
<para>
<emphasis role="bold">Leak</emphasis>
-
which models calcium leak from the ER to the cytosol.
</para>
</listitem>
and
<listitem>
<para>
<emphasis role="bold">Calcium buffering</emphasis>
-
with endogenous buffers.
</para>
</listitem>
</itemizedlist>
</para>
<para>
Their model is based on experimental data. The binding of bradykinin (BK) to its receptor initiates a G-protein cascade, activation of phospholipase C, and degradation of phosphatidylinositol bisphosphate (PIP
<subscript>2</subscript>
) to IP
<subscript>3</subscript>
. IP
<subscript>3</subscript>
then diffuses through the cytosol from the plasma membrane to the ER where it activates Ca
<superscript>2+</superscript>
release through the IP
<subscript>3</subscript>
R channel. The concentration of cytosolic Ca
<superscript>2+</superscript>
rises, and is subsequently reduced as Ca
<superscript>2+</superscript>
binds to calcium buffers and is pumped back into the ER through the SERCA. This Ca
<superscript>2+</superscript>
wave was captured by Fink
<emphasis>et al</emphasis>
. through the use of fluorescent microscopy. The model of this process was assembled using the
<emphasis>Virtual Cell</emphasis>
, a computational system for integrating experimentally recorded image, biochemical and electrophysiological data. The model was tested by comparing several simulation results with the real experimental data, and Fink
<emphasis>et al</emphasis>
. found that there was good spatiotemporal agreement between the two data sets.
</para>
<para>
It should be noted that the following CellML description (for the raw CellML description of the model, see
<xref linkend="sec_download_this_model" />
below) is not quite true to the mathematical model published in the original paper (referenced below). Currently CellML is unable to handle spatial elements, but this will hopefully be possible in the near future with the development of FieldML, an XML based language for spatially variable models. This is important, as the relative positions of the cellular components such as receptors, pumps, channels and enzymes will determine the length of diffusion pathways and therefore the rate of reactions.
</para>
<para>
<ulink url="http://www.biophysj.org/cgi/content/abstract/79/1/163">An Image-Based Model of Calcium Waves in Differentiated Neuroblastoma Cells</ulink>
, Charles C. Fink, Boris Slepchenko, Ion I. Moraru, James Watras, James C. Schaff, and Leslie M. Loew, 2000,
<ulink url="http://www.biophysj.org/">
<emphasis>Biophysical Journal</emphasis>
</ulink>
, 79, 163-183. (
<ulink url="http://www.biophysj.org/cgi/content/full/79/1/163">Full text</ulink>
and
<ulink url="http://www.biophysj.org/cgi/reprint/79/1/163.pdf">PDF versions</ulink>
of the article are available to subscribers on the Biophysical Journal website.)
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10866945&dopt=Abstract">PubMed ID: 10866945</ulink>
</para>
<informalfigure float="0" id="fig_cell_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>Schematic diagram of model</title>
</objectinfo>
<imagedata fileref="fink_2000.png" />
</imageobject>
</mediaobject>
</informalfigure>
</sect1>
</article>
</documentation>
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<unit units="micromolar" />
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</component>
<component name="IP3_dynamics" cmeta:id="submodel_1">
<variable cmeta:id="IP3_dynamics.IP3" initial_value="3.0" name="IP3" public_interface="out" units="micromolar" />
<variable cmeta:id="IP3_dynamics.j_IP3" name="j_IP3" units="micromolar_micrometre_per_second" />
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<variable cmeta:id="IP3_dynamics.time" name="time" public_interface="in" units="second" />
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</math>
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<component name="ER" cmeta:id="submodel_2">
<variable cmeta:id="ER.Ca_ER" initial_value="400.0" name="Ca_ER" public_interface="out" units="micromolar" />
</component>
<component name="Calcium_dynamics" cmeta:id="submodel_3">
<variable cmeta:id="Calcium_dynamics.Ca" initial_value="0.05" name="Ca" public_interface="out" units="micromolar" />
<variable cmeta:id="Calcium_dynamics.alpha" initial_value="0.0" name="alpha" units="dimensionless" />
<variable cmeta:id="Calcium_dynamics.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="Calcium_dynamics.J_channel" name="J_channel" public_interface="in" units="flux" />
<variable cmeta:id="Calcium_dynamics.J_pump" name="J_pump" public_interface="in" units="flux" />
<variable cmeta:id="Calcium_dynamics.J_leak" name="J_leak" public_interface="in" units="flux" />
<variable cmeta:id="Calcium_dynamics.R_buffering" name="R_buffering" public_interface="in" units="flux" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_diff_eq">
<eq />
<apply>
<diff />
<ci>Ca</ci>
<bvar>
<ci>time</ci>
</bvar>
</apply>
<apply>
<plus />
<apply>
<times />
<ci>alpha</ci>
<apply>
<plus />
<ci>J_channel</ci>
<apply>
<minus />
<ci>J_pump</ci>
</apply>
<ci>J_leak</ci>
</apply>
</apply>
<ci>R_buffering</ci>
</apply>
</apply>
</math>
</component>
<component name="Channel_kinetics" cmeta:id="submodel_4">
<variable cmeta:id="Channel_kinetics.J_channel" name="J_channel" public_interface="out" units="flux" />
<variable cmeta:id="Channel_kinetics.J_max" initial_value="3500.0" name="J_max" units="flux" />
<variable cmeta:id="Channel_kinetics.h" initial_value="0.8" name="h" units="dimensionless" />
<variable cmeta:id="Channel_kinetics.K_act" initial_value="0.3" name="K_act" units="micromolar" />
<variable cmeta:id="Channel_kinetics.K_IP3" initial_value="0.8" name="K_IP3" units="micromolar" />
<variable cmeta:id="Channel_kinetics.K_inh" initial_value="0.2" name="K_inh" units="micromolar" />
<variable cmeta:id="Channel_kinetics.k_on" initial_value="2.7" name="k_on" units="second_order_rate_constant" />
<variable cmeta:id="Channel_kinetics.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="Channel_kinetics.IP3" name="IP3" public_interface="in" units="micromolar" />
<variable cmeta:id="Channel_kinetics.Ca" name="Ca" public_interface="in" units="micromolar" />
<variable cmeta:id="Channel_kinetics.Ca_ER" name="Ca_ER" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_channel_calculation">
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<ci>IP3</ci>
<apply>
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<apply>
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<ci>Ca</ci>
<apply>
<plus />
<ci>Ca</ci>
<ci>K_act</ci>
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<ci>h</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">3.0</cn>
</apply>
<apply>
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<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.0</cn>
<apply>
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</apply>
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<apply>
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<apply>
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<ci>K_inh</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="SERCA_pump_kinetics" cmeta:id="submodel_5">
<variable cmeta:id="SERCA_pump_kinetics.J_pump" name="J_pump" public_interface="out" units="flux" />
<variable cmeta:id="SERCA_pump_kinetics.V_max" initial_value="3.75" name="V_max" units="flux" />
<variable cmeta:id="SERCA_pump_kinetics.K_p" initial_value="0.27" name="K_p" units="micromolar" />
<variable cmeta:id="SERCA_pump_kinetics.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="SERCA_pump_kinetics.Ca" name="Ca" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_pump_calculation">
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<ci>J_pump</ci>
<apply>
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<apply>
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<apply>
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<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2.0</cn>
</apply>
<apply>
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<ci>K_p</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2.0</cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Leak" cmeta:id="submodel_6">
<variable cmeta:id="Leak.J_leak" name="J_leak" public_interface="out" units="flux" />
<variable cmeta:id="Leak.L" initial_value="0.1" name="L" units="flux" />
<variable cmeta:id="Leak.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="Leak.Ca" name="Ca" public_interface="in" units="micromolar" />
<variable cmeta:id="Leak.Ca_ER" name="Ca_ER" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_leak_calculation">
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<apply>
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<apply>
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<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.0</cn>
<apply>
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<ci>Ca_ER</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Calcium_buffering" cmeta:id="submodel_7">
<variable cmeta:id="Calcium_buffering.R_buffering" name="R_buffering" public_interface="out" units="flux" />
<variable cmeta:id="Calcium_buffering.R1" initial_value="0.1" name="R1" units="flux" />
<variable cmeta:id="Calcium_buffering.R2" initial_value="0.1" name="R2" units="flux" />
<variable cmeta:id="Calcium_buffering.B1" initial_value="450.0" name="B1" units="micromolar" />
<variable cmeta:id="Calcium_buffering.B2" initial_value="75.0" name="B2" units="micromolar" />
<variable cmeta:id="Calcium_buffering.CaB1" initial_value="0" name="CaB1" units="micromolar" />
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<variable cmeta:id="Plasma_membrane_extrusion_mechanisms.Ca" name="Ca" public_interface="in" units="micromolar" />
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<piecewise>
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<!-- if soma -->
<apply>
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<ci>soma_or_neurite</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0</cn>
</apply>
</piece>
<otherwise>
<ci>gamma_n</ci>
</otherwise>
</piecewise>
</apply>
<apply id="gamma_s_calculation">
<eq />
<ci>gamma_s</ci>
<apply>
<divide />
<apply>
<times />
<ci>gamma_0</ci>
<ci>sigma</ci>
</apply>
<apply>
<plus />
<apply>
<times />
<ci>delta</ci>
<ci>sigma_neurite_2D</ci>
<ci>w_n</ci>
</apply>
<apply>
<times />
<ci>sigma_soma_2D</ci>
<ci>w_s</ci>
</apply>
</apply>
</apply>
</apply>
<apply id="gamma_n_calculation">
<eq />
<ci>gamma_n</ci>
<apply>
<divide />
<apply>
<times />
<ci>gamma_0</ci>
<ci>sigma</ci>
<ci>delta</ci>
</apply>
<apply>
<plus />
<apply>
<times />
<ci>delta</ci>
<ci>sigma_neurite_2D</ci>
<ci>w_n</ci>
</apply>
<apply>
<times />
<ci>sigma_soma_2D</ci>
<ci>w_s</ci>
</apply>
</apply>
</apply>
</apply>
<apply id="j_Ca_calculation">
<eq />
<ci>j_Ca</ci>
<piecewise>
<piece>
<apply>
<times />
<ci>gamma</ci>
<apply>
<minus />
<ci>Ca</ci>
<ci>Ca_c</ci>
</apply>
</apply>
<apply>
<gt />
<ci>Ca</ci>
<ci>Ca_c</ci>
</apply>
</piece>
<otherwise>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="micromolar_micrometre_per_second">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="Calcium_buffering" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="Calcium_dynamics" component_2="Calcium_buffering" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="environment" component_2="Leak" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="Plasma_membrane_extrusion_mechanisms" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="Calcium_buffering" component_2="Calcium_dynamics" />
<map_variables variable_1="R_buffering" variable_2="R_buffering" />
</connection>
<connection>
<map_components component_1="Calcium_dynamics" component_2="Plasma_membrane_extrusion_mechanisms" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="ER" component_2="Leak" />
<map_variables variable_1="Ca_ER" variable_2="Ca_ER" />
</connection>
<connection>
<map_components component_1="environment" component_2="IP3_dynamics" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="SERCA_pump_kinetics" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="SERCA_pump_kinetics" component_2="Calcium_dynamics" />
<map_variables variable_1="J_pump" variable_2="J_pump" />
</connection>
<connection>
<map_components component_1="environment" component_2="Calcium_dynamics" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="ER" component_2="Channel_kinetics" />
<map_variables variable_1="Ca_ER" variable_2="Ca_ER" />
</connection>
<connection>
<map_components component_1="environment" component_2="Channel_kinetics" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="Calcium_dynamics" component_2="Channel_kinetics" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="Calcium_dynamics" component_2="Leak" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="Calcium_dynamics" component_2="SERCA_pump_kinetics" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="IP3_dynamics" component_2="Channel_kinetics" />
<map_variables variable_1="IP3" variable_2="IP3" />
</connection>
<connection>
<map_components component_1="Channel_kinetics" component_2="Calcium_dynamics" />
<map_variables variable_1="J_channel" variable_2="J_channel" />
</connection>
<connection>
<map_components component_1="Leak" component_2="Calcium_dynamics" />
<map_variables variable_1="J_leak" variable_2="J_leak" />
</connection>
<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.J_max">
<dcterms:description>average amplitude of channel release</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.B2">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" dcterms:description="Neuroblastoma" />
<dcterms:description>total concentration of exogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_30">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_4">
<ro:part_of>
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</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.time">
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</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.k_degr">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>degradation rate</dcterms:description>
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<rdf:Description rdf:about="#Channel_kinetics.K_inh">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_11">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>dissociation constant for calcium binding to an inhibition site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Leak.Ca_ER">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_20">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_2">
<ro:part_of>
<rdf:Description rdf:about="#entity_3">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:63842" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:29108" />
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</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the endoplasmic reticulum</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.R1">
<dcterms:description>net calcium flux due to endogranous buffers</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.w_n">
<dcterms:description>neurite volume fraction</dcterms:description>
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<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.j_Ca">
<dcterms:description>flux membrane condition for calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.sigma">
<dcterms:description>average surface-to-volume ratio</dcterms:description>
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<rdf:Description rdf:about="#Channel_kinetics.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_13">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
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</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.J_IP3">
<dcterms:description>average flux density amplitude of IP3</dcterms:description>
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<rdf:Description rdf:about="#IP3_dynamics.k_degr">
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<rdf:Description rdf:about="#Calcium_dynamics.J_pump">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
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</semsim:isComputationalComponentFor>
<dcterms:description>calcium flux due to SERCA pump uptake</dcterms:description>
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<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>total concentration of stationary endogenous buffers</dcterms:description>
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<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_dynamics.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
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<rdf:Description rdf:about="#IP3_dynamics.j_IP3">
<dcterms:description>average flux of IP3</dcterms:description>
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<rdf:Description rdf:about="#SERCA_pump_kinetics.K_p">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_16">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>dissociation constant for calcium binding to a pump</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.k2_on">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="#SERCA_pump_kinetics.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_17">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Channel_kinetics.K_act">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_9">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
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</semsim:isComputationalComponentFor>
<dcterms:description>dissociation constant for calcium binding to an activation site</dcterms:description>
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<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
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<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of rdf:resource="#entity_1" />
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</semsim:isComputationalComponentFor>
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<rdf:Description rdf:about="#Channel_kinetics.k_on">
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<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
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<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the endoplasmic reticulum</dcterms:description>
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<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_32">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
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</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
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<rdf:Description rdf:about="#Channel_kinetics.J_channel">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_8">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
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</semsim:isComputationalComponentFor>
<dcterms:description>calcium flux due to channel release</dcterms:description>
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</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_dynamics.J_channel">
<dcterms:description>calcium flux due to channel release</dcterms:description>
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<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.sigma_soma_2D">
<dcterms:description>soma surface-to-volume ratio</dcterms:description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.R_buffering">
<dcterms:description>net calcium flux due to buffering</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Leak.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.sigma_neurite_2D">
<dcterms:description>neurite surface-to-volume ratio</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.Ca_c">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_31">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>threshold concentration for calcium extrusion at the plasma membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#SERCA_pump_kinetics.V_max">
<dcterms:description>average amplitude of pump uptake</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Channel_kinetics.IP3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_12">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_dynamics.Ca">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
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<rdf:Description rdf:about="#IP3_dynamics.k_0">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>flux time constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.k1_on">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.gamma_s">
<dcterms:description>rate of calcium flux density in the soma</dcterms:description>
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<rdf:Description rdf:about="#Channel_kinetics.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.j_IP3">
<dcterms:description>average flux of IP3</dcterms:description>
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<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.sigma_neurite_2D">
<dcterms:description>neurite surface-to-volume ratio</dcterms:description>
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<rdf:Description rdf:about="#SERCA_pump_kinetics.V_max">
<dcterms:description>average amplitude of pump uptake</dcterms:description>
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<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.IP3">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
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</rdf:Description>
<rdf:Description rdf:about="#IP3_dynamics.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.gamma_n">
<dcterms:description>rate of calcium flux density in the neurite</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#SERCA_pump_kinetics.Ca">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Channel_kinetics.K_IP3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_10">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>dissociation constant for IP3 binding to a channel</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.k1_off">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
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<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Leak.Ca">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
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<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.R2">
<dcterms:description>net calcium flux due to exogenous buffers</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.IP3">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.gamma_0">
<dcterms:description>average rate of calcium flux density at the plasma membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.sigma_soma_2D">
<dcterms:description>soma surface-to-volume ratio</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#ER.Ca_ER">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the endoplasmic reticulum</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.K_act">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>dissociation constant for calcium binding to an activation site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.Ca_c">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>threshold concentration for calcium extrusion at the plasma membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Leak.Ca_ER">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the endoplasmic reticulum</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#SERCA_pump_kinetics.K_p">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>dissociation constant for calcium binding to a pump</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#fink_slepchenko_moraru_watras_schaff_loew_2000_version01" semsim:unknown="Neuroblastoma" bqmodel:isDescribedBy="10866945">
<semsim:modelName>fink_slepchenko_moraru_watras_schaff_loew_2000_version01</semsim:modelName>
<semsim:unknown>Fink et al's 2000 model of calcium waves in differentiated neuroblastoma cells.</semsim:unknown>
<semsim:modelName>fink_slepchenko_moraru_watras_schaff_loew_2000</semsim:modelName>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.CaB1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_26">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_5">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:35225" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium bound to an endogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.B2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_25">
<semsim:physicalPropertyOf rdf:resource="#entity_5" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of exogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.K_IP3">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>dissociation constant for IP3 binding to a channel</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_dynamics.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#Leak.J_leak">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_18">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>calcium flux due to leaks</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Leak.L">
<dcterms:description>leak constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.Ca">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_dynamics.J_pump">
<dcterms:description>calcium flux due to SERCA pump uptake</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.R2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_23">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>net calcium flux due to exogenous buffers</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.k_on">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>on-rate for calcium binding to an inhibition site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.CaB2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_27">
<semsim:physicalPropertyOf rdf:resource="#entity_5" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium bound to an exogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#IP3_dynamics.J_IP3">
<dcterms:description>average flux density amplitude of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.B1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_24">
<semsim:physicalPropertyOf rdf:resource="#entity_5" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of stationary endogenous buffers</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.k1_on">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.k2_off">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.k2_off">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.K_inh">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>dissociation constant for calcium binding to an inhibition site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_dynamics.R_buffering">
<dcterms:description>net calcium flux due to buffering</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.J_channel">
<dcterms:description>calcium flux due to channel release</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_dynamics.J_channel">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>calcium flux due to channel release</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.w_n">
<dcterms:description>neurite volume fraction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Leak.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.R1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_22">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>net calcium flux due to endogranous buffers</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#Calcium_dynamics.R_buffering">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_7">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>net calcium flux due to buffering</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Channel_kinetics.Ca_ER">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_14">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the endoplasmic reticulum</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.gamma_s">
<dcterms:description>rate of calcium flux density in the soma</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.K2">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>dissociation constant for calcium binding to an exogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_dynamics.J_leak">
<dcterms:description>calcium flux due to leaks</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.gamma">
<dcterms:description>rate of calcium flux density</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.h">
<dcterms:description>probability of inhibition site not being occupied</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.k_0">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>flux time constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#IP3_dynamics.IP3_0">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>initial IP3 concentration</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.gamma">
<dcterms:description>rate of calcium flux density</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.K2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_29">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>dissociation constant for calcium binding to an exogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Channel_kinetics.J_max">
<dcterms:description>average amplitude of channel release</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.w_s">
<dcterms:description>soma volume fraction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.R_buffering">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_21">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>net calcium flux due to buffering</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#fink_slepchenko_moraru_watras_schaff_loew_2000_version01" bqmodel:isDescribedBy="10866945" />
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.CaB1">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium bound to an endogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.gamma_0">
<dcterms:description>average rate of calcium flux density at the plasma membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_dynamics.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.k1_off">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Channel_kinetics.Ca_ER">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium in the endoplasmic reticulum</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.sigma">
<dcterms:description>average surface-to-volume ratio</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.k2_on">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.K1">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>dissociation constant for calcium binding to an endogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Channel_kinetics.h">
<dcterms:description>probability of inhibition site not being occupied</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#IP3_dynamics.IP3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_0">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Leak.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_19">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium in the cytoplasm</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.w_s">
<dcterms:description>soma volume fraction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#SERCA_pump_kinetics.J_pump">
<dcterms:description>calcium flux due to SERCA pump uptake</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Leak.J_leak">
<dcterms:description>calcium flux due to leaks</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Plasma_membrane_extrusion_mechanisms.j_Ca">
<dcterms:description>flux membrane condition for calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Leak.L">
<dcterms:description>leak constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_dynamics.J_leak">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_6">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>calcium flux due to leaks</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#SERCA_pump_kinetics.J_pump">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_15">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>calcium flux due to SERCA pump uptake</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Plasma_membrane_extrusion_mechanisms.gamma_n">
<dcterms:description>rate of calcium flux density in the neurite</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Calcium_buffering.K1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_28">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>dissociation constant for calcium binding to an endogenous buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#Calcium_buffering.CaB2">
<bqbiol:isPropertyOf rdf:resource="fink_slepchenko_moraru_watras_schaff_loew_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium bound to an exogenous buffer</dcterms:description>
</rdf:Description>
</rdf:RDF>
</model>
