CompuCell3DAttachment 'delta-notch.cps'
Download 1 <?xml version="1.0" encoding="UTF-8"?>
2 <!-- generated with COPASI 4.19 (Build 140) (http://www.copasi.org) at 2017-07-26 21:17:03 UTC -->
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14 <dcterms:W3CDTF>2017-07-26T17:03:19Z</dcterms:W3CDTF>
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21 <Expression>
22 v * (1 / (1 + b * N^h) - D)
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26 <ParameterDescription key="FunctionParameter_275" name="b" order="1" role="constant"/>
27 <ParameterDescription key="FunctionParameter_281" name="N" order="2" role="modifier"/>
28 <ParameterDescription key="FunctionParameter_284" name="h" order="3" role="constant"/>
29 <ParameterDescription key="FunctionParameter_286" name="D" order="4" role="product"/>
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32 <Function key="Function_42" name="Rate Law for J2" type="UserDefined" reversible="unspecified">
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45
46 </MiriamAnnotation>
47 <Expression>
48 Davg^k / (a + Davg^k) - N
49 </Expression>
50 <ListOfParameterDescriptions>
51 <ParameterDescription key="FunctionParameter_289" name="Davg" order="0" role="modifier"/>
52 <ParameterDescription key="FunctionParameter_276" name="k" order="1" role="constant"/>
53 <ParameterDescription key="FunctionParameter_291" name="a" order="2" role="constant"/>
54 <ParameterDescription key="FunctionParameter_274" name="N" order="3" role="product"/>
55 </ListOfParameterDescriptions>
56 </Function>
57 </ListOfFunctions>
58 <Model key="Model_3" name="New Model" simulationType="time" timeUnit="s" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.022140857e+23">
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71
72 </MiriamAnnotation>
73 <ListOfCompartments>
74 <Compartment key="Compartment_1" name="compartment" simulationType="fixed" dimensionality="3">
75 </Compartment>
76 </ListOfCompartments>
77 <ListOfMetabolites>
78 <Metabolite key="Metabolite_1" name="D" simulationType="reactions" compartment="Compartment_1">
79 <MiriamAnnotation>
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86 <dcterms:W3CDTF>2017-07-26T17:08:02Z</dcterms:W3CDTF>
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92 </MiriamAnnotation>
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94 <Metabolite key="Metabolite_3" name="N" simulationType="reactions" compartment="Compartment_1">
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102 <dcterms:W3CDTF>2017-07-26T17:08:38Z</dcterms:W3CDTF>
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107
108 </MiriamAnnotation>
109 </Metabolite>
110 <Metabolite key="Metabolite_5" name="X" simulationType="fixed" compartment="Compartment_1">
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118 <dcterms:W3CDTF>2017-07-26T17:08:50Z</dcterms:W3CDTF>
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124 </MiriamAnnotation>
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126 <Metabolite key="Metabolite_7" name="Davg" simulationType="fixed" compartment="Compartment_1">
127 <MiriamAnnotation>
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140 </MiriamAnnotation>
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146 <ModelValue key="ModelValue_1" name="a" simulationType="fixed">
147 </ModelValue>
148 <ModelValue key="ModelValue_2" name="v" simulationType="fixed">
149 </ModelValue>
150 <ModelValue key="ModelValue_3" name="b" simulationType="fixed">
151 </ModelValue>
152 <ModelValue key="ModelValue_4" name="h" simulationType="fixed">
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155 <ListOfReactions>
156 <Reaction key="Reaction_0" name="J1" reversible="true" fast="false">
157 <MiriamAnnotation>
158 <rdf:RDF
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170 </MiriamAnnotation>
171 <ListOfSubstrates>
172 <Substrate metabolite="Metabolite_5" stoichiometry="1"/>
173 </ListOfSubstrates>
174 <ListOfProducts>
175 <Product metabolite="Metabolite_1" stoichiometry="1"/>
176 </ListOfProducts>
177 <ListOfModifiers>
178 <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
179 </ListOfModifiers>
180 <ListOfConstants>
181 <Constant key="Parameter_4443" name="v" value="1"/>
182 <Constant key="Parameter_4444" name="b" value="100"/>
183 <Constant key="Parameter_4445" name="h" value="2"/>
184 </ListOfConstants>
185 <KineticLaw function="Function_40" unitType="Default" scalingCompartment="CN=Root,Model=New Model,Vector=Compartments[compartment]">
186 <ListOfCallParameters>
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191 <SourceParameter reference="ModelValue_3"/>
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194 <SourceParameter reference="Metabolite_3"/>
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196 <CallParameter functionParameter="FunctionParameter_284">
197 <SourceParameter reference="ModelValue_4"/>
198 </CallParameter>
199 <CallParameter functionParameter="FunctionParameter_286">
200 <SourceParameter reference="Metabolite_1"/>
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203 </KineticLaw>
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218
219 </MiriamAnnotation>
220 <ListOfSubstrates>
221 <Substrate metabolite="Metabolite_5" stoichiometry="1"/>
222 </ListOfSubstrates>
223 <ListOfProducts>
224 <Product metabolite="Metabolite_3" stoichiometry="1"/>
225 </ListOfProducts>
226 <ListOfModifiers>
227 <Modifier metabolite="Metabolite_7" stoichiometry="1"/>
228 </ListOfModifiers>
229 <ListOfConstants>
230 <Constant key="Parameter_4446" name="k" value="2"/>
231 <Constant key="Parameter_4447" name="a" value="0.01"/>
232 </ListOfConstants>
233 <KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=New Model,Vector=Compartments[compartment]">
234 <ListOfCallParameters>
235 <CallParameter functionParameter="FunctionParameter_289">
236 <SourceParameter reference="Metabolite_7"/>
237 </CallParameter>
238 <CallParameter functionParameter="FunctionParameter_276">
239 <SourceParameter reference="ModelValue_0"/>
240 </CallParameter>
241 <CallParameter functionParameter="FunctionParameter_291">
242 <SourceParameter reference="ModelValue_1"/>
243 </CallParameter>
244 <CallParameter functionParameter="FunctionParameter_274">
245 <SourceParameter reference="Metabolite_3"/>
246 </CallParameter>
247 </ListOfCallParameters>
248 </KineticLaw>
249 </Reaction>
250 </ListOfReactions>
251 <ListOfModelParameterSets activeSet="ModelParameterSet_1">
252 <ModelParameterSet key="ModelParameterSet_1" name="Initial State">
253 <ModelParameterGroup cn="String=Initial Time" type="Group">
254 <ModelParameter cn="CN=Root,Model=New Model" value="0" type="Model" simulationType="time"/>
255 </ModelParameterGroup>
256 <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
257 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/>
258 </ModelParameterGroup>
259 <ModelParameterGroup cn="String=Initial Species Values" type="Group">
260 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[D]" value="3.011070428499999e+23" type="Species" simulationType="reactions"/>
261 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[N]" value="3.011070428499999e+23" type="Species" simulationType="reactions"/>
262 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[X]" value="0" type="Species" simulationType="fixed"/>
263 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[Davg]" value="2.4088563428e+23" type="Species" simulationType="fixed"/>
264 </ModelParameterGroup>
265 <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
266 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[k]" value="2" type="ModelValue" simulationType="fixed"/>
267 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[a]" value="0.01" type="ModelValue" simulationType="fixed"/>
268 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[v]" value="1" type="ModelValue" simulationType="fixed"/>
269 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[b]" value="100" type="ModelValue" simulationType="fixed"/>
270 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[h]" value="2" type="ModelValue" simulationType="fixed"/>
271 </ModelParameterGroup>
272 <ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
273 <ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[J1]" type="Reaction">
274 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[J1],ParameterGroup=Parameters,Parameter=v" value="1" type="ReactionParameter" simulationType="assignment">
275 <InitialExpression>
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279 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[J1],ParameterGroup=Parameters,Parameter=b" value="100" type="ReactionParameter" simulationType="assignment">
280 <InitialExpression>
281 <CN=Root,Model=New Model,Vector=Values[b],Reference=InitialValue>
282 </InitialExpression>
283 </ModelParameter>
284 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[J1],ParameterGroup=Parameters,Parameter=h" value="2" type="ReactionParameter" simulationType="assignment">
285 <InitialExpression>
286 <CN=Root,Model=New Model,Vector=Values[h],Reference=InitialValue>
287 </InitialExpression>
288 </ModelParameter>
289 </ModelParameterGroup>
290 <ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[J2]" type="Reaction">
291 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[J2],ParameterGroup=Parameters,Parameter=k" value="2" type="ReactionParameter" simulationType="assignment">
292 <InitialExpression>
293 <CN=Root,Model=New Model,Vector=Values[k],Reference=InitialValue>
294 </InitialExpression>
295 </ModelParameter>
296 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[J2],ParameterGroup=Parameters,Parameter=a" value="0.01" type="ReactionParameter" simulationType="assignment">
297 <InitialExpression>
298 <CN=Root,Model=New Model,Vector=Values[a],Reference=InitialValue>
299 </InitialExpression>
300 </ModelParameter>
301 </ModelParameterGroup>
302 </ModelParameterGroup>
303 </ModelParameterSet>
304 </ListOfModelParameterSets>
305 <StateTemplate>
306 <StateTemplateVariable objectReference="Model_3"/>
307 <StateTemplateVariable objectReference="Metabolite_1"/>
308 <StateTemplateVariable objectReference="Metabolite_3"/>
309 <StateTemplateVariable objectReference="Metabolite_5"/>
310 <StateTemplateVariable objectReference="Metabolite_7"/>
311 <StateTemplateVariable objectReference="Compartment_1"/>
312 <StateTemplateVariable objectReference="ModelValue_0"/>
313 <StateTemplateVariable objectReference="ModelValue_1"/>
314 <StateTemplateVariable objectReference="ModelValue_2"/>
315 <StateTemplateVariable objectReference="ModelValue_3"/>
316 <StateTemplateVariable objectReference="ModelValue_4"/>
317 </StateTemplate>
318 <InitialState type="initialState">
319 0 3.011070428499999e+23 3.011070428499999e+23 0 2.4088563428e+23 1 2 0.01 1 100 2
320 </InitialState>
321 </Model>
322 <ListOfTasks>
323 <Task key="Task_14" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
324 <Report reference="Report_9" target="" append="1" confirmOverwrite="1"/>
325 <Problem>
326 <Parameter name="JacobianRequested" type="bool" value="1"/>
327 <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
328 </Problem>
329 <Method name="Enhanced Newton" type="EnhancedNewton">
330 <Parameter name="Resolution" type="unsignedFloat" value="1e-09"/>
331 <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
332 <Parameter name="Use Newton" type="bool" value="1"/>
333 <Parameter name="Use Integration" type="bool" value="1"/>
334 <Parameter name="Use Back Integration" type="bool" value="1"/>
335 <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
336 <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
337 <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
338 <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
339 </Method>
340 </Task>
341 <Task key="Task_15" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
342 <Problem>
343 <Parameter name="AutomaticStepSize" type="bool" value="0"/>
344 <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
345 <Parameter name="StepSize" type="float" value="0.01"/>
346 <Parameter name="Duration" type="float" value="1"/>
347 <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
348 <Parameter name="OutputStartTime" type="float" value="0"/>
349 <Parameter name="Output Event" type="bool" value="0"/>
350 <Parameter name="Start in Steady State" type="bool" value="0"/>
351 </Problem>
352 <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
353 <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
354 <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
355 <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
356 <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
357 <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
358 </Method>
359 </Task>
360 <Task key="Task_16" name="Scan" type="scan" scheduled="false" updateModel="false">
361 <Problem>
362 <Parameter name="Subtask" type="unsignedInteger" value="1"/>
363 <ParameterGroup name="ScanItems">
364 </ParameterGroup>
365 <Parameter name="Output in subtask" type="bool" value="1"/>
366 <Parameter name="Adjust initial conditions" type="bool" value="0"/>
367 </Problem>
368 <Method name="Scan Framework" type="ScanFramework">
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371 <Task key="Task_17" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
372 <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
373 <Problem>
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375 <Method name="EFM Algorithm" type="EFMAlgorithm">
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379 <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
380 <Problem>
381 <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
382 <ParameterText name="ObjectiveExpression" type="expression">
383
384 </ParameterText>
385 <Parameter name="Maximize" type="bool" value="0"/>
386 <Parameter name="Randomize Start Values" type="bool" value="0"/>
387 <Parameter name="Calculate Statistics" type="bool" value="1"/>
388 <ParameterGroup name="OptimizationItemList">
389 </ParameterGroup>
390 <ParameterGroup name="OptimizationConstraintList">
391 </ParameterGroup>
392 </Problem>
393 <Method name="Random Search" type="RandomSearch">
394 <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
395 <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
396 <Parameter name="Seed" type="unsignedInteger" value="0"/>
397 </Method>
398 </Task>
399 <Task key="Task_19" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
400 <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
401 <Problem>
402 <Parameter name="Maximize" type="bool" value="0"/>
403 <Parameter name="Randomize Start Values" type="bool" value="0"/>
404 <Parameter name="Calculate Statistics" type="bool" value="1"/>
405 <ParameterGroup name="OptimizationItemList">
406 </ParameterGroup>
407 <ParameterGroup name="OptimizationConstraintList">
408 </ParameterGroup>
409 <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
410 <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
411 <Parameter name="Create Parameter Sets" type="bool" value="0"/>
412 <ParameterGroup name="Experiment Set">
413 </ParameterGroup>
414 <ParameterGroup name="Validation Set">
415 <Parameter name="Threshold" type="unsignedInteger" value="5"/>
416 <Parameter name="Weight" type="unsignedFloat" value="1"/>
417 </ParameterGroup>
418 </Problem>
419 <Method name="Evolutionary Programming" type="EvolutionaryProgram">
420 <Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
421 <Parameter name="Population Size" type="unsignedInteger" value="20"/>
422 <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
423 <Parameter name="Seed" type="unsignedInteger" value="0"/>
424 </Method>
425 </Task>
426 <Task key="Task_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
427 <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
428 <Problem>
429 <Parameter name="Steady-State" type="key" value="Task_14"/>
430 </Problem>
431 <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
432 <Parameter name="Modulation Factor" type="unsignedFloat" value="1e-09"/>
433 <Parameter name="Use Reder" type="bool" value="1"/>
434 <Parameter name="Use Smallbone" type="bool" value="1"/>
435 </Method>
436 </Task>
437 <Task key="Task_21" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
438 <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
439 <Problem>
440 <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
441 <Parameter name="DivergenceRequested" type="bool" value="1"/>
442 <Parameter name="TransientTime" type="float" value="0"/>
443 </Problem>
444 <Method name="Wolf Method" type="WolfMethod">
445 <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
446 <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
447 <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
448 <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
449 <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
450 </Method>
451 </Task>
452 <Task key="Task_22" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
453 <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
454 <Problem>
455 <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
456 <Parameter name="StepSize" type="float" value="0.01"/>
457 <Parameter name="Duration" type="float" value="1"/>
458 <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
459 <Parameter name="OutputStartTime" type="float" value="0"/>
460 </Problem>
461 <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
462 <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="1e-06"/>
463 </Method>
464 </Task>
465 <Task key="Task_23" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
466 <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
467 <Problem>
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469 <ParameterGroup name="TargetFunctions">
470 <Parameter name="SingleObject" type="cn" value=""/>
471 <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
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478 <ParameterGroup name="Variables">
479 <Parameter name="SingleObject" type="cn" value=""/>
480 <Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
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483 </Problem>
484 <Method name="Sensitivities Method" type="SensitivitiesMethod">
485 <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
486 <Parameter name="Delta minimum" type="unsignedFloat" value="1e-12"/>
487 </Method>
488 </Task>
489 <Task key="Task_24" name="Moieties" type="moieties" scheduled="false" updateModel="false">
490 <Problem>
491 </Problem>
492 <Method name="Householder Reduction" type="Householder">
493 </Method>
494 </Task>
495 <Task key="Task_25" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
496 <Problem>
497 <Parameter name="AutomaticStepSize" type="bool" value="0"/>
498 <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
499 <Parameter name="StepSize" type="float" value="0.01"/>
500 <Parameter name="Duration" type="float" value="1"/>
501 <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
502 <Parameter name="OutputStartTime" type="float" value="0"/>
503 <Parameter name="Output Event" type="bool" value="0"/>
504 <Parameter name="Start in Steady State" type="bool" value="0"/>
505 <Parameter name="LimitCrossings" type="bool" value="0"/>
506 <Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
507 <Parameter name="LimitOutTime" type="bool" value="0"/>
508 <Parameter name="LimitOutCrossings" type="bool" value="0"/>
509 <Parameter name="PositiveDirection" type="bool" value="1"/>
510 <Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
511 <Parameter name="LimitUntilConvergence" type="bool" value="0"/>
512 <Parameter name="ConvergenceTolerance" type="float" value="1e-06"/>
513 <Parameter name="Threshold" type="float" value="0"/>
514 <Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
515 <Parameter name="OutputConvergenceTolerance" type="float" value="1e-06"/>
516 <ParameterText name="TriggerExpression" type="expression">
517
518 </ParameterText>
519 <Parameter name="SingleVariable" type="cn" value=""/>
520 </Problem>
521 <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
522 <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
523 <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
524 <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
525 <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
526 <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
527 </Method>
528 </Task>
529 <Task key="Task_26" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
530 <Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
531 <Problem>
532 <Parameter name="Steady-State" type="key" value="Task_14"/>
533 </Problem>
534 <Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
535 </Method>
536 </Task>
537 </ListOfTasks>
538 <ListOfReports>
539 <Report key="Report_9" name="Steady-State" taskType="steadyState" separator="	" precision="6">
540 <Comment>
541 Automatically generated report.
542 </Comment>
543 <Footer>
544 <Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
545 </Footer>
546 </Report>
547 <Report key="Report_10" name="Elementary Flux Modes" taskType="fluxMode" separator="	" precision="6">
548 <Comment>
549 Automatically generated report.
550 </Comment>
551 <Footer>
552 <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
553 </Footer>
554 </Report>
555 <Report key="Report_11" name="Optimization" taskType="optimization" separator="	" precision="6">
556 <Comment>
557 Automatically generated report.
558 </Comment>
559 <Header>
560 <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
561 <Object cn="String=\[Function Evaluations\]"/>
562 <Object cn="Separator=	"/>
563 <Object cn="String=\[Best Value\]"/>
564 <Object cn="Separator=	"/>
565 <Object cn="String=\[Best Parameters\]"/>
566 </Header>
567 <Body>
568 <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
569 <Object cn="Separator=	"/>
570 <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/>
571 <Object cn="Separator=	"/>
572 <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/>
573 </Body>
574 <Footer>
575 <Object cn="String=
"/>
576 <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/>
577 </Footer>
578 </Report>
579 <Report key="Report_12" name="Parameter Estimation" taskType="parameterFitting" separator="	" precision="6">
580 <Comment>
581 Automatically generated report.
582 </Comment>
583 <Header>
584 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/>
585 <Object cn="String=\[Function Evaluations\]"/>
586 <Object cn="Separator=	"/>
587 <Object cn="String=\[Best Value\]"/>
588 <Object cn="Separator=	"/>
589 <Object cn="String=\[Best Parameters\]"/>
590 </Header>
591 <Body>
592 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/>
593 <Object cn="Separator=	"/>
594 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/>
595 <Object cn="Separator=	"/>
596 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/>
597 </Body>
598 <Footer>
599 <Object cn="String=
"/>
600 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/>
601 </Footer>
602 </Report>
603 <Report key="Report_13" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="	" precision="6">
604 <Comment>
605 Automatically generated report.
606 </Comment>
607 <Header>
608 <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/>
609 </Header>
610 <Footer>
611 <Object cn="String=
"/>
612 <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/>
613 </Footer>
614 </Report>
615 <Report key="Report_14" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="	" precision="6">
616 <Comment>
617 Automatically generated report.
618 </Comment>
619 <Header>
620 <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/>
621 </Header>
622 <Footer>
623 <Object cn="String=
"/>
624 <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/>
625 </Footer>
626 </Report>
627 <Report key="Report_15" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="	" precision="6">
628 <Comment>
629 Automatically generated report.
630 </Comment>
631 <Header>
632 <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/>
633 </Header>
634 <Footer>
635 <Object cn="String=
"/>
636 <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Result"/>
637 </Footer>
638 </Report>
639 <Report key="Report_16" name="Sensitivities" taskType="sensitivities" separator="	" precision="6">
640 <Comment>
641 Automatically generated report.
642 </Comment>
643 <Header>
644 <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Description"/>
645 </Header>
646 <Footer>
647 <Object cn="String=
"/>
648 <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Result"/>
649 </Footer>
650 </Report>
651 <Report key="Report_17" name="Linear Noise Approximation" taskType="linearNoiseApproximation" separator="	" precision="6">
652 <Comment>
653 Automatically generated report.
654 </Comment>
655 <Header>
656 <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Description"/>
657 </Header>
658 <Footer>
659 <Object cn="String=
"/>
660 <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result"/>
661 </Footer>
662 </Report>
663 </ListOfReports>
664 <ListOfPlots>
665 <PlotSpecification name="Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1">
666 <Parameter name="log X" type="bool" value="0"/>
667 <Parameter name="log Y" type="bool" value="0"/>
668 <ListOfPlotItems>
669 <PlotItem name="[D]" type="Curve2D">
670 <Parameter name="Line type" type="unsignedInteger" value="0"/>
671 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
672 <Parameter name="Line width" type="unsignedFloat" value="1"/>
673 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
674 <Parameter name="Color" type="string" value="auto"/>
675 <Parameter name="Recording Activity" type="string" value="during"/>
676 <ListOfChannels>
677 <ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
678 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[D],Reference=Concentration"/>
679 </ListOfChannels>
680 </PlotItem>
681 <PlotItem name="[N]" type="Curve2D">
682 <Parameter name="Line type" type="unsignedInteger" value="0"/>
683 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
684 <Parameter name="Line width" type="unsignedFloat" value="1"/>
685 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
686 <Parameter name="Color" type="string" value="auto"/>
687 <Parameter name="Recording Activity" type="string" value="during"/>
688 <ListOfChannels>
689 <ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
690 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[N],Reference=Concentration"/>
691 </ListOfChannels>
692 </PlotItem>
693 </ListOfPlotItems>
694 </PlotSpecification>
695 </ListOfPlots>
696 <GUI>
697 </GUI>
698 <ListOfUnitDefinitions>
699 <UnitDefinition key="Unit_0" name="meter" symbol="m">
700 <Expression>
701 m
702 </Expression>
703 </UnitDefinition>
704 <UnitDefinition key="Unit_2" name="second" symbol="s">
705 <Expression>
706 s
707 </Expression>
708 </UnitDefinition>
709 <UnitDefinition key="Unit_6" name="Avogadro" symbol="Avogadro">
710 <Expression>
711 Avogadro
712 </Expression>
713 </UnitDefinition>
714 <UnitDefinition key="Unit_8" name="item" symbol="#">
715 <Expression>
716 #
717 </Expression>
718 </UnitDefinition>
719 </ListOfUnitDefinitions>
720 </COPASI>
Attached Files
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