CompuCell3DAttachment 'PK_simple_one_compartment.cps'
Download 1 <?xml version="1.0" encoding="UTF-8"?>
2 <!-- generated with COPASI 4.20 (Build 158) (http://www.copasi.org) at 2017-07-31 21:36:46 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="20" versionDevel="158" copasiSourcesModified="0">
5 <ListOfFunctions>
6 <Function key="Function_13" name="Mass action (irreversible)" type="MassAction" reversible="false">
7 <MiriamAnnotation>
8 <rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
9 <rdf:Description rdf:about="#Function_13">
10 <CopasiMT:is rdf:resource="urn:miriam:obo.sbo:SBO:0000041" />
11 </rdf:Description>
12 </rdf:RDF>
13 </MiriamAnnotation>
14 <Comment>
15 <body xmlns="http://www.w3.org/1999/xhtml">
16 <b>Mass action rate law for first order irreversible reactions</b>
17 <p>
18 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant.
19 </p>
20 </body>
21 </Comment>
22 <Expression>
23 k1*PRODUCT<substrate_i>
24 </Expression>
25 <ListOfParameterDescriptions>
26 <ParameterDescription key="FunctionParameter_81" name="k1" order="0" role="constant"/>
27 <ParameterDescription key="FunctionParameter_79" name="substrate" order="1" role="substrate"/>
28 </ListOfParameterDescriptions>
29 </Function>
30 </ListOfFunctions>
31 <Model key="Model_1" name="New Model" simulationType="time" timeUnit="h" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.0221408570000002e+023">
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38 <dcterms:created>
39 <rdf:Description>
40 <dcterms:W3CDTF>2017-07-31T17:07:25Z</dcterms:W3CDTF>
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43 <CopasiMT:is rdf:resource="urn:miriam:mamo:0000019"/>
44 </rdf:Description>
45 </rdf:RDF>
46
47 </MiriamAnnotation>
48 <Comment>
49 Simplest PK model.
50 </Comment>
51 <ListOfCompartments>
52 <Compartment key="Compartment_2" name="WholeBody" simulationType="fixed" dimensionality="3">
53 </Compartment>
54 </ListOfCompartments>
55 <ListOfMetabolites>
56 <Metabolite key="Metabolite_2" name="Xgut" simulationType="reactions" compartment="Compartment_2">
57 <MiriamAnnotation>
58 <rdf:RDF
59 xmlns:dcterms="http://purl.org/dc/terms/"
60 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
61 <rdf:Description rdf:about="#Metabolite_2">
62 <dcterms:created>
63 <rdf:Description>
64 <dcterms:W3CDTF>2017-07-31T17:27:40Z</dcterms:W3CDTF>
65 </rdf:Description>
66 </dcterms:created>
67 </rdf:Description>
68 </rdf:RDF>
69
70 </MiriamAnnotation>
71 <Comment>
72 Xenobiotic in the gut lumen.
73 </Comment>
74 <InitialExpression>
75 <CN=Root,Model=New Model,Vector=Values[XenoDoseGrams],Reference=InitialValue>/<CN=Root,Model=New Model,Vector=Values[XenoMW],Reference=InitialValue>
76 </InitialExpression>
77 </Metabolite>
78 <Metabolite key="Metabolite_1" name="Xbody" simulationType="reactions" compartment="Compartment_2">
79 </Metabolite>
80 <Metabolite key="Metabolite_0" name="XkidTub" simulationType="reactions" compartment="Compartment_2">
81 </Metabolite>
82 </ListOfMetabolites>
83 <ListOfModelValues>
84 <ModelValue key="ModelValue_0" name="kgut2body" simulationType="fixed">
85 </ModelValue>
86 <ModelValue key="ModelValue_1" name="kbody2kidtub" simulationType="fixed">
87 <MiriamAnnotation>
88 <rdf:RDF
89 xmlns:dcterms="http://purl.org/dc/terms/"
90 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
91 <rdf:Description rdf:about="#ModelValue_1">
92 <dcterms:created>
93 <rdf:Description>
94 <dcterms:W3CDTF>2017-07-31T17:16:06Z</dcterms:W3CDTF>
95 </rdf:Description>
96 </dcterms:created>
97 </rdf:Description>
98 </rdf:RDF>
99
100 </MiriamAnnotation>
101 </ModelValue>
102 <ModelValue key="ModelValue_2" name="XenoMW" simulationType="fixed">
103 <MiriamAnnotation>
104 <rdf:RDF
105 xmlns:dcterms="http://purl.org/dc/terms/"
106 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
107 <rdf:Description rdf:about="#ModelValue_2">
108 <dcterms:created>
109 <rdf:Description>
110 <dcterms:W3CDTF>2017-07-31T17:32:28Z</dcterms:W3CDTF>
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113 </rdf:Description>
114 </rdf:RDF>
115
116 </MiriamAnnotation>
117 </ModelValue>
118 <ModelValue key="ModelValue_3" name="XenoDoseGrams" simulationType="fixed">
119 </ModelValue>
120 <ModelValue key="ModelValue_4" name="XbodyGrams" simulationType="assignment">
121 <MiriamAnnotation>
122 <rdf:RDF
123 xmlns:dcterms="http://purl.org/dc/terms/"
124 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
125 <rdf:Description rdf:about="#ModelValue_4">
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127 <rdf:Description>
128 <dcterms:W3CDTF>2017-07-31T17:33:44Z</dcterms:W3CDTF>
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131 </rdf:Description>
132 </rdf:RDF>
133
134 </MiriamAnnotation>
135 <Expression>
136 <CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xbody],Reference=Concentration>*<CN=Root,Model=New Model,Vector=Values[XenoMW],Reference=InitialValue>
137 </Expression>
138 <Unit>
139 gram
140 </Unit>
141 </ModelValue>
142 </ListOfModelValues>
143 <ListOfReactions>
144 <Reaction key="Reaction_1" name="R1" reversible="false" fast="false">
145 <MiriamAnnotation>
146 <rdf:RDF
147 xmlns:dcterms="http://purl.org/dc/terms/"
148 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
149 <rdf:Description rdf:about="#Reaction_1">
150 <dcterms:created>
151 <rdf:Description>
152 <dcterms:W3CDTF>2017-07-31T17:15:24Z</dcterms:W3CDTF>
153 </rdf:Description>
154 </dcterms:created>
155 </rdf:Description>
156 </rdf:RDF>
157
158 </MiriamAnnotation>
159 <ListOfSubstrates>
160 <Substrate metabolite="Metabolite_2" stoichiometry="1"/>
161 </ListOfSubstrates>
162 <ListOfProducts>
163 <Product metabolite="Metabolite_1" stoichiometry="1"/>
164 </ListOfProducts>
165 <ListOfConstants>
166 <Constant key="Parameter_4568" name="k1" value="1"/>
167 </ListOfConstants>
168 <KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=New Model,Vector=Compartments[WholeBody]">
169 <ListOfCallParameters>
170 <CallParameter functionParameter="FunctionParameter_81">
171 <SourceParameter reference="ModelValue_0"/>
172 </CallParameter>
173 <CallParameter functionParameter="FunctionParameter_79">
174 <SourceParameter reference="Metabolite_2"/>
175 </CallParameter>
176 </ListOfCallParameters>
177 </KineticLaw>
178 </Reaction>
179 <Reaction key="Reaction_0" name="R2" reversible="false" fast="false">
180 <MiriamAnnotation>
181 <rdf:RDF
182 xmlns:dcterms="http://purl.org/dc/terms/"
183 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
184 <rdf:Description rdf:about="#Reaction_0">
185 <dcterms:created>
186 <rdf:Description>
187 <dcterms:W3CDTF>2017-07-31T17:15:56Z</dcterms:W3CDTF>
188 </rdf:Description>
189 </dcterms:created>
190 </rdf:Description>
191 </rdf:RDF>
192
193 </MiriamAnnotation>
194 <ListOfSubstrates>
195 <Substrate metabolite="Metabolite_1" stoichiometry="1"/>
196 </ListOfSubstrates>
197 <ListOfProducts>
198 <Product metabolite="Metabolite_0" stoichiometry="1"/>
199 </ListOfProducts>
200 <ListOfConstants>
201 <Constant key="Parameter_4468" name="k1" value="1"/>
202 </ListOfConstants>
203 <KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=New Model,Vector=Compartments[WholeBody]">
204 <ListOfCallParameters>
205 <CallParameter functionParameter="FunctionParameter_81">
206 <SourceParameter reference="ModelValue_1"/>
207 </CallParameter>
208 <CallParameter functionParameter="FunctionParameter_79">
209 <SourceParameter reference="Metabolite_1"/>
210 </CallParameter>
211 </ListOfCallParameters>
212 </KineticLaw>
213 </Reaction>
214 </ListOfReactions>
215 <ListOfModelParameterSets activeSet="ModelParameterSet_1">
216 <ModelParameterSet key="ModelParameterSet_1" name="Initial State">
217 <ModelParameterGroup cn="String=Initial Time" type="Group">
218 <ModelParameter cn="CN=Root,Model=New Model" value="0" type="Model" simulationType="time"/>
219 </ModelParameterGroup>
220 <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
221 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody]" value="70" type="Compartment" simulationType="fixed"/>
222 </ModelParameterGroup>
223 <ModelParameterGroup cn="String=Initial Species Values" type="Group">
224 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xgut]" value="2.8103323999333334e+023" type="Species" simulationType="reactions">
225 <InitialExpression>
226 <CN=Root,Model=New Model,Vector=Values[XenoDoseGrams],Reference=InitialValue>/<CN=Root,Model=New Model,Vector=Values[XenoMW],Reference=InitialValue>
227 </InitialExpression>
228 </ModelParameter>
229 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xbody]" value="0" type="Species" simulationType="reactions"/>
230 <ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[XkidTub]" value="0" type="Species" simulationType="reactions"/>
231 </ModelParameterGroup>
232 <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
233 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[kgut2body]" value="1" type="ModelValue" simulationType="fixed"/>
234 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[kbody2kidtub]" value="1" type="ModelValue" simulationType="fixed"/>
235 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[XenoMW]" value="150" type="ModelValue" simulationType="fixed"/>
236 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[XenoDoseGrams]" value="1" type="ModelValue" simulationType="fixed"/>
237 <ModelParameter cn="CN=Root,Model=New Model,Vector=Values[XbodyGrams]" value="0" type="ModelValue" simulationType="assignment"/>
238 </ModelParameterGroup>
239 <ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
240 <ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[R1]" type="Reaction">
241 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[R1],ParameterGroup=Parameters,Parameter=k1" value="1" type="ReactionParameter" simulationType="assignment">
242 <InitialExpression>
243 <CN=Root,Model=New Model,Vector=Values[kgut2body],Reference=InitialValue>
244 </InitialExpression>
245 </ModelParameter>
246 </ModelParameterGroup>
247 <ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[R2]" type="Reaction">
248 <ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[R2],ParameterGroup=Parameters,Parameter=k1" value="1" type="ReactionParameter" simulationType="assignment">
249 <InitialExpression>
250 <CN=Root,Model=New Model,Vector=Values[kbody2kidtub],Reference=InitialValue>
251 </InitialExpression>
252 </ModelParameter>
253 </ModelParameterGroup>
254 </ModelParameterGroup>
255 </ModelParameterSet>
256 </ListOfModelParameterSets>
257 <StateTemplate>
258 <StateTemplateVariable objectReference="Model_1"/>
259 <StateTemplateVariable objectReference="Metabolite_1"/>
260 <StateTemplateVariable objectReference="Metabolite_2"/>
261 <StateTemplateVariable objectReference="Metabolite_0"/>
262 <StateTemplateVariable objectReference="ModelValue_4"/>
263 <StateTemplateVariable objectReference="Compartment_2"/>
264 <StateTemplateVariable objectReference="ModelValue_0"/>
265 <StateTemplateVariable objectReference="ModelValue_1"/>
266 <StateTemplateVariable objectReference="ModelValue_2"/>
267 <StateTemplateVariable objectReference="ModelValue_3"/>
268 </StateTemplate>
269 <InitialState type="initialState">
270 0 0 2.8103323999333334e+023 0 0 70 1 1 150 1
271 </InitialState>
272 </Model>
273 <ListOfTasks>
274 <Task key="Task_26" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
275 <Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
276 <Problem>
277 <Parameter name="JacobianRequested" type="bool" value="1"/>
278 <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
279 </Problem>
280 <Method name="Enhanced Newton" type="EnhancedNewton">
281 <Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-009"/>
282 <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
283 <Parameter name="Use Newton" type="bool" value="1"/>
284 <Parameter name="Use Integration" type="bool" value="1"/>
285 <Parameter name="Use Back Integration" type="bool" value="1"/>
286 <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
287 <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
288 <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
289 <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
290 </Method>
291 </Task>
292 <Task key="Task_25" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
293 <Problem>
294 <Parameter name="AutomaticStepSize" type="bool" value="0"/>
295 <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
296 <Parameter name="StepSize" type="float" value="0.10000000000000001"/>
297 <Parameter name="Duration" type="float" value="10"/>
298 <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
299 <Parameter name="OutputStartTime" type="float" value="0"/>
300 <Parameter name="Output Event" type="bool" value="0"/>
301 <Parameter name="Start in Steady State" type="bool" value="0"/>
302 </Problem>
303 <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
304 <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
305 <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-007"/>
306 <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-013"/>
307 <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
308 <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
309 </Method>
310 </Task>
311 <Task key="Task_24" name="Scan" type="scan" scheduled="false" updateModel="false">
312 <Problem>
313 <Parameter name="Subtask" type="unsignedInteger" value="1"/>
314 <ParameterGroup name="ScanItems">
315 <ParameterGroup name="ScanItem">
316 <Parameter name="Number of steps" type="unsignedInteger" value="10"/>
317 <Parameter name="Type" type="unsignedInteger" value="1"/>
318 <Parameter name="Object" type="cn" value="CN=Root,Model=New Model,Vector=Values[kgut2body],Reference=InitialValue"/>
319 <Parameter name="Minimum" type="float" value="0.10000000000000001"/>
320 <Parameter name="Maximum" type="float" value="10"/>
321 <Parameter name="log" type="bool" value="0"/>
322 </ParameterGroup>
323 </ParameterGroup>
324 <Parameter name="Output in subtask" type="bool" value="1"/>
325 <Parameter name="Adjust initial conditions" type="bool" value="0"/>
326 </Problem>
327 <Method name="Scan Framework" type="ScanFramework">
328 </Method>
329 </Task>
330 <Task key="Task_23" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
331 <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
332 <Problem>
333 </Problem>
334 <Method name="EFM Algorithm" type="EFMAlgorithm">
335 </Method>
336 </Task>
337 <Task key="Task_22" name="Optimization" type="optimization" scheduled="false" updateModel="false">
338 <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
339 <Problem>
340 <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
341 <ParameterText name="ObjectiveExpression" type="expression">
342
343 </ParameterText>
344 <Parameter name="Maximize" type="bool" value="0"/>
345 <Parameter name="Randomize Start Values" type="bool" value="0"/>
346 <Parameter name="Calculate Statistics" type="bool" value="1"/>
347 <ParameterGroup name="OptimizationItemList">
348 </ParameterGroup>
349 <ParameterGroup name="OptimizationConstraintList">
350 </ParameterGroup>
351 </Problem>
352 <Method name="Random Search" type="RandomSearch">
353 <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
354 <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
355 <Parameter name="Seed" type="unsignedInteger" value="0"/>
356 </Method>
357 </Task>
358 <Task key="Task_21" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
359 <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
360 <Problem>
361 <Parameter name="Maximize" type="bool" value="0"/>
362 <Parameter name="Randomize Start Values" type="bool" value="0"/>
363 <Parameter name="Calculate Statistics" type="bool" value="1"/>
364 <ParameterGroup name="OptimizationItemList">
365 </ParameterGroup>
366 <ParameterGroup name="OptimizationConstraintList">
367 </ParameterGroup>
368 <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
369 <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
370 <Parameter name="Create Parameter Sets" type="bool" value="0"/>
371 <ParameterGroup name="Experiment Set">
372 </ParameterGroup>
373 <ParameterGroup name="Validation Set">
374 <Parameter name="Weight" type="unsignedFloat" value="1"/>
375 <Parameter name="Threshold" type="unsignedInteger" value="5"/>
376 </ParameterGroup>
377 </Problem>
378 <Method name="Evolutionary Programming" type="EvolutionaryProgram">
379 <Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
380 <Parameter name="Population Size" type="unsignedInteger" value="20"/>
381 <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
382 <Parameter name="Seed" type="unsignedInteger" value="0"/>
383 </Method>
384 </Task>
385 <Task key="Task_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
386 <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
387 <Problem>
388 <Parameter name="Steady-State" type="key" value="Task_26"/>
389 </Problem>
390 <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
391 <Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-009"/>
392 <Parameter name="Use Reder" type="bool" value="1"/>
393 <Parameter name="Use Smallbone" type="bool" value="1"/>
394 </Method>
395 </Task>
396 <Task key="Task_19" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
397 <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
398 <Problem>
399 <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
400 <Parameter name="DivergenceRequested" type="bool" value="1"/>
401 <Parameter name="TransientTime" type="float" value="0"/>
402 </Problem>
403 <Method name="Wolf Method" type="WolfMethod">
404 <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
405 <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
406 <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-007"/>
407 <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-013"/>
408 <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
409 </Method>
410 </Task>
411 <Task key="Task_18" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
412 <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
413 <Problem>
414 <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
415 <Parameter name="StepSize" type="float" value="0.01"/>
416 <Parameter name="Duration" type="float" value="1"/>
417 <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
418 <Parameter name="OutputStartTime" type="float" value="0"/>
419 </Problem>
420 <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
421 <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="9.9999999999999995e-007"/>
422 </Method>
423 </Task>
424 <Task key="Task_17" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
425 <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
426 <Problem>
427 <Parameter name="SubtaskType" type="unsignedInteger" value="2"/>
428 <ParameterGroup name="TargetFunctions">
429 <Parameter name="SingleObject" type="cn" value=""/>
430 <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
431 </ParameterGroup>
432 <ParameterGroup name="ListOfVariables">
433 <ParameterGroup name="Variables">
434 <Parameter name="SingleObject" type="cn" value=""/>
435 <Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
436 </ParameterGroup>
437 <ParameterGroup name="Variables">
438 <Parameter name="SingleObject" type="cn" value=""/>
439 <Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
440 </ParameterGroup>
441 </ParameterGroup>
442 </Problem>
443 <Method name="Sensitivities Method" type="SensitivitiesMethod">
444 <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
445 <Parameter name="Delta minimum" type="unsignedFloat" value="9.9999999999999998e-013"/>
446 </Method>
447 </Task>
448 <Task key="Task_16" name="Moieties" type="moieties" scheduled="false" updateModel="false">
449 <Problem>
450 </Problem>
451 <Method name="Householder Reduction" type="Householder">
452 </Method>
453 </Task>
454 <Task key="Task_15" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
455 <Problem>
456 <Parameter name="AutomaticStepSize" type="bool" value="0"/>
457 <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
458 <Parameter name="StepSize" type="float" value="0.01"/>
459 <Parameter name="Duration" type="float" value="1"/>
460 <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
461 <Parameter name="OutputStartTime" type="float" value="0"/>
462 <Parameter name="Output Event" type="bool" value="0"/>
463 <Parameter name="Start in Steady State" type="bool" value="0"/>
464 <Parameter name="LimitCrossings" type="bool" value="0"/>
465 <Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
466 <Parameter name="LimitOutTime" type="bool" value="0"/>
467 <Parameter name="LimitOutCrossings" type="bool" value="0"/>
468 <Parameter name="PositiveDirection" type="bool" value="1"/>
469 <Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
470 <Parameter name="LimitUntilConvergence" type="bool" value="0"/>
471 <Parameter name="ConvergenceTolerance" type="float" value="9.9999999999999995e-007"/>
472 <Parameter name="Threshold" type="float" value="0"/>
473 <Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
474 <Parameter name="OutputConvergenceTolerance" type="float" value="9.9999999999999995e-007"/>
475 <ParameterText name="TriggerExpression" type="expression">
476
477 </ParameterText>
478 <Parameter name="SingleVariable" type="cn" value=""/>
479 </Problem>
480 <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
481 <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
482 <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-007"/>
483 <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-013"/>
484 <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
485 <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
486 </Method>
487 </Task>
488 <Task key="Task_27" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
489 <Report reference="Report_9" target="" append="1" confirmOverwrite="1"/>
490 <Problem>
491 <Parameter name="Steady-State" type="key" value="Task_26"/>
492 </Problem>
493 <Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
494 </Method>
495 </Task>
496 </ListOfTasks>
497 <ListOfReports>
498 <Report key="Report_17" name="Steady-State" taskType="steadyState" separator="	" precision="6">
499 <Comment>
500 Automatically generated report.
501 </Comment>
502 <Footer>
503 <Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
504 </Footer>
505 </Report>
506 <Report key="Report_16" name="Elementary Flux Modes" taskType="fluxMode" separator="	" precision="6">
507 <Comment>
508 Automatically generated report.
509 </Comment>
510 <Footer>
511 <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
512 </Footer>
513 </Report>
514 <Report key="Report_15" name="Optimization" taskType="optimization" separator="	" precision="6">
515 <Comment>
516 Automatically generated report.
517 </Comment>
518 <Header>
519 <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
520 <Object cn="String=\[Function Evaluations\]"/>
521 <Object cn="Separator=	"/>
522 <Object cn="String=\[Best Value\]"/>
523 <Object cn="Separator=	"/>
524 <Object cn="String=\[Best Parameters\]"/>
525 </Header>
526 <Body>
527 <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
528 <Object cn="Separator=	"/>
529 <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/>
530 <Object cn="Separator=	"/>
531 <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/>
532 </Body>
533 <Footer>
534 <Object cn="String=
"/>
535 <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/>
536 </Footer>
537 </Report>
538 <Report key="Report_14" name="Parameter Estimation" taskType="parameterFitting" separator="	" precision="6">
539 <Comment>
540 Automatically generated report.
541 </Comment>
542 <Header>
543 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/>
544 <Object cn="String=\[Function Evaluations\]"/>
545 <Object cn="Separator=	"/>
546 <Object cn="String=\[Best Value\]"/>
547 <Object cn="Separator=	"/>
548 <Object cn="String=\[Best Parameters\]"/>
549 </Header>
550 <Body>
551 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/>
552 <Object cn="Separator=	"/>
553 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/>
554 <Object cn="Separator=	"/>
555 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/>
556 </Body>
557 <Footer>
558 <Object cn="String=
"/>
559 <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/>
560 </Footer>
561 </Report>
562 <Report key="Report_13" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="	" precision="6">
563 <Comment>
564 Automatically generated report.
565 </Comment>
566 <Header>
567 <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/>
568 </Header>
569 <Footer>
570 <Object cn="String=
"/>
571 <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/>
572 </Footer>
573 </Report>
574 <Report key="Report_12" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="	" precision="6">
575 <Comment>
576 Automatically generated report.
577 </Comment>
578 <Header>
579 <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/>
580 </Header>
581 <Footer>
582 <Object cn="String=
"/>
583 <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/>
584 </Footer>
585 </Report>
586 <Report key="Report_11" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="	" precision="6">
587 <Comment>
588 Automatically generated report.
589 </Comment>
590 <Header>
591 <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/>
592 </Header>
593 <Footer>
594 <Object cn="String=
"/>
595 <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Result"/>
596 </Footer>
597 </Report>
598 <Report key="Report_10" name="Sensitivities" taskType="sensitivities" separator="	" precision="6">
599 <Comment>
600 Automatically generated report.
601 </Comment>
602 <Header>
603 <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Description"/>
604 </Header>
605 <Footer>
606 <Object cn="String=
"/>
607 <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Result"/>
608 </Footer>
609 </Report>
610 <Report key="Report_9" name="Linear Noise Approximation" taskType="linearNoiseApproximation" separator="	" precision="6">
611 <Comment>
612 Automatically generated report.
613 </Comment>
614 <Header>
615 <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Description"/>
616 </Header>
617 <Footer>
618 <Object cn="String=
"/>
619 <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result"/>
620 </Footer>
621 </Report>
622 </ListOfReports>
623 <ListOfPlots>
624 <PlotSpecification name="Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1">
625 <Parameter name="log X" type="bool" value="0"/>
626 <Parameter name="log Y" type="bool" value="0"/>
627 <ListOfPlotItems>
628 <PlotItem name="[Xgut]" type="Curve2D">
629 <Parameter name="Line type" type="unsignedInteger" value="0"/>
630 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
631 <Parameter name="Line width" type="unsignedFloat" value="1"/>
632 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
633 <Parameter name="Color" type="string" value="auto"/>
634 <Parameter name="Recording Activity" type="string" value="during"/>
635 <ListOfChannels>
636 <ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
637 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xgut],Reference=Concentration"/>
638 </ListOfChannels>
639 </PlotItem>
640 <PlotItem name="[Xbody]" type="Curve2D">
641 <Parameter name="Line type" type="unsignedInteger" value="0"/>
642 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
643 <Parameter name="Line width" type="unsignedFloat" value="1"/>
644 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
645 <Parameter name="Color" type="string" value="auto"/>
646 <Parameter name="Recording Activity" type="string" value="during"/>
647 <ListOfChannels>
648 <ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
649 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xbody],Reference=Concentration"/>
650 </ListOfChannels>
651 </PlotItem>
652 <PlotItem name="[XkidTub]" type="Curve2D">
653 <Parameter name="Line type" type="unsignedInteger" value="0"/>
654 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
655 <Parameter name="Line width" type="unsignedFloat" value="1"/>
656 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
657 <Parameter name="Color" type="string" value="auto"/>
658 <Parameter name="Recording Activity" type="string" value="during"/>
659 <ListOfChannels>
660 <ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
661 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[XkidTub],Reference=Concentration"/>
662 </ListOfChannels>
663 </PlotItem>
664 </ListOfPlotItems>
665 </PlotSpecification>
666 <PlotSpecification name="Scan of Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1">
667 <Parameter name="log X" type="bool" value="0"/>
668 <Parameter name="log Y" type="bool" value="0"/>
669 <ListOfPlotItems>
670 <PlotItem name="[Xgut]" type="Curve2D">
671 <Parameter name="Line type" type="unsignedInteger" value="0"/>
672 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
673 <Parameter name="Line width" type="unsignedFloat" value="1"/>
674 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
675 <Parameter name="Color" type="string" value="auto"/>
676 <Parameter name="Recording Activity" type="string" value="during"/>
677 <ListOfChannels>
678 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Values[kgut2body],Reference=InitialValue"/>
679 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xgut],Reference=Concentration"/>
680 </ListOfChannels>
681 </PlotItem>
682 <PlotItem name="[Xbody]" type="Curve2D">
683 <Parameter name="Line type" type="unsignedInteger" value="0"/>
684 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
685 <Parameter name="Line width" type="unsignedFloat" value="1"/>
686 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
687 <Parameter name="Color" type="string" value="auto"/>
688 <Parameter name="Recording Activity" type="string" value="during"/>
689 <ListOfChannels>
690 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Values[kgut2body],Reference=InitialValue"/>
691 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[Xbody],Reference=Concentration"/>
692 </ListOfChannels>
693 </PlotItem>
694 <PlotItem name="[XkidTub]" type="Curve2D">
695 <Parameter name="Line type" type="unsignedInteger" value="0"/>
696 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
697 <Parameter name="Line width" type="unsignedFloat" value="1"/>
698 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
699 <Parameter name="Color" type="string" value="auto"/>
700 <Parameter name="Recording Activity" type="string" value="during"/>
701 <ListOfChannels>
702 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Values[kgut2body],Reference=InitialValue"/>
703 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[WholeBody],Vector=Metabolites[XkidTub],Reference=Concentration"/>
704 </ListOfChannels>
705 </PlotItem>
706 </ListOfPlotItems>
707 </PlotSpecification>
708 <PlotSpecification name="Amounts instead of concentration" type="Plot2D" active="1">
709 <Parameter name="log X" type="bool" value="0"/>
710 <Parameter name="log Y" type="bool" value="0"/>
711 <ListOfPlotItems>
712 <PlotItem name="Values[XbodyGrams]|Time" type="Curve2D">
713 <Parameter name="Color" type="string" value="auto"/>
714 <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
715 <Parameter name="Line type" type="unsignedInteger" value="0"/>
716 <Parameter name="Line width" type="unsignedFloat" value="1"/>
717 <Parameter name="Recording Activity" type="string" value="during"/>
718 <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
719 <ListOfChannels>
720 <ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
721 <ChannelSpec cn="CN=Root,Model=New Model,Vector=Values[XbodyGrams],Reference=Value"/>
722 </ListOfChannels>
723 </PlotItem>
724 </ListOfPlotItems>
725 </PlotSpecification>
726 </ListOfPlots>
727 <GUI>
728 </GUI>
729 <ListOfUnitDefinitions>
730 <UnitDefinition key="Unit_0" name="meter" symbol="m">
731 <Expression>
732 m
733 </Expression>
734 </UnitDefinition>
735 <UnitDefinition key="Unit_1" name="gram" symbol="g">
736 <Expression>
737 g
738 </Expression>
739 </UnitDefinition>
740 <UnitDefinition key="Unit_2" name="second" symbol="s">
741 <Expression>
742 s
743 </Expression>
744 </UnitDefinition>
745 <UnitDefinition key="Unit_6" name="Avogadro" symbol="Avogadro">
746 <Expression>
747 Avogadro
748 </Expression>
749 </UnitDefinition>
750 <UnitDefinition key="Unit_8" name="item" symbol="#">
751 <Expression>
752 #
753 </Expression>
754 </UnitDefinition>
755 </ListOfUnitDefinitions>
756 </COPASI>
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