Ticket #3: TCR_SBML_fail.mdl

File TCR_SBML_fail.mdl, 63.9 KB (added by ginkel, 19 years ago)

The failed model

Line 
1(define-variable
2  :class "var-real-parameter"
3  :super-classes ("variable")
4  :system-theoretic "real-parameter")
5
6(define-variable
7  :class "var-output"
8  :super-classes ("variable")
9  :system-theoretic "output")
10
11(define-variable
12  :class "concentration"
13  :super-classes ("variable")
14  :unit "mol/l")
15
16(define-module
17  :class "library"
18  :super-classes ("module")
19  :documentation "Library")
20
21(define-variable
22  :class "var-input"
23  :super-classes ("variable")
24  :system-theoretic "input")
25
26(define-variable
27  :class "var-rate"
28  :super-classes ("variable")
29  :value "100.0d0"
30  :minimum "0.0d0"
31  :maximum "100000.0d0"
32  :unit "1/h")
33
34(define-variable
35  :class "scaling-parameter"
36  :super-classes ("variable")
37  :documentation "parameter to perform manual numeric scaling of rate-laws
38  etc. for optimization. It is marked as a help-variable to eventually
39remove it by the equation-optimizer in Promot."
40  :system-theoretic "help"
41  :value "1.0d0")
42
43(define-variable
44  :class "molar-flux"
45  :super-classes ("variable")
46  :minimum "0.0d0"
47  :maximum "1000.0d0"
48  :unit "mol/s")
49
50(define-module
51  :class "tcell-signaling"
52  :super-classes ("module"))
53
54(define-module
55  :class "tcr-prox-events"
56  :super-classes ("tcell-signaling"))
57
58(define-module
59  :class "predefined"
60  :super-classes ("library"))
61
62(define-module
63  :class "c2"
64  :super-classes ("predefined"))
65
66(define-module
67  :class "c2a"
68  :super-classes ("c2")
69  :icon "ProMoT_models/SignalTransd/TCR/predefined/icons/C2a.gif")
70
71(define-module
72  :class "reaction"
73  :super-classes ("library"))
74
75(define-module
76  :class "special-reaction"
77  :super-classes ("reaction"))
78
79(define-variable
80  :class "var-activity"
81  :super-classes ("var-real-parameter"))
82
83(define-variable
84  :class "reaction-rate"
85  :super-classes ("molar-flux")
86  :unit "mol/s")
87
88(define-module
89  :class "kinetics"
90  :super-classes ("reaction")
91  :variables
92  (("r"
93    :is-a "reaction-rate"
94    :documentation "reaction-rate"
95    :system-theoretic "help"
96    :report "lumped"
97    :unit "umol/g_dw/h")
98   ("skal"
99    :is-a "scaling-parameter")))
100
101(define-module
102  :class "catalytic"
103  :super-classes ("kinetics"))
104
105(define-module
106  :class "structure"
107  :super-classes ("reaction")
108  :variables
109  (("r")))
110
111(define-variable
112  :class "var-concentration"
113  :super-classes ("concentration")
114  :value "1.0d-4"
115  :minimum "0.0d0"
116  :maximum "10.0d0")
117
118(define-variable
119  :class "var-concentration-in"
120  :super-classes ("var-concentration" "var-input")
121  :absolute-error "1.0d-8")
122
123(define-terminal
124  :class "term-concentration-in"
125  :super-classes ("terminal")
126  :icon "icons/term_concentration_in.gif"
127  :link-color "green"
128  :variables
129  (("c"
130    :is-a "var-concentration-in"
131    :unit "umol/g_dw")))
132
133(define-module
134  :class "enz-0eff"
135  :super-classes ("structure")
136  :terminals
137  (("t_enz"
138    :is-a "term-concentration-in"
139    :geometry-side "top"
140    :geometry-position "0.5")))
141
142(define-module
143  :class "en1"
144  :super-classes ("catalytic" "enz-0eff")
145  :documentation "enzimatic reaction with 1st order kinetics"
146  :parameters
147  (("r"
148    :value "t_enz.c*sa*a.c"))
149  :variables
150  (("sa"
151    :is-a "var-activity")))
152
153(define-variable
154  :class "var-rate-out"
155  :super-classes ("var-rate" "var-output")
156  :absolute-error "1.0d-8")
157
158(define-terminal
159  :class "term-reaction-flux"
160  :super-classes ("terminal")
161  :icon "icons/term_react_blue.gif"
162  :link-color "blue"
163  :variables
164  (("c"
165    :is-a "var-concentration-in"
166    :unit "umol/g_dw")
167   ("r"
168    :is-a "var-rate-out"
169    :positive-vector-direction "out"
170    :unit "umol/g_dw/h")))
171
172(define-module
173  :class "s-a-b"
174  :super-classes ("structure")
175  :terminals
176  (("a"
177    :is-a "term-reaction-flux")
178   ("b"
179    :is-a "term-reaction-flux"))
180  :equations
181  (("stoech_a"
182    :relation "a.r == -r")
183   ("stoech_b"
184    :relation "b.r == r")))
185
186(define-module
187  :class "s-a-b_l"
188  :super-classes ("s-a-b")
189  :terminals
190  (("a"
191    :geometry-side "right"
192    :geometry-position "0.5")
193   ("b"
194    :geometry-side "left"
195    :geometry-position "0.5")))
196
197(define-module
198  :class "trans2a-en1_l"
199  :super-classes ("en1" "s-a-b_l")
200  :properties
201  (("abstract"
202    :value "no"))
203  :icon "icons/irrev_l")
204
205(define-module
206  :class "s-a-b_r"
207  :super-classes ("s-a-b")
208  :terminals
209  (("a"
210    :geometry-side "left"
211    :geometry-position "0.5")
212   ("b"
213    :geometry-side "right"
214    :geometry-position "0.5")))
215
216(define-module
217  :class "trans2a-en1_r"
218  :super-classes ("en1" "s-a-b_r")
219  :properties
220  (("abstract"
221    :value "no"))
222  :icon "icons/irrev_r")
223
224(define-module
225  :class "help"
226  :super-classes ("library"))
227
228(define-module
229  :class "adapter"
230  :super-classes ("help"))
231
232(define-variable
233  :class "var-concentration-out"
234  :super-classes ("var-concentration" "var-output")
235  :absolute-error "1.0d-8")
236
237(define-variable
238  :class "var-state-concentration-out"
239  :super-classes ("var-concentration-out")
240  :system-theoretic "output")
241
242(define-variable
243  :class "var-rate-in"
244  :super-classes ("var-rate" "var-input")
245  :absolute-error "1.0d-8")
246
247(define-terminal
248  :class "term-storage-flux"
249  :super-classes ("terminal")
250  :icon "icons/term_stor_blue.gif"
251  :link-color "blue"
252  :variables
253  (("c"
254    :is-a "var-concentration-out")
255   ("r"
256    :is-a "var-rate-in"
257    :positive-vector-direction "in"
258    :unit "umol/g_dw/h")))
259
260(define-module
261  :class "adapter-flux"
262  :super-classes ("adapter")
263  :documentation "splits a flux-terminal into 2"
264  :properties
265  (("abstract"
266    :value "no"))
267  :icon "icons/adapter.gif"
268  :terminals
269  (("in"
270    :is-a "term-reaction-flux"
271    :geometry-side "LEFT"
272    :geometry-position "0.47333333"
273    :variables
274    (("r"
275      :is-eq-to "parent.r")))
276   ("out"
277    :is-a "term-storage-flux"
278    :geometry-side "RIGHT"
279    :geometry-position "0.47333333"
280    :variables
281    (("c"
282      :is-eq-to "parent.c"))))
283  :variables
284  (("c"
285    :is-a "var-state-concentration-out")
286   ("r"
287    :is-a "var-rate-out"
288    :positive-vector-direction "out"
289    :value "0.0d0"))
290  :equations
291  (("hurg"
292    :relation "c == in.c")
293   ("rate"
294    :relation "r == out.r")))
295
296(define-module
297  :class "cyclic_en1"
298  :super-classes ("special-reaction")
299  :documentation "two 1st-order reactions in a cycle"
300  :properties
301  (("abstract"
302    :value "no"))
303  :icon "icons/cyclic.gif"
304  :geometry-width "273"
305  :geometry-height "252"
306  :terminals
307  (("a"
308    :is-eq-to "aa.in"
309    :geometry-side "LEFT"
310    :geometry-position "0.47619048")
311   ("b"
312    :is-eq-to "ab.in"
313    :geometry-side "RIGHT"
314    :geometry-position "0.50396824")
315   ("enz1"
316    :is-eq-to "reaction1.t_enz"
317    :geometry-side "TOP"
318    :geometry-position "0.45421246")
319   ("enz2"
320    :is-eq-to "reaction2.t_enz"
321    :geometry-side "BOTTOM"
322    :geometry-position "0.46153846"))
323  :modules
324  (("aa"
325    :is-a "adapter-flux"
326    :geometry-x "42"
327    :geometry-y "120")
328   ("ab"
329    :is-a "adapter-flux"
330    :geometry-x "204"
331    :geometry-y "127")
332   ("reaction1"
333    :is-a "trans2a-en1_r"
334    :geometry-x "124"
335    :geometry-y "89"
336    :variables
337    (("sa"
338      :is-eq-to "parent.r1_sa")))
339   ("reaction2"
340    :is-a "trans2a-en1_l"
341    :geometry-x "127"
342    :geometry-y "154"
343    :variables
344    (("sa"
345      :is-eq-to "parent.r2_sa"))))
346  :links
347  (("aaout_reaction1a_467359"
348    :terminals ("aa.out" "reaction1.a" "reaction2.b")
349    :nodes (("57" "121"))
350    :edges (("0" "-1" (("48" "120"))) ("1" "-1" nil) ("2" "-1" nil)))
351   ("reaction1b_abin_467365"
352    :terminals ("reaction1.b" "ab.out" "reaction2.a")
353    :nodes (("190" "124"))
354    :edges (("0" "-1" (("174" "108"))) ("1" "-1" nil) ("2" "-1" nil))))
355  :variables
356  (("r1_sa"
357    :is-a "var-activity"
358    :system-theoretic "real-parameter")
359   ("r2_sa"
360    :is-a "var-activity"
361    :system-theoretic "real-parameter")))
362
363(define-module
364  :class "cyclic_en1_ud"
365  :super-classes ("cyclic_en1")
366  :documentation "two 1st-order reactions in a cycle"
367  :properties
368  (("abstract"
369    :value "no"))
370  :icon "icons/cyclic_ud.gif"
371  :geometry-width "273"
372  :geometry-height "252"
373  :terminals
374  (("a"
375    :is-eq-to "aa.in"
376    :geometry-side "TOP"
377    :geometry-position "0.47619048")
378   ("b"
379    :is-eq-to "ab.in"
380    :geometry-side "BOTTOM"
381    :geometry-position "0.50396824")
382   ("enz1"
383    :is-eq-to "reaction1.t_enz"
384    :geometry-side "RIGHT"
385    :geometry-position "0.45421246")
386   ("enz2"
387    :is-eq-to "reaction2.t_enz"
388    :geometry-side "LEFT"
389    :geometry-position "0.46153846")))
390
391(define-module
392  :class "storage"
393  :super-classes ("library"))
394
395(define-terminal
396  :class "term-concentration-out"
397  :super-classes ("terminal")
398  :icon "icons/term_concentration_out.gif"
399  :link-color "green"
400  :variables
401  (("c"
402    :is-a "var-concentration-out"
403    :unit "umol/g_dw")))
404
405(define-module
406  :class "storage-intra-const_c"
407  :super-classes ("storage")
408  :documentation "Constant concentration with concentration-terminals"
409  :properties
410  (("abstract"
411    :value "no"))
412  :icon "icons/storage_small"
413  :terminals
414  (("co"
415    :is-a "term-concentration-out"
416    :geometry-side "bottom"
417    :geometry-position "0.5"))
418  :variables
419  (("c0"
420    :is-a "var-real-parameter"
421    :documentation "Constant concentration value"
422    :report "lumped"
423    :value "1.0d0"))
424  :equations
425  (("hurg"
426    :relation "co.c == c0")))
427
428(define-module
429  :class "term-conv"
430  :super-classes ("help")
431  :documentation "converts different terminal-types")
432
433(define-module
434  :class "cf2co"
435  :super-classes ("term-conv")
436  :documentation "converts a cf-term to a co-term"
437  :properties
438  (("abstract"
439    :value "no"))
440  :icon "icons/adapter"
441  :terminals
442  (("cf"
443    :is-a "term-reaction-flux"
444    :geometry-side "LEFT"
445    :geometry-position "0.52666664"
446    :variables
447    (("c"
448      :is-eq-to "parent.c")))
449   ("co"
450    :is-a "term-concentration-out"
451    :geometry-side "RIGHT"
452    :geometry-position "0.52666664"))
453  :variables
454  (("c"
455    :is-a "var-concentration-in"))
456  :equations
457  (("free"
458    :relation "co.c == c")
459   ("rate"
460    :relation "cf.r == 0.0d0")))
461
462(define-module
463  :class "c2a-en1-nost"
464  :super-classes ("c2a")
465  :documentation "protein in 2 states, active-inactive, storages not included, reactiosn are 1st order"
466  :properties
467  (("abstract"
468    :value "no"))
469  :icon "ProMoT_models/SignalTransd/TCR/predefined/icons/C2a-nost.gif"
470  :terminals
471  (("a"
472    :is-eq-to "reaction.a"
473    :geometry-side "LEFT"
474    :geometry-position "0.05")
475   ("b"
476    :is-eq-to "adapter_flux.in"
477    :geometry-side "LEFT"
478    :geometry-position "0.9")
479   ("input"
480    :is-eq-to "reaction.enz1"
481    :geometry-side "RIGHT"
482    :geometry-position "0.45")
483   ("output"
484    :is-eq-to "aco.co"
485    :geometry-side "BOTTOM"
486    :geometry-position "0.5233333"))
487  :modules
488  (("aco"
489    :is-a "cf2co"
490    :geometry-x "165"
491    :geometry-y "200")
492   ("adapter_flux"
493    :is-a "adapter-flux"
494    :geometry-x "147"
495    :geometry-y "175")
496   ("phosphatase"
497    :is-a "storage-intra-const_c"
498    :geometry-x "84"
499    :geometry-y "215")
500   ("reaction"
501    :is-a "cyclic_en1_ud"
502    :geometry-x "153"
503    :geometry-y "126"
504    :variables
505    (("r1_sa"
506      :is-eq-to "parent.r1_sa")
507     ("r2_sa"
508      :is-eq-to "parent.r2_sa"))))
509  :links
510  (("adapter_fluxout_reactionb"
511    :terminals ("adapter_flux.out" "reaction.b" "aco.cf")
512    :nodes (("176" "176"))
513    :edges (("0" "-1" (("176" "176"))) ("1" "-1" nil) ("2" "-1" nil)))
514   ("phos7953"
515    :terminals ("phosphatase.co" "reaction.enz2")))
516  :variables
517  (("r1_sa"
518    :is-a "var-real-parameter")
519   ("r2_sa"
520    :is-a "var-real-parameter")))
521
522(define-module
523  :class "c2a-en1-nost-prep"
524  :super-classes ("c2a-en1-nost")
525  :documentation "just give values to the parameters of the class c2a-en1-bs-nost"
526  :parameters
527  (("r1_sa"
528    :value "1.0d0")
529   ("r2_sa"
530    :value "1.0d0")))
531
532(define-module
533  :class "multistage-storage"
534  :super-classes ("storage"))
535
536(define-module
537  :class "storage-intra"
538  :super-classes ("storage")
539  :documentation "intracellular storage without mue with flux-terminals"
540  :properties
541  (("abstract"
542    :value "no"))
543  :icon "icons/storage"
544  :terminals
545  (("cf"
546    :is-a "term-storage-flux"
547    :geometry-side "right"
548    :geometry-position "0.5"
549    :variables
550    (("c"
551      :is-eq-to "parent.c0"))))
552  :variables
553  (("c0"
554    :is-a "var-state-concentration-out"
555    :documentation "Initial concentration"
556    :report "lumped"))
557  :equations
558  (("bal"
559    :relation ":diff<t> c0 == cf.r")))
560
561(define-module
562  :class "storage-mult-2st"
563  :super-classes ("multistage-storage")
564  :properties
565  (("abstract"
566    :value "no"))
567  :icon "icons/1bs-2st"
568  :geometry-width "406"
569  :geometry-height "401"
570  :parameters
571  (("st1.c0"
572    :value "parent.totalconc"))
573  :terminals
574  (("cf1"
575    :is-eq-to "st1.cf"
576    :geometry-side "RIGHT"
577    :geometry-position "0.3")
578   ("cf2"
579    :is-eq-to "st2.cf"
580    :geometry-side "RIGHT"
581    :geometry-position "0.7")
582   ("cot"
583    :is-a "term-concentration-in"
584    :documentation "terminal for the reactions where the total molecule is involved"
585    :geometry-side "top"
586    :geometry-position "0.5"))
587  :modules
588  (("st1"
589    :is-a "storage-intra"
590    :geometry-x "78"
591    :geometry-y "125")
592   ("st2"
593    :is-a "storage-intra"
594    :geometry-x "77"
595    :geometry-y "218"))
596  :variables
597  (("totalconc"
598    :is-eq-to "cot.c")))
599
600(define-module
601  :class "storage-mult-3st"
602  :super-classes ("storage-mult-2st")
603  :properties
604  (("abstract"
605    :value "no"))
606  :icon "icons/1bs-3st"
607  :terminals
608  (("cf1"
609    :geometry-position "0.2")
610   ("cf2"
611    :geometry-position "0.5")
612   ("cf3"
613    :is-eq-to "st3.cf"
614    :geometry-side "RIGHT"
615    :geometry-position "0.8"))
616  :modules
617  (("st3"
618    :is-a "storage-intra"
619    :geometry-x "77"
620    :geometry-y "316")))
621
622(define-module
623  :class "storage-mult-4st"
624  :super-classes ("storage-mult-3st")
625  :properties
626  (("abstract"
627    :value "no"))
628  :icon "icons/1bs-4st"
629  :terminals
630  (("cf1"
631    :geometry-position "0.12")
632   ("cf2"
633    :geometry-position "0.35")
634   ("cf3"
635    :geometry-position "0.6")
636   ("cf4"
637    :is-eq-to "st4.cf"
638    :geometry-side "RIGHT"
639    :geometry-position "0.8"))
640  :modules
641  (("st4"
642    :is-a "storage-intra"
643    :geometry-x "77"
644    :geometry-y "336")))
645
646(define-module
647  :class "storage-mult-5st"
648  :super-classes ("storage-mult-4st")
649  :properties
650  (("abstract"
651    :value "no"))
652  :icon "icons/1bs-5st"
653  :terminals
654  (("cf3"
655    :geometry-position "0.5")
656   ("cf4"
657    :geometry-position "0.75")
658   ("cf5"
659    :is-eq-to "st5.cf"
660    :geometry-side "RIGHT"
661    :geometry-position "0.8"))
662  :modules
663  (("st5"
664    :is-a "storage-intra"
665    :geometry-x "77"
666    :geometry-y "356")))
667
668(define-module
669  :class "storage-mult-6st"
670  :super-classes ("storage-mult-5st")
671  :properties
672  (("abstract"
673    :value "no"))
674  :icon "icons/1bs-6st"
675  :terminals
676  (("cf2"
677    :geometry-position "0.27")
678   ("cf3"
679    :geometry-position "0.42")
680   ("cf4"
681    :geometry-position "0.55")
682   ("cf5"
683    :geometry-position "0.71")
684   ("cf6"
685    :is-eq-to "st6.cf"
686    :geometry-side "RIGHT"
687    :geometry-position "0.87"))
688  :modules
689  (("st6"
690    :is-a "storage-intra"
691    :geometry-x "77"
692    :geometry-y "356")))
693
694(define-module
695  :class "storage-mult-6st-spec"
696  :super-classes ("storage-mult-6st")
697  :documentation "this particular storage for zap, where we are interested in
698      the phosphorylation at p319 because it is measured; thsi corresponds to
699      c_4+c_5, and at the total concentration (all except degradated)"
700  :parameters
701  (("st6.c0"
702    :model-name "degradzap_c0"))
703  :variables
704  (("totphosp"
705    :is-a "var-state-concentration-out"
706    :dont-optimize "yes"
707    :model-name "totp"))
708  :equations
709  (("totphospeq"
710    :relation "totphosp == st4.c0+st5.c0")))
711
712(define-module
713  :class "formal"
714  :super-classes ("kinetics"))
715
716(define-module
717  :class "reversible"
718  :super-classes ("formal"))
719
720(define-module
721  :class "fr1"
722  :super-classes ("reversible")
723  :documentation "A <-> B (dynamical)"
724  :parameters
725  (("r"
726    :value "k1*a.c-k2*b.c"))
727  :variables
728  (("k1"
729    :is-a "var-real-parameter"
730    :documentation "Rate constant A -> B"
731    :value "1.0d0"
732    :unit "1/h")
733   ("k2"
734    :is-a "var-real-parameter"
735    :documentation "Rate constant A <- B"
736    :value "1.0d0"
737    :unit "1/h")))
738
739(define-module
740  :class "trans2a-fr1_l"
741  :super-classes ("fr1" "s-a-b_l")
742  :properties
743  (("abstract"
744    :value "no"))
745  :icon "icons/rev_l")
746
747(define-module
748  :class "c2b1"
749  :super-classes ("predefined"))
750
751(define-module
752  :class "fr4b"
753  :super-classes ("reversible")
754  :documentation "Reversible Doppelsubstratkinetik-only one (C) product
755  influences the kinetic; needed for bindsites module"
756  :parameters
757  (("r"
758    :value "k1*a.c*b.c-k2*c.c"))
759  :variables
760  (("k1"
761    :is-a "var-real-parameter")
762   ("k2"
763    :is-a "var-real-parameter")))
764
765(define-module
766  :class "s-ab-cd"
767  :super-classes ("structure")
768  :terminals
769  (("a"
770    :is-a "term-reaction-flux")
771   ("b"
772    :is-a "term-reaction-flux")
773   ("c"
774    :is-a "term-reaction-flux")
775   ("d"
776    :is-a "term-reaction-flux"))
777  :equations
778  (("stoech_a"
779    :relation "a.r == -r")
780   ("stoech_b"
781    :relation "b.r == -r")
782   ("stoech_c"
783    :relation "c.r == r")
784   ("stoech_d"
785    :relation "d.r == r")))
786
787(define-module
788  :class "s-ab-cd_d"
789  :super-classes ("s-ab-cd")
790  :terminals
791  (("a"
792    :geometry-side "left"
793    :geometry-position "0.2")
794   ("b"
795    :geometry-side "right"
796    :geometry-position "0.2")
797   ("c"
798    :geometry-side "left"
799    :geometry-position "0.8")
800   ("d"
801    :geometry-side "right"
802    :geometry-position "0.8")))
803
804(define-module
805  :class "trans4a-fr4b_d"
806  :super-classes ("fr4b" "s-ab-cd_d")
807  :properties
808  (("abstract"
809    :value "no"))
810  :icon "icons/rev_4_d")
811
812(define-module
813  :class "c2b1-en1-nost-noout"
814  :super-classes ("c2b1")
815  :documentation "c2b1 but the storages are left out"
816  :properties
817  (("abstract"
818    :value "no"))
819  :icon "ProMoT_models/SignalTransd/TCR/predefined/icons/C2B1-nost.gif"
820  :geometry-width "347"
821  :geometry-height "298"
822  :terminals
823  (("a"
824    :is-eq-to "reaction.a"
825    :geometry-side "LEFT"
826    :geometry-position "0.02")
827   ("a2"
828    :is-eq-to "reactionbind.b"
829    :geometry-side "RIGHT"
830    :geometry-position "0.5")
831   ("b"
832    :is-eq-to "adapter_flux0.in"
833    :geometry-side "LEFT"
834    :geometry-position "0.5")
835   ("b2"
836    :is-eq-to "reactionbind.d"
837    :geometry-side "RIGHT"
838    :geometry-position "0.92")
839   ("c"
840    :is-eq-to "adapter_flux.in"
841    :geometry-side "LEFT"
842    :geometry-position "0.92")
843   ("input"
844    :is-eq-to "reaction.enz1"
845    :geometry-side "RIGHT"
846    :geometry-position "0.25"))
847  :modules
848  (("adapter_flux"
849    :is-a "adapter-flux"
850    :geometry-x "56"
851    :geometry-y "209")
852   ("adapter_flux0"
853    :is-a "adapter-flux"
854    :geometry-x "66"
855    :geometry-y "139")
856   ("phosphatase"
857    :is-a "storage-intra-const_c"
858    :geometry-x "164"
859    :geometry-y "136")
860   ("reaction"
861    :is-a "cyclic_en1_ud"
862    :geometry-x "161"
863    :geometry-y "94")
864   ("reactionbind"
865    :is-a "trans4a-fr4b_d"
866    :geometry-x "162"
867    :geometry-y "180"
868    :variables
869    (("k1"
870      :is-eq-to "parent.k1")
871     ("k2"
872      :is-eq-to "parent.k2"))))
873  :links
874  (("adapter_flux0out_reactionb"
875    :terminals ("adapter_flux0.out" "reaction.b" "reactionbind.a")
876    :nodes (("96" "152"))
877    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
878   ("adapter_fluxout_reactionbindc"
879    :terminals ("adapter_flux.out" "reactionbind.c")
880    :nodes (("104" "200"))
881    :edges (("0" "-1" nil) ("1" "-1" nil)))
882   ("phos7953"
883    :terminals ("phosphatase.co" "reaction.enz2")))
884  :variables
885  (("k1"
886    :is-a "var-real-parameter")
887   ("k2"
888    :is-a "var-real-parameter")))
889
890(define-module
891  :class "c2b1-en1-nost-noout-prep"
892  :super-classes ("c2b1-en1-nost-noout")
893  :parameters
894  (("k1"
895    :value "1.0d0")
896   ("k2"
897    :value "1.0d0")
898   ("reaction.r1_sa"
899    :value "1.0d0")
900   ("reaction.r2_sa"
901    :value "1.0d0")))
902
903(define-module
904  :class "storage-mult-2bs"
905  :super-classes ("multistage-storage"))
906
907(define-module
908  :class "adapter-conc"
909  :super-classes ("adapter")
910  :documentation "splits a concentration-terminal into 2"
911  :properties
912  (("abstract"
913    :value "no"))
914  :icon "icons/adapter.gif"
915  :terminals
916  (("in"
917    :is-a "term-concentration-in"
918    :geometry-side "LEFT"
919    :geometry-position "0.5")
920   ("out"
921    :is-a "term-concentration-out"
922    :geometry-side "RIGHT"
923    :geometry-position "0.50666666"
924    :variables
925    (("c"
926      :is-eq-to "parent.c"))))
927  :variables
928  (("c"
929    :is-a "var-state-concentration-out"))
930  :equations
931  (("hurg"
932    :relation "c == in.c")))
933
934(define-module
935  :class "storage-mult-2bs-23st"
936  :super-classes ("storage-mult-2bs")
937  :properties
938  (("abstract"
939    :value "no"))
940  :icon "icons/2bs-23st"
941  :geometry-width "258"
942  :geometry-height "306"
943  :terminals
944  (("cf11"
945    :is-eq-to "bs1.cf1"
946    :geometry-side "RIGHT"
947    :geometry-position "0.16")
948   ("cf12"
949    :is-eq-to "bs1.cf2"
950    :geometry-side "RIGHT"
951    :geometry-position "0.3")
952   ("cf21"
953    :is-eq-to "bs2.cf1"
954    :geometry-side "RIGHT"
955    :geometry-position "0.55")
956   ("cf22"
957    :is-eq-to "bs2.cf2"
958    :geometry-side "RIGHT"
959    :geometry-position "0.73")
960   ("cf23"
961    :is-eq-to "bs2.cf3"
962    :geometry-side "RIGHT"
963    :geometry-position "0.9")
964   ("cot"
965    :is-eq-to "adapter_conc.in"
966    :geometry-side "TOP"
967    :geometry-position "0.47"))
968  :modules
969  (("adapter_conc"
970    :is-a "adapter-conc"
971    :geometry-x "59"
972    :geometry-y "59")
973   ("bs1"
974    :is-a "storage-mult-2st"
975    :geometry-x "104"
976    :geometry-y "99")
977   ("bs2"
978    :is-a "storage-mult-3st"
979    :geometry-x "108"
980    :geometry-y "221"))
981  :links
982  (("adapter_concout_bs1cot"
983    :terminals ("adapter_conc.out" "bs1.cot" "bs2.cot")
984    :nodes (("90" "126"))
985    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))))
986
987(define-module
988  :class "sum"
989  :super-classes ("help")
990  :documentation "These classes are needed for add signals, eg enz_tot=enz1+enz2")
991
992(define-module
993  :class "sum-2-signal"
994  :super-classes ("sum")
995  :documentation "add 2 concentrations"
996  :properties
997  (("abstract"
998    :value "no"))
999  :icon "icons/sumsignals.gif"
1000  :terminals
1001  (("in1"
1002    :is-a "term-concentration-in"
1003    :geometry-side "TOP"
1004    :geometry-position "0.1")
1005   ("in2"
1006    :is-a "term-concentration-in"
1007    :geometry-side "TOP"
1008    :geometry-position "0.9")
1009   ("out"
1010    :is-a "term-concentration-out"
1011    :geometry-side "BOTTOM"
1012    :geometry-position "0.5"
1013    :variables
1014    (("c"
1015      :is-eq-to "parent.c"))))
1016  :variables
1017  (("c"
1018    :is-a "var-state-concentration-out"
1019    :documentation "sum of both concentrations"
1020    :report "lumped")
1021   ("k1"
1022    :is-a "var-real-parameter"
1023    :value "1.0d0")
1024   ("k2"
1025    :is-a "var-real-parameter"
1026    :value "1.0d0"))
1027  :equations
1028  (("hurg"
1029    :relation "c == k1*in1.c+k2*in2.c")))
1030
1031(define-module
1032  :class "sum-3-signal"
1033  :super-classes ("sum-2-signal")
1034  :documentation "add 2 concentrations"
1035  :properties
1036  (("abstract"
1037    :value "no"))
1038  :icon "icons/sum3signals.gif"
1039  :parameters
1040  (("hurg"
1041    :relation "c == k1*in1.c+k2*in2.c+k3*in3.c")
1042   ("k1"
1043    :value "1.0d0")
1044   ("k2"
1045    :value "1.0d0"))
1046  :terminals
1047  (("in3"
1048    :is-a "term-concentration-in"
1049    :geometry-side "LEFT"
1050    :geometry-position "0.5")
1051   ("out"
1052    :is-a "term-concentration-out"
1053    :variables
1054    (("c"
1055      :is-eq-to "parent.c"))))
1056  :variables
1057  (("c"
1058    :is-a "var-state-concentration-out"
1059    :documentation "sum of both concentrations"
1060    :report "lumped")
1061   ("k3"
1062    :is-a "var-real-parameter"
1063    :value "1.0d0")))
1064
1065(define-module
1066  :class "b1"
1067  :super-classes ("predefined")
1068  :documentation "binding of 2 proteins/domains")
1069
1070(define-module
1071  :class "b1-en1-nost-noout"
1072  :super-classes ("b1" "trans4a-fr4b_d")
1073  :icon "ProMoT_models/SignalTransd/TCR/predefined/icons/B1-nost.gif"
1074  :terminals
1075  (("a"
1076    :geometry-side "LEFT"
1077    :geometry-position "0.06")
1078   ("b"
1079    :geometry-side "RIGHT"
1080    :geometry-position "0.06")
1081   ("c"
1082    :geometry-side "LEFT"
1083    :geometry-position "0.94")
1084   ("d"
1085    :geometry-side "RIGHT"
1086    :geometry-position "0.94")))
1087
1088(define-module
1089  :class "b1-en1-nost-noout-prep"
1090  :super-classes ("b1-en1-nost-noout")
1091  :parameters
1092  (("k1"
1093    :value "1.0d0")
1094   ("k2"
1095    :value "1.0d0")))
1096
1097(define-module
1098  :class "tcrcd8zap-2"
1099  :super-classes ("tcr-prox-events")
1100  :documentation "includes degradation of ZAP via cCBl in a simple manner, shp,
1101  pagcsk, erk protection as tcrcd8zap, but the output is cd3crossl, no cd8 crossl"
1102  :properties
1103  (("abstract"
1104    :value "no"))
1105  :geometry-width "807"
1106  :geometry-height "746"
1107  :parameters
1108  (("cd8.st_2"
1109    :model-name "cd8occupancy")
1110   ("cd8tot.c0"
1111    :model-name "cd8tot_c0")
1112   ("ligcd8tot.c0"
1113    :model-name "ligcd8tot_c0")
1114   ("sumzapact.k1"
1115    :documentation "not to be changed,ie do not fit  it!"
1116    :value "1.0d0"
1117    :model-name "sumzapactk1")
1118   ("sumzapact.k2"
1119    :documentation "not to be changed,ie do not fit  it!"
1120    :value "1.0d0"
1121    :model-name "sumzapactk2")
1122   ("sumzapact.k3"
1123    :documentation "not to be changed,ie do not fit  it!"
1124    :value "1.0d0"
1125    :model-name "sumzapactk3")
1126   ("tcr.bs1.st_2"
1127    :model-name "tcrligoccupancy")
1128   ("tcr.bs2.st_3"
1129    :model-name "tcrzapoccupancy")
1130   ("tcrzap.phosphatase.c0"
1131    :model-name "tcrp_phos_c0")
1132   ("zap70.totphosp"
1133    :report "lumped"
1134    :model-name "zapphosp292")
1135   ("zapactivation.phosphatase.c0"
1136    :model-name "zapact_phos_c0")
1137   ("zapautophosp.phosphatase.c0"
1138    :model-name "zapautop_phos_c0")
1139   ("zapdeg.k1"
1140    :documentation "not to be changed,ie do not fit  it! reversible reaction of the degradation"
1141    :value "0.0d0"))
1142  :terminals
1143  (("inpsrckinact"
1144    :is-eq-to "srckinactada.in"
1145    :geometry-side "RIGHT"
1146    :geometry-position "0.8096515"
1147    :line (("624" "592")))
1148   ("outcd8crossl"
1149    :is-eq-to "cd8crosslad.out"
1150    :geometry-side "RIGHT"
1151    :geometry-position "0.37265417")
1152   ("outtcrcossl"
1153    :is-eq-to "cf2co1.co"
1154    :geometry-side "BOTTOM"
1155    :geometry-position "0.58488226"
1156    :line (("472" "192")))
1157   ("zapout"
1158    :is-eq-to "sumzapact.out"
1159    :geometry-side "BOTTOM"
1160    :geometry-position "0.2695829"))
1161  :modules
1162  (("cd8"
1163    :is-a "storage-mult-2st"
1164    :geometry-x "573"
1165    :geometry-y "138")
1166   ("cd8crosslad"
1167    :is-a "adapter-conc"
1168    :geometry-x "615"
1169    :geometry-y "277")
1170   ("cd8ligbind"
1171    :is-a "b1-en1-nost-noout-prep"
1172    :geometry-x "652"
1173    :geometry-y "134"
1174    :model-name "cd8lb")
1175   ("cd8tot"
1176    :is-a "storage-intra-const_c"
1177    :geometry-x "572"
1178    :geometry-y "73")
1179   ("cf2co"
1180    :is-a "cf2co"
1181    :geometry-x "609"
1182    :geometry-y "191")
1183   ("cf2co0"
1184    :is-a "cf2co"
1185    :geometry-x "246"
1186    :geometry-y "566")
1187   ("cf2co1"
1188    :is-a "cf2co"
1189    :geometry-x "125"
1190    :geometry-y "188")
1191   ("ligand"
1192    :is-a "storage-mult-2st"
1193    :geometry-x "261"
1194    :geometry-y "128"
1195    :model-name "lig")
1196   ("ligandtotal"
1197    :is-a "storage-intra-const_c"
1198    :geometry-x "258"
1199    :geometry-y "68"
1200    :model-name "ligt")
1201   ("ligcd8"
1202    :is-a "storage-mult-2st"
1203    :geometry-x "727"
1204    :geometry-y "139")
1205   ("ligcd8tot"
1206    :is-a "storage-intra-const_c"
1207    :geometry-x "729"
1208    :geometry-y "73")
1209   ("srckinactada"
1210    :is-a "adapter-conc"
1211    :geometry-x "592"
1212    :geometry-y "369")
1213   ("sumzapact"
1214    :is-a "sum-3-signal"
1215    :geometry-x "340"
1216    :geometry-y "614")
1217   ("tcr"
1218    :is-a "storage-mult-2bs-23st"
1219    :geometry-x "81"
1220    :geometry-y "189"
1221    :model-name "tcr")
1222   ("tcrligandbind"
1223    :is-a "b1-en1-nost-noout-prep"
1224    :geometry-x "167"
1225    :geometry-y "125"
1226    :model-name "tcrlb")
1227   ("tcrtotal"
1228    :is-a "storage-intra-const_c"
1229    :geometry-x "75"
1230    :geometry-y "64"
1231    :model-name "tcrt")
1232   ("tcrzap"
1233    :is-a "c2b1-en1-nost-noout-prep"
1234    :geometry-x "213"
1235    :geometry-y "242"
1236    :model-name "tcrzab")
1237   ("trans2a_fr1_l"
1238    :is-a "trans2a-fr1_l"
1239    :geometry-x "285"
1240    :geometry-y "554")
1241   ("zap70"
1242    :is-a "storage-mult-6st-spec"
1243    :geometry-x "217"
1244    :geometry-y "506"
1245    :model-name "zap")
1246   ("zap70total"
1247    :is-a "storage-intra-const_c"
1248    :geometry-x "212"
1249    :geometry-y "345"
1250    :model-name "zapt")
1251   ("zapactivation"
1252    :is-a "c2a-en1-nost-prep"
1253    :geometry-x "339"
1254    :geometry-y "461")
1255   ("zapautophosp"
1256    :is-a "c2a-en1-nost-prep"
1257    :geometry-x "339"
1258    :geometry-y "519")
1259   ("zapdeg"
1260    :is-a "b1-en1-nost-noout-prep"
1261    :geometry-x "139"
1262    :geometry-y "574"
1263    :model-name "zdeg"))
1264  :links
1265  (("cd8cf2_cd8ligbindc"
1266    :terminals ("cd8.cf2" "cd8ligbind.c" "cf2co.cf")
1267    :nodes (("607" "160"))
1268    :edges (("0" "-1" (("615" "176"))) ("1" "-1" nil) ("2" "-1" nil)))
1269   ("cd8cot_cd8totco"
1270    :terminals ("cd8.cot" "cd8tot.co"))
1271   ("cd8ligbinda_cd8cf1"
1272    :terminals ("cd8ligbind.a" "cd8.cf1"))
1273   ("cd8ligbindd_ligcd8cf2"
1274    :terminals ("cd8ligbind.d" "ligcd8.cf2"))
1275   ("cf2coco_cocrosslin2"
1276    :terminals ("cf2co.co" "cd8crosslad.in")
1277    :nodes (("608" "200"))
1278    :edges (("0" "-1" nil) ("2" "-1" nil)))
1279   ("ligandcf2_tcrligandbindd"
1280    :terminals ("ligand.cf2" "tcrligandbind.d"))
1281   ("ligandcot_ligandtotalco"
1282    :terminals ("ligand.cot" "ligandtotal.co"))
1283   ("ligcd8cf1_cd8ligbindb"
1284    :terminals ("ligcd8.cf1" "cd8ligbind.b"))
1285   ("ligcd8cot_ligcd8totco"
1286    :terminals ("ligcd8.cot" "ligcd8tot.co"))
1287   ("srckinactadaout_tcrzapinput"
1288    :terminals ("srckinactada.out" "tcrzap.input" "zapactivation.input")
1289    :nodes (("400" "336"))
1290    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1291   ("sumzapactin1_zapautophospoutput"
1292    :terminals ("sumzapact.in1" "zapautophosp.output")
1293    :edges (("-1" "1" nil)))
1294   ("sumzapactin3_cf2co0co"
1295    :terminals ("sumzapact.in3" "cf2co0.co"))
1296   ("tcrcf11_tcrligandbinda"
1297    :terminals ("tcr.cf11" "tcrligandbind.a"))
1298   ("tcrcf21_tcrzapa"
1299    :terminals ("tcr.cf21" "tcrzap.a"))
1300   ("tcrcot_tcrtotalco"
1301    :terminals ("tcr.cot" "tcrtotal.co"))
1302   ("tcrligandbindb_ligandcf1"
1303    :terminals ("tcrligandbind.b" "ligand.cf1"))
1304   ("tcrligandbindc_tcrcf12"
1305    :terminals ("tcrligandbind.c" "tcr.cf12" "cf2co1.cf")
1306    :nodes (("118" "143"))
1307    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1308   ("tcrzapa2_zap70cf11"
1309    :terminals ("tcrzap.a2" "zap70.cf1")
1310    :edges (("0" "1" (("248" "240")))))
1311   ("tcrzapb_tcrcf22"
1312    :terminals ("tcrzap.b" "tcr.cf22" "zapdeg.b")
1313    :nodes (("113" "241"))
1314    :edges (("0" "-1" (("128" "240"))) ("1" "-1" nil) ("2" "-1" nil)))
1315   ("tcrzapc_tcrcf23"
1316    :terminals ("tcrzap.c" "tcr.cf23" "zapdeg.d")
1317    :nodes (("114" "283"))
1318    :edges (("0" "-1" (("112" "280"))) ("1" "-1" nil) ("2" "-1" nil)))
1319   ("trans2a_fr1_lb_zap70cf5"
1320    :terminals ("trans2a_fr1_l.b" "zap70.cf5" "zapdeg.c" "cf2co0.cf")
1321    :nodes (("248" "566"))
1322    :edges (("0" "-1" (("272" "552"))) ("1" "-1" nil) ("2" "-1" nil)
1323            ("3" "-1" nil)))
1324   ("zap70cf2_tcrzapb2"
1325    :terminals ("zap70.cf2" "tcrzap.b2" "zapactivation.a")
1326    :nodes (("248" "453"))
1327    :edges (("0" "-1" (("248" "431")))
1328            ("1" "-1" (("304" "280") ("304" "440"))) ("2" "-1" nil)))
1329   ("zap70cf3_zapactivationb"
1330    :terminals ("zap70.cf3" "zapactivation.b" "zapautophosp.a")
1331    :nodes (("248" "485"))
1332    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1333   ("zap70totalco_zap70cot"
1334    :terminals ("zap70total.co" "zap70.cot"))
1335   ("zapautophospb_zap70cf4"
1336    :terminals ("zapautophosp.b" "zap70.cf4" "trans2a_fr1_l.a")
1337    :nodes (("253" "520"))
1338    :edges (("0" "-1" (("312" "520"))) ("1" "-1" nil) ("2" "-1" nil)))
1339   ("zapautophospinput_zapactivationoutput"
1340    :terminals ("zapautophosp.input" "zapactivation.output"
1341                "sumzapact.in2")
1342    :nodes (("371" "522"))
1343    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1344   ("zapdegc_zap70cf6"
1345    :terminals ("zapdeg.a" "zap70.cf6"))))
1346
1347(define-module
1348  :class "srckinases"
1349  :super-classes ("tcr-prox-events")
1350  :icon "ProMoT_models/SignalTransd/TCR/icons/Srckinase.gif")
1351
1352(define-module
1353  :class "c2a-en1-bs"
1354  :super-classes ("c2a")
1355  :documentation "protein in 2 states, active-inactive, using multistage, reactiosn are 1st order"
1356  :properties
1357  (("abstract"
1358    :value "no"))
1359  :icon "ProMoT_models/SignalTransd/TCR/predefined/icons/C2a.gif"
1360  :geometry-width "378"
1361  :geometry-height "275"
1362  :terminals
1363  (("input"
1364    :is-eq-to "reaction.enz1"
1365    :geometry-side "TOP"
1366    :geometry-position "0.5")
1367   ("output"
1368    :is-eq-to "aco.co"
1369    :geometry-side "BOTTOM"
1370    :geometry-position "0.5233333"))
1371  :modules
1372  (("aco"
1373    :is-a "cf2co"
1374    :geometry-x "206"
1375    :geometry-y "199")
1376   ("activ"
1377    :is-a "storage-mult-2st"
1378    :geometry-x "266"
1379    :geometry-y "167")
1380   ("activtotal"
1381    :is-a "storage-intra-const_c"
1382    :geometry-x "271"
1383    :geometry-y "77")
1384   ("phosphatase"
1385    :is-a "storage-intra-const_c"
1386    :geometry-x "84"
1387    :geometry-y "215")
1388   ("reaction"
1389    :is-a "cyclic_en1"
1390    :geometry-x "153"
1391    :geometry-y "126"
1392    :variables
1393    (("r1_sa"
1394      :is-eq-to "parent.r1_sa")
1395     ("r2_sa"
1396      :is-eq-to "parent.r2_sa"))))
1397  :links
1398  (("activcot_activtotalco"
1399    :terminals ("activ.cot" "activtotal.co"))
1400   ("deact204"
1401    :terminals ("activ.cf1" "reaction.a"))
1402   ("phos7953"
1403    :terminals ("phosphatase.co" "reaction.enz2"))
1404   ("reactionb_acocf_473370"
1405    :terminals ("reaction.b" "aco.cf" "activ.cf2")
1406    :nodes (("201" "127"))
1407    :edges (("0" "-1" (("176" "128"))) ("1" "-1" nil) ("2" "-1" nil))))
1408  :variables
1409  (("r1_sa"
1410    :is-a "var-real-parameter")
1411   ("r2_sa"
1412    :is-a "var-real-parameter")))
1413
1414(define-module
1415  :class "c2a-en1-bs-prep"
1416  :super-classes ("c2a-en1-bs")
1417  :documentation "just give values to the parameters of the class c2a-en1-bs"
1418  :parameters
1419  (("r1_sa"
1420    :value "1.0d0")
1421   ("r2_sa"
1422    :value "1.0d0")))
1423
1424(define-module
1425  :class "phospd-crossldepandindep"
1426  :super-classes ("srckinases")
1427  :properties
1428  (("abstract"
1429    :value "no"))
1430  :icon "ProMoT_models/SignalTransd/TCR/icons/phospd-crossldepandindep.gif"
1431  :geometry-width "300"
1432  :geometry-height "178"
1433  :parameters
1434  (("sum_2_signal.k1"
1435    :model-name "phospd_src_crosslk1su")
1436   ("sum_2_signal.k2"
1437    :model-name "phospd_src_crosslk2su"))
1438  :terminals
1439  (("inpcrossl"
1440    :is-eq-to "phospdcrossldep.input"
1441    :geometry-side "LEFT"
1442    :geometry-position "0.5")
1443   ("outphospd"
1444    :is-eq-to "sum_2_signal.out"
1445    :geometry-side "RIGHT"
1446    :geometry-position "0.5"))
1447  :modules
1448  (("phospdconst"
1449    :is-a "storage-intra-const_c"
1450    :geometry-x "84"
1451    :geometry-y "97")
1452   ("phospdcrossldep"
1453    :is-a "c2a-en1-bs-prep"
1454    :geometry-x "175"
1455    :geometry-y "65")
1456   ("sum_2_signal"
1457    :is-a "sum-2-signal"
1458    :geometry-x "174"
1459    :geometry-y "113"))
1460  :links
1461  (("phospdconstco_sum_2_signalin1"
1462    :terminals ("phospdconst.co" "sum_2_signal.in1"))
1463   ("sum_2_signalin2_phospdcrossldepoutput"
1464    :terminals ("sum_2_signal.in2" "phospdcrossldep.output")
1465    :edges (("0" "1" (("176" "104")))))))
1466
1467(define-module
1468  :class "c2b1-en1-nost-noout-inpinh"
1469  :super-classes ("c2b1")
1470  :documentation "c2b1-en1-nost-noout with a second input for inhibitoy enzime
1471  (tipically phosphatase)"
1472  :properties
1473  (("abstract"
1474    :value "no"))
1475  :icon "ProMoT_models/SignalTransd/TCR/predefined/icons/C2B1-nost.gif"
1476  :geometry-width "347"
1477  :geometry-height "298"
1478  :terminals
1479  (("a"
1480    :is-eq-to "reaction.a"
1481    :geometry-side "LEFT"
1482    :geometry-position "0.02")
1483   ("a2"
1484    :is-eq-to "reactionbind.b"
1485    :geometry-side "RIGHT"
1486    :geometry-position "0.5")
1487   ("b"
1488    :is-eq-to "adapter_flux0.in"
1489    :geometry-side "LEFT"
1490    :geometry-position "0.5")
1491   ("b2"
1492    :is-eq-to "reactionbind.d"
1493    :geometry-side "RIGHT"
1494    :geometry-position "0.92")
1495   ("c"
1496    :is-eq-to "adapter_flux.in"
1497    :geometry-side "LEFT"
1498    :geometry-position "0.92")
1499   ("input"
1500    :is-eq-to "reaction.enz1"
1501    :geometry-side "RIGHT"
1502    :geometry-position "0.25")
1503   ("input2"
1504    :is-eq-to "reaction.enz2"
1505    :geometry-side "LEFT"
1506    :geometry-position "0.2885906"))
1507  :modules
1508  (("adapter_flux"
1509    :is-a "adapter-flux"
1510    :geometry-x "56"
1511    :geometry-y "209")
1512   ("adapter_flux0"
1513    :is-a "adapter-flux"
1514    :geometry-x "66"
1515    :geometry-y "139")
1516   ("reaction"
1517    :is-a "cyclic_en1_ud"
1518    :geometry-x "161"
1519    :geometry-y "94")
1520   ("reactionbind"
1521    :is-a "trans4a-fr4b_d"
1522    :geometry-x "162"
1523    :geometry-y "180"
1524    :variables
1525    (("k1"
1526      :is-eq-to "parent.k1")
1527     ("k2"
1528      :is-eq-to "parent.k2"))))
1529  :links
1530  (("adapter_flux0out_reactionb"
1531    :terminals ("adapter_flux0.out" "reaction.b" "reactionbind.a")
1532    :nodes (("96" "152"))
1533    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1534   ("adapter_fluxout_reactionbindc"
1535    :terminals ("adapter_flux.out" "reactionbind.c")
1536    :nodes (("104" "200"))
1537    :edges (("0" "-1" nil) ("1" "-1" nil))))
1538  :variables
1539  (("k1"
1540    :is-a "var-real-parameter")
1541   ("k2"
1542    :is-a "var-real-parameter")))
1543
1544(define-module
1545  :class "c2b1-en1-nost-noout-inpinh-prep"
1546  :super-classes ("c2b1-en1-nost-noout-inpinh")
1547  :parameters
1548  (("k1"
1549    :value "1.0d0")
1550   ("k2"
1551    :value "1.0d0")
1552   ("reaction.r1_sa"
1553    :value "1.0d0")
1554   ("reaction.r2_sa"
1555    :value "1.0d0")))
1556
1557(define-module
1558  :class "pagcsk"
1559  :super-classes ("tcr-prox-events")
1560  :documentation "module with pag and csk"
1561  :properties
1562  (("abstract"
1563    :value "no"))
1564  :icon "ProMoT_models/SignalTransd/TCR/icons/Pagcsk.gif"
1565  :geometry-width "616"
1566  :geometry-height "300"
1567  :parameters
1568  (("csktot.c0"
1569    :model-name "csktot_c0")
1570   ("pagtot.c0"
1571    :model-name "pagtot_c0"))
1572  :terminals
1573  (("cskout"
1574    :is-eq-to "convcsk.co"
1575    :geometry-side "BOTTOM"
1576    :geometry-position "0.425")
1577   ("inppagdephosp"
1578    :is-eq-to "pagcskbind.input"
1579    :geometry-side "TOP"
1580    :geometry-position "0.28733766")
1581   ("inppagphosp"
1582    :is-eq-to "pagcskbind.input2"
1583    :geometry-side "RIGHT"
1584    :geometry-position "0.33666667"))
1585  :modules
1586  (("convcsk"
1587    :is-a "cf2co"
1588    :geometry-x "308"
1589    :geometry-y "244")
1590   ("csk"
1591    :is-a "storage-mult-2st"
1592    :geometry-x "308"
1593    :geometry-y "132")
1594   ("csktot"
1595    :is-a "storage-intra-const_c"
1596    :geometry-x "303"
1597    :geometry-y "59")
1598   ("pag"
1599    :is-a "storage-mult-3st"
1600    :geometry-x "98"
1601    :geometry-y "177")
1602   ("pagcskbind"
1603    :is-a "c2b1-en1-nost-noout-inpinh-prep"
1604    :geometry-x "203"
1605    :geometry-y "167")
1606   ("pagtot"
1607    :is-a "storage-intra-const_c"
1608    :geometry-x "98"
1609    :geometry-y "92"))
1610  :links
1611  (("cskcf1_pagcskbinda2"
1612    :terminals ("csk.cf1" "pagcskbind.a2")
1613    :edges (("0" "-1" nil)))
1614   ("cskcot_csktotco"
1615    :terminals ("csk.cot" "csktot.co"))
1616   ("pagcf1_pagcskbinda"
1617    :terminals ("pag.cf1" "pagcskbind.a")
1618    :edges (("0" "-1" nil)))
1619   ("pagcf2_pagcskbindb"
1620    :terminals ("pag.cf2" "pagcskbind.b")
1621    :edges (("0" "-1" nil)))
1622   ("pagcot_pagtotco"
1623    :terminals ("pag.cot" "pagtot.co"))
1624   ("pagcskbindb2_cskcf2"
1625    :terminals ("pagcskbind.b2" "csk.cf2" "convcsk.cf")
1626    :nodes (("272" "200"))
1627    :edges (("-1" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1628   ("pagcskbindc_pagcf3"
1629    :terminals ("pagcskbind.c" "pag.cf3")
1630    :edges (("-1" "1" nil)))))
1631
1632(define-module
1633  :class "sum-4-signal"
1634  :super-classes ("sum-3-signal")
1635  :documentation "add 4 concentrations"
1636  :properties
1637  (("abstract"
1638    :value "no"))
1639  :icon "icons/sum3signals.gif"
1640  :parameters
1641  (("hurg"
1642    :relation "c == k1*in1.c+k2*in2.c+k3*in3.c+k4*in4.c")
1643   ("k1"
1644    :value "1.0d0")
1645   ("k2"
1646    :value "1.0d0")
1647   ("k3"
1648    :value "1.0d0"))
1649  :terminals
1650  (("in1"
1651    :geometry-side "TOP"
1652    :geometry-position "0.1")
1653   ("in2"
1654    :geometry-side "TOP"
1655    :geometry-position "0.9")
1656   ("in3"
1657    :geometry-side "LEFT"
1658    :geometry-position "0.5")
1659   ("in4"
1660    :is-a "term-concentration-in"
1661    :geometry-side "RIGHT"
1662    :geometry-position "0.5")
1663   ("out"
1664    :is-a "term-concentration-out"
1665    :variables
1666    (("c"
1667      :is-eq-to "parent.c"))))
1668  :variables
1669  (("c"
1670    :is-a "var-state-concentration-out"
1671    :documentation "weighted sum of all concentrations"
1672    :report "lumped")
1673   ("k4"
1674    :is-a "var-real-parameter"
1675    :value "1.0d0")))
1676
1677(define-module
1678  :class "prod-2-signal"
1679  :super-classes ("sum")
1680  :documentation "multiplies 2 concentrations"
1681  :properties
1682  (("abstract"
1683    :value "no"))
1684  :icon "icons/prodsignals.gif"
1685  :terminals
1686  (("in1"
1687    :is-a "term-concentration-in"
1688    :geometry-side "TOP"
1689    :geometry-position "0.1")
1690   ("in2"
1691    :is-a "term-concentration-in"
1692    :geometry-side "TOP"
1693    :geometry-position "0.9")
1694   ("out"
1695    :is-a "term-concentration-out"
1696    :geometry-side "BOTTOM"
1697    :geometry-position "0.5"
1698    :variables
1699    (("c"
1700      :is-eq-to "parent.c"))))
1701  :variables
1702  (("c"
1703    :is-a "var-state-concentration-out"
1704    :documentation "sum of both concentrations"
1705    :report "lumped")
1706   ("k1"
1707    :is-a "var-real-parameter"
1708    :value "1.0d0"))
1709  :equations
1710  (("hurg"
1711    :relation "c == k1*in1.c*in2.c")))
1712
1713(define-module
1714  :class "lck-protec-2"
1715  :super-classes ("srckinases")
1716  :documentation "module defining lck activation and protection via ERK
1717  including effect of crosslinking"
1718  :properties
1719  (("abstract"
1720    :value "no"))
1721  :geometry-width "735"
1722  :geometry-height "619"
1723  :parameters
1724  (("lck.c_1"
1725    :model-name "lckdconc")
1726   ("lck.c_2"
1727    :model-name "lckiconc")
1728   ("lck.c_3"
1729    :model-name "lckaconc")
1730   ("lck.c_4"
1731    :model-name "lckdpconc")
1732   ("lck.c_5"
1733    :model-name "lckipconc")
1734   ("lck.c_6"
1735    :model-name "lckapconc")
1736   ("lck.st_1"
1737    :model-name "lckd")
1738   ("lck.st_2"
1739    :model-name "lcki")
1740   ("lck.st_3"
1741    :model-name "lcka")
1742   ("lck.st_4"
1743    :model-name "lckdp")
1744   ("lck.st_5"
1745    :model-name "lckip")
1746   ("lck.st_6"
1747    :model-name "lckap")
1748   ("lckautop.c"
1749    :model-name "lckautop")
1750   ("lckautop.k1"
1751    :model-name "lckautopk1su")
1752   ("lckautop.k2"
1753    :model-name "lckautopk2su")
1754   ("lckautop.kprod"
1755    :model-name "lckautopkprod")
1756   ("phosp.c0"
1757    :model-name "lckprph")
1758   ("sumlck.c"
1759    :model-name "lckactiv")
1760   ("sumlckphosp.k1"
1761    :documentation "should be removed from fitting, is redundant to r22_sa"
1762    :model-name "sumlckphok1su")
1763   ("sumlckphosp.k2"
1764    :model-name "sumlckphok2su"))
1765  :terminals
1766  (("cd8crossl"
1767    :is-eq-to "lckautop.in2"
1768    :geometry-side "RIGHT"
1769    :geometry-position "0.8368336")
1770   ("inerk"
1771    :is-eq-to "adapter_conc.in"
1772    :geometry-side "RIGHT"
1773    :geometry-position "0.5")
1774   ("inphospd"
1775    :is-eq-to "adapterphosp.in"
1776    :geometry-side "LEFT"
1777    :geometry-position "0.7399031")
1778   ("inpkind"
1779    :is-eq-to "adaptercsk.in"
1780    :geometry-side "TOP"
1781    :geometry-position "0.43")
1782   ("inpphospa"
1783    :is-eq-to "inputconv.in"
1784    :geometry-side "right"
1785    :geometry-position "0.4")
1786   ("inshp"
1787    :is-eq-to "sumlckphosp.in2"
1788    :geometry-side "BOTTOM"
1789    :geometry-position "0.069767445")
1790   ("outlck"
1791    :is-eq-to "sum_2_signal.out"
1792    :geometry-side "BOTTOM"
1793    :geometry-position "0.55668604"))
1794  :modules
1795  (("adaptercsk"
1796    :is-a "adapter-conc"
1797    :geometry-x "87"
1798    :geometry-y "70")
1799   ("adapterphosp"
1800    :is-a "adapter-conc"
1801    :geometry-x "67"
1802    :geometry-y "457")
1803   ("adapter_conc"
1804    :is-a "adapter-conc"
1805    :geometry-x "632"
1806    :geometry-y "233")
1807   ("cf2co"
1808    :is-a "cf2co"
1809    :geometry-x "291"
1810    :geometry-y "370")
1811   ("cf2co0"
1812    :is-a "cf2co"
1813    :geometry-x "294"
1814    :geometry-y "325")
1815   ("cf2co1"
1816    :is-a "cf2co"
1817    :geometry-x "303"
1818    :geometry-y "239")
1819   ("cf2co2"
1820    :is-a "cf2co"
1821    :geometry-x "313"
1822    :geometry-y "189")
1823   ("inputconv"
1824    :is-a "adapter-conc"
1825    :geometry-x "338"
1826    :geometry-y "60")
1827   ("lck"
1828    :is-a "storage-mult-6st"
1829    :geometry-x "263"
1830    :geometry-y "262"
1831    :model-name "lck")
1832   ("lckautop"
1833    :is-a "prod-2-signal"
1834    :geometry-x "426"
1835    :geometry-y "450")
1836   ("lckprot1"
1837    :is-a "cyclic_en1_ud"
1838    :geometry-x "496"
1839    :geometry-y "169"
1840    :model-name "lckp"
1841    :variables
1842    (("r1_sa"
1843      :is-eq-to "parent.lckp_r1_sa")
1844     ("r2_sa"
1845      :is-eq-to "parent.lckp_r2_sa")))
1846   ("lckprot2"
1847    :is-a "cyclic_en1_ud"
1848    :geometry-x "492"
1849    :geometry-y "236"
1850    :model-name "lckp2"
1851    :variables
1852    (("r1_sa"
1853      :is-eq-to "parent.lckp_r1_sa")
1854     ("r2_sa"
1855      :is-eq-to "parent.lckp_r2_sa")))
1856   ("lckprot3"
1857    :is-a "cyclic_en1_ud"
1858    :geometry-x "494"
1859    :geometry-y "344"
1860    :model-name "lckp3"
1861    :variables
1862    (("r1_sa"
1863      :is-eq-to "parent.lckp_r1_sa")
1864     ("r2_sa"
1865      :is-eq-to "parent.lckp_r2_sa")))
1866   ("lcktot"
1867    :is-a "storage-intra-const_c"
1868    :geometry-x "254"
1869    :geometry-y "116"
1870    :model-name "lckt")
1871   ("phosp"
1872    :is-a "storage-intra-const_c"
1873    :geometry-x "496"
1874    :geometry-y "290")
1875   ("phosp1"
1876    :is-a "cyclic_en1_ud"
1877    :geometry-x "110"
1878    :geometry-y "169"
1879    :variables
1880    (("r1_sa"
1881      :is-eq-to "parent.lcka_r11_sa")
1882     ("r2_sa"
1883      :is-eq-to "parent.lcka_r12_sa")))
1884   ("phosp1p"
1885    :is-a "cyclic_en1_ud"
1886    :geometry-x "110"
1887    :geometry-y "282"
1888    :variables
1889    (("r1_sa"
1890      :is-eq-to "parent.lcka_r11_sa")
1891     ("r2_sa"
1892      :is-eq-to "parent.lcka_r12_sa")))
1893   ("phosp2"
1894    :is-a "cyclic_en1_ud"
1895    :geometry-x "110"
1896    :geometry-y "226"
1897    :variables
1898    (("r1_sa"
1899      :is-eq-to "parent.lcka_r21_sa")
1900     ("r2_sa"
1901      :is-eq-to "parent.lcka_r22_sa")))
1902   ("phosp2p"
1903    :is-a "cyclic_en1_ud"
1904    :geometry-x "111"
1905    :geometry-y "343"
1906    :variables
1907    (("r1_sa"
1908      :is-eq-to "parent.lcka_r21_sa")
1909     ("r2_sa"
1910      :is-eq-to "parent.lcka_r22_sa")))
1911   ("sumlck"
1912    :is-a "sum-4-signal"
1913    :geometry-x "346"
1914    :geometry-y "413"
1915    :variables
1916    (("k1"
1917      :is-eq-to "parent.lcka_sumk1")
1918     ("k2"
1919      :is-eq-to "parent.lcka_sumk2")
1920     ("k3"
1921      :is-eq-to "parent.lcka_sumk1")
1922     ("k4"
1923      :is-eq-to "parent.lcka_sumk2")))
1924   ("sumlckphosp"
1925    :is-a "sum-2-signal"
1926    :geometry-x "34"
1927    :geometry-y "310")
1928   ("sum_2_signal"
1929    :is-a "adapter-conc"
1930    :geometry-x "357"
1931    :geometry-y "504"))
1932  :links
1933  (("adaptercskout_phosp1enz2"
1934    :terminals ("adaptercsk.out" "phosp1.enz2" "phosp1p.enz2")
1935    :nodes (("16" "160"))
1936    :edges (("0" "-1" (("16" "72"))) ("1" "-1" nil) ("2" "-1" nil)))
1937   ("adapter_concout_lckprot1enz1"
1938    :terminals ("adapter_conc.out" "lckprot1.enz1" "lckprot2.enz1"
1939                "lckprot3.enz1")
1940    :nodes (("576" "235"))
1941    :edges (("0" "-1" (("616" "240"))) ("1" "-1" nil) ("2" "-1" nil)
1942            ("3" "-1" nil)))
1943   ("cf2coco_sumlckin1"
1944    :terminals ("cf2co.co" "sumlck.in1")
1945    :edges (("0" "-1" nil)))
1946   ("inputconvout_phosp1enz1"
1947    :terminals ("inputconv.out" "phosp1.enz1" "phosp1p.enz1")
1948    :nodes (("192" "85"))
1949    :edges (("0" "-1" (("344" "88"))) ("1" "-1" (("192" "160")))
1950            ("2" "-1" (("192" "280")))))
1951   ("lckautopout_phosp2enz1"
1952    :terminals ("lckautop.out" "phosp2.enz1" "phosp2p.enz1")
1953    :nodes (("168" "405"))
1954    :edges (("0" "-1" (("424" "480") ("168" "480")))
1955            ("1" "-1" (("168" "224"))) ("2" "-1" (("168" "336")))))
1956   ("lckcf1_phosp1a"
1957    :terminals ("lck.cf1" "phosp1.a" "lckprot1.a")
1958    :nodes (("302" "149"))
1959    :edges (("0" "-1" (("304" "147"))) ("1" "-1" nil) ("2" "-1" nil)))
1960   ("lckcf2_phosp1b"
1961    :terminals ("lck.cf2" "phosp1.b" "phosp2.a" "lckprot2.a"
1962                "cf2co2.cf")
1963    :nodes (("302" "189"))
1964    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1965            ("4" "-1" nil)))
1966   ("lckcf3_phosp2b"
1967    :terminals ("lck.cf3" "phosp2.b" "cf2co1.cf")
1968    :nodes (("297" "240"))
1969    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1970   ("lckcf6_phosp2pb"
1971    :terminals ("lck.cf6" "phosp2p.b" "lckprot3.b" "cf2co.cf")
1972    :nodes (("296" "363"))
1973    :edges (("0" "-1" (("288" "363"))) ("1" "-1" nil) ("2" "-1" nil)
1974            ("3" "-1" nil)))
1975   ("lckcot_lcktotco"
1976    :terminals ("lck.cot" "lcktot.co"))
1977   ("phosp1pa_lckcf4"
1978    :terminals ("phosp1p.a" "lck.cf4" "lckprot1.b" "lckprot3.a")
1979    :nodes (("294" "269"))
1980    :edges (("0" "-1" (("160" "267"))) ("1" "-1" nil) ("2" "-1" nil)
1981            ("3" "-1" (("304" "272")))))
1982   ("phosp2pa_lckcf5"
1983    :terminals ("phosp2p.a" "lck.cf5" "phosp1p.b" "lckprot2.b"
1984                "cf2co0.cf")
1985    :nodes (("302" "317"))
1986    :edges (("0" "-1" (("152" "323"))) ("1" "-1" nil)
1987            ("2" "-1" (("184" "307"))) ("3" "-1" (("440" "261")))
1988            ("4" "-1" nil)))
1989   ("phospco_lckprot1enz2"
1990    :terminals ("phosp.co" "lckprot1.enz2" "lckprot2.enz2"
1991                "lckprot3.enz2")
1992    :nodes (("496" "293"))
1993    :edges (("0" "-1" (("496" "293"))) ("1" "-1" nil) ("2" "-1" nil)
1994            ("3" "-1" nil)))
1995   ("sumlckin2_cf2co0co"
1996    :terminals ("sumlck.in2" "cf2co0.co")
1997    :edges (("-1" "1" nil)))
1998   ("sumlckin3_cf2co1co"
1999    :terminals ("sumlck.in3" "cf2co1.co"))
2000   ("sumlckin4_cf2co2co"
2001    :terminals ("sumlck.in4" "cf2co2.co"))
2002   ("sumlckout_lckautopin1"
2003    :terminals ("sumlck.out" "lckautop.in1" "sum_2_signal.in")
2004    :nodes (("360" "440"))
2005    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
2006   ("sumlckphospin1_adapterphospout"
2007    :terminals ("sumlckphosp.in1" "adapterphosp.out" "phosp2p.enz2")
2008    :nodes (("72" "384"))
2009    :edges (("0" "-1" (("24" "384"))) ("1" "-1" nil)
2010            ("2" "-1" (("72" "344")))))
2011   ("sumlckphospout_phosp2enz2"
2012    :terminals ("sumlckphosp.out" "phosp2.enz2")
2013    :edges (("0" "1" (("32" "224"))))))
2014  :variables
2015  (("lcka_r11_sa"
2016    :is-a "var-real-parameter"
2017    :value "1.0d0"
2018    :model-name "lckar11_sa")
2019   ("lcka_r12_sa"
2020    :is-a "var-real-parameter"
2021    :value "1.0d0"
2022    :model-name "lckar12_sa")
2023   ("lcka_r21_sa"
2024    :is-a "var-real-parameter"
2025    :value "1.0d0"
2026    :model-name "lckar21_sa")
2027   ("lcka_r22_sa"
2028    :is-a "var-real-parameter"
2029    :value "1.0d0"
2030    :model-name "lckar22_sa")
2031   ("lcka_sumk1"
2032    :is-a "var-real-parameter"
2033    :value "3.0d0"
2034    :model-name "lckasumk1su")
2035   ("lcka_sumk2"
2036    :is-a "var-real-parameter"
2037    :documentation "should be out of fitting"
2038    :value "1.0d0"
2039    :model-name "lckasumk2su")
2040   ("lckp_r1_sa"
2041    :is-a "var-real-parameter"
2042    :value "1.0d0"
2043    :model-name "lckpr1_sa")
2044   ("lckp_r2_sa"
2045    :is-a "var-real-parameter"
2046    :value "1.0d0"
2047    :model-name "lckpr2_sa")))
2048
2049(define-module
2050  :class "srccrossl"
2051  :super-classes ("srckinases")
2052  :documentation "as srcsimple plus the influence of crosslinking"
2053  :properties
2054  (("abstract"
2055    :value "no"))
2056  :icon "ProMoT_models/SignalTransd/TCR/icons/Srckinase.gif"
2057  :geometry-width "405"
2058  :geometry-height "400"
2059  :parameters
2060  (("phosp1.r1_sa"
2061    :value "1.0d0")
2062   ("phosp1.r2_sa"
2063    :value "1.0d0")
2064   ("phosp2.r1_sa"
2065    :value "1.0d0")
2066   ("phosp2.r2_sa"
2067    :value "1.0d0")
2068   ("prod.kprod"
2069    :model-name "srcprodkprod")
2070   ("sumsrca.k1"
2071    :documentation "activity of intermediate"
2072    :value "1.0d0"
2073    :model-name "sumsrcak1su")
2074   ("sumsrca.k2"
2075    :documentation "activity of activ"
2076    :value "1.0d0"
2077    :model-name "sumsrcak2su")
2078   ("sumsrcphosp.k1"
2079    :model-name "sumsrcphosk1su")
2080   ("sumsrcphosp.k2"
2081    :model-name "sumsrcphosk2su"))
2082  :terminals
2083  (("inpcrossl"
2084    :is-eq-to "prod.in2"
2085    :geometry-side "RIGHT"
2086    :geometry-position "0.5375")
2087   ("inpkina"
2088    :is-eq-to "sumsrcphosp.in2"
2089    :geometry-side "RIGHT"
2090    :geometry-position "0.815")
2091   ("inpkind"
2092    :is-eq-to "phosp1.enz2"
2093    :geometry-side "TOP"
2094    :geometry-position "0.4327416")
2095   ("inpphospa"
2096    :is-eq-to "phosp1.enz1"
2097    :geometry-side "RIGHT"
2098    :geometry-position "0.4")
2099   ("inpphospd"
2100    :is-eq-to "phosp2.enz2"
2101    :geometry-side "LEFT"
2102    :geometry-position "0.8525")
2103   ("srcact"
2104    :is-eq-to "adapter_conc.out"
2105    :geometry-side "BOTTOM"
2106    :geometry-position "0.61563516"))
2107  :modules
2108  (("adapter_conc"
2109    :is-a "adapter-conc"
2110    :geometry-x "256"
2111    :geometry-y "338")
2112   ("cf2co"
2113    :is-a "cf2co"
2114    :geometry-x "115"
2115    :geometry-y "264")
2116   ("cf2co0"
2117    :is-a "cf2co"
2118    :geometry-x "101"
2119    :geometry-y "212")
2120   ("phosp1"
2121    :is-a "cyclic_en1_ud"
2122    :geometry-x "181"
2123    :geometry-y "162")
2124   ("phosp2"
2125    :is-a "cyclic_en1_ud"
2126    :geometry-x "181"
2127    :geometry-y "231")
2128   ("prod"
2129    :is-a "prod-2-signal"
2130    :geometry-x "283"
2131    :geometry-y "271")
2132   ("srcmolec"
2133    :is-a "storage-mult-3st"
2134    :geometry-x "72"
2135    :geometry-y "199")
2136   ("srctot"
2137    :is-a "storage-intra-const_c"
2138    :geometry-x "73"
2139    :geometry-y "120")
2140   ("sumsrca"
2141    :is-a "sum-2-signal"
2142    :geometry-x "187"
2143    :geometry-y "344")
2144   ("sumsrcphosp"
2145    :is-a "sum-2-signal"
2146    :geometry-x "260"
2147    :geometry-y "228"))
2148  :links
2149  (("phosp2a_srccf2"
2150    :terminals ("phosp2.a" "srcmolec.cf2" "phosp1.b" "cf2co0.cf")
2151    :nodes (("104" "200"))
2152    :edges (("0" "-1" (("104" "200"))) ("1" "-1" nil) ("2" "-1" nil)
2153            ("3" "-1" nil)))
2154   ("prodout_sumsrcphospin1"
2155    :terminals ("prod.out" "sumsrcphosp.in1"))
2156   ("srccf1_phosp1a"
2157    :terminals ("srcmolec.cf1" "phosp1.a"))
2158   ("srccf3_phosp2b"
2159    :terminals ("srcmolec.cf3" "phosp2.b" "cf2co.cf")
2160    :nodes (("112" "240"))
2161    :edges (("0" "-1" (("112" "248"))) ("1" "-1" nil) ("2" "-1" nil)))
2162   ("srctotco_srccot"
2163    :terminals ("srctot.co" "srcmolec.cot"))
2164   ("sumsrcain1_cf2coco"
2165    :terminals ("sumsrca.in1" "cf2co.co"))
2166   ("sumsrcain2_cf2co0co"
2167    :terminals ("sumsrca.in2" "cf2co0.co"))
2168   ("sumsrcaout_adapter_concin"
2169    :terminals ("sumsrca.out" "adapter_conc.in" "prod.in1")
2170    :nodes (("224" "312"))
2171    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
2172   ("sumsrcphospout_phosp2enz1"
2173    :terminals ("sumsrcphosp.out" "phosp2.enz1"))))
2174
2175(define-module
2176  :class "lck-fyn-pagcsk"
2177  :super-classes ("tcr-prox-events")
2178  :properties
2179  (("abstract"
2180    :value "no"))
2181  :geometry-width "790"
2182  :geometry-height "550"
2183  :parameters
2184  (("cocrossl.k1"
2185    :model-name "recepcocrosslkprod")
2186   ("fyn.srcmolec"
2187    :model-name "fyn")
2188   ("fyn.srctot.c0"
2189    :model-name "fyntot_c0")
2190   ("fyn.sumsrca.c"
2191    :model-name "fynactiv")
2192   ("kindsrconst.c0"
2193    :model-name "kindsrconst_c0")
2194   ("lck.phosp.c0"
2195    :model-name "lckprotphosp_c0")
2196   ("lck.srcmolec"
2197    :model-name "lck")
2198   ("lck.srctot.c0"
2199    :model-name "lcktot_c0")
2200   ("lckacttcr.c"
2201    :model-name "lckacttcr")
2202   ("shp1.activtotal.c0"
2203    :model-name "shp1tot_c0")
2204   ("shp1.phosphatase.c0"
2205    :model-name "shp1deact_c0")
2206   ("sum_kindsrc.k1"
2207    :model-name "sum_kindsrck1su")
2208   ("sum_kindsrc.k2"
2209    :model-name "sum_kindsrck2su"))
2210  :terminals
2211  (("inerk"
2212    :is-eq-to "lck.inerk"
2213    :geometry-side "RIGHT"
2214    :geometry-position "0.5690909")
2215   ("inpcd8cross"
2216    :is-eq-to "aca.in"
2217    :geometry-side "TOP"
2218    :geometry-position "0.3886076")
2219   ("inphospdlck"
2220    :is-eq-to "lck.inphospd"
2221    :geometry-side "LEFT"
2222    :geometry-position "0.82")
2223   ("inppagdephosp"
2224    :is-eq-to "pagcsk.inppagdephosp"
2225    :geometry-side "TOP"
2226    :geometry-position "0.18860759")
2227   ("inpphospafyn"
2228    :is-eq-to "fyn.inpphospa"
2229    :geometry-side "LEFT"
2230    :geometry-position "0.34363636"
2231    :line (("80" "192")))
2232   ("inpphospalck"
2233    :is-eq-to "lck.inpphospa"
2234    :geometry-side "LEFT"
2235    :geometry-position "0.55454546"
2236    :line (("64" "304")))
2237   ("inpphospdfyn"
2238    :is-eq-to "fyn.inpphospd"
2239    :geometry-side "LEFT"
2240    :geometry-position "0.06909091"
2241    :line (("88" "232") ("88" "32")))
2242   ("intcrcross"
2243    :is-eq-to "adapter_conc.in"
2244    :geometry-side "TOP"
2245    :geometry-position "0.77468354")
2246   ("outfyn"
2247    :is-eq-to "adapterfyn.out"
2248    :geometry-side "BOTTOM"
2249    :geometry-position "0.7721519")
2250   ("outlck"
2251    :is-eq-to "adapter_conc0.out"
2252    :geometry-side "BOTTOM"
2253    :geometry-position "0.5037975"))
2254  :modules
2255  (("aca"
2256    :is-a "adapter-conc"
2257    :geometry-x "311"
2258    :geometry-y "63")
2259   ("adapterfyn"
2260    :is-a "adapter-conc"
2261    :geometry-x "605"
2262    :geometry-y "263")
2263   ("adapter_conc"
2264    :is-a "adapter-conc"
2265    :geometry-x "617"
2266    :geometry-y "63")
2267   ("adapter_conc0"
2268    :is-a "adapter-conc"
2269    :geometry-x "435"
2270    :geometry-y "483")
2271   ("cocrossl"
2272    :is-a "prod-2-signal"
2273    :geometry-x "392"
2274    :geometry-y "73")
2275   ("fyn"
2276    :is-a "srccrossl"
2277    :geometry-x "475"
2278    :geometry-y "200")
2279   ("kindsrconst"
2280    :is-a "storage-intra-const_c"
2281    :geometry-x "118"
2282    :geometry-y "179")
2283   ("lck"
2284    :is-a "lck-protec-2"
2285    :geometry-x "247"
2286    :geometry-y "313")
2287   ("lckacttcr"
2288    :is-a "prod-2-signal"
2289    :geometry-x "378"
2290    :geometry-y "423")
2291   ("pagcsk"
2292    :is-a "pagcsk"
2293    :geometry-x "183"
2294    :geometry-y "103")
2295   ("shp1"
2296    :is-a "c2a-en1-bs-prep"
2297    :geometry-x "255"
2298    :geometry-y "464")
2299   ("sum_kindsrc"
2300    :is-a "sum-2-signal"
2301    :geometry-x "164"
2302    :geometry-y "167"))
2303  :links
2304  (("acaout_lck_protec_2cd8crossl"
2305    :terminals ("aca.out" "lck.cd8crossl" "cocrossl.in1")
2306    :nodes (("329" "64"))
2307    :edges (("0" "-1" (("320" "64"))) ("1" "-1" (("328" "352")))
2308            ("2" "-1" nil)))
2309   ("adapter_concout_fyninpcrossl"
2310    :terminals ("adapter_conc.out" "fyn.inpcrossl" "cocrossl.in2")
2311    :nodes (("576" "64"))
2312    :edges (("0" "-1" (("568" "64"))) ("1" "-1" (("576" "208")))
2313            ("2" "-1" nil)))
2314   ("cocrosslout_lckacttcrin2"
2315    :terminals ("cocrossl.out" "lckacttcr.in2"))
2316   ("fynsrcact_pagcskinppagphosp"
2317    :terminals ("fyn.srcact" "pagcsk.inppagphosp" "adapterfyn.in")
2318    :nodes (("488" "264"))
2319    :edges (("0" "-1" (("488" "264")))
2320            ("1" "-1" (("368" "88") ("368" "264"))) ("2" "-1" nil)))
2321   ("kindsrconstco_sum_kindsrkconstin1"
2322    :terminals ("kindsrconst.co" "sum_kindsrc.in1"))
2323   ("lckacttcrout_fyninpkina"
2324    :terminals ("lckacttcr.out" "fyn.inpkina" "adapter_conc0.in")
2325    :nodes (("432" "448"))
2326    :edges (("0" "-1" (("376" "448")))
2327            ("1" "-1" (("528" "376") ("432" "376"))) ("2" "-1" nil)))
2328   ("pagcskcskout_lck_protec_2inpcsk"
2329    :terminals ("lck.inpkind" "fyn.inpkind" "sum_kindsrc.out")
2330    :nodes (("239" "167"))
2331    :edges (("0" "-1" nil)
2332            ("1" "-1" (("464" "136") ("400" "136") ("400" "168")))
2333            ("2" "-1" nil)))
2334   ("shp1input_lck_protec_2outlck"
2335    :terminals ("shp1.input" "lck.outlck" "lckacttcr.in1")
2336    :nodes (("256" "414"))
2337    :edges (("0" "-1" (("256" "402"))) ("1" "-1" nil) ("2" "-1" nil)))
2338   ("shp1output_lck_protec_2inshp"
2339    :terminals ("shp1.output" "lck.inshp")
2340    :edges (("0" "1" (("256" "520") ("192" "520")))))
2341   ("sum_kindsrkconstin2_pagcskcskout"
2342    :terminals ("sum_kindsrc.in2" "pagcsk.cskout"))))
2343
2344(define-module
2345  :class "prodsum-2-signal"
2346  :super-classes ("sum")
2347  :documentation "sums and multiplies 2 concentrations, for e.g. test effect of one of them and/or product of both"
2348  :properties
2349  (("abstract"
2350    :value "no"))
2351  :icon "../libraries/icons/prodsignals.gif"
2352  :terminals
2353  (("in1"
2354    :is-a "term-concentration-in"
2355    :geometry-side "TOP"
2356    :geometry-position "0.1")
2357   ("in2"
2358    :is-a "term-concentration-in"
2359    :geometry-side "TOP"
2360    :geometry-position "0.9")
2361   ("out"
2362    :is-a "term-concentration-out"
2363    :geometry-side "BOTTOM"
2364    :geometry-position "0.5"
2365    :variables
2366    (("c"
2367      :is-eq-to "parent.c"))))
2368  :variables
2369  (("c"
2370    :is-a "var-state-concentration-out"
2371    :documentation "sum of both concentrations"
2372    :report "lumped")
2373   ("k1"
2374    :is-a "var-real-parameter"
2375    :value "1.0d0")
2376   ("k2"
2377    :is-a "var-real-parameter"
2378    :value "1.0d0")
2379   ("kprod"
2380    :is-a "var-real-parameter"
2381    :value "1.0d0"))
2382  :equations
2383  (("hurg"
2384    :relation "c == k1*in1.c+k2*in2.c+kprod*in1.c*in2.c")))
2385
2386(define-module
2387  :class "srccrossl-2"
2388  :super-classes ("srccrossl")
2389  :parameters
2390  (("prod.k1"
2391    :model-name "srcprodk1su")
2392   ("prod.k2"
2393    :model-name "srcprodk2su"))
2394  :modules
2395  (("prod"
2396    :is-a "prodsum-2-signal")))
2397
2398(define-module
2399  :class "lck-protec-2b"
2400  :super-classes ("lck-protec-2")
2401  :modules
2402  (("lckautop"
2403    :is-a "prodsum-2-signal")))
2404
2405(define-module
2406  :class "lck-fyn-pagcsk-2"
2407  :super-classes ("lck-fyn-pagcsk")
2408  :parameters
2409  (("lckacttcr.k1"
2410    :model-name "lckacttcrk1su")
2411   ("lckacttcr.k2"
2412    :model-name "lckacttcrk2su")
2413   ("lckacttcr.kprod"
2414    :model-name "lckacttcrkprod"))
2415  :modules
2416  (("fyn"
2417    :is-a "srccrossl-2")
2418   ("lck"
2419    :is-a "lck-protec-2b")
2420   ("lckacttcr"
2421    :is-a "prodsum-2-signal")))
2422
2423(define-module
2424  :class "tcr-prox-events-4-lckout"
2425  :super-classes ("tcr-prox-events")
2426  :documentation "output for lck and lck-fyn-pagcsk is lck-fyn-pagcsk-2, with prodsums"
2427  :properties
2428  (("abstract"
2429    :value "no"))
2430  :icon "ProMoT_models/SignalTransd/TCR/icons/proxevents.gif"
2431  :geometry-width "777"
2432  :geometry-height "513"
2433  :parameters
2434  (("phospa_fyn.phospdconst.c0"
2435    :model-name "phospa_fyn_phospdconst_c0")
2436   ("phospa_fyn.phospdcrossldep.activtotal.c0"
2437    :model-name "phospa_fyn_ph_c0")
2438   ("phospa_fyn.phospdcrossldep.phosphatase.c0"
2439    :model-name "phospa_fyn_deact_c0")
2440   ("phospa_lck.phospdconst.c0"
2441    :model-name "phospa_lck_phospdconst_c0")
2442   ("phospa_lck.phospdcrossldep.activtotal.c0"
2443    :model-name "phospa_lck_ph_c0")
2444   ("phospa_lck.phospdcrossldep.phosphatase.c0"
2445    :model-name "phospa_lck_deact_c0")
2446   ("phospa_pagcsk.phospdconst.c0"
2447    :model-name "phospa_pagcsk_phospdconst_c0")
2448   ("phospdsrc.c0"
2449    :model-name "phospdsrc_c0")
2450   ("phospd_pagcsk.phospdconst.c0"
2451    :model-name "phospa_pagcsk_phcons_c0")
2452   ("phospd_pagcsk.phospdcrossldep.activtotal.c0"
2453    :model-name "phospa_pagcsk_phdep_c0")
2454   ("phospd_pagcsk.phospdcrossldep.phosphatase.c0"
2455    :model-name "phospa_pagcsk_deact_c0")
2456   ("sumsrckin.k1"
2457    :model-name "sumsrckink1su")
2458   ("sumsrckin.k2"
2459    :model-name "sumsrckink2su"))
2460  :terminals
2461  (("inerk"
2462    :is-eq-to "lck_fyn_pagcsk.inerk"
2463    :geometry-side "RIGHT"
2464    :geometry-position "0.4659091")
2465   ("outlck"
2466    :is-eq-to "adapter_conc.out"
2467    :geometry-side "RIGHT"
2468    :geometry-position "0.7368421")
2469   ("zapout"
2470    :is-eq-to "tcrcd8zap_2.zapout"
2471    :geometry-side "BOTTOM"
2472    :geometry-position "0.081571"))
2473  :modules
2474  (("adapter_conc"
2475    :is-a "adapter-conc"
2476    :geometry-x "646"
2477    :geometry-y "377")
2478   ("lck_fyn_pagcsk"
2479    :is-a "lck-fyn-pagcsk-2"
2480    :geometry-x "512"
2481    :geometry-y "263")
2482   ("phospa_fyn"
2483    :is-a "phospd-crossldepandindep"
2484    :geometry-x "304"
2485    :geometry-y "223")
2486   ("phospa_lck"
2487    :is-a "phospd-crossldepandindep"
2488    :geometry-x "304"
2489    :geometry-y "279")
2490   ("phospdsrc"
2491    :is-a "storage-intra-const_c"
2492    :geometry-x "372"
2493    :geometry-y "431")
2494   ("phospd_pagcsk"
2495    :is-a "phospd-crossldepandindep"
2496    :geometry-x "303"
2497    :geometry-y "168")
2498   ("sumsrckin"
2499    :is-a "sum-2-signal"
2500    :geometry-x "524"
2501    :geometry-y "340")
2502   ("tcrcd8zap_2"
2503    :is-a "tcrcd8zap-2"
2504    :geometry-x "99"
2505    :geometry-y "209"))
2506  :links
2507  (("lck_fyn_pagcskinpcd8cross_tcrcd8zap_2outcd8crossl"
2508    :terminals ("lck_fyn_pagcsk.inpcd8cross" "tcrcd8zap_2.outcd8crossl")
2509    :edges (("0" "1" (("496" "192")))))
2510   ("lck_fyn_pagcskinppagdephosp_phospd_pagcskoutphospd"
2511    :terminals ("lck_fyn_pagcsk.inppagdephosp"
2512                "phospd_pagcsk.outphospd"))
2513   ("lck_fyn_pagcskinpphospalck_phospa_lckoutphospd"
2514    :terminals ("lck_fyn_pagcsk.inpphospalck" "phospa_lck.outphospd"))
2515   ("phospa_fynoutphospa_lck_fyn_pagcskinpphospafyn"
2516    :terminals ("phospa_fyn.outphospd" "lck_fyn_pagcsk.inpphospafyn"))
2517   ("phospdsrcco_lck_fyn_pagcskinphospdlck"
2518    :terminals ("phospdsrc.co" "lck_fyn_pagcsk.inphospdlck"
2519                "lck_fyn_pagcsk.inpphospdfyn")
2520    :nodes (("368" "435"))
2521    :edges (("0" "-1" (("368" "435"))) ("1" "-1" (("368" "296")))
2522            ("2" "-1" (("368" "216")))))
2523   ("sumsrckinin1_lck_fyn_pagcskoutlck"
2524    :terminals ("sumsrckin.in1" "lck_fyn_pagcsk.outlck"
2525                "adapter_conc.in")
2526    :nodes (("512" "313"))
2527    :edges (("0" "-1" (("512" "320"))) ("1" "-1" nil) ("2" "-1" nil)))
2528   ("sumsrckinin2_lck_fyn_pagcskoutfyn"
2529    :terminals ("sumsrckin.in2" "lck_fyn_pagcsk.outfyn"))
2530   ("sumsrckinout_tcrcd8zap_2inpsrckinact"
2531    :terminals ("sumsrckin.out" "tcrcd8zap_2.inpsrckinact")
2532    :edges (("0" "1" (("528" "360") ("224" "360") ("224" "256")))))
2533   ("tcrcd8zap_2outtcrcossl_lck_fyn_pagcskintcrcross"
2534    :terminals ("tcrcd8zap_2.outtcrcossl" "lck_fyn_pagcsk.intcrcross"
2535                "phospd_pagcsk.inpcrossl" "phospa_fyn.inpcrossl"
2536                "phospa_lck.inpcrossl")
2537    :nodes (("240" "136"))
2538    :edges (("0" "-1" (("112" "304") ("240" "304")))
2539            ("1" "-1" (("552" "136"))) ("2" "-1" nil)
2540            ("3" "-1" (("240" "224"))) ("4" "-1" (("240" "280")))))))
2541
2542(define-module
2543  :class "conc-sink"
2544  :super-classes ("help" "storage")
2545  :properties
2546  (("abstract"
2547    :value "no"))
2548  :icon "icons/storage_sink.gif"
2549  :terminals
2550  (("co"
2551    :is-a "term-concentration-in"
2552    :geometry-side "top"
2553    :geometry-position "0.5")))
2554
2555(define-module
2556  :class "export-proxevents"
2557  :super-classes ("tcr-prox-events")
2558  :documentation "class to create a model of only the prox-events"
2559  :properties
2560  (("abstract"
2561    :value "no"))
2562  :geometry-width "362"
2563  :geometry-height "446"
2564  :modules
2565  (("erkin"
2566    :is-a "storage-intra-const_c"
2567    :geometry-x "312"
2568    :geometry-y "228")
2569   ("lckout"
2570    :is-a "conc-sink"
2571    :geometry-x "260"
2572    :geometry-y "301")
2573   ("proxevents"
2574    :is-a "tcr-prox-events-4-lckout"
2575    :geometry-x "152"
2576    :geometry-y "249")
2577   ("zapout"
2578    :is-a "conc-sink"
2579    :geometry-x "44"
2580    :geometry-y "368"))
2581  :links
2582  (("lckoutco_proxeventsoutlck"
2583    :terminals ("lckout.co" "proxevents.outlck"))
2584   ("proxeventsinerk_erkinco"
2585    :terminals ("proxevents.inerk" "erkin.co"))
2586   ("zapoutco_proxeventszapout"
2587    :terminals ("zapout.co" "proxevents.zapout"))))
2588