22 #include "utilities.hpp"
28 #include "sbml/SBMLDocument.h"
29 #include "sbml/Model.h"
30 #include "sbml/Rule.h"
31 #include "sbml/Species.h"
32 #include "sbml/Parameter.h"
33 #include "sbml/math/ASTNode.h"
59 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
61 CPPUNIT_ASSERT(pDocument == NULL);
64 const Model* pSBMLModel = pDocument->getModel();
65 CPPUNIT_ASSERT(pSBMLModel != NULL);
66 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 3);
67 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
68 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 3);
69 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 8);
70 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
71 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 0);
76 CPPUNIT_ASSERT(pModifiedMM != NULL);
78 CPPUNIT_ASSERT(pModifiedCF != NULL);
80 CPPUNIT_ASSERT(pConstantFlux != NULL);
81 unsigned int i, iMax = pSBMLModel->getListOfReactions()->size();
82 const Reaction* pReaction = NULL;
83 const ASTNode* pRoot = NULL;
84 const std::map<CCopasiObject*, SBase*>& copasi2sbmlmap = pDataModel->
getCopasi2SBMLMap();
85 std::map<CCopasiObject*, SBase*>::const_iterator mappos;
87 for (i = 0; i < iMax; ++i)
89 pReaction = pSBMLModel->getReaction(i);
90 CPPUNIT_ASSERT(pReaction != NULL);
91 CPPUNIT_ASSERT(pReaction->getKineticLaw() != NULL);
92 pRoot = pReaction->getKineticLaw()->getMath();
93 CPPUNIT_ASSERT(pRoot != NULL);
94 CPPUNIT_ASSERT(pRoot->getType() == AST_TIMES);
96 if (pRoot->getChild(0)->getType() == AST_NAME && pRoot->getChild(0)->getName() == pSBMLModel->getCompartment(0)->getId())
98 pRoot = pRoot->getChild(1);
102 pRoot = pRoot->getChild(0);
105 if (pReaction->getName() ==
"y0Prod" || pReaction->getName() ==
"y1Prod" || pReaction->getName() ==
"xProdLin")
108 CPPUNIT_ASSERT(pRoot->getType() == AST_FUNCTION);
109 mappos = copasi2sbmlmap.find(pModifiedCF);
110 CPPUNIT_ASSERT(mappos != copasi2sbmlmap.end());
111 CPPUNIT_ASSERT(mappos->second != NULL);
112 CPPUNIT_ASSERT(pRoot->getName() == mappos->second->getId());
114 else if (pReaction->getName() ==
"xDegMM")
117 CPPUNIT_ASSERT(pRoot->getType() == AST_FUNCTION);
118 mappos = copasi2sbmlmap.find(pModifiedMM);
119 CPPUNIT_ASSERT(mappos != copasi2sbmlmap.end());
120 CPPUNIT_ASSERT(mappos->second != NULL);
121 CPPUNIT_ASSERT(pRoot->getName() == mappos->second->getId());
123 else if (pReaction->getName() ==
"xProd")
126 CPPUNIT_ASSERT(pRoot->getType() == AST_FUNCTION);
127 mappos = copasi2sbmlmap.find(pConstantFlux);
128 CPPUNIT_ASSERT(mappos != copasi2sbmlmap.end());
129 CPPUNIT_ASSERT(mappos->second != NULL);
130 CPPUNIT_ASSERT(pRoot->getName() == mappos->second->getId());
135 CPPUNIT_ASSERT(pRoot->getType() == AST_TIMES);
142 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
143 "<!-- generated with COPASI 4.4 (Build 26) (http://www.copasi.org) at 2008-08-04 15:57:12 UTC -->\n"
144 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"26\">\n"
145 " <ListOfFunctions>\n"
146 " <Function key=\"Function_6\" name=\"Constant flux (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
150 " <ListOfParameterDescriptions>\n"
151 " <ParameterDescription key=\"FunctionParameter_49\" name=\"v\" order=\"0\" role=\"constant\"/>\n"
152 " </ListOfParameterDescriptions>\n"
154 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
156 " k1*PRODUCT<substrate_i>\n"
158 " <ListOfParameterDescriptions>\n"
159 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
160 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
161 " </ListOfParameterDescriptions>\n"
163 " <Function key=\"Function_60\" name=\"Objective Function 1\" type=\"Expression\">\n"
168 " <Function key=\"Function_46\" name=\"Objective Function\" type=\"Expression\">\n"
173 " <Function key=\"Function_63\" name=\"modified constant flux\" type=\"UserDefined\" reversible=\"unspecified\">\n"
177 " <ListOfParameterDescriptions>\n"
178 " <ParameterDescription key=\"FunctionParameter_297\" name=\"k\" order=\"0\" role=\"constant\"/>\n"
179 " <ParameterDescription key=\"FunctionParameter_268\" name=\"M\" order=\"1\" role=\"modifier\"/>\n"
180 " </ListOfParameterDescriptions>\n"
182 " <Function key=\"Function_52\" name=\"Modified MM\" type=\"UserDefined\" reversible=\"unspecified\">\n"
186 " <ListOfParameterDescriptions>\n"
187 " <ParameterDescription key=\"FunctionParameter_272\" name=\"a_k\" order=\"0\" role=\"constant\"/>\n"
188 " <ParameterDescription key=\"FunctionParameter_250\" name=\"y\" order=\"1\" role=\"modifier\"/>\n"
189 " <ParameterDescription key=\"FunctionParameter_278\" name=\"x\" order=\"2\" role=\"substrate\"/>\n"
190 " <ParameterDescription key=\"FunctionParameter_264\" name=\"k\" order=\"3\" role=\"constant\"/>\n"
191 " </ListOfParameterDescriptions>\n"
193 " <Function key=\"Function_67\" name=\"Objective Function 2\" type=\"Expression\">\n"
198 " </ListOfFunctions>\n"
199 " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"min\" volumeUnit=\"ml\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
201 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
205 " <ListOfCompartments>\n"
206 " <Compartment key=\"Compartment_1\" name=\"compartment\" simulationType=\"fixed\">\n"
208 " </ListOfCompartments>\n"
209 " <ListOfMetabolites>\n"
210 " <Metabolite key=\"Metabolite_5\" name=\"x\" simulationType=\"reactions\" compartment=\"Compartment_1\">\n"
211 " <InitialExpression>\n"
213 " </InitialExpression>\n"
215 " <Metabolite key=\"Metabolite_4\" name=\"y0\" simulationType=\"reactions\" compartment=\"Compartment_1\">\n"
217 " <Metabolite key=\"Metabolite_3\" name=\"y1\" simulationType=\"reactions\" compartment=\"Compartment_1\">\n"
218 " <InitialExpression>\n"
220 " </InitialExpression>\n"
222 " </ListOfMetabolites>\n"
223 " <ListOfReactions>\n"
224 " <Reaction key=\"Reaction_15\" name=\"y0Prod\" reversible=\"false\">\n"
225 " <ListOfProducts>\n"
226 " <Product metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
227 " </ListOfProducts>\n"
228 " <ListOfModifiers>\n"
229 " <Modifier metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
230 " </ListOfModifiers>\n"
231 " <ListOfConstants>\n"
232 " <Constant key=\"Parameter_290\" name=\"k\" value=\"0.1\"/>\n"
233 " </ListOfConstants>\n"
234 " <KineticLaw function=\"Function_63\">\n"
235 " <ListOfCallParameters>\n"
236 " <CallParameter functionParameter=\"FunctionParameter_297\">\n"
237 " <SourceParameter reference=\"Parameter_290\"/>\n"
238 " </CallParameter>\n"
239 " <CallParameter functionParameter=\"FunctionParameter_268\">\n"
240 " <SourceParameter reference=\"Metabolite_5\"/>\n"
241 " </CallParameter>\n"
242 " </ListOfCallParameters>\n"
245 " <Reaction key=\"Reaction_14\" name=\"y0toy1\" reversible=\"false\">\n"
246 " <ListOfSubstrates>\n"
247 " <Substrate metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
248 " </ListOfSubstrates>\n"
249 " <ListOfProducts>\n"
250 " <Product metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
251 " </ListOfProducts>\n"
252 " <ListOfConstants>\n"
253 " <Constant key=\"Parameter_203\" name=\"k1\" value=\"0.1\"/>\n"
254 " </ListOfConstants>\n"
255 " <KineticLaw function=\"Function_13\">\n"
256 " <ListOfCallParameters>\n"
257 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
258 " <SourceParameter reference=\"Parameter_203\"/>\n"
259 " </CallParameter>\n"
260 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
261 " <SourceParameter reference=\"Metabolite_4\"/>\n"
262 " </CallParameter>\n"
263 " </ListOfCallParameters>\n"
266 " <Reaction key=\"Reaction_12\" name=\"y1Deg\" reversible=\"false\">\n"
267 " <ListOfSubstrates>\n"
268 " <Substrate metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
269 " </ListOfSubstrates>\n"
270 " <ListOfConstants>\n"
271 " <Constant key=\"Parameter_102\" name=\"k1\" value=\"0.1\"/>\n"
272 " </ListOfConstants>\n"
273 " <KineticLaw function=\"Function_13\">\n"
274 " <ListOfCallParameters>\n"
275 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
276 " <SourceParameter reference=\"Parameter_102\"/>\n"
277 " </CallParameter>\n"
278 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
279 " <SourceParameter reference=\"Metabolite_3\"/>\n"
280 " </CallParameter>\n"
281 " </ListOfCallParameters>\n"
284 " <Reaction key=\"Reaction_11\" name=\"y0Deg\" reversible=\"false\">\n"
285 " <ListOfSubstrates>\n"
286 " <Substrate metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
287 " </ListOfSubstrates>\n"
288 " <ListOfConstants>\n"
289 " <Constant key=\"Parameter_282\" name=\"k1\" value=\"0.1\"/>\n"
290 " </ListOfConstants>\n"
291 " <KineticLaw function=\"Function_13\">\n"
292 " <ListOfCallParameters>\n"
293 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
294 " <SourceParameter reference=\"Parameter_282\"/>\n"
295 " </CallParameter>\n"
296 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
297 " <SourceParameter reference=\"Metabolite_4\"/>\n"
298 " </CallParameter>\n"
299 " </ListOfCallParameters>\n"
302 " <Reaction key=\"Reaction_8\" name=\"xDegMM\" reversible=\"false\">\n"
303 " <ListOfSubstrates>\n"
304 " <Substrate metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
305 " </ListOfSubstrates>\n"
306 " <ListOfModifiers>\n"
307 " <Modifier metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
308 " </ListOfModifiers>\n"
309 " <ListOfConstants>\n"
310 " <Constant key=\"Parameter_412\" name=\"a_k\" value=\"0.1\"/>\n"
311 " <Constant key=\"Parameter_139\" name=\"k\" value=\"0.1\"/>\n"
312 " </ListOfConstants>\n"
313 " <KineticLaw function=\"Function_52\">\n"
314 " <ListOfCallParameters>\n"
315 " <CallParameter functionParameter=\"FunctionParameter_272\">\n"
316 " <SourceParameter reference=\"Parameter_412\"/>\n"
317 " </CallParameter>\n"
318 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
319 " <SourceParameter reference=\"Metabolite_3\"/>\n"
320 " </CallParameter>\n"
321 " <CallParameter functionParameter=\"FunctionParameter_278\">\n"
322 " <SourceParameter reference=\"Metabolite_5\"/>\n"
323 " </CallParameter>\n"
324 " <CallParameter functionParameter=\"FunctionParameter_264\">\n"
325 " <SourceParameter reference=\"Parameter_139\"/>\n"
326 " </CallParameter>\n"
327 " </ListOfCallParameters>\n"
330 " <Reaction key=\"Reaction_7\" name=\"y1Prod\" reversible=\"false\">\n"
331 " <ListOfProducts>\n"
332 " <Product metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
333 " </ListOfProducts>\n"
334 " <ListOfModifiers>\n"
335 " <Modifier metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
336 " </ListOfModifiers>\n"
337 " <ListOfConstants>\n"
338 " <Constant key=\"Parameter_275\" name=\"k\" value=\"0.1\"/>\n"
339 " </ListOfConstants>\n"
340 " <KineticLaw function=\"Function_63\">\n"
341 " <ListOfCallParameters>\n"
342 " <CallParameter functionParameter=\"FunctionParameter_297\">\n"
343 " <SourceParameter reference=\"Parameter_275\"/>\n"
344 " </CallParameter>\n"
345 " <CallParameter functionParameter=\"FunctionParameter_268\">\n"
346 " <SourceParameter reference=\"Metabolite_4\"/>\n"
347 " </CallParameter>\n"
348 " </ListOfCallParameters>\n"
351 " <Reaction key=\"Reaction_1\" name=\"xProd\" reversible=\"false\">\n"
352 " <ListOfProducts>\n"
353 " <Product metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
354 " </ListOfProducts>\n"
355 " <ListOfModifiers>\n"
356 " <Modifier metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
357 " </ListOfModifiers>\n"
358 " <ListOfConstants>\n"
359 " <Constant key=\"Parameter_339\" name=\"v\" value=\"0.1\"/>\n"
360 " </ListOfConstants>\n"
361 " <KineticLaw function=\"Function_6\">\n"
362 " <ListOfCallParameters>\n"
363 " <CallParameter functionParameter=\"FunctionParameter_49\">\n"
364 " <SourceParameter reference=\"Parameter_339\"/>\n"
365 " </CallParameter>\n"
366 " </ListOfCallParameters>\n"
369 " <Reaction key=\"Reaction_0\" name=\"xProdLin\" reversible=\"false\">\n"
370 " <ListOfProducts>\n"
371 " <Product metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
372 " </ListOfProducts>\n"
373 " <ListOfModifiers>\n"
374 " <Modifier metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
375 " </ListOfModifiers>\n"
376 " <ListOfConstants>\n"
377 " <Constant key=\"Parameter_306\" name=\"k\" value=\"0.1\"/>\n"
378 " </ListOfConstants>\n"
379 " <KineticLaw function=\"Function_63\">\n"
380 " <ListOfCallParameters>\n"
381 " <CallParameter functionParameter=\"FunctionParameter_297\">\n"
382 " <SourceParameter reference=\"Parameter_306\"/>\n"
383 " </CallParameter>\n"
384 " <CallParameter functionParameter=\"FunctionParameter_268\">\n"
385 " <SourceParameter reference=\"Metabolite_5\"/>\n"
386 " </CallParameter>\n"
387 " </ListOfCallParameters>\n"
390 " </ListOfReactions>\n"
392 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
393 " <StateTemplateVariable objectReference=\"Metabolite_5\"/>\n"
394 " <StateTemplateVariable objectReference=\"Metabolite_4\"/>\n"
395 " <StateTemplateVariable objectReference=\"Metabolite_3\"/>\n"
396 " <StateTemplateVariable objectReference=\"Compartment_1\"/>\n"
397 " </StateTemplate>\n"
398 " <InitialState type=\"initialState\">\n"
399 " 0 3.974613390000001e+20 1.2044283e+20 5.540370180000001e+20 1\n"
403 " <Task key=\"Task_15\" name=\"Steady-State\" type=\"steadyState\" scheduled=\"false\" updateModel=\"false\">\n"
404 " <Report reference=\"Report_13\" target=\"\" append=\"1\"/>\n"
406 " <Parameter name=\"JacobianRequested\" type=\"bool\" value=\"1\"/>\n"
407 " <Parameter name=\"StabilityAnalysisRequested\" type=\"bool\" value=\"1\"/>\n"
409 " <Method name=\"Enhanced Newton\" type=\"EnhancedNewton\">\n"
410 " <Parameter name=\"Resolution\" type=\"unsignedFloat\" value=\"1e-09\"/>\n"
411 " <Parameter name=\"Derivation Factor\" type=\"unsignedFloat\" value=\"0.001\"/>\n"
412 " <Parameter name=\"Use Newton\" type=\"bool\" value=\"1\"/>\n"
413 " <Parameter name=\"Use Integration\" type=\"bool\" value=\"1\"/>\n"
414 " <Parameter name=\"Use Back Integration\" type=\"bool\" value=\"1\"/>\n"
415 " <Parameter name=\"Accept Negative Concentrations\" type=\"bool\" value=\"0\"/>\n"
416 " <Parameter name=\"Iteration Limit\" type=\"unsignedInteger\" value=\"50\"/>\n"
419 " <Task key=\"Task_7\" name=\"Time-Course\" type=\"timeCourse\" scheduled=\"false\" updateModel=\"false\">\n"
421 " <Parameter name=\"StepNumber\" type=\"unsignedInteger\" value=\"3500\"/>\n"
422 " <Parameter name=\"StepSize\" type=\"float\" value=\"0.01\"/>\n"
423 " <Parameter name=\"Duration\" type=\"float\" value=\"35\"/>\n"
424 " <Parameter name=\"TimeSeriesRequested\" type=\"bool\" value=\"1\"/>\n"
425 " <Parameter name=\"OutputStartTime\" type=\"float\" value=\"0\"/>\n"
427 " <Method name=\"Deterministic (LSODA)\" type=\"Deterministic(LSODA)\">\n"
428 " <Parameter name=\"Integrate Reduced Model\" type=\"bool\" value=\"0\"/>\n"
429 " <Parameter name=\"Relative Tolerance\" type=\"unsignedFloat\" value=\"1e-06\"/>\n"
430 " <Parameter name=\"Absolute Tolerance\" type=\"unsignedFloat\" value=\"1e-12\"/>\n"
431 " <Parameter name=\"Adams Max Order\" type=\"unsignedInteger\" value=\"12\"/>\n"
432 " <Parameter name=\"BDF Max Order\" type=\"unsignedInteger\" value=\"5\"/>\n"
433 " <Parameter name=\"Max Internal Steps\" type=\"unsignedInteger\" value=\"10000\"/>\n"
436 " <Task key=\"Task_13\" name=\"Scan\" type=\"scan\" scheduled=\"false\" updateModel=\"false\">\n"
438 " <Parameter name=\"Subtask\" type=\"unsignedInteger\" value=\"1\"/>\n"
439 " <ParameterGroup name=\"ScanItems\">\n"
440 " </ParameterGroup>\n"
441 " <Parameter name=\"Output in subtask\" type=\"bool\" value=\"1\"/>\n"
442 " <Parameter name=\"Adjust initial conditions\" type=\"bool\" value=\"0\"/>\n"
444 " <Method name=\"Scan Framework\" type=\"ScanFramework\">\n"
447 " <Task key=\"Task_8\" name=\"Elementary Flux Modes\" type=\"fluxMode\" scheduled=\"false\" updateModel=\"false\">\n"
448 " <Report reference=\"Report_12\" target=\"\" append=\"1\"/>\n"
451 " <Method name=\"EFM Algorithm\" type=\"EFMAlgorithm\">\n"
454 " <Task key=\"Task_11\" name=\"Optimization\" type=\"optimization\" scheduled=\"false\" updateModel=\"false\">\n"
455 " <Report reference=\"Report_11\" target=\"\" append=\"1\"/>\n"
457 " <Parameter name=\"Steady-State\" type=\"key\" value=\"\"/>\n"
458 " <Parameter name=\"Time-Course\" type=\"key\" value=\"Task_7\"/>\n"
459 " <Parameter name=\"ObjectiveFunction\" type=\"key\" value=\"Function_67\"/>\n"
460 " <Parameter name=\"Maximize\" type=\"bool\" value=\"0\"/>\n"
461 " <ParameterGroup name=\"OptimizationItemList\">\n"
462 " </ParameterGroup>\n"
463 " <ParameterGroup name=\"OptimizationConstraintList\">\n"
464 " </ParameterGroup>\n"
466 " <Method name=\"Random Search\" type=\"RandomSearch\">\n"
467 " <Parameter name=\"Number of Iterations\" type=\"unsignedInteger\" value=\"100000\"/>\n"
468 " <Parameter name=\"Random Number Generator\" type=\"unsignedInteger\" value=\"1\"/>\n"
469 " <Parameter name=\"Seed\" type=\"unsignedInteger\" value=\"0\"/>\n"
472 " <Task key=\"Task_20\" name=\"Parameter Estimation\" type=\"parameterFitting\" scheduled=\"true\" updateModel=\"true\">\n"
473 " <Report reference=\"Report_10\" target=\"\" append=\"1\"/>\n"
475 " <Parameter name=\"Steady-State\" type=\"key\" value=\"Task_15\"/>\n"
476 " <Parameter name=\"Time-Course\" type=\"key\" value=\"Task_7\"/>\n"
477 " <ParameterGroup name=\"OptimizationItemList\">\n"
478 " <ParameterGroup name=\"FitItem\">\n"
479 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y0Prod],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
480 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
481 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
482 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
483 " <ParameterGroup name=\"Affected Experiments\">\n"
484 " </ParameterGroup>\n"
485 " </ParameterGroup>\n"
486 " <ParameterGroup name=\"FitItem\">\n"
487 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y0toy1],ParameterGroup=Parameters,Parameter=k1,Reference=Value\"/>\n"
488 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
489 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
490 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
491 " <ParameterGroup name=\"Affected Experiments\">\n"
492 " </ParameterGroup>\n"
493 " </ParameterGroup>\n"
494 " <ParameterGroup name=\"FitItem\">\n"
495 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y1Deg],ParameterGroup=Parameters,Parameter=k1,Reference=Value\"/>\n"
496 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
497 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
498 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
499 " <ParameterGroup name=\"Affected Experiments\">\n"
500 " </ParameterGroup>\n"
501 " </ParameterGroup>\n"
502 " <ParameterGroup name=\"FitItem\">\n"
503 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y0Deg],ParameterGroup=Parameters,Parameter=k1,Reference=Value\"/>\n"
504 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
505 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
506 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
507 " <ParameterGroup name=\"Affected Experiments\">\n"
508 " </ParameterGroup>\n"
509 " </ParameterGroup>\n"
510 " <ParameterGroup name=\"FitItem\">\n"
511 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[xDegMM],ParameterGroup=Parameters,Parameter=a_k,Reference=Value\"/>\n"
512 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
513 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
514 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
515 " <ParameterGroup name=\"Affected Experiments\">\n"
516 " </ParameterGroup>\n"
517 " </ParameterGroup>\n"
518 " <ParameterGroup name=\"FitItem\">\n"
519 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[xDegMM],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
520 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
521 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
522 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
523 " <ParameterGroup name=\"Affected Experiments\">\n"
524 " </ParameterGroup>\n"
525 " </ParameterGroup>\n"
526 " <ParameterGroup name=\"FitItem\">\n"
527 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y1Prod],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
528 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
529 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
530 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
531 " <ParameterGroup name=\"Affected Experiments\">\n"
532 " </ParameterGroup>\n"
533 " </ParameterGroup>\n"
534 " <ParameterGroup name=\"FitItem\">\n"
535 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[xProd],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
536 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
537 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
538 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
539 " <ParameterGroup name=\"Affected Experiments\">\n"
540 " </ParameterGroup>\n"
541 " </ParameterGroup>\n"
542 " <ParameterGroup name=\"FitItem\">\n"
543 " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y0],Reference=InitialConcentration\"/>\n"
544 " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.01\"/>\n"
545 " <Parameter name=\"UpperBound\" type=\"cn\" value=\"1\"/>\n"
546 " <Parameter name=\"StartValue\" type=\"float\" value=\"0.2\"/>\n"
547 " <ParameterGroup name=\"Affected Experiments\">\n"
548 " </ParameterGroup>\n"
549 " </ParameterGroup>\n"
550 " </ParameterGroup>\n"
551 " <ParameterGroup name=\"OptimizationConstraintList\">\n"
552 " </ParameterGroup>\n"
553 " <ParameterGroup name=\"Experiment Set\">\n"
554 " <ParameterGroup name=\"Experiment\">\n"
555 " <Parameter name=\"Key\" type=\"key\" value=\"Experiment_2\"/>\n"
556 " <Parameter name=\"File Name\" type=\"file\" value=\"Geva-ZatorskyCutoff.txt\"/>\n"
557 " <Parameter name=\"First Row\" type=\"unsignedInteger\" value=\"1\"/>\n"
558 " <Parameter name=\"Last Row\" type=\"unsignedInteger\" value=\"93\"/>\n"
559 " <Parameter name=\"Experiment Type\" type=\"unsignedInteger\" value=\"1\"/>\n"
560 " <Parameter name=\"Separator\" type=\"string\" value=\"	\"/>\n"
561 " <Parameter name=\"Weight Method\" type=\"unsignedInteger\" value=\"2\"/>\n"
562 " <Parameter name=\"Data is Row Oriented\" type=\"bool\" value=\"1\"/>\n"
563 " <Parameter name=\"Row containing Names\" type=\"unsignedInteger\" value=\"1\"/>\n"
564 " <Parameter name=\"Number of Columns\" type=\"unsignedInteger\" value=\"3\"/>\n"
565 " <ParameterGroup name=\"Object Map\">\n"
566 " <ParameterGroup name=\"0\">\n"
567 " <Parameter name=\"Role\" type=\"unsignedInteger\" value=\"3\"/>\n"
568 " </ParameterGroup>\n"
569 " <ParameterGroup name=\"1\">\n"
570 " <Parameter name=\"Role\" type=\"unsignedInteger\" value=\"2\"/>\n"
571 " <Parameter name=\"Object CN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[x],Reference=Concentration\"/>\n"
572 " </ParameterGroup>\n"
573 " <ParameterGroup name=\"2\">\n"
574 " <Parameter name=\"Role\" type=\"unsignedInteger\" value=\"2\"/>\n"
575 " <Parameter name=\"Object CN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y1],Reference=Concentration\"/>\n"
576 " </ParameterGroup>\n"
577 " </ParameterGroup>\n"
578 " </ParameterGroup>\n"
579 " </ParameterGroup>\n"
581 " <Method name=\"Evolutionary Programming\" type=\"EvolutionaryProgram\">\n"
582 " <Parameter name=\"Number of Generations\" type=\"unsignedInteger\" value=\"2000\"/>\n"
583 " <Parameter name=\"Population Size\" type=\"unsignedInteger\" value=\"100\"/>\n"
584 " <Parameter name=\"Random Number Generator\" type=\"unsignedInteger\" value=\"1\"/>\n"
585 " <Parameter name=\"Seed\" type=\"unsignedInteger\" value=\"0\"/>\n"
588 " <Task key=\"Task_19\" name=\"Metabolic Control Analysis\" type=\"metabolicControlAnalysis\" scheduled=\"false\" updateModel=\"false\">\n"
589 " <Report reference=\"Report_9\" target=\"\" append=\"1\"/>\n"
591 " <Parameter name=\"Steady-State\" type=\"key\" value=\"Task_15\"/>\n"
593 " <Method name=\"MCA Method (Reder)\" type=\"MCAMethod(Reder)\">\n"
594 " <Parameter name=\"Modulation Factor\" type=\"unsignedFloat\" value=\"1e-09\"/>\n"
597 " <Task key=\"Task_18\" name=\"Lyapunov Exponents\" type=\"lyapunovExponents\" scheduled=\"false\" updateModel=\"false\">\n"
598 " <Report reference=\"Report_8\" target=\"\" append=\"1\"/>\n"
600 " <Parameter name=\"ExponentNumber\" type=\"unsignedInteger\" value=\"3\"/>\n"
601 " <Parameter name=\"DivergenceRequested\" type=\"bool\" value=\"1\"/>\n"
602 " <Parameter name=\"TransientTime\" type=\"float\" value=\"0\"/>\n"
604 " <Method name=\"Wolf Method\" type=\"WolfMethod\">\n"
605 " <Parameter name=\"Orthonormalization Interval\" type=\"unsignedFloat\" value=\"1\"/>\n"
606 " <Parameter name=\"Overall time\" type=\"unsignedFloat\" value=\"1000\"/>\n"
607 " <Parameter name=\"Relative Tolerance\" type=\"unsignedFloat\" value=\"1e-06\"/>\n"
608 " <Parameter name=\"Use Default Absolute Tolerance\" type=\"bool\" value=\"1\"/>\n"
609 " <Parameter name=\"Absolute Tolerance\" type=\"unsignedFloat\" value=\"1e-12\"/>\n"
610 " <Parameter name=\"Adams Max Order\" type=\"unsignedInteger\" value=\"12\"/>\n"
611 " <Parameter name=\"BDF Max Order\" type=\"unsignedInteger\" value=\"5\"/>\n"
612 " <Parameter name=\"Max Internal Steps\" type=\"unsignedInteger\" value=\"10000\"/>\n"
615 " <Task key=\"Task_17\" name=\"Sensitivities\" type=\"sensitivities\" scheduled=\"false\" updateModel=\"false\">\n"
616 " <Report reference=\"Report_7\" target=\"\" append=\"1\"/>\n"
618 " <Parameter name=\"SubtaskType\" type=\"unsignedInteger\" value=\"1\"/>\n"
619 " <ParameterGroup name=\"TargetFunctions\">\n"
620 " <Parameter name=\"SingleObject\" type=\"cn\" value=\"\"/>\n"
621 " <Parameter name=\"ObjectListType\" type=\"unsignedInteger\" value=\"7\"/>\n"
622 " </ParameterGroup>\n"
623 " <ParameterGroup name=\"ListOfVariables\">\n"
624 " <ParameterGroup name=\"Variables\">\n"
625 " <Parameter name=\"SingleObject\" type=\"cn\" value=\"\"/>\n"
626 " <Parameter name=\"ObjectListType\" type=\"unsignedInteger\" value=\"41\"/>\n"
627 " </ParameterGroup>\n"
628 " </ParameterGroup>\n"
630 " <Method name=\"Sensitivities Method\" type=\"SensitivitiesMethod\">\n"
631 " <Parameter name=\"Delta factor\" type=\"unsignedFloat\" value=\"1e-06\"/>\n"
632 " <Parameter name=\"Delta minimum\" type=\"unsignedFloat\" value=\"1e-12\"/>\n"
635 " <Task key=\"Task_10\" name=\"Moieties\" type=\"moieties\" scheduled=\"false\" updateModel=\"false\">\n"
638 " <Method name=\"Householder Reduction\" type=\"Householder\">\n"
643 " <Report key=\"Report_13\" name=\"Steady-State\" taskType=\"steadyState\" separator=\"	\" precision=\"6\">\n"
645 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
646 " Automatically generated report.\n"
650 " <Object cn=\"CN=Root,Vector=TaskList[Steady-State]\"/>\n"
653 " <Report key=\"Report_12\" name=\"Elementary Flux Modes\" taskType=\"fluxMode\" separator=\"	\" precision=\"6\">\n"
655 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
656 " Automatically generated report.\n"
660 " <Object cn=\"CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result\"/>\n"
663 " <Report key=\"Report_11\" name=\"Optimization\" taskType=\"optimization\" separator=\"	\" precision=\"6\">\n"
665 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
666 " Automatically generated report.\n"
670 " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Object=Description\"/>\n"
671 " <Object cn=\"String=\\[Function Evaluations\\]\"/>\n"
672 " <Object cn=\"Separator=	\"/>\n"
673 " <Object cn=\"String=\\[Best Value\\]\"/>\n"
674 " <Object cn=\"Separator=	\"/>\n"
675 " <Object cn=\"String=\\[Best Parameters\\]\"/>\n"
678 " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations\"/>\n"
679 " <Object cn=\"Separator=	\"/>\n"
680 " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value\"/>\n"
681 " <Object cn=\"Separator=	\"/>\n"
682 " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters\"/>\n"
685 " <Object cn=\"String=
\"/>\n"
686 " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Object=Result\"/>\n"
689 " <Report key=\"Report_10\" name=\"Parameter Estimation\" taskType=\"parameterFitting\" separator=\"	\" precision=\"6\">\n"
691 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
692 " Automatically generated report.\n"
696 " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Object=Description\"/>\n"
697 " <Object cn=\"String=\\[Function Evaluations\\]\"/>\n"
698 " <Object cn=\"Separator=	\"/>\n"
699 " <Object cn=\"String=\\[Best Value\\]\"/>\n"
700 " <Object cn=\"Separator=	\"/>\n"
701 " <Object cn=\"String=\\[Best Parameters\\]\"/>\n"
704 " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations\"/>\n"
705 " <Object cn=\"Separator=	\"/>\n"
706 " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value\"/>\n"
707 " <Object cn=\"Separator=	\"/>\n"
708 " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters\"/>\n"
711 " <Object cn=\"String=
\"/>\n"
712 " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Object=Result\"/>\n"
715 " <Report key=\"Report_9\" name=\"Metabolic Control Analysis\" taskType=\"metabolicControlAnalysis\" separator=\"	\" precision=\"6\">\n"
717 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
718 " Automatically generated report.\n"
722 " <Object cn=\"CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description\"/>\n"
725 " <Object cn=\"String=
\"/>\n"
726 " <Object cn=\"CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result\"/>\n"
729 " <Report key=\"Report_8\" name=\"Lyapunov Exponents\" taskType=\"lyapunovExponents\" separator=\"	\" precision=\"6\">\n"
731 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
732 " Automatically generated report.\n"
736 " <Object cn=\"CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description\"/>\n"
739 " <Object cn=\"String=
\"/>\n"
740 " <Object cn=\"CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result\"/>\n"
743 " <Report key=\"Report_7\" name=\"Sensitivities\" taskType=\"sensitivities\" separator=\"	\" precision=\"6\">\n"
745 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
746 " Automatically generated report.\n"
750 " <Object cn=\"CN=Root,Vector=TaskList[Sensitivities],Object=Description\"/>\n"
753 " <Object cn=\"String=
\"/>\n"
754 " <Object cn=\"CN=Root,Vector=TaskList[Sensitivities],Object=Result\"/>\n"
757 " </ListOfReports>\n"
759 " <PlotSpecification name=\"Concentrations, Volumes, and Global Quantity Values\" type=\"Plot2D\" active=\"1\">\n"
760 " <Parameter name=\"log X\" type=\"bool\" value=\"0\"/>\n"
761 " <Parameter name=\"log Y\" type=\"bool\" value=\"0\"/>\n"
762 " <ListOfPlotItems>\n"
763 " <PlotItem name=\"[x]\" type=\"Curve2D\">\n"
764 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
765 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"during\"/>\n"
766 " <ListOfChannels>\n"
767 " <ChannelSpec cn=\"CN=Root,Model=New Model,Reference=Time\"/>\n"
768 " <ChannelSpec cn=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[x],Reference=Concentration\"/>\n"
769 " </ListOfChannels>\n"
771 " <PlotItem name=\"[y0]\" type=\"Curve2D\">\n"
772 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
773 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"during\"/>\n"
774 " <ListOfChannels>\n"
775 " <ChannelSpec cn=\"CN=Root,Model=New Model,Reference=Time\"/>\n"
776 " <ChannelSpec cn=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y0],Reference=Concentration\"/>\n"
777 " </ListOfChannels>\n"
779 " <PlotItem name=\"[y]\" type=\"Curve2D\">\n"
780 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
781 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"during\"/>\n"
782 " <ListOfChannels>\n"
783 " <ChannelSpec cn=\"CN=Root,Model=New Model,Reference=Time\"/>\n"
784 " <ChannelSpec cn=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y1],Reference=Concentration\"/>\n"
785 " </ListOfChannels>\n"
787 " </ListOfPlotItems>\n"
788 " </PlotSpecification>\n"
789 " <PlotSpecification name=\"Experiment\" type=\"Plot2D\" active=\"1\">\n"
790 " <Parameter name=\"log X\" type=\"bool\" value=\"0\"/>\n"
791 " <Parameter name=\"log Y\" type=\"bool\" value=\"0\"/>\n"
792 " <ListOfPlotItems>\n"
793 " <PlotItem name=\"[x](Measured Value)\" type=\"Curve2D\">\n"
794 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"2\"/>\n"
795 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
796 " <ListOfChannels>\n"
797 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
798 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Measured Value\"/>\n"
799 " </ListOfChannels>\n"
801 " <PlotItem name=\"[x](Fitted Value)\" type=\"Curve2D\">\n"
802 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
803 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
804 " <ListOfChannels>\n"
805 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
806 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Fitted Value\"/>\n"
807 " </ListOfChannels>\n"
809 " <PlotItem name=\"[y](Measured Value)\" type=\"Curve2D\">\n"
810 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"2\"/>\n"
811 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
812 " <ListOfChannels>\n"
813 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
814 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[1],Reference=Measured Value\"/>\n"
815 " </ListOfChannels>\n"
817 " <PlotItem name=\"[y](Fitted Value)\" type=\"Curve2D\">\n"
818 " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
819 " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
820 " <ListOfChannels>\n"
821 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
822 " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[1],Reference=Fitted Value\"/>\n"
823 " </ListOfChannels>\n"
825 " </ListOfPlotItems>\n"
826 " </PlotSpecification>\n"
830 " <SBMLReference file=\"MasterModel.xml\">\n"
831 " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_1\"/>\n"
832 " <SBMLMap SBMLid=\"function_1\" COPASIkey=\"Function_52\"/>\n"
833 " <SBMLMap SBMLid=\"function_2\" COPASIkey=\"Function_63\"/>\n"
834 " <SBMLMap SBMLid=\"reaction_3\" COPASIkey=\"Reaction_15\"/>\n"
835 " <SBMLMap SBMLid=\"reaction_4\" COPASIkey=\"Reaction_14\"/>\n"
836 " <SBMLMap SBMLid=\"reaction_5\" COPASIkey=\"Reaction_12\"/>\n"
837 " <SBMLMap SBMLid=\"reaction_8\" COPASIkey=\"Reaction_11\"/>\n"
838 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_5\"/>\n"
839 " <SBMLMap SBMLid=\"species_2\" COPASIkey=\"Metabolite_4\"/>\n"
840 " <SBMLMap SBMLid=\"species_3\" COPASIkey=\"Metabolite_3\"/>\n"
841 " </SBMLReference>\n"
SBMLDocument * getCurrentSBMLDocument()
Header file of class CModelEntity and CModelValue.
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
static bool checkIfIdsUnique(const Model *pSBMLModel)
static const char * MODEL_STRING1
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
static CFunctionDB * getFunctionList()
static CCopasiDataModel * addDatamodel()
static CCopasiDataModel * pCOPASIDATAMODEL
static void init(int argc, char *argv[], const bool &withGui=false)
std::map< CCopasiObject *, SBase * > & getCopasi2SBMLMap()
CFunction * findFunction(const std::string &functionName)