- 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/wierschem_2004/model/wierschem_2004.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="./wierschem_2004.cellml#n">
<dcterms:description>potassium channel activation variable</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_influx.k_c">
<dcterms:description>rate of calcium pumping out of the cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#I_KATP">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>ATP-sensitive potassium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_current.V_K">
<dcterms:description>potassium reversal potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_influx.I_Ca">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>calcium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_activated_K_current.k_D">
<bqbiol:isPropertyOf>
<rdf:Description rdf:about="./wierschem_2004.cellml#entity_0">
<bqbiol:isPartOf>
<rdf:Description rdf:about="./wierschem_2004.cellml#entity_1">
<bqbiol:isPartOf>
<rdf:Description rdf:about="./wierschem_2004.cellml#entity_2">
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA:85704"/>
</rdf:Description>
</bqbiol:isPartOf>
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA:260691"/>
</rdf:Description>
</bqbiol:isPartOf>
<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>calcium dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_influx.alpha">
<dcterms:description>current to flux conversion variable</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ATP_sensitive_K_current.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#nucleotides.tau_c">
<dcterms:description>time constant of phosphofructokinase reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#V">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00506"/>
<dcterms:description>membrane potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#I_Ca">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>calcium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_channel_activation.tau_n">
<dcterms:description>activation time constant for potassium channel</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_influx.f">
<dcterms:description>ratio of free to total cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_current.n">
<dcterms:description>potassium channel activation variable</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_activated_K_current.g_KCa_">
<dcterms:description>calcium-dependent potassium current conductance</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ATP">
<dcterms:description>concentration of ATP nucleotides</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_current.V">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00506"/>
<dcterms:description>membrane potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#n_infinity">
<dcterms:description>steady state function of potassium channel activation variable</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_current.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_current.g_Ca_">
<dcterms:description>calcium current conductance</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ADP">
<dcterms:description>concentration of ADP nucleotides</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#nucleotides.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#c">
<bqbiol:isPropertyOf rdf:resource="./wierschem_2004.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ATP_sensitive_K_current.V">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00506"/>
<dcterms:description>membrane potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_activated_K_current.V">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00506"/>
<dcterms:description>membrane potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#nucleotides.v">
<dcterms:description>constant ATP influx into the cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#membrane.I_KCa">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>calcium-activated potassium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_channel_activation.v_n">
<dcterms:description>activation potential of potassium channel</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#membrane.I_Ca">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>calcium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ATP_sensitive_K_current.g_KATP_">
<dcterms:description>ATP-sensitive potassium current conductance</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#m_infinity">
<dcterms:description>steady state function of calcium channel activation variable</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_channel_activation.s_n">
<dcterms:description>potassium channel saturation potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#nucleotides.k">
<dcterms:description>ratio of forward and reverse reaction rates of substrate ATP binding to phosphofructokinase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_channel_activation.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#membrane.C_m">
<dcterms:description>membrane capacitance</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#nucleotides.phi">
<dcterms:description>phosphofructokinase-catalysed reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_activated_K_current.c">
<bqbiol:isPropertyOf rdf:resource="./wierschem_2004.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#wierschem_2004"
semsim:modelName="wierschem_2004"
bqmodel:isDescribedBy="15178199">
<semsim:hasCellMLdocumentation><documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Complex bursting in pancreatic islets: a potential glycolytic mechanism</title>
<author>
<firstname>Ethan</firstname>
<surname>Choi</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 has been built with the differential expressions in Wierschem's 2004 paper and also the XPPAUT code from Richard Bertram. This file is known to run in PCEnv and COR, however the model works in milliseconds, and must be run for at least 600000 time units or more (to simulate 10 minutes) and could not be changed to portray minutes instead. Due to the large iterations, and large point density required to run the model, problems were found in PCEnv and COR where the model would crash or not display properly giving an memory exceded error. Current parameterization of the model replicates Figure 9 of the paper. The initial conditions for all variables were provided in the Bertram code (given as V=-66, n=0, c=0.17, ATP=2.4, ADP=0.05) however these figures still required a warmup period for the functions so they were changed by running the model to steady state then cloning to the output to better replicate the figures from the paper.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>ABSTRACT: The electrical activity of insulin-secreting pancreatic islets of Langerhans is characterized by bursts of action potentials. Most often this bursting is periodic, but in some cases it is modulated by an underlying slower rhythm. We suggest that the modulatory rhythm for this complex bursting pattern is due to oscillations in glycolysis, while the bursting itself is generated by some other slow process. To demonstrate this hypothesis, we couple a minimal model of glycolytic oscillations to a minimal model for activity-dependent bursting in islets. We show that the combined model can reproduce several complex bursting patterns from mouse islets published in the literature, and we illustrate how these complex oscillations are produced through the use of a fast/slow analysis.</para>
<para>
Complex bursting in pancreatic islets: a potential glycolytic mechanism, Wierschem, Bertram, 2004,
<emphasis>Journal of Theoretical Biology</emphasis>
, 228, 513-521.
<ulink url="http://www.ncbi.nlm.nih.gov/pubmed/15178199">PubMed ID: 15178199</ulink>
</para>
<informalfigure>
<mediaobject>
<imageobject>
<objectinfo>
<title>Model Diagram</title>
</objectinfo>
<imagedata fileref="wierschem_2004.png" />
</imageobject>
</mediaobject>
<caption>Schematic diagram of the composite model.</caption>
</informalfigure>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
<semsim:unknown>pancreatic beta cell@en</semsim:unknown>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_current.V">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00506"/>
<dcterms:description>membrane potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#nucleotides.eta">
<dcterms:description>ATP degradation rate</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#membrane.I_KATP">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>ATP-sensitive potassium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_activated_K_current.V_K">
<dcterms:description>potassium reversal potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ATP_sensitive_K_current.ATP">
<dcterms:description>concentration of ATP nucleotides</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#ATP_sensitive_K_current.V_K">
<dcterms:description>potassium reversal potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_influx.c">
<bqbiol:isPropertyOf rdf:resource="./wierschem_2004.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_current.V_Ca">
<dcterms:description>calcium reversal potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#J_mem">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium influx into the cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#membrane.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_current.s_m">
<dcterms:description>calcium channel saturation potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#I_KCa">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>calcium-activated potassium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#omega">
<dcterms:description>activation variable of calcium-dependent potassium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#cytosolic_Ca.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#cytosolic_Ca.J_mem">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium influx into the cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#membrane.I_K">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>potassium current</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_channel_activation.V">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00506"/>
<dcterms:description>membrane potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#K_current.g_K_">
<dcterms:description>potassium current conductance</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#Ca_current.v_m">
<dcterms:description>activation potential of calcium channel</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#environment_time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./wierschem_2004.cellml#I_K">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00318"/>
<dcterms:description>potassium current</dcterms:description>
</rdf:Description>
</rdf:RDF>
