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  • Committer: srba.jiri at gmail
  • Date: 2020-09-11 14:23:39 UTC
  • mfrom: (213.1.151 interval_tar)
  • Revision ID: srba.jiri@gmail.com-20200911142339-bq9328s1gppw24uj
merged in lp:~verifypn-maintainers/verifypn/interval_tar doing 
- Implements TAR w/o z3, but using a simple integer inference engine for Hoare logic.
 - Replaces LP-Solve with GLPK, reduces computation-time and memory overhead
 - Implements new global properties, translated into CTL formulae.

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test_models/MAPK-test001/model.pnml
 
1
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 
2
<pnml xmlns="http://www.pnml.org/version-2009/grammar/pnml">
 
3
    <net id="ComposedModel" type="http://www.pnml.org/version-2009/grammar/ptnet">
 
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        <page id="page0">
 
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            <place id="Raf">
 
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                <graphics>
 
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                </graphics>
 
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                <name>
 
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                    <graphics>
 
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                        <offset x="-5" y="35"/>
 
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                    </graphics>
 
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                    <text>Raf</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>2</text>
 
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                </initialMarking>
 
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            </place>
 
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                <graphics>
 
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                <name>
 
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                    </graphics>
 
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                    <text>RasGTP</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>2</text>
 
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            </place>
 
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                </graphics>
 
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                <name>
 
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                    <graphics>
 
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                    </graphics>
 
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                    <text>RafP_Phase1</text>
 
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                </name>
 
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                    <text>0</text>
 
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                    <text>Phase3</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>2</text>
 
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            <place id="Phase2">
 
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                    <text>Phase2</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>2</text>
 
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                    <text>MEKPP</text>
 
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                    <text>0</text>
 
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            </place>
 
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                <name>
 
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                    <text>ERKP_Phase3</text>
 
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                </name>
 
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                    <text>0</text>
 
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            <place id="ERKPP_Phase3">
 
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                <name>
 
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                    <graphics>
 
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                        <offset x="-5" y="35"/>
 
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                    </graphics>
 
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                    <text>ERKPP_Phase3</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>0</text>
 
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            </place>
 
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            <place id="MEK">
 
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                <graphics>
 
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                <name>
 
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                    <graphics>
 
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                        <offset x="-5" y="35"/>
 
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                    </graphics>
 
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                    <text>MEK</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>2</text>
 
269
                </initialMarking>
 
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            </place>
 
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            <place id="Phase1">
 
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                <graphics>
 
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                    <position x="675" y="1230"/>
 
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                </graphics>
 
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                <name>
 
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                    <graphics>
 
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                        <offset x="-5" y="35"/>
 
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                    </graphics>
 
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                    <text>Phase1</text>
 
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                </name>
 
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                <initialMarking>
 
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                    <text>2</text>
 
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                </initialMarking>
 
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            </place>
 
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            <place id="ERKP_MEKPP">
 
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                <graphics>
 
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                    </graphics>
 
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                    <text>ERKP_MEKPP</text>
 
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                </name>
 
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                    <text>0</text>
 
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            </place>
 
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                    </graphics>
 
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                    <text>ERK_MEKPP</text>
 
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                </name>
 
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511
            <transition id="k26">
 
512
                <name>
 
513
                    <graphics>
 
514
                        <offset x="-5" y="35"/>
 
515
                    </graphics>
 
516
                    <text>k26</text>
 
517
                </name>
 
518
                <graphics>
 
519
                    <position x="1770" y="1125"/>
 
520
                </graphics>
 
521
            </transition>
 
522
            <transition id="k25">
 
523
                <name>
 
524
                    <graphics>
 
525
                        <offset x="-5" y="35"/>
 
526
                    </graphics>
 
527
                    <text>k25</text>
 
528
                </name>
 
529
                <graphics>
 
530
                    <position x="1740" y="1065"/>
 
531
                </graphics>
 
532
            </transition>
 
533
            <transition id="k15">
 
534
                <name>
 
535
                    <graphics>
 
536
                        <offset x="-5" y="35"/>
 
537
                    </graphics>
 
538
                    <text>k15</text>
 
539
                </name>
 
540
                <graphics>
 
541
                    <position x="1095" y="1125"/>
 
542
                </graphics>
 
543
            </transition>
 
544
            <transition id="k24">
 
545
                <name>
 
546
                    <graphics>
 
547
                        <offset x="-5" y="35"/>
 
548
                    </graphics>
 
549
                    <text>k24</text>
 
550
                </name>
 
551
                <graphics>
 
552
                    <position x="1440" y="1215"/>
 
553
                </graphics>
 
554
            </transition>
 
555
            <transition id="k9">
 
556
                <name>
 
557
                    <graphics>
 
558
                        <offset x="-5" y="35"/>
 
559
                    </graphics>
 
560
                    <text>k9</text>
 
561
                </name>
 
562
                <graphics>
 
563
                    <position x="855" y="1230"/>
 
564
                </graphics>
 
565
            </transition>
 
566
            <transition id="k12">
 
567
                <name>
 
568
                    <graphics>
 
569
                        <offset x="-5" y="35"/>
 
570
                    </graphics>
 
571
                    <text>k12</text>
 
572
                </name>
 
573
                <graphics>
 
574
                    <position x="945" y="1395"/>
 
575
                </graphics>
 
576
            </transition>
 
577
            <transition id="k21">
 
578
                <name>
 
579
                    <graphics>
 
580
                        <offset x="-5" y="35"/>
 
581
                    </graphics>
 
582
                    <text>k21</text>
 
583
                </name>
 
584
                <graphics>
 
585
                    <position x="1395" y="1125"/>
 
586
                </graphics>
 
587
            </transition>
 
588
            <transition id="k18">
 
589
                <name>
 
590
                    <graphics>
 
591
                        <offset x="-5" y="35"/>
 
592
                    </graphics>
 
593
                    <text>k18</text>
 
594
                </name>
 
595
                <graphics>
 
596
                    <position x="930" y="1095"/>
 
597
                </graphics>
 
598
            </transition>
 
599
            <transition id="k3">
 
600
                <name>
 
601
                    <graphics>
 
602
                        <offset x="-5" y="35"/>
 
603
                    </graphics>
 
604
                    <text>k3</text>
 
605
                </name>
 
606
                <graphics>
 
607
                    <position x="375" y="1365"/>
 
608
                </graphics>
 
609
            </transition>
 
610
            <transition id="k6">
 
611
                <name>
 
612
                    <graphics>
 
613
                        <offset x="-5" y="35"/>
 
614
                    </graphics>
 
615
                    <text>k6</text>
 
616
                </name>
 
617
                <graphics>
 
618
                    <position x="600" y="1320"/>
 
619
                </graphics>
 
620
            </transition>
 
621
            <transition id="k1">
 
622
                <name>
 
623
                    <graphics>
 
624
                        <offset x="-5" y="35"/>
 
625
                    </graphics>
 
626
                    <text>k1</text>
 
627
                </name>
 
628
                <graphics>
 
629
                    <position x="465" y="1275"/>
 
630
                </graphics>
 
631
            </transition>
 
632
            <transition id="k2">
 
633
                <name>
 
634
                    <graphics>
 
635
                        <offset x="-5" y="35"/>
 
636
                    </graphics>
 
637
                    <text>k2</text>
 
638
                </name>
 
639
                <graphics>
 
640
                    <position x="555" y="1365"/>
 
641
                </graphics>
 
642
            </transition>
 
643
            <arc id="Phase3_to_k28" source="Phase3" target="k28" type="normal"/>
 
644
            <arc id="ERKP_to_k28" source="ERKP" target="k28" type="normal"/>
 
645
            <arc id="MEKP_to_k16" source="MEKP" target="k16" type="normal"/>
 
646
            <arc id="Phase2_to_k16" source="Phase2" target="k16" type="normal"/>
 
647
            <arc id="MEKP_Phase2_to_k17" source="MEKP_Phase2" target="k17" type="normal"/>
 
648
            <arc id="MEKPP_Phase2_to_k14" source="MEKPP_Phase2" target="k14" type="normal"/>
 
649
            <arc id="ERKP_Phase3_to_k29" source="ERKP_Phase3" target="k29" type="normal"/>
 
650
            <arc id="ERKP_MEKPP_to_k24" source="ERKP_MEKPP" target="k24" type="normal"/>
 
651
            <arc id="RasGTP_to_k1" source="RasGTP" target="k1" type="normal"/>
 
652
            <arc id="Raf_to_k1" source="Raf" target="k1" type="normal"/>
 
653
            <arc id="Raf_RasGTP_to_k2" source="Raf_RasGTP" target="k2" type="normal"/>
 
654
            <arc id="ERKP_Phase3_to_k30" source="ERKP_Phase3" target="k30" type="normal"/>
 
655
            <arc id="ERKPP_Phase3_to_k27" source="ERKPP_Phase3" target="k27" type="normal"/>
 
656
            <arc id="RafP_to_k10" source="RafP" target="k10" type="normal"/>
 
657
            <arc id="MEKP_RafP_to_k12" source="MEKP_RafP" target="k12" type="normal"/>
 
658
            <arc id="ERKP_to_k22" source="ERKP" target="k22" type="normal"/>
 
659
            <arc id="MEKPP_to_k22" source="MEKPP" target="k22" type="normal"/>
 
660
            <arc id="MEKPP_to_k19" source="MEKPP" target="k19" type="normal"/>
 
661
            <arc id="ERK_to_k19" source="ERK" target="k19" type="normal"/>
 
662
            <arc id="MEKP_to_k10" source="MEKP" target="k10" type="normal"/>
 
663
            <arc id="Raf_RasGTP_to_k3" source="Raf_RasGTP" target="k3" type="normal"/>
 
664
            <arc id="MEKP_Phase2_to_k18" source="MEKP_Phase2" target="k18" type="normal"/>
 
665
            <arc id="MEKPP_Phase2_to_k15" source="MEKPP_Phase2" target="k15" type="normal"/>
 
666
            <arc id="MEK_RafP_to_k9" source="MEK_RafP" target="k9" type="normal"/>
 
667
            <arc id="ERKP_MEKPP_to_k23" source="ERKP_MEKPP" target="k23" type="normal"/>
 
668
            <arc id="ERK_MEKPP_to_k21" source="ERK_MEKPP" target="k21" type="normal"/>
 
669
            <arc id="RafP_Phase1_to_k6" source="RafP_Phase1" target="k6" type="normal"/>
 
670
            <arc id="RafP_to_k7" source="RafP" target="k7" type="normal"/>
 
671
            <arc id="MEK_to_k7" source="MEK" target="k7" type="normal"/>
 
672
            <arc id="ERK_MEKPP_to_k20" source="ERK_MEKPP" target="k20" type="normal"/>
 
673
            <arc id="ERKPP_Phase3_to_k26" source="ERKPP_Phase3" target="k26" type="normal"/>
 
674
            <arc id="MEKP_RafP_to_k11" source="MEKP_RafP" target="k11" type="normal"/>
 
675
            <arc id="ERKPP_to_k25" source="ERKPP" target="k25" type="normal"/>
 
676
            <arc id="MEK_RafP_to_k8" source="MEK_RafP" target="k8" type="normal"/>
 
677
            <arc id="Phase2_to_k13" source="Phase2" target="k13" type="normal"/>
 
678
            <arc id="MEKPP_to_k13" source="MEKPP" target="k13" type="normal"/>
 
679
            <arc id="Phase3_to_k25" source="Phase3" target="k25" type="normal"/>
 
680
            <arc id="RafP_to_k4" source="RafP" target="k4" type="normal"/>
 
681
            <arc id="RafP_Phase1_to_k5" source="RafP_Phase1" target="k5" type="normal"/>
 
682
            <arc id="Phase1_to_k4" source="Phase1" target="k4" type="normal"/>
 
683
            <arc id="k29_to_ERKP" source="k29" target="ERKP" type="normal"/>
 
684
            <arc id="k28_to_ERKP_Phase3" source="k28" target="ERKP_Phase3" type="normal"/>
 
685
            <arc id="k16_to_MEKP_Phase2" source="k16" target="MEKP_Phase2" type="normal"/>
 
686
            <arc id="k14_to_Phase2" source="k14" target="Phase2" type="normal"/>
 
687
            <arc id="k17_to_Phase2" source="k17" target="Phase2" type="normal"/>
 
688
            <arc id="k17_to_MEKP" source="k17" target="MEKP" type="normal"/>
 
689
            <arc id="k29_to_Phase3" source="k29" target="Phase3" type="normal"/>
 
690
            <arc id="k15_to_MEKP" source="k15" target="MEKP" type="normal"/>
 
691
            <arc id="k24_to_MEKPP" source="k24" target="MEKPP" type="normal"/>
 
692
            <arc id="k24_to_ERKPP" source="k24" target="ERKPP" type="normal"/>
 
693
            <arc id="k1_to_Raf_RasGTP" source="k1" target="Raf_RasGTP" type="normal"/>
 
694
            <arc id="k30_to_ERK" source="k30" target="ERK" type="normal"/>
 
695
            <arc id="k30_to_Phase3" source="k30" target="Phase3" type="normal"/>
 
696
            <arc id="k27_to_ERKP" source="k27" target="ERKP" type="normal"/>
 
697
            <arc id="k27_to_Phase3" source="k27" target="Phase3" type="normal"/>
 
698
            <arc id="k2_to_Raf" source="k2" target="Raf" type="normal"/>
 
699
            <arc id="k2_to_RasGTP" source="k2" target="RasGTP" type="normal"/>
 
700
            <arc id="k7_to_MEK_RafP" source="k7" target="MEK_RafP" type="normal"/>
 
701
            <arc id="k9_to_RafP" source="k9" target="RafP" type="normal"/>
 
702
            <arc id="k12_to_RafP" source="k12" target="RafP" type="normal"/>
 
703
            <arc id="k12_to_MEKPP" source="k12" target="MEKPP" type="normal"/>
 
704
            <arc id="k18_to_Phase2" source="k18" target="Phase2" type="normal"/>
 
705
            <arc id="k18_to_MEK" source="k18" target="MEK" type="normal"/>
 
706
            <arc id="k22_to_ERKP_MEKPP" source="k22" target="ERKP_MEKPP" type="normal"/>
 
707
            <arc id="k19_to_ERK_MEKPP" source="k19" target="ERK_MEKPP" type="normal"/>
 
708
            <arc id="k10_to_MEKP_RafP" source="k10" target="MEKP_RafP" type="normal"/>
 
709
            <arc id="k3_to_RafP" source="k3" target="RafP" type="normal"/>
 
710
            <arc id="k21_to_MEKPP" source="k21" target="MEKPP" type="normal"/>
 
711
            <arc id="k15_to_Phase2" source="k15" target="Phase2" type="normal"/>
 
712
            <arc id="k9_to_MEKP" source="k9" target="MEKP" type="normal"/>
 
713
            <arc id="k23_to_MEKPP" source="k23" target="MEKPP" type="normal"/>
 
714
            <arc id="k21_to_ERKP" source="k21" target="ERKP" type="normal"/>
 
715
            <arc id="k6_to_Phase1" source="k6" target="Phase1" type="normal"/>
 
716
            <arc id="k6_to_Raf" source="k6" target="Raf" type="normal"/>
 
717
            <arc id="k3_to_RasGTP" source="k3" target="RasGTP" type="normal"/>
 
718
            <arc id="k23_to_ERKP" source="k23" target="ERKP" type="normal"/>
 
719
            <arc id="k20_to_MEKPP" source="k20" target="MEKPP" type="normal"/>
 
720
            <arc id="k20_to_ERK" source="k20" target="ERK" type="normal"/>
 
721
            <arc id="k8_to_RafP" source="k8" target="RafP" type="normal"/>
 
722
            <arc id="k8_to_MEK" source="k8" target="MEK" type="normal"/>
 
723
            <arc id="k26_to_Phase3" source="k26" target="Phase3" type="normal"/>
 
724
            <arc id="k11_to_RafP" source="k11" target="RafP" type="normal"/>
 
725
            <arc id="k25_to_ERKPP_Phase3" source="k25" target="ERKPP_Phase3" type="normal"/>
 
726
            <arc id="k11_to_MEKP" source="k11" target="MEKP" type="normal"/>
 
727
            <arc id="k14_to_MEKPP" source="k14" target="MEKPP" type="normal"/>
 
728
            <arc id="k13_to_MEKPP_Phase2" source="k13" target="MEKPP_Phase2" type="normal"/>
 
729
            <arc id="k26_to_ERKPP" source="k26" target="ERKPP" type="normal"/>
 
730
            <arc id="k4_to_RafP_Phase1" source="k4" target="RafP_Phase1" type="normal"/>
 
731
            <arc id="k5_to_Phase1" source="k5" target="Phase1" type="normal"/>
 
732
            <arc id="k5_to_RafP" source="k5" target="RafP" type="normal"/>
 
733
        </page>
 
734
        <name>
 
735
            <text>ComposedModel</text>
 
736
        </name>
 
737
    </net>
 
738
</pnml>