Attachment 'Chaotic Lorenz in COPASI.cps'

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   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- generated with COPASI 4.16 (Build 104) (http://www.copasi.org) at 2017-07-28 15:01:21 UTC -->
   3 <?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
   4 <COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="16" versionDevel="104" copasiSourcesModified="0">
   5   <Model key="Model_3" name="New Model" simulationType="time" timeUnit="s" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.02214179e+023">
   6     <MiriamAnnotation>
   7 <rdf:RDF
   8    xmlns:dcterms="http://purl.org/dc/terms/"
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  10   <rdf:Description rdf:about="#Model_3">
  11     <dcterms:created>
  12       <rdf:Description>
  13         <dcterms:W3CDTF>2017-07-26T11:01:30Z</dcterms:W3CDTF>
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  15     </dcterms:created>
  16   </rdf:Description>
  17 </rdf:RDF>
  18 
  19     </MiriamAnnotation>
  20     <Comment>
  21       After Herbert Sauro&apos;s version of the Chaotic Lorenz System
  22 See https://en.wikipedia.org/wiki/Lorenz_system
  23 Model is a set of ODE&apos;s, not chemical reactions, so x, y, z are treated as variables set by ODEs (instead of chemical species)
  24 https://en.wikipedia.org/wiki/Lorenz_system
  25 
  26     </Comment>
  27     <ListOfCompartments>
  28       <Compartment key="Compartment_1" name="compartment" simulationType="fixed" dimensionality="3">
  29       </Compartment>
  30     </ListOfCompartments>
  31     <ListOfModelValues>
  32       <ModelValue key="ModelValue_0" name="sigma" simulationType="fixed">
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  34       <ModelValue key="ModelValue_1" name="rho" simulationType="fixed">
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  40         <dcterms:W3CDTF>2017-07-26T11:04:36Z</dcterms:W3CDTF>
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  42     </dcterms:created>
  43   </rdf:Description>
  44 </rdf:RDF>
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  46       </ModelValue>
  47       <ModelValue key="ModelValue_2" name="beta" simulationType="fixed">
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  59       </ModelValue>
  60       <ModelValue key="ModelValue_3" name="x" simulationType="ode">
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  76           &lt;CN=Root,Model=New Model,Vector=Values[sigma],Reference=InitialValue&gt;*(&lt;CN=Root,Model=New Model,Vector=Values[y],Reference=Value&gt;-&lt;CN=Root,Model=New Model,Vector=Values[x],Reference=Value&gt;)
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  78       </ModelValue>
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  92           &lt;CN=Root,Model=New Model,Vector=Values[x],Reference=Value&gt;*(&lt;CN=Root,Model=New Model,Vector=Values[rho],Reference=InitialValue&gt;-&lt;CN=Root,Model=New Model,Vector=Values[z],Reference=Value&gt;)-&lt;CN=Root,Model=New Model,Vector=Values[y],Reference=Value&gt;
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  94       </ModelValue>
  95       <ModelValue key="ModelValue_5" name="z" simulationType="ode">
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 118           <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/>
 119         </ModelParameterGroup>
 120         <ModelParameterGroup cn="String=Initial Species Values" type="Group">
 121         </ModelParameterGroup>
 122         <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
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 143     </StateTemplate>
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 145       0 0.96259 2.07272 18.65888 1 10 28 2.67 
 146     </InitialState>
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 150       <Report reference="Report_9" target="" append="1" confirmOverwrite="1"/>
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 176       </Problem>
 177       <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
 178         <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
 179         <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
 180         <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
 181         <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
 182       </Method>
 183     </Task>
 184     <Task key="Task_16" name="Scan" type="scan" scheduled="false" updateModel="false">
 185       <Problem>
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 187         <ParameterGroup name="ScanItems">
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 219         <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
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 225       <Problem>
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 227         <Parameter name="Randomize Start Values" type="bool" value="0"/>
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 230         </ParameterGroup>
 231         <ParameterGroup name="OptimizationConstraintList">
 232         </ParameterGroup>
 233         <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
 234         <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
 235         <Parameter name="Create Parameter Sets" type="bool" value="0"/>
 236         <ParameterGroup name="Experiment Set">
 237         </ParameterGroup>
 238         <ParameterGroup name="Validation Set">
 239           <Parameter name="Threshold" type="unsignedInteger" value="5"/>
 240           <Parameter name="Weight" type="unsignedFloat" value="1"/>
 241         </ParameterGroup>
 242       </Problem>
 243       <Method name="Evolutionary Programming" type="EvolutionaryProgram">
 244         <Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
 245         <Parameter name="Population Size" type="unsignedInteger" value="20"/>
 246         <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
 247         <Parameter name="Seed" type="unsignedInteger" value="0"/>
 248       </Method>
 249     </Task>
 250     <Task key="Task_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
 251       <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
 252       <Problem>
 253         <Parameter name="Steady-State" type="key" value="Task_14"/>
 254       </Problem>
 255       <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
 256         <Parameter name="Modulation Factor" type="unsignedFloat" value="1e-009"/>
 257         <Parameter name="Use Reeder" type="bool" value="1"/>
 258         <Parameter name="Use Smallbone" type="bool" value="1"/>
 259       </Method>
 260     </Task>
 261     <Task key="Task_21" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
 262       <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
 263       <Problem>
 264         <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
 265         <Parameter name="DivergenceRequested" type="bool" value="1"/>
 266         <Parameter name="TransientTime" type="float" value="0"/>
 267       </Problem>
 268       <Method name="Wolf Method" type="WolfMethod">
 269         <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
 270         <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
 271         <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
 272         <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
 273         <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
 274       </Method>
 275     </Task>
 276     <Task key="Task_22" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
 277       <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
 278       <Problem>
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 280         <Parameter name="StepSize" type="float" value="0.01"/>
 281         <Parameter name="Duration" type="float" value="1"/>
 282         <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
 283         <Parameter name="OutputStartTime" type="float" value="0"/>
 284       </Problem>
 285       <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
 286         <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="1e-006"/>
 287       </Method>
 288     </Task>
 289     <Task key="Task_23" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
 290       <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
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 293         <ParameterGroup name="TargetFunctions">
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 306         <Parameter name="Delta minimum" type="unsignedFloat" value="1e-012"/>
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 308     </Task>
 309     <Task key="Task_24" name="Moieties" type="moieties" scheduled="false" updateModel="false">
 310       <Problem>
 311       </Problem>
 312       <Method name="Householder Reduction" type="Householder">
 313       </Method>
 314     </Task>
 315     <Task key="Task_25" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
 316       <Problem>
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 318         <Parameter name="StepSize" type="float" value="0.01"/>
 319         <Parameter name="Duration" type="float" value="1"/>
 320         <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
 321         <Parameter name="OutputStartTime" type="float" value="0"/>
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 324         <Parameter name="LimitCrossings" type="bool" value="0"/>
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 326         <Parameter name="LimitOutTime" type="bool" value="0"/>
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 338         <Parameter name="SingleVariable" type="cn" value=""/>
 339       </Problem>
 340       <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
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 344         <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
 345       </Method>
 346     </Task>
 347     <Task key="Task_26" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
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  • [get | view] (2017-07-27 19:18:45, 142.4 KB) [[attachment:Acetaminophen_PBPK.cps]]
  • [get | view] (2017-07-31 17:20:41, 1449.3 KB) [[attachment:Andy RK.zip]]
  • [get | view] (2017-07-27 19:18:53, 59.4 KB) [[attachment:BIOMD0000000619.xml]]
  • [get | view] (2017-08-09 16:50:30, 13731.9 KB) [[attachment:Belmonte_thesis.pdf]]
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  • [get | view] (2017-08-02 19:58:08, 69593.2 KB) [[attachment:CC3D Intro.pptx]]
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  • [get | view] (2017-08-04 21:38:26, 180.5 KB) [[attachment:CancerFlowCgart.pdf]]
  • [get | view] (2017-08-04 17:24:52, 5066.1 KB) [[attachment:CellCompartmentsAndLinks.pptx]]
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  • [get | view] (2017-07-27 19:19:01, 1.1 KB) [[attachment:Critchley_human_APAP_data.csv]]
  • [get | view] (2017-08-02 14:44:17, 550.8 KB) [[attachment:Defining ODEs in COPASI--SBML.pptx]]
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  • [get | view] (2017-08-04 17:40:32, 7.2 KB) [[attachment:DirectedMovement.zip]]
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  • [get | view] (2017-08-02 16:55:16, 1753.5 KB) [[attachment:Hirashima_et_al-2017-Development_Growt.pdf]]
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  • [get | view] (2017-07-31 21:35:05, 38.2 KB) [[attachment:PK_simple_one_compartment.cps]]
  • [get | view] (2017-07-30 19:38:10, 738.3 KB) [[attachment:Priyom Verbal Model from Mark Alber Epithelial paper with annotations.docx]]
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  • [get | view] (2017-08-04 17:47:09, 92.6 KB) [[attachment:class_photo.jpg]]
  • [get | view] (2017-08-02 19:59:01, 34.5 KB) [[attachment:delta-notch.cps]]
  • [get | view] (2017-08-02 20:05:06, 987.6 KB) [[attachment:delta-notch.pptx]]
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  • [get | view] (2017-08-04 17:20:14, 6.9 KB) [[attachment:gradient_2.zip]]
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  • [get | view] (2017-07-28 21:48:18, 3377.8 KB) [[attachment:holmes_et_al.gene_exp_enh_blas.pdf]]
  • [get | view] (2017-07-28 21:48:28, 2700.3 KB) [[attachment:holmes_sup_material.pdf]]
  • [get | view] (2017-07-31 13:25:51, 18008.4 KB) [[attachment:journal.pcbi.1005533.pdf]]
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