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added showcase model for paper
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tgeb committed Aug 27, 2020
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4 changes: 4 additions & 0 deletions index.html
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Expand Up @@ -32,6 +32,10 @@ <h4>DiVil</h4>
<div id="modelSelection">
<h1> Select two model versions </h1>
<select id="versionChoice" class="box" size="10">
<optgroup label="Kummer2000 from BioModels">
<option class="opt" value="test">Kumm2000-v1</option>
<option class="opt" value="test">Kummer2000-v2</option>
</optgroup>
<optgroup label="Liebal from BioModels">
<option class="opt" value="test">Liebal1-BIOMD0000000461</option>
<option class="opt" value="test">Liebal2-BIOMD0000000461</option>
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240 changes: 240 additions & 0 deletions testModels/Kummer2000-v1.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="metaid_0000001" version="4">
<model id="Kummer2000_CalciumSpiking" metaid="metaid_0000002" name="Kummer2000_CalciumSpiking">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>
This model is from the article:
<br/>
<strong> Switching from simple to complex oscillations in calcium signaling.
</strong>
<br/>
Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G.
<em>Biophys J.</em>2000 Sep;79(3):1188-95.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/10968983">10968983</a>,
<br/>
<strong>Abstract:</strong>
<br/>
We present a new model for calcium oscillations based on experiments in hepatocytes. The model considers feedback inhibition on the initial agonist receptor complex by calcium and activated phospholipase C, as well as receptor type-dependent self-enhanced behavior of the activated G(alpha) subunit. It is able to show simple periodic oscillations and periodic bursting, and it is the first model to display chaotic bursting in response to agonist stimulations. Moreover, our model offers a possible explanation for the differences in dynamic behavior observed in response to different agonists in hepatocytes.
</p>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
<rdf:Description rdf:about="#model01">
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2011-05-05T12:59:47+00:00</dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2011-05-05T14:19:55+00:00</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfCompartments>
<compartment id="cytoplasm" metaid="metaid_0000003" name="cytoplasm" size="1"/>
<compartment id="ER" metaid="metaid_0000004" name="ER" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species compartment="cytoplasm" id="a" initialConcentration="0.01" metaid="metaid_0000005" name="G-alpha"/>
<species compartment="cytoplasm" id="b" initialAmount="0.01" metaid="metaid_0000006" name="PLC"/>
<species compartment="cytoplasm" id="c" initialAmount="0.01" metaid="metaid_0000007" name="Calcium-Cyt"/>
<species compartment="ER" id="d" initialAmount="20" metaid="metaid_0000008" name="Calcium-ER"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="k1" metaid="metaid_0000009" name="k1" value="0.09"/>
<parameter constant="true" id="k2" metaid="metaid_0000010" name="k2" value="1.3"/>
<parameter constant="true" id="k3" metaid="metaid_0000011" name="k3" value="0.64"/>
<parameter constant="true" id="K4" metaid="metaid_0000012" name="K4" value="0.19"/>
<parameter constant="true" id="k5" metaid="metaid_0000013" name="k5" value="4.88"/>
<parameter constant="true" id="K6" metaid="metaid_0000014" name="K6" value="1.18"/>
<parameter constant="true" id="k7" metaid="metaid_0000015" name="k7" value="2.08"/>
<parameter constant="true" id="k8" metaid="metaid_0000016" name="k8" value="32.24"/>
<parameter constant="true" id="K9" metaid="metaid_0000017" name="K9" value="29.09"/>
<parameter constant="true" id="k10" metaid="metaid_0000018" name="k10" value="5.0"/>
<parameter constant="true" id="K11" metaid="metaid_0000019" name="K11" value="2.67"/>
<parameter constant="true" id="k12" metaid="metaid_0000020" name="k12" value="0.7"/>
<parameter constant="true" id="k13" metaid="metaid_0000021" name="k13" value="13.58"/>
<parameter constant="true" id="k14" metaid="metaid_0000022" name="k14" value="153"/>
<parameter constant="true" id="K15" metaid="metaid_0000023" name="K15" value="0.16"/>
<parameter constant="true" id="k16" metaid="metaid_0000024" name="k16" value="4.85"/>
<parameter constant="true" id="K17" metaid="metaid_0000025" name="K17" value="0.05"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="metaid_0000026" variable="a">
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</math>
</rateRule>
</listOfRules>
</model>
</sbml>
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