-
Notifications
You must be signed in to change notification settings - Fork 0
/
PulsedDrugLadder.cps
952 lines (947 loc) · 49.4 KB
/
PulsedDrugLadder.cps
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
<?xml version="1.0" encoding="UTF-8"?>
<!-- generated with COPASI 4.38 (Build 268) (http://www.copasi.org) at 2022-12-14T14:33:58Z -->
<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="38" versionDevel="268" copasiSourcesModified="0">
<ListOfFunctions>
<Function key="Function_13" name="Mass action (irreversible)" type="MassAction" reversible="false">
<MiriamAnnotation>
<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#">
<rdf:Description rdf:about="#Function_13">
<CopasiMT:is rdf:resource="urn:miriam:obo.sbo:SBO:0000163" />
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
<body xmlns="http://www.w3.org/1999/xhtml">
<b>Mass action rate law for irreversible reactions</b>
<p>
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.
</p>
</body>
</Comment>
<Expression>
k1*PRODUCT<substrate_i>
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_80" name="k1" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_81" name="substrate" order="1" role="substrate"/>
</ListOfParameterDescriptions>
</Function>
<Function key="Function_19" name="Noncompetitive inhibition (irr)" type="PreDefined" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_19">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
V*substrate/((Km+substrate)*(1+Inhibitor/Ki))
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_119" name="substrate" order="0" role="substrate"/>
<ParameterDescription key="FunctionParameter_118" name="Inhibitor" order="1" role="modifier"/>
<ParameterDescription key="FunctionParameter_117" name="Km" order="2" role="constant"/>
<ParameterDescription key="FunctionParameter_116" name="V" order="3" role="constant"/>
<ParameterDescription key="FunctionParameter_115" name="Ki" order="4" role="constant"/>
</ListOfParameterDescriptions>
</Function>
</ListOfFunctions>
<Model key="Model_1" name="Model with pulsed drug" simulationType="time" timeUnit="s" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.0221407599999999e+23">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
<rdf:Description rdf:about="#Model_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-09-30T13:00:28Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
<dcterms:creator>
<rdf:Description>
<vCard:EMAIL>pmendes@uchc.edu</vCard:EMAIL>
<vCard:N>
<rdf:Description>
<vCard:Family>Mendes</vCard:Family>
<vCard:Given>Pedro</vCard:Given>
</rdf:Description>
</vCard:N>
<vCard:ORG>
<rdf:Description>
<vCard:Orgname>University of Connecticut</vCard:Orgname>
</rdf:Description>
</vCard:ORG>
</rdf:Description>
</dcterms:creator>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
<body xmlns="http://www.w3.org/1999/xhtml"><h1>Example of using events to provide pulses of a species</h1>
<h2>Description</h2>
<p>The model consists of a simple linear pathway with two intermediates (<b>A</b> and <b>B</b>), where the reaction that converts <b>A</b> into <b>B</b> is inhibited by another species <b>drug</b>. There are two external species, a substrate <b>S</b> and a product <b>P</b> of the pathway that are kept fixed.</p>
<pre>
drug
|
v
S ---> A ---> B ---> P
</pre>
<p>The main point of this example is to demonstrate how to set events such that they can simulate a pulse in the drug concentration (ie change its concentration at specific time points). The example here is to turn it "on" for 1 second (set it to a fixed value) and then turn it "off" for 3 second (set it to zero). In this case we also make it more complicated as the drug dose increases every time it is applied. Something like this:</p>
<pre>
▁▁▁▁▁▁▁▁▁▃▃▁▁▁▁▁▁▁▁▁▅▅▁▁▁▁▁▁▁▁▁██▁▁ . . .
</pre>
<h2>Approach</h2>
<p>A few auxiliary <b>global quantities</b> are created:</p>
<table>
<tr><td>Drug_dose </td><td>to set the value of the [drug] during on time</td></tr>
<tr><td>Drug_increase </td><td>to set the value by which the [drug] increases from event to event</td></tr>
<tr><td>off_time</td><td>to set the duration of the off time (here 3 second)</td></tr>
<tr><td>on_time</td><td>to set the duration of the on time (here 1 second)</td></tr>
<tr><td>Next_On</td><td>to store the next time when the drug pulse is turned on</td></tr>
<tr><td>Next_Off</td><td>to store the next time when the drug pulse is turned off</td></tr>
</table>
<p>Then two <b>events</b> are created to turn on and turn off the pulse:</p>
<table>
<tr><td>Drug_On </td><td>happens when time > Next_On<br />sets the [drug]=Drug_dose<br />adds the time of a whole period (off_time+on_time) to Next_On (so that it can turn on the next time).</td></tr>
<tr><td>Drug_Off</td><td>happens when time > Next_Off<br />sets the [drug]=0<br />adds the time of a whole period (off_time+on_time) to Next_Off (so that it can turn off the next time). It also increases the drug dose for the next time.</td></tr>
</table>
<h2>Further improvements</h2>
<p>It is possible to change the on and off times, simply by adjusting the global quantities <b>on_time</b> and <b>off_time</b>.</p>
<p>It is possible to adjust the drug dose by adjusting <b>Drug_dose</b>. </p>
<p>It is even possible to change these values at some point in time by adding another event that changes any of these global quantitites...</p>
<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p>
</body>
</Comment>
<ListOfCompartments>
<Compartment key="Compartment_0" name="compartment" simulationType="fixed" dimensionality="3" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Compartment_0">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Compartment>
</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_3" name="A" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_3">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_2" name="S" simulationType="fixed" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_0">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_102" name="B" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_102">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_103" name="P" simulationType="fixed" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_104" name="drug" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</Metabolite>
</ListOfMetabolites>
<ListOfModelValues>
<ModelValue key="ModelValue_4" name="Next_On" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<InitialExpression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[off_time],Reference=InitialValue>
</InitialExpression>
<Unit>
s
</Unit>
</ModelValue>
<ModelValue key="ModelValue_0" name="Drug_dose" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_1" name="on_time" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#ModelValue_1">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_2" name="off_time" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#ModelValue_2">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_3" name="Next_Off" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<InitialExpression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[off_time],Reference=InitialValue>+<CN=Root,Model=Model with pulsed drug,Vector=Values[on_time],Reference=InitialValue>
</InitialExpression>
<Unit>
s
</Unit>
</ModelValue>
<ModelValue key="ModelValue_5" name="Drug_increase" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</ModelValue>
</ListOfModelValues>
<ListOfReactions>
<Reaction key="Reaction_3" name="R1" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_12307" name="k1" value="4"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_12307"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_201" name="R2" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_102" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_104" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_11324" name="Km" value="0.05"/>
<Constant key="Parameter_7552" name="V" value="5"/>
<Constant key="Parameter_6957" name="Ki" value="0.5"/>
</ListOfConstants>
<KineticLaw function="Function_19" unitType="Default" scalingCompartment="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_119">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_118">
<SourceParameter reference="Metabolite_104"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_117">
<SourceParameter reference="Parameter_11324"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_116">
<SourceParameter reference="Parameter_7552"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_115">
<SourceParameter reference="Parameter_6957"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_202" name="R3" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_102" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_103" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_5593" name="k1" value="15"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_5593"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_102"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<ListOfEvents>
<Event key="Event_0" name="Drug on" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<TriggerExpression>
<CN=Root,Model=Model with pulsed drug,Reference=Time> > <CN=Root,Model=Model with pulsed drug,Vector=Values[Next_On],Reference=Value>
</TriggerExpression>
<ListOfAssignments>
<Assignment target="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[drug]" targetKey="Metabolite_104">
<Expression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[Drug_dose],Reference=Value>
</Expression>
</Assignment>
<Assignment target="CN=Root,Model=Model with pulsed drug,Vector=Values[Next_On]" targetKey="ModelValue_4">
<Expression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[Next_On],Reference=Value>+<CN=Root,Model=Model with pulsed drug,Vector=Values[off_time],Reference=Value>+<CN=Root,Model=Model with pulsed drug,Vector=Values[on_time],Reference=Value>
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
<Event key="Event_1" name="Drug_off" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<TriggerExpression>
<CN=Root,Model=Model with pulsed drug,Reference=Time> > <CN=Root,Model=Model with pulsed drug,Vector=Values[Next_Off],Reference=Value>
</TriggerExpression>
<ListOfAssignments>
<Assignment target="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[drug]" targetKey="Metabolite_104">
<Expression>
0
</Expression>
</Assignment>
<Assignment target="CN=Root,Model=Model with pulsed drug,Vector=Values[Next_Off]" targetKey="ModelValue_3">
<Expression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[Next_Off],Reference=Value>+<CN=Root,Model=Model with pulsed drug,Vector=Values[off_time],Reference=Value>+<CN=Root,Model=Model with pulsed drug,Vector=Values[on_time],Reference=Value>
</Expression>
</Assignment>
<Assignment target="CN=Root,Model=Model with pulsed drug,Vector=Values[Drug_dose]" targetKey="ModelValue_0">
<Expression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[Drug_dose],Reference=Value>+<CN=Root,Model=Model with pulsed drug,Vector=Values[Drug_increase],Reference=Value>
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
</ListOfEvents>
<ListOfModelParameterSets activeSet="ModelParameterSet_1">
<ModelParameterSet key="ModelParameterSet_1" name="Initial State">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#ModelParameterSet_1">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ModelParameterGroup cn="String=Initial Time" type="Group">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[A]" value="1.204428151999984e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[S]" value="6.0221407599999744e+23" type="Species" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[B]" value="1.6059042026666633e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[P]" value="0" type="Species" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[drug]" value="0" type="Species" simulationType="reactions"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Values[Next_On]" value="3" type="ModelValue" simulationType="fixed">
<InitialExpression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[off_time],Reference=InitialValue>
</InitialExpression>
</ModelParameter>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Values[Drug_dose]" value="0.10000000000000001" type="ModelValue" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Values[on_time]" value="1" type="ModelValue" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Values[off_time]" value="3" type="ModelValue" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Values[Next_Off]" value="4" type="ModelValue" simulationType="fixed">
<InitialExpression>
<CN=Root,Model=Model with pulsed drug,Vector=Values[off_time],Reference=InitialValue>+<CN=Root,Model=Model with pulsed drug,Vector=Values[on_time],Reference=InitialValue>
</InitialExpression>
</ModelParameter>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Values[Drug_increase]" value="0.050000000000000003" type="ModelValue" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
<ModelParameterGroup cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R1]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R1],ParameterGroup=Parameters,Parameter=k1" value="4" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R2]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R2],ParameterGroup=Parameters,Parameter=Km" value="0.050000000000000003" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R2],ParameterGroup=Parameters,Parameter=V" value="5" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R2],ParameterGroup=Parameters,Parameter=Ki" value="0.5" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R3]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Model with pulsed drug,Vector=Reactions[R3],ParameterGroup=Parameters,Parameter=k1" value="15" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
</ModelParameterGroup>
</ModelParameterSet>
</ListOfModelParameterSets>
<StateTemplate>
<StateTemplateVariable objectReference="Model_1"/>
<StateTemplateVariable objectReference="Metabolite_3"/>
<StateTemplateVariable objectReference="Metabolite_102"/>
<StateTemplateVariable objectReference="Metabolite_2"/>
<StateTemplateVariable objectReference="Metabolite_103"/>
<StateTemplateVariable objectReference="Metabolite_104"/>
<StateTemplateVariable objectReference="Compartment_0"/>
<StateTemplateVariable objectReference="ModelValue_4"/>
<StateTemplateVariable objectReference="ModelValue_0"/>
<StateTemplateVariable objectReference="ModelValue_1"/>
<StateTemplateVariable objectReference="ModelValue_2"/>
<StateTemplateVariable objectReference="ModelValue_3"/>
<StateTemplateVariable objectReference="ModelValue_5"/>
</StateTemplate>
<InitialState type="initialState">
0 1.204428151999984e+23 1.6059042026666633e+23 6.0221407599999744e+23 0 0 1 3 0.10000000000000001 1 3 4 0.050000000000000003
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_28" name="Steady-State" type="steadyState" scheduled="false" updateModel="true">
<Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="JacobianRequested" type="bool" value="1"/>
<Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
</Problem>
<Method name="Enhanced Newton" type="EnhancedNewton">
<Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-09"/>
<Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
<Parameter name="Use Newton" type="bool" value="1"/>
<Parameter name="Use Integration" type="bool" value="1"/>
<Parameter name="Use Back Integration" type="bool" value="0"/>
<Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
<Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
<Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
<Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
<Parameter name="Target Criterion" type="string" value="Distance and Rate"/>
</Method>
</Task>
<Task key="Task_27" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
<Report reference="Report_21" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="0"/>
<Parameter name="StepNumber" type="unsignedInteger" value="1000"/>
<Parameter name="StepSize" type="float" value="0.050000000000000003"/>
<Parameter name="Duration" type="float" value="50"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
<Parameter name="Start in Steady State" type="bool" value="0"/>
<Parameter name="Use Values" type="bool" value="0"/>
<Parameter name="Values" type="string" value=""/>
</Problem>
<Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
<Task key="Task_26" name="Scan" type="scan" scheduled="false" updateModel="false">
<Problem>
<Parameter name="Subtask" type="unsignedInteger" value="1"/>
<ParameterGroup name="ScanItems">
</ParameterGroup>
<Parameter name="Output in subtask" type="bool" value="1"/>
<Parameter name="Adjust initial conditions" type="bool" value="0"/>
<Parameter name="Continue on Error" type="bool" value="0"/>
</Problem>
<Method name="Scan Framework" type="ScanFramework">
</Method>
</Task>
<Task key="Task_17" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
<Report reference="Report_20" target="" append="1" confirmOverwrite="1"/>
<Problem>
</Problem>
<Method name="EFM Algorithm" type="EFMAlgorithm">
</Method>
</Task>
<Task key="Task_33" name="Optimization" type="optimization" scheduled="false" updateModel="false">
<Report reference="Report_19" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<ParameterText name="ObjectiveExpression" type="expression">
</ParameterText>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
</Problem>
<Method name="Random Search" type="RandomSearch">
<Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
<Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_25" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
<Report reference="Report_18" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
<Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
<Parameter name="Create Parameter Sets" type="bool" value="0"/>
<Parameter name="Use Time Sens" type="bool" value="0"/>
<Parameter name="Time-Sens" type="cn" value=""/>
<ParameterGroup name="Experiment Set">
</ParameterGroup>
<ParameterGroup name="Validation Set">
<Parameter name="Weight" type="unsignedFloat" value="1"/>
<Parameter name="Threshold" type="unsignedInteger" value="5"/>
</ParameterGroup>
</Problem>
<Method name="Evolutionary Programming" type="EvolutionaryProgram">
<Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
<Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
<Parameter name="Population Size" type="unsignedInteger" value="20"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
<Parameter name="Stop after # Stalled Generations" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_24" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_28"/>
</Problem>
<Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
<Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-09"/>
<Parameter name="Use Reder" type="bool" value="1"/>
<Parameter name="Use Smallbone" type="bool" value="1"/>
</Method>
</Task>
<Task key="Task_23" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
<Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
<Parameter name="DivergenceRequested" type="bool" value="1"/>
<Parameter name="TransientTime" type="float" value="0"/>
</Problem>
<Method name="Wolf Method" type="WolfMethod">
<Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
<Parameter name="Overall time" type="unsignedFloat" value="1000"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_32" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
</Problem>
<Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
<Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="0.0001"/>
</Method>
</Task>
<Task key="Task_30" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
<Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
<ParameterGroup name="TargetFunctions">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
</ParameterGroup>
<ParameterGroup name="ListOfVariables">
<ParameterGroup name="Variables">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
</ParameterGroup>
<ParameterGroup name="Variables">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
</ParameterGroup>
</ParameterGroup>
</Problem>
<Method name="Sensitivities Method" type="SensitivitiesMethod">
<Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
<Parameter name="Delta minimum" type="unsignedFloat" value="9.9999999999999998e-13"/>
</Method>
</Task>
<Task key="Task_31" name="Moieties" type="moieties" scheduled="false" updateModel="false">
<Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
<Problem>
</Problem>
<Method name="Householder Reduction" type="Householder">
</Method>
</Task>
<Task key="Task_22" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="0"/>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
<Parameter name="Start in Steady State" type="bool" value="0"/>
<Parameter name="Use Values" type="bool" value="0"/>
<Parameter name="Values" type="string" value=""/>
<Parameter name="LimitCrossings" type="bool" value="0"/>
<Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
<Parameter name="LimitOutTime" type="bool" value="0"/>
<Parameter name="LimitOutCrossings" type="bool" value="0"/>
<Parameter name="PositiveDirection" type="bool" value="1"/>
<Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
<Parameter name="LimitUntilConvergence" type="bool" value="0"/>
<Parameter name="ConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
<Parameter name="Threshold" type="float" value="0"/>
<Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
<Parameter name="OutputConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
<ParameterText name="TriggerExpression" type="expression">
</ParameterText>
<Parameter name="SingleVariable" type="cn" value=""/>
</Problem>
<Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
<Task key="Task_21" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
<Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_28"/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
<Task key="Task_20" name="Time-Course Sensitivities" type="timeSensitivities" scheduled="false" updateModel="false">
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="0"/>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
<Parameter name="Start in Steady State" type="bool" value="0"/>
<Parameter name="Use Values" type="bool" value="0"/>
<Parameter name="Values" type="string" value=""/>
<ParameterGroup name="ListOfParameters">
</ParameterGroup>
<ParameterGroup name="ListOfTargets">
</ParameterGroup>
</Problem>
<Method name="LSODA Sensitivities" type="Sensitivities(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
</ListOfTasks>
<ListOfReports>
<Report key="Report_10" name="Steady-State" taskType="steadyState" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
</Footer>
</Report>
<Report key="Report_21" name="Time-Course" taskType="timeCourse" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Time-Course],Object=Description"/>
</Header>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Time-Course],Object=Result"/>
</Footer>
</Report>
<Report key="Report_20" name="Elementary Flux Modes" taskType="fluxMode" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
</Footer>
</Report>
<Report key="Report_19" name="Optimization" taskType="optimization" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
<Object cn="String=\[Function Evaluations\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Value\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Parameters\]"/>
</Header>
<Body>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/>
</Body>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/>
</Footer>
</Report>
<Report key="Report_18" name="Parameter Estimation" taskType="parameterFitting" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/>
<Object cn="String=\[Function Evaluations\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Value\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Parameters\]"/>
</Header>
<Body>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/>
</Body>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/>
</Footer>
</Report>
<Report key="Report_17" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/>
</Footer>
</Report>
<Report key="Report_16" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/>
</Footer>
</Report>
<Report key="Report_15" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Result"/>
</Footer>
</Report>
<Report key="Report_14" name="Sensitivities" taskType="sensitivities" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Result"/>
</Footer>
</Report>
<Report key="Report_13" name="Moieties" taskType="moieties" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Moieties],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Moieties],Object=Result"/>
</Footer>
</Report>
<Report key="Report_12" name="Linear Noise Approximation" taskType="linearNoiseApproximation" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result"/>
</Footer>
</Report>
</ListOfReports>
<ListOfPlots>
<PlotSpecification name="Time course" type="Plot2D" active="1" taskTypes="">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="[A]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=Model with pulsed drug,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[B]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=Model with pulsed drug,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[B],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[drug]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=Model with pulsed drug,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Model with pulsed drug,Vector=Compartments[compartment],Vector=Metabolites[drug],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
</ListOfPlots>
<GUI>
</GUI>
<ListOfUnitDefinitions>
<UnitDefinition key="Unit_1" name="meter" symbol="m">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Unit_0">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
m
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_5" name="second" symbol="s">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Unit_4">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
s
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_13" name="Avogadro" symbol="Avogadro">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Unit_12">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
Avogadro
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_17" name="item" symbol="#">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Unit_16">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
#
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_35" name="liter" symbol="l">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Unit_34">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
0.001*m^3
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_41" name="mole" symbol="mol">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Unit_40">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
Avogadro*#
</Expression>
</UnitDefinition>
</ListOfUnitDefinitions>
</COPASI>