source: Promot/trunk/promot/kb/testsuite/mdl/teusink.mdl

Last change on this file was 9135, checked in by rempel, 15 years ago

model comparison with explorer + test models
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1(define-module
2  :class "library"
3  :super-classes ("module")
4  :documentation "Superclass for all library elements.")
5
6
7(define-module
8  :class "sbml-rules"
9  :super-classes ("module")
10  :documentation "Rules for SBML models.")
11
12
13(define-variable
14  :class "var-rate"
15  :super-classes ("variable")
16  :value "100.0d0"
17  :minimum "0.0d0"
18  :maximum "100000.0d0"
19  :unit "1/h")
20
21
22(define-variable
23  :class "concentration"
24  :super-classes ("variable")
25  :unit "mol/l")
26
27
28(define-variable
29  :class "molar-flux"
30  :super-classes ("variable")
31  :minimum "0.0d0"
32  :maximum "1000.0d0"
33  :unit "mol/s")
34
35
36(define-variable
37  :class "mass"
38  :super-classes ("variable")
39  :minimum "0.0d0"
40  :maximum "10000.0d0"
41  :unit "mol")
42
43
44(define-variable
45  :class "scaling-parameter"
46  :super-classes ("variable")
47  :documentation "parameter to perform manual numeric scaling of rate-laws
48  etc. for optimization. It is marked as a help-variable to eventually
49remove it by the equation-optimizer in Promot."
50  :system-theoretic "help"
51  :value "1.0d0")
52
53
54(define-variable
55  :class "kinetic-parameter"
56  :super-classes ("variable")
57  :system-theoretic "real-parameter")
58
59
60(define-variable
61  :class "stoichiometry"
62  :super-classes ("variable")
63  :documentation "Don't know what is the best solution, but these parameters
64  should not be changed by the user during simulation, therefore I consider them
65  as helps, which means they can be optimized away."
66  :system-theoretic "help"
67  :value "1.0d0"
68  :unit "1")
69
70
71(define-variable
72  :class "sbml-parameter"
73  :super-classes ("variable")
74  :documentation "`Parameters' (can be real-parameters, helps, states  read from sbml-files")
75
76
77(define-variable
78  :class "volume"
79  :super-classes ("variable")
80  :minimum "0.0d0"
81  :maximum "10.0d0"
82  :unit "l")
83
84
85(define-variable
86  :class "var-output"
87  :super-classes ("variable")
88  :system-theoretic "output")
89
90
91(define-module
92  :class "sbml-model"
93  :super-classes ("module"))
94
95
96(define-variable
97  :class "var-input"
98  :super-classes ("variable")
99  :system-theoretic "input")
100
101
102(define-terminal
103  :class "tsig"
104  :super-classes ("terminal")
105  :icon "icons/term_concentration_in.gif"
106  :link-color "green"
107  :variables
108  (("c"
109    :is-a "concentration"
110    :system-theoretic "state"
111    :value "0.0d0")))
112
113
114(define-module
115  :class "teusink2000_glycolysis-rules"
116  :super-classes ("sbml-rules")
117  :geometry-width "585"
118  :geometry-height "200"
119  :terminals
120  (("t_adp"
121    :is-a "tsig"
122    :geometry-side "top"
123    :geometry-position "0.5")
124   ("t_amp"
125    :is-a "tsig"
126    :geometry-side "top"
127    :geometry-position "0.8333333")
128   ("t_atp"
129    :is-a "tsig"
130    :geometry-side "top"
131    :geometry-position "0.6666667")
132   ("t_p"
133    :is-a "tsig"
134    :geometry-side "top"
135    :geometry-position "0.33333334")
136   ("t_sum_p"
137    :is-a "tsig"
138    :geometry-side "top"
139    :geometry-position "0.16666667"))
140  :equations
141  (("adp"
142    :relation "0.0d0 == t_adp.c-(t_sum_p.c-(t_p.c ^ 2*(1-4*root.keqak)+2*t_sum_p.c*t_p.c*(4*root.keqak+-1)+t_sum_p.c ^ 2) ^ 0.5d0)/(1-4*root.keqak)")
143   ("amp"
144    :relation "0.0d0 == t_amp.c-t_sum_p.c+t_atp.c+t_adp.c")
145   ("atp"
146    :relation "0.0d0 == t_atp.c-(t_p.c-t_adp.c)/2")))
147
148
149(define-module
150  :class "compartment"
151  :super-classes ("module")
152  :variables
153  (("v"
154    :is-a "volume"
155    :system-theoretic "real-parameter"
156    :value "1.0d0")))
157
158
159(define-module
160  :class "reaction"
161  :super-classes ("library")
162  :documentation "Superclass containing all reaction definitions.")
163
164
165(define-module
166  :class "structure"
167  :super-classes ("reaction")
168  :documentation "Superclass containing all possible reaction structures."
169  :variables
170  (("r")))
171
172
173(define-terminal
174  :class "tflux"
175  :super-classes ("tsig")
176  :icon "icons/term_react_blue.gif"
177  :link-color "blue"
178  :variables
179  (("r"
180    :is-a "molar-flux"
181    :system-theoretic "state"
182    :positive-vector-direction "out"
183    :value "0.0d0")))
184
185
186(define-module
187  :class "s-1-1"
188  :super-classes ("structure")
189  :terminals
190  (("t_p1"
191    :is-a "tflux"
192    :geometry-side "right"
193    :geometry-position "0.5")
194   ("t_r1"
195    :is-a "tflux"
196    :geometry-side "left"
197    :geometry-position "0.5"))
198  :variables
199  (("gamma_p1"
200    :is-a "stoichiometry"
201    :value "1.0d0")
202   ("gamma_r1"
203    :is-a "stoichiometry"
204    :value "-1.0d0"))
205  :equations
206  (("e_p1"
207    :relation "t_p1.r == gamma_p1*r")
208   ("e_r1"
209    :relation "t_r1.r == gamma_r1*r")))
210
211
212(define-variable
213  :class "reaction-rate"
214  :super-classes ("molar-flux")
215  :unit "mol/s")
216
217
218(define-module
219  :class "kinetics"
220  :super-classes ("reaction")
221  :documentation "Superclass containing all kinetics."
222  :variables
223  (("r"
224    :is-a "reaction-rate"
225    :documentation "reaction-rate"
226    :system-theoretic "help"
227    :report "lumped"
228    :unit "umol/g_dw/h")
229   ("skal"
230    :is-a "scaling-parameter")))
231
232
233(define-module
234  :class "kin-1-1_0_tglco_keqglt_kmgltglci34f"
235  :super-classes ("s-1-1" "kinetics")
236  :icon "icons/rev_l"
237  :variables
238  (("keqglt"
239    :is-a "kinetic-parameter")
240   ("kmgltglci"
241    :is-a "kinetic-parameter")
242   ("kmgltglco"
243    :is-a "kinetic-parameter")
244   ("vmglt"
245    :is-a "kinetic-parameter")))
246
247
248(define-module
249  :class "storage"
250  :super-classes ("library")
251  :documentation "Superclass for species in the network.")
252
253
254(define-module
255  :class "species"
256  :super-classes ("storage")
257  :documentation "Constant species"
258  :icon "icons/species"
259  :parameters
260  (("cf.r"
261    :positive-vector-direction "in"
262    :value "0.0d0"))
263  :terminals
264  (("cf"
265    :is-a "tflux"
266    :variables
267    (("c"
268      :is-eq-to "parent.c"))))
269  :variables
270  (("c"
271    :is-a "concentration"
272    :system-theoretic "help"
273    :report "lumped"
274    :value "n/v")
275   ("n"
276    :is-a "mass"
277    :system-theoretic "real-parameter")
278   ("v"
279    :is-eq-to "parent.v")))
280
281
282(define-module
283  :class "dyn-adapter"
284  :super-classes ("library")
285  :documentation "Superclass containing adapters. Useful for instance for propagating terminals already connected to other elements.")
286
287
288(define-variable
289  :class "var-rate-out"
290  :super-classes ("var-rate" "var-output")
291  :absolute-error "1.0d-8")
292
293
294(define-variable
295  :class "var-concentration"
296  :super-classes ("concentration")
297  :value "1.0d-4"
298  :minimum "0.0d0"
299  :maximum "10.0d0")
300
301
302(define-variable
303  :class "var-concentration-out"
304  :super-classes ("var-concentration" "var-output")
305  :absolute-error "1.0d-8")
306
307
308(define-variable
309  :class "var-state-concentration-out"
310  :super-classes ("var-concentration-out")
311  :system-theoretic "output")
312
313
314(define-variable
315  :class "var-rate-in"
316  :super-classes ("var-rate" "var-input")
317  :absolute-error "1.0d-8")
318
319
320(define-terminal
321  :class "term-storage-flux"
322  :super-classes ("terminal")
323  :documentation "Terminal for a flux in a storage."
324  :icon "icons/term_stor_blue.gif"
325  :link-color "blue"
326  :variables
327  (("c"
328    :is-a "var-concentration-out")
329   ("r"
330    :is-a "var-rate-in"
331    :positive-vector-direction "in"
332    :unit "umol/g_dw/h")))
333
334
335(define-variable
336  :class "var-concentration-in"
337  :super-classes ("var-concentration" "var-input")
338  :absolute-error "1.0d-8")
339
340
341(define-terminal
342  :class "term-reaction-flux"
343  :super-classes ("terminal")
344  :documentation "Terminal for a flux in a reaction."
345  :icon "icons/term_react_blue.gif"
346  :link-color "blue"
347  :variables
348  (("c"
349    :is-a "var-concentration-in"
350    :unit "umol/g_dw")
351   ("r"
352    :is-a "var-rate-out"
353    :positive-vector-direction "out"
354    :unit "umol/g_dw/h")))
355
356
357(define-module
358  :class "adapter-flux"
359  :super-classes ("dyn-adapter")
360  :documentation "Flux -> Flux"
361  :properties
362  (("abstract"
363    :value "no"))
364  :icon "icons/adapter.gif"
365  :terminals
366  (("in"
367    :is-a "term-reaction-flux"
368    :geometry-side "LEFT"
369    :geometry-position "0.47333333"
370    :variables
371    (("r"
372      :is-eq-to "parent.r")))
373   ("out"
374    :is-a "term-storage-flux"
375    :geometry-side "RIGHT"
376    :geometry-position "0.47333333"
377    :variables
378    (("c"
379      :is-eq-to "parent.c"))))
380  :variables
381  (("c"
382    :is-a "var-state-concentration-out")
383   ("r"
384    :is-a "var-rate-out"
385    :positive-vector-direction "out"
386    :value "0.0d0"))
387  :equations
388  (("hurg"
389    :relation "c == in.c")
390   ("rate"
391    :relation "r == out.r")))
392
393
394(define-module
395  :class "s-2-1"
396  :super-classes ("structure")
397  :terminals
398  (("t_p1"
399    :is-a "tflux"
400    :geometry-side "right"
401    :geometry-position "0.5")
402   ("t_r1"
403    :is-a "tflux"
404    :geometry-side "left"
405    :geometry-position "0.33333334")
406   ("t_r2"
407    :is-a "tflux"
408    :geometry-side "left"
409    :geometry-position "0.6666667"))
410  :variables
411  (("gamma_p1"
412    :is-a "stoichiometry"
413    :value "1.0d0")
414   ("gamma_r1"
415    :is-a "stoichiometry"
416    :value "-1.0d0")
417   ("gamma_r2"
418    :is-a "stoichiometry"
419    :value "-1.0d0"))
420  :equations
421  (("e_p1"
422    :relation "t_p1.r == gamma_p1*r")
423   ("e_r1"
424    :relation "t_r1.r == gamma_r1*r")
425   ("e_r2"
426    :relation "t_r2.r == gamma_r2*r")))
427
428
429(define-terminal
430  :class "tvol"
431  :super-classes ("terminal")
432  :link-color "yellow"
433  :variables
434  (("v"
435    :is-a "volume"
436    :system-theoretic "state")))
437
438
439(define-module
440  :class "kin-2-1_0_1_ktrehalose"
441  :super-classes ("s-2-1" "kinetics")
442  :icon "icons/irrev_r"
443  :terminals
444  (("t_c1"
445    :is-a "tvol"
446    :geometry-side "bottom"
447    :geometry-position "0.5"))
448  :variables
449  (("ktrehalose"
450    :is-a "kinetic-parameter")))
451
452
453(define-module
454  :class "s-3-2"
455  :super-classes ("structure")
456  :terminals
457  (("t_p1"
458    :is-a "tflux"
459    :geometry-side "right"
460    :geometry-position "0.33333334")
461   ("t_p2"
462    :is-a "tflux"
463    :geometry-side "right"
464    :geometry-position "0.6666667")
465   ("t_r1"
466    :is-a "tflux"
467    :geometry-side "left"
468    :geometry-position "0.25")
469   ("t_r2"
470    :is-a "tflux"
471    :geometry-side "left"
472    :geometry-position "0.5")
473   ("t_r3"
474    :is-a "tflux"
475    :geometry-side "left"
476    :geometry-position "0.75"))
477  :variables
478  (("gamma_p1"
479    :is-a "stoichiometry"
480    :value "1.0d0")
481   ("gamma_p2"
482    :is-a "stoichiometry"
483    :value "1.0d0")
484   ("gamma_r1"
485    :is-a "stoichiometry"
486    :value "-1.0d0")
487   ("gamma_r2"
488    :is-a "stoichiometry"
489    :value "-1.0d0")
490   ("gamma_r3"
491    :is-a "stoichiometry"
492    :value "-1.0d0"))
493  :equations
494  (("e_p1"
495    :relation "t_p1.r == gamma_p1*r")
496   ("e_p2"
497    :relation "t_p2.r == gamma_p2*r")
498   ("e_r1"
499    :relation "t_r1.r == gamma_r1*r")
500   ("e_r2"
501    :relation "t_r2.r == gamma_r2*r")
502   ("e_r3"
503    :relation "t_r3.r == gamma_r3*r")))
504
505
506(define-module
507  :class "kin-3-2_0_1_ksucc"
508  :super-classes ("s-3-2" "kinetics")
509  :icon "icons/irrev_r"
510  :terminals
511  (("t_c1"
512    :is-a "tvol"
513    :geometry-side "bottom"
514    :geometry-position "0.5"))
515  :variables
516  (("ksucc"
517    :is-a "kinetic-parameter")))
518
519
520(define-module
521  :class "s-1-2"
522  :super-classes ("structure")
523  :terminals
524  (("t_p1"
525    :is-a "tflux"
526    :geometry-side "right"
527    :geometry-position "0.33333334")
528   ("t_p2"
529    :is-a "tflux"
530    :geometry-side "right"
531    :geometry-position "0.6666667")
532   ("t_r1"
533    :is-a "tflux"
534    :geometry-side "left"
535    :geometry-position "0.5"))
536  :variables
537  (("gamma_p1"
538    :is-a "stoichiometry"
539    :value "1.0d0")
540   ("gamma_p2"
541    :is-a "stoichiometry"
542    :value "1.0d0")
543   ("gamma_r1"
544    :is-a "stoichiometry"
545    :value "-1.0d0"))
546  :equations
547  (("e_p1"
548    :relation "t_p1.r == gamma_p1*r")
549   ("e_p2"
550    :relation "t_p2.r == gamma_p2*r")
551   ("e_r1"
552    :relation "t_r1.r == gamma_r1*r")))
553
554
555(define-module
556  :class "kin-1-2_2_1_kpep_kmpykadp_keqpyk_kmpykpyr_kmpykatpos3"
557  :super-classes ("s-1-2" "kinetics")
558  :icon "icons/rev_l"
559  :terminals
560  (("t_c1"
561    :is-a "tvol"
562    :geometry-side "bottom"
563    :geometry-position "0.5")
564   ("t_m1"
565    :is-a "tsig"
566    :geometry-side "top"
567    :geometry-position "0.33333334")
568   ("t_m2"
569    :is-a "tsig"
570    :geometry-side "top"
571    :geometry-position "0.6666667"))
572  :variables
573  (("keqpyk"
574    :is-a "kinetic-parameter")
575   ("kmpykadp"
576    :is-a "kinetic-parameter")
577   ("kmpykatp"
578    :is-a "kinetic-parameter")
579   ("kmpykpep"
580    :is-a "kinetic-parameter")
581   ("kmpykpyr"
582    :is-a "kinetic-parameter")
583   ("vmpyk"
584    :is-a "kinetic-parameter")))
585
586
587(define-module
588  :class "kin-1-1_0_1_mp3g_keqpgm_kmpgmp2g6me"
589  :super-classes ("s-1-1" "kinetics")
590  :icon "icons/rev_l"
591  :terminals
592  (("t_c1"
593    :is-a "tvol"
594    :geometry-side "bottom"
595    :geometry-position "0.5"))
596  :variables
597  (("keqpgm"
598    :is-a "kinetic-parameter")
599   ("kmpgmp2g"
600    :is-a "kinetic-parameter")
601   ("kmpgmp3g"
602    :is-a "kinetic-parameter")
603   ("vmpgm"
604    :is-a "kinetic-parameter")))
605
606
607(define-module
608  :class "kin-1-2_2_1_kp3g_kmpgkatp_keqpgk_kmpgkbpg_kmpgkadp7d8"
609  :super-classes ("s-1-2" "kinetics")
610  :icon "icons/rev_l"
611  :terminals
612  (("t_c1"
613    :is-a "tvol"
614    :geometry-side "bottom"
615    :geometry-position "0.5")
616   ("t_m1"
617    :is-a "tsig"
618    :geometry-side "top"
619    :geometry-position "0.33333334")
620   ("t_m2"
621    :is-a "tsig"
622    :geometry-side "top"
623    :geometry-position "0.6666667"))
624  :variables
625  (("keqpgk"
626    :is-a "kinetic-parameter")
627   ("kmpgkadp"
628    :is-a "kinetic-parameter")
629   ("kmpgkatp"
630    :is-a "kinetic-parameter")
631   ("kmpgkbpg"
632    :is-a "kinetic-parameter")
633   ("kmpgkp3g"
634    :is-a "kinetic-parameter")
635   ("vmpgk"
636    :is-a "kinetic-parameter")))
637
638
639(define-module
640  :class "kin-1-1_0_1_pgig6p_2_keqpgi_2_kmpgif6p_213yw"
641  :super-classes ("s-1-1" "kinetics")
642  :icon "icons/rev_l"
643  :terminals
644  (("t_c1"
645    :is-a "tvol"
646    :geometry-side "bottom"
647    :geometry-position "0.5"))
648  :variables
649  (("keqpgi_2"
650    :is-a "kinetic-parameter")
651   ("kmpgif6p_2"
652    :is-a "kinetic-parameter")
653   ("kmpgig6p_2"
654    :is-a "kinetic-parameter")
655   ("vmpgi_2"
656    :is-a "kinetic-parameter")))
657
658
659(define-module
660  :class "kin-2-1_3_1_vmpfk"
661  :super-classes ("s-2-1" "kinetics")
662  :icon "icons/irrev_r"
663  :terminals
664  (("t_c1"
665    :is-a "tvol"
666    :geometry-side "bottom"
667    :geometry-position "0.5")
668   ("t_m1"
669    :is-a "tsig"
670    :geometry-side "top"
671    :geometry-position "0.25")
672   ("t_m2"
673    :is-a "tsig"
674    :geometry-side "top"
675    :geometry-position "0.5")
676   ("t_m3"
677    :is-a "tsig"
678    :geometry-side "top"
679    :geometry-position "0.75"))
680  :variables
681  (("vmpfk"
682    :is-a "kinetic-parameter")))
683
684
685(define-module
686  :class "kin-1-2_0_1_vmpdc_npdc_kmpdcpyr"
687  :super-classes ("s-1-2" "kinetics")
688  :icon "icons/irrev_r"
689  :terminals
690  (("t_c1"
691    :is-a "tvol"
692    :geometry-side "bottom"
693    :geometry-position "0.5"))
694  :variables
695  (("kmpdcpyr"
696    :is-a "kinetic-parameter")
697   ("npdc"
698    :is-a "kinetic-parameter")
699   ("vmpdc"
700    :is-a "kinetic-parameter")))
701
702
703(define-module
704  :class "kin-2-1_0_1_kglycogen_3"
705  :super-classes ("s-2-1" "kinetics")
706  :icon "icons/irrev_r"
707  :terminals
708  (("t_c1"
709    :is-a "tvol"
710    :geometry-side "bottom"
711    :geometry-position "0.5"))
712  :variables
713  (("kglycogen_3"
714    :is-a "kinetic-parameter")))
715
716
717(define-module
718  :class "kin-2-1_2_1_kglci_kmglkatp_keqglk_kmglkg6p_kmglkadpuxj"
719  :super-classes ("s-2-1" "kinetics")
720  :icon "icons/rev_l"
721  :terminals
722  (("t_c1"
723    :is-a "tvol"
724    :geometry-side "bottom"
725    :geometry-position "0.5")
726   ("t_m1"
727    :is-a "tsig"
728    :geometry-side "top"
729    :geometry-position "0.33333334")
730   ("t_m2"
731    :is-a "tsig"
732    :geometry-side "top"
733    :geometry-position "0.6666667"))
734  :variables
735  (("keqglk"
736    :is-a "kinetic-parameter")
737   ("kmglkadp"
738    :is-a "kinetic-parameter")
739   ("kmglkatp"
740    :is-a "kinetic-parameter")
741   ("kmglkg6p"
742    :is-a "kinetic-parameter")
743   ("kmglkglci"
744    :is-a "kinetic-parameter")
745   ("vmglk"
746    :is-a "kinetic-parameter")))
747
748
749(define-module
750  :class "s-2-2"
751  :super-classes ("structure")
752  :terminals
753  (("t_p1"
754    :is-a "tflux"
755    :geometry-side "right"
756    :geometry-position "0.33333334")
757   ("t_p2"
758    :is-a "tflux"
759    :geometry-side "right"
760    :geometry-position "0.6666667")
761   ("t_r1"
762    :is-a "tflux"
763    :geometry-side "left"
764    :geometry-position "0.33333334")
765   ("t_r2"
766    :is-a "tflux"
767    :geometry-side "left"
768    :geometry-position "0.6666667"))
769  :variables
770  (("gamma_p1"
771    :is-a "stoichiometry"
772    :value "1.0d0")
773   ("gamma_p2"
774    :is-a "stoichiometry"
775    :value "1.0d0")
776   ("gamma_r1"
777    :is-a "stoichiometry"
778    :value "-1.0d0")
779   ("gamma_r2"
780    :is-a "stoichiometry"
781    :value "-1.0d0"))
782  :equations
783  (("e_p1"
784    :relation "t_p1.r == gamma_p1*r")
785   ("e_p2"
786    :relation "t_p2.r == gamma_p2*r")
787   ("e_r1"
788    :relation "t_r1.r == gamma_r1*r")
789   ("e_r2"
790    :relation "t_r2.r == gamma_r2*r")))
791
792
793(define-module
794  :class "kin-2-2_0_1_mgapdhgap_kmgapdhnad_vmgapdhr_kmgapdhbpg_kmgapdhnadh1e35"
795  :super-classes ("s-2-2" "kinetics")
796  :icon "icons/rev_l"
797  :terminals
798  (("t_c1"
799    :is-a "tvol"
800    :geometry-side "bottom"
801    :geometry-position "0.5"))
802  :variables
803  (("kmgapdhbpg"
804    :is-a "kinetic-parameter")
805   ("kmgapdhgap"
806    :is-a "kinetic-parameter")
807   ("kmgapdhnad"
808    :is-a "kinetic-parameter")
809   ("kmgapdhnadh"
810    :is-a "kinetic-parameter")
811   ("vmgapdhf"
812    :is-a "kinetic-parameter")
813   ("vmgapdhr"
814    :is-a "kinetic-parameter")))
815
816
817(define-module
818  :class "kin-2-2_0_1_g3pdhdhap_kmg3pdhnadh_keqg3pdh_kmg3pdhgly_kmg3pdhnad15uq"
819  :super-classes ("s-2-2" "kinetics")
820  :icon "icons/irrev_r"
821  :terminals
822  (("t_c1"
823    :is-a "tvol"
824    :geometry-side "bottom"
825    :geometry-position "0.5"))
826  :variables
827  (("keqg3pdh"
828    :is-a "kinetic-parameter")
829   ("kmg3pdhdhap"
830    :is-a "kinetic-parameter")
831   ("kmg3pdhgly"
832    :is-a "kinetic-parameter")
833   ("kmg3pdhnad"
834    :is-a "kinetic-parameter")
835   ("kmg3pdhnadh"
836    :is-a "kinetic-parameter")
837   ("vmg3pdh"
838    :is-a "kinetic-parameter")))
839
840
841(define-module
842  :class "kin-1-1_0_1_op2g_keqeno_kmenopep1e60"
843  :super-classes ("s-1-1" "kinetics")
844  :icon "icons/rev_l"
845  :terminals
846  (("t_c1"
847    :is-a "tvol"
848    :geometry-side "bottom"
849    :geometry-position "0.5"))
850  :variables
851  (("keqeno"
852    :is-a "kinetic-parameter")
853   ("kmenop2g"
854    :is-a "kinetic-parameter")
855   ("kmenopep"
856    :is-a "kinetic-parameter")
857   ("vmeno"
858    :is-a "kinetic-parameter")))
859
860
861(define-module
862  :class "s-1-_"
863  :super-classes ("structure")
864  :terminals
865  (("t_r1"
866    :is-a "tflux"
867    :geometry-side "left"
868    :geometry-position "0.5"))
869  :variables
870  (("gamma_r1"
871    :is-a "stoichiometry"
872    :value "-1.0d0"))
873  :equations
874  (("e_r1"
875    :relation "t_r1.r == gamma_r1*r")))
876
877
878(define-module
879  :class "kin-1-__1_1_katpase"
880  :super-classes ("s-1-_" "kinetics")
881  :icon "icons/rev_l"
882  :terminals
883  (("t_c1"
884    :is-a "tvol"
885    :geometry-side "bottom"
886    :geometry-position "0.5")
887   ("t_m1"
888    :is-a "tsig"
889    :geometry-side "top"
890    :geometry-position "0.5"))
891  :variables
892  (("katpase"
893    :is-a "kinetic-parameter")))
894
895
896(define-module
897  :class "kin-1-1_0_1_df16p_keqald_kmaldgap_kmalddhap_kmaldgapideg"
898  :super-classes ("s-1-1" "kinetics")
899  :icon "icons/rev_l"
900  :terminals
901  (("t_c1"
902    :is-a "tvol"
903    :geometry-side "bottom"
904    :geometry-position "0.5"))
905  :variables
906  (("keqald"
907    :is-a "kinetic-parameter")
908   ("kmalddhap"
909    :is-a "kinetic-parameter")
910   ("kmaldf16p"
911    :is-a "kinetic-parameter")
912   ("kmaldgap"
913    :is-a "kinetic-parameter")
914   ("kmaldgapi"
915    :is-a "kinetic-parameter")
916   ("vmald"
917    :is-a "kinetic-parameter")))
918
919
920(define-module
921  :class "kin-2-2_0_1_hnad_kmadhetoh_keqadh_kmadhnad_kmadhnadh_kiadhnadh_kmadhace_kiadhace_kiadhetohcon"
922  :super-classes ("s-2-2" "kinetics")
923  :icon "icons/rev_l"
924  :terminals
925  (("t_c1"
926    :is-a "tvol"
927    :geometry-side "bottom"
928    :geometry-position "0.5"))
929  :variables
930  (("keqadh"
931    :is-a "kinetic-parameter")
932   ("kiadhace"
933    :is-a "kinetic-parameter")
934   ("kiadhetoh"
935    :is-a "kinetic-parameter")
936   ("kiadhnad"
937    :is-a "kinetic-parameter")
938   ("kiadhnadh"
939    :is-a "kinetic-parameter")
940   ("kmadhace"
941    :is-a "kinetic-parameter")
942   ("kmadhetoh"
943    :is-a "kinetic-parameter")
944   ("kmadhnad"
945    :is-a "kinetic-parameter")
946   ("kmadhnadh"
947    :is-a "kinetic-parameter")
948   ("vmadh"
949    :is-a "kinetic-parameter")))
950
951
952(define-module
953  :class "adapter-vol"
954  :super-classes ("dyn-adapter"))
955
956
957(define-module
958  :class "adapter-volume-pop"
959  :super-classes ("adapter-vol")
960  :parent-type "compartment"
961  :documentation "exports one tvol as volume out of parent"
962  :properties
963  (("abstract"
964    :value "no"))
965  :icon "icons/adapter.gif"
966  :terminals
967  (("out"
968    :is-a "tvol"
969    :geometry-side "RIGHT"
970    :variables
971    (("v"
972      :is-eq-to "parent.v"))))
973  :variables
974  (("v"
975    :is-eq-to "parent.v")))
976
977
978(define-module
979  :class "help"
980  :super-classes ("library")
981  :documentation "Superclass containing accessories for making basic operations on signals or converting terminals.")
982
983
984(define-module
985  :class "term-conv"
986  :super-classes ("help")
987  :documentation "Superclass containing elements for converting different terminal types.")
988
989
990(define-terminal
991  :class "term-concentration-out"
992  :super-classes ("terminal")
993  :documentation "Output terminal for a concentration (signal)"
994  :icon "icons/term_concentration_out.gif"
995  :link-color "green"
996  :variables
997  (("c"
998    :is-a "var-concentration-out"
999    :unit "umol/g_dw")))
1000
1001
1002(define-module
1003  :class "cf2co"
1004  :super-classes ("term-conv")
1005  :documentation "Flux -> Signal. Converts a cf-term to a co-term ."
1006  :properties
1007  (("abstract"
1008    :value "no"))
1009  :icon "icons/adapter"
1010  :terminals
1011  (("cf"
1012    :is-a "term-reaction-flux"
1013    :geometry-side "LEFT"
1014    :geometry-position "0.52666664"
1015    :variables
1016    (("c"
1017      :is-eq-to "parent.c")))
1018   ("co"
1019    :is-a "term-concentration-out"
1020    :geometry-side "RIGHT"
1021    :geometry-position "0.52666664"))
1022  :variables
1023  (("c"
1024    :is-a "var-concentration-in"))
1025  :equations
1026  (("free"
1027    :relation "co.c == c")
1028   ("rate"
1029    :relation "cf.r == 0.0d0")))
1030
1031
1032(define-module
1033  :class "speciesb"
1034  :super-classes ("species")
1035  :documentation "Non-constant boundary species, value of c! (not n)
1036is fixed by some external rule.
1037The rule is necessary, n is unused."
1038  :icon "icons/speciesb"
1039  :parameters
1040  (("c"
1041    :system-theoretic "state"
1042    :value "0")
1043   ("n"
1044    :system-theoretic "help"
1045    :value "c*v")))
1046
1047
1048(define-module
1049  :class "speciesv"
1050  :super-classes ("species")
1051  :documentation "Species with molar balance, defined by connected reactions.
1052Concentration calculated using surrounding compartment"
1053  :icon "icons/speciesv"
1054  :parameters
1055  (("n"
1056    :system-theoretic "state"))
1057  :equations
1058  (("balc"
1059    :relation ":diff<t> n == cf.r")))
1060
1061
1062(define-module
1063  :class "teusink2000_glycolysis-cytosol"
1064  :super-classes ("compartment")
1065  :rdf-annotation ((:name "BQB_IS" :resources
1066                    ("urn:miriam:obo.go:GO%3A0005829")))
1067  :geometry-width "1299"
1068  :geometry-height "1194"
1069  :parameters
1070  (("ace.c"
1071    :label "Acetaldehyde"
1072    :model-name "ACE")
1073   ("ace.n"
1074    :value "0.17d0*v")
1075   ("bpg.c"
1076    :label "1,3-bisphosphoglycerate"
1077    :model-name "BPG")
1078   ("bpg.n"
1079    :value "0.0d0")
1080   ("co2.c"
1081    :label "CO2"
1082    :model-name "CO2")
1083   ("co2.n"
1084    :value "v")
1085   ("etoh.c"
1086    :label "Ethanol"
1087    :model-name "ETOH")
1088   ("etoh.n"
1089    :value "50.0d0*v")
1090   ("f16p.c"
1091    :label "Fructose-1,6 bisphosphate"
1092    :model-name "F16P")
1093   ("f16p.n"
1094    :value "5.51d0*v")
1095   ("f26bp.c"
1096    :label "F2,6P"
1097    :model-name "F26BP")
1098   ("f26bp.n"
1099    :value "0.02d0*v")
1100   ("f6p.c"
1101    :label "Fructose 6 Phosphate"
1102    :model-name "F6P")
1103   ("f6p.n"
1104    :value "0.62d0*v")
1105   ("g6p.c"
1106    :label "Glucose 6 Phosphate"
1107    :model-name "G6P")
1108   ("g6p.n"
1109    :value "2.45d0*v")
1110   ("glci.c"
1111    :label "Glucose in Cytosol"
1112    :model-name "GLCi")
1113   ("glci.n"
1114    :value "0.087d0*v")
1115   ("gly.c"
1116    :label "Glycerol"
1117    :model-name "GLY")
1118   ("gly.n"
1119    :value "0.15d0*v")
1120   ("glyc.c"
1121    :label "Glycogen"
1122    :model-name "Glyc")
1123   ("glyc.n"
1124    :value "0.0d0")
1125   ("nad.c"
1126    :label "NAD"
1127    :model-name "NAD")
1128   ("nad.n"
1129    :value "1.2d0*v")
1130   ("nadh.c"
1131    :label "NADH"
1132    :model-name "NADH")
1133   ("nadh.n"
1134    :value "0.39d0*v")
1135   ("p.c"
1136    :label "High energy phosphates"
1137    :model-name "P")
1138   ("p.n"
1139    :value "6.31d0*v")
1140   ("p2g.c"
1141    :label "2-phosphoglycerate"
1142    :model-name "P2G")
1143   ("p2g.n"
1144    :value "0.12d0*v")
1145   ("p3g.c"
1146    :label "3-phosphoglycerate"
1147    :model-name "P3G")
1148   ("p3g.n"
1149    :value "0.9d0*v")
1150   ("pep.c"
1151    :label "Phosphoenolpyruvate"
1152    :model-name "PEP")
1153   ("pep.n"
1154    :value "0.07d0*v")
1155   ("pyr.c"
1156    :label "Pyruvate"
1157    :model-name "PYR")
1158   ("pyr.n"
1159    :value "1.85d0*v")
1160   ("succ.c"
1161    :label "Succinate"
1162    :model-name "SUCC")
1163   ("succ.n"
1164    :value "0.0d0")
1165   ("sum_p.c"
1166    :label "sum of AXP conc"
1167    :model-name "SUM_P")
1168   ("sum_p.n"
1169    :value "4.1d0*v")
1170   ("trh.c"
1171    :label "Trehalose"
1172    :model-name "Trh")
1173   ("trh.n"
1174    :value "0.0d0")
1175   ("trio.c"
1176    :label "Triose-phosphate"
1177    :model-name "TRIO")
1178   ("trio.n"
1179    :value "0.96d0*v")
1180   ("v"
1181    :value "1.0d0"
1182    :model-name "cytosol")
1183   ("vadh.keqadh"
1184    :value "6.9d-5")
1185   ("vadh.kiadhace"
1186    :value "1.1d0")
1187   ("vadh.kiadhetoh"
1188    :value "90.0d0")
1189   ("vadh.kiadhnad"
1190    :value "0.92d0")
1191   ("vadh.kiadhnadh"
1192    :value "0.031d0")
1193   ("vadh.kmadhace"
1194    :value "1.11d0")
1195   ("vadh.kmadhetoh"
1196    :value "17.0d0")
1197   ("vadh.kmadhnad"
1198    :value "0.17d0")
1199   ("vadh.kmadhnadh"
1200    :value "0.11d0")
1201   ("vadh.r"
1202    :label "Alcohol dehydrogenase"
1203    :value "vmadh/(kiadhnad*kmadhetoh)*(t_p1.c*t_p2.c-t_r2.c*t_r1.c/keqadh)/(1+t_p1.c/kiadhnad+kmadhnad*t_p2.c/(kiadhnad*kmadhetoh)+kmadhnadh*t_r1.c/(kiadhnadh*kmadhace)+t_r2.c/kiadhnadh+t_p1.c*t_p2.c/(kiadhnad*kmadhetoh)+kmadhnadh*t_p1.c*t_r1.c/(kiadhnad*kiadhnadh*kmadhace)+kmadhnad*t_p2.c*t_r2.c/(kiadhnad*kmadhetoh*kiadhnadh)+t_r2.c*t_r1.c/(kiadhnadh*kmadhace)+t_p1.c*t_p2.c*t_r1.c/(kiadhnad*kmadhetoh*kiadhace)+t_p2.c*t_r2.c*t_r1.c/(kiadhetoh*kiadhnadh*kmadhace))*(-t_c1.v)"
1204    :model-name "vADH")
1205   ("vadh.vmadh"
1206    :value "810.0d0")
1207   ("vald.gamma_p1"
1208    :value "2.0d0")
1209   ("vald.keqald"
1210    :value "0.069d0")
1211   ("vald.kmalddhap"
1212    :value "2.4d0")
1213   ("vald.kmaldf16p"
1214    :value "0.3d0")
1215   ("vald.kmaldgap"
1216    :value "2.0d0")
1217   ("vald.kmaldgapi"
1218    :value "10.0d0")
1219   ("vald.r"
1220    :label "Aldolase"
1221    :value "t_c1.v*vmald/kmaldf16p*(t_r1.c-root.keqtpi/(1+root.keqtpi)*t_p1.c/(1+root.keqtpi)*t_p1.c/keqald)/(1+t_r1.c/kmaldf16p+root.keqtpi/(1+root.keqtpi)*t_p1.c/kmaldgap+(1/(1+root.keqtpi))*t_p1.c/kmalddhap+root.keqtpi/(1+root.keqtpi)*t_p1.c/(1+root.keqtpi)*t_p1.c/(kmaldgap*kmalddhap)+root.keqtpi/(1+root.keqtpi)*t_r1.c*t_p1.c/(kmaldgapi*kmaldf16p))"
1222    :model-name "vALD")
1223   ("vald.vmald"
1224    :value "322.258d0")
1225   ("vatp.katpase"
1226    :value "33.7d0")
1227   ("vatp.r"
1228    :label "ATPase activity"
1229    :value "t_c1.v*katpase*t_m1.c"
1230    :model-name "vATP")
1231   ("veno.keqeno"
1232    :value "6.7d0")
1233   ("veno.kmenop2g"
1234    :value "0.04d0")
1235   ("veno.kmenopep"
1236    :value "0.5d0")
1237   ("veno.r"
1238    :label "Enolase"
1239    :value "t_c1.v*vmeno/kmenop2g*(t_r1.c-t_p1.c/keqeno)/(1+t_r1.c/kmenop2g+t_p1.c/kmenopep)"
1240    :model-name "vENO")
1241   ("veno.vmeno"
1242    :value "365.806d0")
1243   ("vg3pdh.keqg3pdh"
1244    :value "4300.0d0")
1245   ("vg3pdh.kmg3pdhdhap"
1246    :value "0.4d0")
1247   ("vg3pdh.kmg3pdhgly"
1248    :value "1.0d0")
1249   ("vg3pdh.kmg3pdhnad"
1250    :value "0.93d0")
1251   ("vg3pdh.kmg3pdhnadh"
1252    :value "0.023d0")
1253   ("vg3pdh.r"
1254    :label "Glycerol 3-phosphate dehydrogenase"
1255    :value "t_c1.v*vmg3pdh/(kmg3pdhdhap*kmg3pdhnadh)*((1/(1+root.keqtpi))*t_r1.c*t_r2.c-t_p2.c*t_p1.c/keqg3pdh)/((1+(1/(1+root.keqtpi))*t_r1.c/kmg3pdhdhap+t_p2.c/kmg3pdhgly)*(1+t_r2.c/kmg3pdhnadh+t_p1.c/kmg3pdhnad))"
1256    :model-name "vG3PDH")
1257   ("vg3pdh.reversible"
1258    :value "0")
1259   ("vg3pdh.vmg3pdh"
1260    :value "70.15d0")
1261   ("vgapdh.kmgapdhbpg"
1262    :value "0.0098d0")
1263   ("vgapdh.kmgapdhgap"
1264    :value "0.21d0")
1265   ("vgapdh.kmgapdhnad"
1266    :value "0.09d0")
1267   ("vgapdh.kmgapdhnadh"
1268    :value "0.06d0")
1269   ("vgapdh.r"
1270    :label "Glyceraldehyde 3-phosphate dehydrogenase"
1271    :value "t_c1.v*(root.keqtpi/(1+root.keqtpi)*vmgapdhf*t_r1.c*t_r2.c/(kmgapdhgap*kmgapdhnad)-vmgapdhr*t_p1.c*t_p2.c/(kmgapdhbpg*kmgapdhnadh))/((1+root.keqtpi/(1+root.keqtpi)*t_r1.c/kmgapdhgap+t_p1.c/kmgapdhbpg)*(1+t_r2.c/kmgapdhnad+t_p2.c/kmgapdhnadh))"
1272    :model-name "vGAPDH")
1273   ("vgapdh.vmgapdhf"
1274    :value "1184.52d0")
1275   ("vgapdh.vmgapdhr"
1276    :value "6549.8d0")
1277   ("vglk.keqglk"
1278    :value "3800.0d0")
1279   ("vglk.kmglkadp"
1280    :value "0.23d0")
1281   ("vglk.kmglkatp"
1282    :value "0.15d0")
1283   ("vglk.kmglkg6p"
1284    :value "30.0d0")
1285   ("vglk.kmglkglci"
1286    :value "0.08d0")
1287   ("vglk.r"
1288    :label "Hexokinase"
1289    :value "t_c1.v*vmglk/(kmglkglci*kmglkatp)*(t_r1.c*t_m1.c-t_p1.c*t_m2.c/keqglk)/((1+t_r1.c/kmglkglci+t_p1.c/kmglkg6p)*(1+t_m1.c/kmglkatp+t_m2.c/kmglkadp))"
1290    :model-name "vGLK")
1291   ("vglk.vmglk"
1292    :value "226.452d0")
1293   ("vglyco.kglycogen_3"
1294    :value "6.0d0")
1295   ("vglyco.r"
1296    :label "Glycogen synthesis"
1297    :value "t_c1.v*kglycogen_3"
1298    :model-name "vGLYCO")
1299   ("vglyco.reversible"
1300    :value "0")
1301   ("vpdc.kmpdcpyr"
1302    :value "4.33d0")
1303   ("vpdc.npdc"
1304    :value "1.9d0")
1305   ("vpdc.r"
1306    :label "Pyruvate decarboxylase"
1307    :value "t_c1.v*vmpdc*t_r1.c ^ npdc/kmpdcpyr ^ npdc/(1+t_r1.c ^ npdc/kmpdcpyr ^ npdc)"
1308    :model-name "vPDC")
1309   ("vpdc.reversible"
1310    :value "0")
1311   ("vpdc.vmpdc"
1312    :value "174.194d0")
1313   ("vpfk.r"
1314    :label "Phosphofructokinase"
1315    :value "t_c1.v*vmpfk*root.gr*t_r1.c/root.kmpfkf6p*t_m2.c/root.kmpfkatp*(1+t_r1.c/root.kmpfkf6p+t_m2.c/root.kmpfkatp+t_r1.c/root.kmpfkf6p*root.gr*t_m2.c/root.kmpfkatp)/((1+t_r1.c/root.kmpfkf6p+t_m2.c/root.kmpfkatp+t_r1.c/root.kmpfkf6p*root.gr*t_m2.c/root.kmpfkatp) ^ 2+root.lzero*((1+t_m2.c/root.kipfkatp*root.cipfkatp)/(1+t_m2.c/root.kipfkatp)) ^ 2*((1+t_m1.c/root.kpfkamp*root.cpfkamp)/(1+t_m1.c/root.kpfkamp)) ^ 2*((1+root.cpfkf26bp*t_m3.c/root.kpfkf26bp+root.cpfkf16bp*t_p1.c/root.kpfkf16bp)/(1+t_m3.c/root.kpfkf26bp+t_p1.c/root.kpfkf16bp)) ^ 2*(1+t_m2.c/root.kmpfkatp*root.cpfkatp) ^ 2)"
1316    :model-name "vPFK")
1317   ("vpfk.reversible"
1318    :value "0")
1319   ("vpfk.vmpfk"
1320    :value "182.903d0")
1321   ("vpgi.keqpgi_2"
1322    :value "0.314d0")
1323   ("vpgi.kmpgif6p_2"
1324    :value "0.3d0")
1325   ("vpgi.kmpgig6p_2"
1326    :value "1.4d0")
1327   ("vpgi.r"
1328    :label "Glucose-6-phosphate isomerase"
1329    :value "t_c1.v*vmpgi_2/kmpgig6p_2*(t_r1.c-t_p1.c/keqpgi_2)/(1+t_r1.c/kmpgig6p_2+t_p1.c/kmpgif6p_2)"
1330    :model-name "vPGI")
1331   ("vpgi.vmpgi_2"
1332    :value "339.677d0")
1333   ("vpgk.keqpgk"
1334    :value "3200.0d0")
1335   ("vpgk.kmpgkadp"
1336    :value "0.2d0")
1337   ("vpgk.kmpgkatp"
1338    :value "0.3d0")
1339   ("vpgk.kmpgkbpg"
1340    :value "0.003d0")
1341   ("vpgk.kmpgkp3g"
1342    :value "0.53d0")
1343   ("vpgk.r"
1344    :label "Phosphoglycerate kinase"
1345    :value "t_c1.v*vmpgk/(kmpgkp3g*kmpgkatp)*(keqpgk*t_r1.c*t_m2.c-t_p1.c*t_m1.c)/((1+t_r1.c/kmpgkbpg+t_p1.c/kmpgkp3g)*(1+t_m1.c/kmpgkatp+t_m2.c/kmpgkadp))"
1346    :model-name "vPGK")
1347   ("vpgk.vmpgk"
1348    :value "1306.45d0")
1349   ("vpgm.keqpgm"
1350    :value "0.19d0")
1351   ("vpgm.kmpgmp2g"
1352    :value "0.08d0")
1353   ("vpgm.kmpgmp3g"
1354    :value "1.2d0")
1355   ("vpgm.r"
1356    :label "Phosphoglycerate mutase"
1357    :value "t_c1.v*vmpgm/kmpgmp3g*(t_r1.c-t_p1.c/keqpgm)/(1+t_r1.c/kmpgmp3g+t_p1.c/kmpgmp2g)"
1358    :model-name "vPGM")
1359   ("vpgm.vmpgm"
1360    :value "2525.81d0")
1361   ("vpyk.keqpyk"
1362    :value "6500.0d0")
1363   ("vpyk.kmpykadp"
1364    :value "0.53d0")
1365   ("vpyk.kmpykatp"
1366    :value "1.5d0")
1367   ("vpyk.kmpykpep"
1368    :value "0.14d0")
1369   ("vpyk.kmpykpyr"
1370    :value "21.0d0")
1371   ("vpyk.r"
1372    :label "Pyruvate kinase"
1373    :value "t_c1.v*vmpyk/(kmpykpep*kmpykadp)*(t_r1.c*t_m2.c-t_p1.c*t_m1.c/keqpyk)/((1+t_r1.c/kmpykpep+t_p1.c/kmpykpyr)*(1+t_m1.c/kmpykatp+t_m2.c/kmpykadp))"
1374    :model-name "vPYK")
1375   ("vpyk.vmpyk"
1376    :value "1088.71d0")
1377   ("vsuc.gamma_p1"
1378    :value "3.0d0")
1379   ("vsuc.gamma_r1"
1380    :value "-2.0d0")
1381   ("vsuc.gamma_r2"
1382    :value "-3.0d0")
1383   ("vsuc.gamma_r3"
1384    :value "-4.0d0")
1385   ("vsuc.ksucc"
1386    :value "21.4d0")
1387   ("vsuc.r"
1388    :label "Succinate synthesis"
1389    :value "t_c1.v*ksucc*t_r1.c"
1390    :model-name "vSUC")
1391   ("vsuc.reversible"
1392    :value "0")
1393   ("vtreha.gamma_r1"
1394    :value "-2.0d0")
1395   ("vtreha.ktrehalose"
1396    :value "2.4d0")
1397   ("vtreha.r"
1398    :label "Trehalose 6-phosphate synthase"
1399    :value "t_c1.v*ktrehalose"
1400    :model-name "vTreha")
1401   ("vtreha.reversible"
1402    :value "0"))
1403  :terminals
1404  (("t_adp"
1405    :is-eq-to "fa_adp.out"
1406    :geometry-side "TOP"
1407    :geometry-position "0.65165514")
1408   ("t_amp"
1409    :is-eq-to "fa_amp.out"
1410    :geometry-side "BOTTOM"
1411    :geometry-position "0.92494226")
1412   ("t_atp"
1413    :is-eq-to "fa_atp.out"
1414    :geometry-side "BOTTOM"
1415    :geometry-position "0.92494226")
1416   ("t_glci"
1417    :is-eq-to "fa_glci.out"
1418    :geometry-side "RIGHT"
1419    :geometry-position "0.92504185")
1420   ("t_p"
1421    :is-eq-to "fa_p.out"
1422    :geometry-side "RIGHT"
1423    :geometry-position "0.92504185")
1424   ("t_sum_p"
1425    :is-eq-to "fa_sum_p.out"
1426    :geometry-side "LEFT"
1427    :geometry-position "0.22152428"))
1428  :modules
1429  (("ace"
1430    :is-a "speciesv"
1431    :rdf-annotation ((:name "BQB_IS" :resources
1432                      ("urn:miriam:obo.chebi:CHEBI%3A15343"
1433                       "urn:miriam:kegg.compound:C00084")))
1434    :geometry-x "470"
1435    :geometry-y "438")
1436   ("adp"
1437    :is-a "speciesb"
1438    :rdf-annotation ((:name "BQB_IS" :resources
1439                      ("urn:miriam:obo.chebi:CHEBI%3A16761"
1440                       "urn:miriam:kegg.compound:C00008")))
1441    :geometry-x "433"
1442    :geometry-y "184")
1443   ("amp"
1444    :is-a "speciesb"
1445    :rdf-annotation ((:name "BQB_IS" :resources
1446                      ("urn:miriam:obo.chebi:CHEBI%3A16027"
1447                       "urn:miriam:kegg.compound:C00020")))
1448    :geometry-x "954"
1449    :geometry-y "124")
1450   ("atp"
1451    :is-a "speciesb"
1452    :rdf-annotation ((:name "BQB_IS" :resources
1453                      ("urn:miriam:obo.chebi:CHEBI%3A15422"
1454                       "urn:miriam:kegg.compound:C00002")))
1455    :geometry-x "1166"
1456    :geometry-y "925")
1457   ("bpg"
1458    :is-a "speciesv"
1459    :rdf-annotation ((:name "BQB_IS" :resources
1460                      ("urn:miriam:obo.chebi:CHEBI%3A16001"
1461                       "urn:miriam:kegg.compound:C00236")))
1462    :geometry-x "509"
1463    :geometry-y "854")
1464   ("ca_adp"
1465    :is-a "cf2co"
1466    :geometry-x "573"
1467    :geometry-y "307")
1468   ("ca_amp"
1469    :is-a "cf2co"
1470    :geometry-x "878"
1471    :geometry-y "284")
1472   ("ca_atp"
1473    :is-a "cf2co"
1474    :geometry-x "1029"
1475    :geometry-y "769")
1476   ("ca_f26bp"
1477    :is-a "cf2co"
1478    :geometry-x "1073"
1479    :geometry-y "518")
1480   ("co2"
1481    :is-a "species"
1482    :rdf-annotation ((:name "BQB_IS" :resources
1483                      ("urn:miriam:obo.chebi:CHEBI%3A16526"
1484                       "urn:miriam:kegg.compound:C00011")))
1485    :geometry-x "625"
1486    :geometry-y "407")
1487   ("etoh"
1488    :is-a "species"
1489    :rdf-annotation ((:name "BQB_IS" :resources
1490                      ("urn:miriam:obo.chebi:CHEBI%3A16236"
1491                       "urn:miriam:kegg.compound:C00469")))
1492    :geometry-x "447"
1493    :geometry-y "572")
1494   ("f16p"
1495    :is-a "speciesv"
1496    :rdf-annotation ((:name "BQB_IS" :resources
1497                      ("urn:miriam:obo.chebi:CHEBI%3A16905"
1498                       "urn:miriam:kegg.compound:C00354")))
1499    :geometry-x "695"
1500    :geometry-y "280")
1501   ("f26bp"
1502    :is-a "species"
1503    :rdf-annotation ((:name "BQB_IS" :resources
1504                      ("urn:miriam:obo.chebi:CHEBI%3A28602"
1505                       "urn:miriam:kegg.compound:C00665")))
1506    :geometry-x "1187"
1507    :geometry-y "511")
1508   ("f6p"
1509    :is-a "speciesv"
1510    :rdf-annotation ((:name "BQB_IS" :resources
1511                      ("urn:miriam:obo.chebi:CHEBI%3A15946"
1512                       "urn:miriam:kegg.compound:C05345")))
1513    :geometry-x "1093"
1514    :geometry-y "668")
1515   ("fa_adp"
1516    :is-a "adapter-flux"
1517    :geometry-x "464"
1518    :geometry-y "122")
1519   ("fa_amp"
1520    :is-a "adapter-flux"
1521    :geometry-x "863"
1522    :geometry-y "78")
1523   ("fa_atp"
1524    :is-a "adapter-flux"
1525    :geometry-x "1211"
1526    :geometry-y "866")
1527   ("fa_glci"
1528    :is-a "adapter-flux"
1529    :geometry-x "693"
1530    :geometry-y "1113")
1531   ("fa_p"
1532    :is-a "adapter-flux"
1533    :geometry-x "594"
1534    :geometry-y "927")
1535   ("fa_sum_p"
1536    :is-a "adapter-flux"
1537    :geometry-x "93"
1538    :geometry-y "397")
1539   ("g6p"
1540    :is-a "speciesv"
1541    :rdf-annotation ((:name "BQB_IS" :resources
1542                      ("urn:miriam:obo.chebi:CHEBI%3A17665"
1543                       "urn:miriam:kegg.compound:C00668")))
1544    :geometry-x "944"
1545    :geometry-y "921")
1546   ("glci"
1547    :is-a "speciesv"
1548    :rdf-annotation ((:name "BQB_IS" :resources
1549                      ("urn:miriam:obo.chebi:CHEBI%3A17234"
1550                       "urn:miriam:kegg.compound:C00293")))
1551    :geometry-x "771"
1552    :geometry-y "1107")
1553   ("gly"
1554    :is-a "species"
1555    :rdf-annotation ((:name "BQB_IS" :resources
1556                      ("urn:miriam:obo.chebi:CHEBI%3A17754"
1557                       "urn:miriam:kegg.compound:C00116")))
1558    :geometry-x "310"
1559    :geometry-y "626")
1560   ("glyc"
1561    :is-a "species"
1562    :rdf-annotation ((:name "BQB_IS" :resources
1563                      ("urn:miriam:obo.chebi:CHEBI%3A28087"
1564                       "urn:miriam:kegg.compound:C00182")))
1565    :geometry-x "888"
1566    :geometry-y "902")
1567   ("nad"
1568    :is-a "speciesv"
1569    :rdf-annotation ((:name "BQB_IS" :resources
1570                      ("urn:miriam:obo.chebi:CHEBI%3A15846"
1571                       "urn:miriam:kegg.compound:C00003")))
1572    :geometry-x "314"
1573    :geometry-y "717")
1574   ("nadh"
1575    :is-a "speciesv"
1576    :rdf-annotation ((:name "BQB_IS" :resources
1577                      ("urn:miriam:obo.chebi:CHEBI%3A16908"
1578                       "urn:miriam:kegg.compound:C00004")))
1579    :geometry-x "348"
1580    :geometry-y "788")
1581   ("p"
1582    :is-a "speciesv"
1583    :rdf-annotation ((:name "BQB_HAS_PART" :resources
1584                      ("urn:miriam:obo.chebi:CHEBI%3A15422"
1585                       "urn:miriam:obo.chebi:CHEBI%3A16761"))
1586                     (:name "BQB_HAS_PART" :resources
1587                      ("urn:miriam:kegg.compound:C00002"
1588                       "urn:miriam:kegg.compound:C00008")))
1589    :geometry-x "690"
1590    :geometry-y "851")
1591   ("p2g"
1592    :is-a "speciesv"
1593    :rdf-annotation ((:name "BQB_IS" :resources
1594                      ("urn:miriam:obo.chebi:CHEBI%3A17835"
1595                       "urn:miriam:kegg.compound:C00631")))
1596    :geometry-x "1076"
1597    :geometry-y "334")
1598   ("p3g"
1599    :is-a "speciesv"
1600    :rdf-annotation ((:name "BQB_IS" :resources
1601                      ("urn:miriam:obo.chebi:CHEBI%3A17794"
1602                       "urn:miriam:kegg.compound:C00197")))
1603    :geometry-x "910"
1604    :geometry-y "372")
1605   ("pep"
1606    :is-a "speciesv"
1607    :rdf-annotation ((:name "BQB_IS" :resources
1608                      ("urn:miriam:obo.chebi:CHEBI%3A26055"
1609                       "urn:miriam:kegg.compound:C00074")))
1610    :geometry-x "1098"
1611    :geometry-y "455")
1612   ("pyr"
1613    :is-a "speciesv"
1614    :rdf-annotation ((:name "BQB_IS" :resources
1615                      ("urn:miriam:obo.chebi:CHEBI%3A32816"
1616                       "urn:miriam:kegg.compound:C00022")))
1617    :geometry-x "769"
1618    :geometry-y "350")
1619   ("succ"
1620    :is-a "species"
1621    :rdf-annotation ((:name "BQB_IS" :resources
1622                      ("urn:miriam:obo.chebi:CHEBI%3A30031")))
1623    :geometry-x "495"
1624    :geometry-y "787")
1625   ("sum_p"
1626    :is-a "species"
1627    :rdf-annotation ((:name "BQB_HAS_PART" :resources
1628                      ("urn:miriam:kegg.compound:C00020"
1629                       "urn:miriam:kegg.compound:C00008"
1630                       "urn:miriam:kegg.compound:C00002"))
1631                     (:name "BQB_HAS_PART" :resources
1632                      ("urn:miriam:obo.chebi:CHEBI%3A16027"
1633                       "urn:miriam:obo.chebi:CHEBI%3A16761"
1634                       "urn:miriam:obo.chebi:CHEBI%3A15422")))
1635    :geometry-x "77"
1636    :geometry-y "458")
1637   ("trh"
1638    :is-a "species"
1639    :rdf-annotation ((:name "BQB_IS" :resources
1640                      ("urn:miriam:obo.chebi:CHEBI%3A27082"
1641                       "urn:miriam:kegg.compound:C01083")))
1642    :geometry-x "810"
1643    :geometry-y "941")
1644   ("trio"
1645    :is-a "speciesv"
1646    :rdf-annotation ((:name "BQB_HAS_PART" :resources
1647                      ("urn:miriam:kegg.compound:C00111"
1648                       "urn:miriam:kegg.compound:C00118"))
1649                     (:name "BQB_HAS_PART" :resources
1650                      ("urn:miriam:obo.chebi:CHEBI%3A29052"
1651                       "urn:miriam:obo.chebi:CHEBI%3A16108")))
1652    :geometry-x "345"
1653    :geometry-y "470")
1654   ("va"
1655    :is-a "adapter-volume-pop"
1656    :geometry-x "670"
1657    :geometry-y "688")
1658   ("vadh"
1659    :is-a "kin-2-2_0_1_hnad_kmadhetoh_keqadh_kmadhnad_kmadhnadh_kiadhnadh_kmadhace_kiadhace_kiadhetohcon"
1660    :geometry-x "493"
1661    :geometry-y "614")
1662   ("vald"
1663    :is-a "kin-1-1_0_1_df16p_keqald_kmaldgap_kmalddhap_kmaldgapideg"
1664    :geometry-x "589"
1665    :geometry-y "500")
1666   ("vatp"
1667    :is-a "kin-1-__1_1_katpase"
1668    :geometry-x "780"
1669    :geometry-y "689")
1670   ("veno"
1671    :is-a "kin-1-1_0_1_op2g_keqeno_kmenopep1e60"
1672    :geometry-x "932"
1673    :geometry-y "478")
1674   ("vg3pdh"
1675    :is-a "kin-2-2_0_1_g3pdhdhap_kmg3pdhnadh_keqg3pdh_kmg3pdhgly_kmg3pdhnad15uq"
1676    :geometry-x "415"
1677    :geometry-y "622")
1678   ("vgapdh"
1679    :is-a "kin-2-2_0_1_mgapdhgap_kmgapdhnad_vmgapdhr_kmgapdhbpg_kmgapdhnadh1e35"
1680    :geometry-x "502"
1681    :geometry-y "662")
1682   ("vglk"
1683    :is-a "kin-2-1_2_1_kglci_kmglkatp_keqglk_kmglkg6p_kmglkadpuxj"
1684    :geometry-x "780"
1685    :geometry-y "744")
1686   ("vglyco"
1687    :is-a "kin-2-1_0_1_kglycogen_3"
1688    :geometry-x "806"
1689    :geometry-y "796")
1690   ("vpdc"
1691    :is-a "kin-1-2_0_1_vmpdc_npdc_kmpdcpyr"
1692    :geometry-x "639"
1693    :geometry-y "499")
1694   ("vpfk"
1695    :is-a "kin-2-1_3_1_vmpfk"
1696    :geometry-x "860"
1697    :geometry-y "569")
1698   ("vpgi"
1699    :is-a "kin-1-1_0_1_pgig6p_2_keqpgi_2_kmpgif6p_213yw"
1700    :geometry-x "890"
1701    :geometry-y "727")
1702   ("vpgk"
1703    :is-a "kin-1-2_2_1_kp3g_kmpgkatp_keqpgk_kmpgkbpg_kmpgkadp7d8"
1704    :geometry-x "744"
1705    :geometry-y "634")
1706   ("vpgm"
1707    :is-a "kin-1-1_0_1_mp3g_keqpgm_kmpgmp2g6me"
1708    :geometry-x "884"
1709    :geometry-y "456")
1710   ("vpyk"
1711    :is-a "kin-1-2_2_1_kpep_kmpykadp_keqpyk_kmpykpyr_kmpykatpos3"
1712    :geometry-x "790"
1713    :geometry-y "589")
1714   ("vsuc"
1715    :is-a "kin-3-2_0_1_ksucc"
1716    :geometry-x "545"
1717    :geometry-y "679")
1718   ("vtreha"
1719    :is-a "kin-2-1_0_1_ktrehalose"
1720    :geometry-x "760"
1721    :geometry-y "818"))
1722  :links
1723  (("cl_adp"
1724    :terminals ("ca_adp.co" "vglk.t_m2" "vpgk.t_m2" "vpyk.t_m2")
1725    :nodes (("731" "558"))
1726    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1727   ("cl_amp"
1728    :terminals ("ca_amp.co" "vpfk.t_m1"))
1729   ("cl_atp"
1730    :terminals ("ca_atp.co" "vglk.t_m1" "vpfk.t_m2" "vpgk.t_m1"
1731                "vpyk.t_m1" "vatp.t_m1")
1732    :nodes (("840" "654"))
1733    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1734            ("4" "-1" nil) ("5" "-1" nil)))
1735   ("cl_f26bp"
1736    :terminals ("ca_f26bp.co" "vpfk.t_m3"))
1737   ("fl_ace"
1738    :terminals ("ace.cf" "vpdc.t_p1" "vsuc.t_r1" "vadh.t_r1")
1739    :nodes (("524" "542"))
1740    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1741   ("fl_adp"
1742    :terminals ("adp.cf" "ca_adp.cf" "fa_adp.in")
1743    :nodes (("484" "213"))
1744    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1745   ("fl_amp"
1746    :terminals ("amp.cf" "ca_amp.cf" "fa_amp.in")
1747    :nodes (("883" "169"))
1748    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1749   ("fl_atp"
1750    :terminals ("atp.cf" "ca_atp.cf" "fa_atp.in")
1751    :nodes (("1129" "861"))
1752    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1753   ("fl_bpg"
1754    :terminals ("bpg.cf" "vgapdh.t_p1" "vpgk.t_r1")
1755    :nodes (("567" "742"))
1756    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1757   ("fl_co2"
1758    :terminals ("co2.cf" "vpdc.t_p2"))
1759   ("fl_etoh"
1760    :terminals ("etoh.cf" "vadh.t_p2"))
1761   ("fl_f16p"
1762    :terminals ("f16p.cf" "vpfk.t_p1" "vald.t_r1")
1763    :nodes (("698" "409"))
1764    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1765   ("fl_f26bp"
1766    :terminals ("f26bp.cf" "ca_f26bp.cf"))
1767   ("fl_f6p"
1768    :terminals ("f6p.cf" "vpgi.t_p1" "vpfk.t_r1")
1769    :nodes (("974" "660"))
1770    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1771   ("fl_g6p"
1772    :terminals ("g6p.cf" "vglk.t_p1" "vpgi.t_r1" "vglyco.t_r1"
1773                "vtreha.t_r1")
1774    :nodes (("845" "821"))
1775    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1776            ("4" "-1" nil)))
1777   ("fl_glci"
1778    :terminals ("glci.cf" "vglk.t_r1" "fa_glci.in")
1779    :nodes (("729" "1030"))
1780    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1781   ("fl_gly"
1782    :terminals ("gly.cf" "vg3pdh.t_p2"))
1783   ("fl_glyc"
1784    :terminals ("glyc.cf" "vglyco.t_p1"))
1785   ("fl_nad"
1786    :terminals ("nad.cf" "vgapdh.t_r2" "vsuc.t_r2" "vadh.t_p1"
1787                "vg3pdh.t_p1")
1788    :nodes (("426" "673"))
1789    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1790            ("4" "-1" nil)))
1791   ("fl_nadh"
1792    :terminals ("nadh.cf" "vgapdh.t_p2" "vsuc.t_p1" "vadh.t_r2"
1793                "vg3pdh.t_r2")
1794    :nodes (("443" "700"))
1795    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1796            ("4" "-1" nil)))
1797   ("fl_p"
1798    :terminals ("p.cf" "vglk.t_r2" "vglyco.t_r2" "vtreha.t_r2"
1799                "vpfk.t_r2" "vpgk.t_p2" "vpyk.t_p2" "vsuc.t_r3"
1800                "vatp.t_r1" "fa_p.in")
1801    :nodes (("722" "746"))
1802    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1803            ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil)
1804            ("8" "-1" nil) ("9" "-1" nil)))
1805   ("fl_p2g"
1806    :terminals ("p2g.cf" "vpgm.t_p1" "veno.t_r1")
1807    :nodes (("981" "402"))
1808    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1809   ("fl_p3g"
1810    :terminals ("p3g.cf" "vpgk.t_p1" "vpgm.t_r1")
1811    :nodes (("835" "475"))
1812    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1813   ("fl_pep"
1814    :terminals ("pep.cf" "veno.t_p1" "vpyk.t_r1")
1815    :nodes (("981" "510"))
1816    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1817   ("fl_pyr"
1818    :terminals ("pyr.cf" "vpyk.t_p1" "vpdc.t_r1")
1819    :nodes (("732" "463"))
1820    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1821   ("fl_succ"
1822    :terminals ("succ.cf" "vsuc.t_p2"))
1823   ("fl_sum_p"
1824    :terminals ("sum_p.cf" "fa_sum_p.in"))
1825   ("fl_trh"
1826    :terminals ("trh.cf" "vtreha.t_p1"))
1827   ("fl_trio"
1828    :terminals ("trio.cf" "vald.t_p1" "vgapdh.t_r1" "vg3pdh.t_r1")
1829    :nodes (("426" "540"))
1830    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1831   ("vl_cytosol"
1832    :terminals ("va.out" "vglk.t_c1" "vpgi.t_c1" "vglyco.t_c1"
1833                "vtreha.t_c1" "vpfk.t_c1" "vald.t_c1" "vgapdh.t_c1"
1834                "vpgk.t_c1" "vpgm.t_c1" "veno.t_c1" "vpyk.t_c1"
1835                "vpdc.t_c1" "vsuc.t_c1" "vadh.t_c1" "vg3pdh.t_c1"
1836                "vatp.t_c1")
1837    :nodes (("707" "652"))
1838    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1839            ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil)
1840            ("8" "-1" nil) ("9" "-1" nil) ("10" "-1" nil)
1841            ("11" "-1" nil) ("12" "-1" nil) ("13" "-1" nil)
1842            ("14" "-1" nil) ("15" "-1" nil) ("16" "-1" nil)))))
1843
1844
1845(define-module
1846  :class "teusink2000_glycolysis-extracellular"
1847  :super-classes ("compartment")
1848  :rdf-annotation ((:name "BQB_IS" :resources
1849                    ("urn:miriam:obo.go:GO%3A0005576")))
1850  :geometry-width "528"
1851  :geometry-height "550"
1852  :parameters
1853  (("glco.c"
1854    :label "Extracellular Glucose"
1855    :model-name "GLCo")
1856   ("glco.n"
1857    :value "50.0d0*v")
1858   ("v"
1859    :value "1.0d0"
1860    :model-name "extracellular")
1861   ("vglt.keqglt"
1862    :value "1.0d0")
1863   ("vglt.kmgltglci"
1864    :value "1.1918d0")
1865   ("vglt.kmgltglco"
1866    :value "1.1918d0")
1867   ("vglt.r"
1868    :label "Glucose transport"
1869    :value "vmglt/kmgltglco*(t_r1.c-t_p1.c/keqglt)/(1+t_r1.c/kmgltglco+t_p1.c/kmgltglci+0.91d0*t_r1.c*t_p1.c/(kmgltglco*kmgltglci))"
1870    :model-name "vGLT")
1871   ("vglt.vmglt"
1872    :value "97.264d0"))
1873  :terminals
1874  (("t_adp"
1875    :is-eq-to "fa_adp.out"
1876    :geometry-side "BOTTOM"
1877    :geometry-position "0.9251894")
1878   ("t_amp"
1879    :is-eq-to "fa_amp.out"
1880    :geometry-side "RIGHT"
1881    :geometry-position "0.92454547")
1882   ("t_atp"
1883    :is-eq-to "fa_atp.out"
1884    :geometry-side "BOTTOM"
1885    :geometry-position "0.9251894")
1886   ("t_p"
1887    :is-eq-to "fa_p.out"
1888    :geometry-side "RIGHT"
1889    :geometry-position "0.88454545")
1890   ("t_sum_p"
1891    :is-eq-to "fa_sum_p.out"
1892    :geometry-side "LEFT"
1893    :geometry-position "0.57545453"))
1894  :modules
1895  (("cytosol"
1896    :is-a "teusink2000_glycolysis-cytosol"
1897    :geometry-x "244"
1898    :geometry-y "264")
1899   ("fa_adp"
1900    :is-a "adapter-flux"
1901    :geometry-x "297"
1902    :geometry-y "78")
1903   ("fa_amp"
1904    :is-a "adapter-flux"
1905    :geometry-x "357"
1906    :geometry-y "469")
1907   ("fa_atp"
1908    :is-a "adapter-flux"
1909    :geometry-x "440"
1910    :geometry-y "409")
1911   ("fa_p"
1912    :is-a "adapter-flux"
1913    :geometry-x "438"
1914    :geometry-y "307")
1915   ("fa_sum_p"
1916    :is-a "adapter-flux"
1917    :geometry-x "65"
1918    :geometry-y "180")
1919   ("glco"
1920    :is-a "species"
1921    :rdf-annotation ((:name "BQB_IS" :resources
1922                      ("urn:miriam:obo.chebi:CHEBI%3A17234"
1923                       "urn:miriam:kegg.compound:C00293")))
1924    :geometry-x "239"
1925    :geometry-y "437")
1926   ("vglt"
1927    :is-a "kin-1-1_0_tglco_keqglt_kmgltglci34f"
1928    :geometry-x "296"
1929    :geometry-y "409"))
1930  :links
1931  (("fl_adp"
1932    :terminals ("cytosol.t_adp" "fa_adp.in"))
1933   ("fl_amp"
1934    :terminals ("cytosol.t_amp" "fa_amp.in"))
1935   ("fl_atp"
1936    :terminals ("cytosol.t_atp" "fa_atp.in"))
1937   ("fl_glci"
1938    :terminals ("cytosol.t_glci" "vglt.t_p1"))
1939   ("fl_glco"
1940    :terminals ("glco.cf" "vglt.t_r1"))
1941   ("fl_p"
1942    :terminals ("cytosol.t_p" "fa_p.in"))
1943   ("fl_sum_p"
1944    :terminals ("cytosol.t_sum_p" "fa_sum_p.in"))))
1945
1946
1947(define-module
1948  :class "teusink2000_glycolysis"
1949  :super-classes ("sbml-model")
1950  :documentation "
1951      <body xmlns=\"http://www.w3.org/1999/xhtml\">
1952        <p>
1953          <b>Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.</b>
1954          <br></br>
1955          <i>Teusink,B et al.: Eur J Biochem 2000 Sep;267(17):5313-29.</i>
1956          <br></br>
1957        The model reproduces the steady-state fluxes and metabolite concentrations of the branched model as given in Table 4 of the paper. It is derived from the model on JWS online, but has the ATP consumption in the succinate branch with the same stoichiometrie as in the publication. The model was successfully tested on copasi v.4.4(build 26).
1958     
1959         
1960         
1961     
1962         
1963         
1964          <br></br>
1965For Vmax values, please note that there is a conversion factor of approx. 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol). The equilibrium constant for the ADH reaction in the paper is given for the reverse reaction (Keq = 1.45*10
1966     
1967         
1968         
1969     
1970         
1971         
1972          <sup>4</sup>). The value used in this model is for the forward reaction: 1/Keq = 6.9*10
1973     
1974         
1975         
1976     
1977         
1978         
1979          <sup>-5</sup> .
1980     
1981         
1982         
1983     
1984         
1985         
1986          <br></br>
1987Vmax parameters values used (in [mM/min] except VmGLT):
1988       
1989     
1990         
1991         
1992     
1993         
1994         
1995          <table border=\"0\" cellpadding=\"2\" cellspacing=\"0\">
1996            <tr>
1997              <td>
1998                <b>VmGLT</b>
1999              </td>
2000              <td>97.264</td>
2001              <td>mmol/min</td>
2002            </tr>
2003            <tr>
2004              <td>
2005                <b>VmGLK</b>
2006              </td>
2007              <td>226.45</td>
2008              <td></td>
2009            </tr>
2010            <tr>
2011              <td>
2012                <b>VmPGI</b>
2013              </td>
2014              <td>339.667</td>
2015              <td></td>
2016            </tr>
2017            <tr>
2018              <td>
2019                <b>VmPFK</b>
2020              </td>
2021              <td>182.903</td>
2022              <td></td>
2023            </tr>
2024            <tr>
2025              <td>
2026                <b>VmALD</b>
2027              </td>
2028              <td>322.258</td>
2029              <td></td>
2030            </tr>
2031            <tr>
2032              <td>
2033                <b>VmGAPDH_f</b>
2034              </td>
2035              <td>1184.52</td>
2036              <td></td>
2037            </tr>
2038            <tr>
2039              <td>
2040                <b>VmGAPDH_r</b>
2041              </td>
2042              <td>6549.68</td>
2043              <td></td>
2044            </tr>
2045            <tr>
2046              <td>
2047                <b>VmPGK</b>
2048              </td>
2049              <td>1306.45</td>
2050              <td></td>
2051            </tr>
2052            <tr>
2053              <td>
2054                <b>VmPGM</b>
2055              </td>
2056              <td>2525.81</td>
2057              <td></td>
2058            </tr>
2059            <tr>
2060              <td>
2061                <b>VmENO</b>
2062              </td>
2063              <td>365.806</td>
2064              <td></td>
2065            </tr>
2066            <tr>
2067              <td>
2068                <b>VmPYK</b>
2069              </td>
2070              <td>1088.71</td>
2071              <td></td>
2072            </tr>
2073            <tr>
2074              <td>
2075                <b>VmPDC</b>
2076              </td>
2077              <td>174.194</td>
2078              <td></td>
2079            </tr>
2080            <tr>
2081              <td>
2082                <b>VmG3PDH</b>
2083              </td>
2084              <td>70.15</td>
2085              <td></td>
2086            </tr>
2087          </table>
2088
2089The result of the G6P steady state concentration (marked in red) differs slightly from the one given in table 4. of the publication
2090     
2091         
2092         
2093     
2094         
2095         
2096          <br></br>
2097Results for steady state:
2098       
2099          <table border=\"0\" cellpadding=\"2\" cellspacing=\"0\">
2100            <thead>
2101              <tr>
2102                <th align=\"left\" bgcolor=\"#eeeeee\" valign=\"middle\"></th>
2103                <th align=\"left\" bgcolor=\"#eeeeee\" valign=\"middle\">orig. article </th>
2104                <th align=\"center\" bgcolor=\"#eeeeee\" valign=\"middle\"> this model</th>
2105              </tr>
2106            </thead>
2107            <tbody>
2108              <tr>
2109                <td>
2110                  <b>Fluxes[mM/min]</b>&#xA0;</td>
2111                  <td></td>
2112                  <td></td>
2113                </tr>
2114                <tr>
2115                  <td>Glucose&#xA0;</td>
2116                  <td>88&#xA0;</td>
2117                  <td>88&#xA0;</td>
2118                </tr>
2119                <tr>
2120                  <td>Ethanol&#xA0;</td>
2121                  <td>129&#xA0;</td>
2122                  <td>129&#xA0;</td>
2123                </tr>
2124                <tr>
2125                  <td>Glycogen&#xA0;</td>
2126                  <td>6&#xA0;</td>
2127                  <td>6&#xA0;</td>
2128                </tr>
2129                <tr>
2130                  <td>Trehalose&#xA0;</td>
2131                  <td>4.8&#xA0;</td>
2132                  <td>4.8&#xA0;</td>
2133                  <td> (G6P flux through trehalose branch) </td>
2134                </tr>
2135                <tr>
2136                  <td>Glycerol&#xA0;</td>
2137                  <td>18.2&#xA0;</td>
2138                  <td>18.2&#xA0;</td>
2139                </tr>
2140                <tr>
2141                  <td>Succinate&#xA0;</td>
2142                  <td>3.6&#xA0;</td>
2143                  <td>3.6&#xA0;</td>
2144                </tr>
2145                <tr>
2146                  <td>
2147                    <b>Conc.[mM]</b>&#xA0;</td>
2148                    <td></td>
2149                    <td></td>
2150                  </tr>
2151                  <tr>
2152                    <td>G6P&#xA0;</td>
2153                    <td>1.07&#xA0;</td>
2154                    <td style=\"color: red\">1.03&#xA0;</td>
2155                  </tr>
2156                  <tr>
2157                    <td>F6P&#xA0;</td>
2158                    <td>0.11&#xA0;</td>
2159                    <td>0.11&#xA0;</td>
2160                  </tr>
2161                  <tr>
2162                    <td>F1,6P&#xA0;</td>
2163                    <td>0.6&#xA0;</td>
2164                    <td>0.6&#xA0;</td>
2165                  </tr>
2166                  <tr>
2167                    <td>DHAP&#xA0;</td>
2168                    <td>0.74&#xA0;</td>
2169                    <td>0.74&#xA0;</td>
2170                  </tr>
2171                  <tr>
2172                    <td>3PGA&#xA0;</td>
2173                    <td>0.36&#xA0;</td>
2174                    <td>0.36&#xA0;</td>
2175                  </tr>
2176                  <tr>
2177                    <td>2PGA&#xA0;</td>
2178                    <td>0.04&#xA0;</td>
2179                    <td>0.04&#xA0;</td>
2180                  </tr>
2181                  <tr>
2182                    <td>PEP&#xA0;</td>
2183                    <td>0.07&#xA0;</td>
2184                    <td>0.07&#xA0;</td>
2185                  </tr>
2186                  <tr>
2187                    <td>PYR&#xA0;</td>
2188                    <td>8.52&#xA0;</td>
2189                    <td>8.52&#xA0;</td>
2190                  </tr>
2191                  <tr>
2192                    <td>AcAld&#xA0;</td>
2193                    <td>0.17&#xA0;</td>
2194                    <td>0.17&#xA0;</td>
2195                  </tr>
2196                  <tr>
2197                    <td>ATP&#xA0;</td>
2198                    <td>2.51&#xA0;</td>
2199                    <td>2.51&#xA0;</td>
2200                  </tr>
2201                  <tr>
2202                    <td>ADP&#xA0;</td>
2203                    <td>1.29&#xA0;</td>
2204                    <td>1.29&#xA0;</td>
2205                  </tr>
2206                  <tr>
2207                    <td>AMP&#xA0;</td>
2208                    <td>0.3&#xA0;</td>
2209                    <td>0.3&#xA0;</td>
2210                  </tr>
2211                  <tr>
2212                    <td>NAD&#xA0;</td>
2213                    <td>1.55&#xA0;</td>
2214                    <td>1.55&#xA0;</td>
2215                  </tr>
2216                  <tr>
2217                    <td>NADH&#xA0;</td>
2218                    <td>0.04&#xA0;</td>
2219                    <td>0.04&#xA0;</td>
2220                  </tr>
2221                </tbody>
2222              </table>
2223        Authors of the publication also mentioned a few misprints in the original article:
2224     
2225         
2226         
2227     
2228         
2229         
2230              <br></br>
2231        in the kinetic law for
2232     
2233         
2234         
2235     
2236         
2237         
2238              <em>ADH</em>:
2239       
2240     
2241         
2242         
2243     
2244         
2245         
2246              <ol>
2247                <li>    the species
2248       
2249           
2250           
2251       
2252           
2253           
2254                <em>a</em> should denote
2255       
2256           
2257           
2258       
2259           
2260           
2261                <em>NAD</em> and 
2262       
2263           
2264           
2265       
2266           
2267           
2268                <em>b </em>
2269                <em>Ethanol</em>
2270              </li>
2271              <li>      the last term in the equation should read
2272     
2273         
2274         
2275     
2276         
2277         
2278              <em>bpq</em>/(
2279     
2280         
2281         
2282     
2283         
2284         
2285              <em>K
2286     
2287         
2288         
2289     
2290         
2291         
2292              <sub>ib</sub>K
2293     
2294         
2295         
2296     
2297         
2298         
2299              <sub>iq</sub>K
2300     
2301         
2302         
2303     
2304         
2305         
2306              <sub>p</sub>
2307            </em>)</li>
2308          </ol>
2309        in the kinetic law for
2310 
2311     
2312     
2313 
2314     
2315     
2316          <em>PFK</em>:
2317       
2318 
2319     
2320     
2321 
2322     
2323     
2324          <ol>
2325            <li>        R = 1 + &#x3BB;
2326            <sub>1</sub> + &#x3BB;
2327            <sub>2</sub>  + g
2328            <sub>r</sub> &#x3BB;
2329            <sub>1</sub> &#x3BB;
2330            <sub>2</sub>
2331          </li>
2332          <li> equation L  should read: L = L0*(..)
2333   
2334       
2335       
2336   
2337       
2338       
2339          <sup>2</sup>*(..)
2340   
2341       
2342       
2343   
2344       
2345       
2346          <sup>2</sup>*(..)
2347   
2348       
2349       
2350   
2351       
2352       
2353          <sup>2</sup> not L = L0*(..)
2354   
2355       
2356       
2357   
2358       
2359       
2360          <sup>2</sup>*(..)
2361   
2362       
2363       
2364   
2365       
2366       
2367          <sup>2</sup>*(..)</li>
2368        </ol>
2369       
2370        To make the model easier to curate, the species
2371 
2372     
2373     
2374 
2375     
2376     
2377        <em>ATP</em>,
2378 
2379     
2380     
2381 
2382     
2383     
2384        <em>ADP</em> and
2385 
2386     
2387     
2388 
2389     
2390     
2391        <em>AMP</em> were added. These are calculated via assignment rules from the active phosphate species,
2392 
2393     
2394     
2395 
2396     
2397     
2398        <em>P</em>, and the sum of all
2399 
2400     
2401     
2402 
2403     
2404     
2405        <em>AXP</em>,
2406 
2407     
2408     
2409 
2410     
2411     
2412        <em>SUM_P</em>.</p>
2413        <p>This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.<br></br>For more information see the <a href=\"http://www.ebi.ac.uk/biomodels/legal.html\" target=\"_blank\">terms of use</a>.<br></br>To cite BioModels Database, please use <a href=\"http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=16381960\" target=\"_blank\">Le Nov&#xe8;re N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.</a>
2414      </p>
2415    </body>
2416  "
2417  :rdf-annotation ((:name "BQM_IS" :resources
2418                    ("urn:miriam:biomodels.db:BIOMD0000000064"))
2419                   (:name "BQM_IS_DESCRIBED_BY" :resources
2420                    ("urn:miriam:pubmed:10951190"))
2421                   (:name "BQB_IS_HOMOLOG_TO" :resources
2422                    ("urn:miriam:reactome:REACT_723"))
2423                   (:name "BQB_IS" :resources
2424                    ("urn:miriam:kegg.pathway:sce00010"
2425                     "urn:miriam:obo.go:GO%3A0019642"))
2426                   (:name "BQB_OCCURS_IN" :resources
2427                    ("urn:miriam:taxonomy:4932")))
2428  :geometry-width "317"
2429  :geometry-height "281"
2430  :modules
2431  (("ca_adp"
2432    :is-a "cf2co"
2433    :geometry-x "127"
2434    :geometry-y "109")
2435   ("ca_amp"
2436    :is-a "cf2co"
2437    :geometry-x "218"
2438    :geometry-y "119")
2439   ("ca_atp"
2440    :is-a "cf2co"
2441    :geometry-x "77"
2442    :geometry-y "156")
2443   ("ca_p"
2444    :is-a "cf2co"
2445    :geometry-x "96"
2446    :geometry-y "199")
2447   ("ca_sum_p"
2448    :is-a "cf2co"
2449    :geometry-x "65"
2450    :geometry-y "143")
2451   ("extracellular"
2452    :is-a "teusink2000_glycolysis-extracellular"
2453    :geometry-x "172"
2454    :geometry-y "128")
2455   ("rules"
2456    :is-a "teusink2000_glycolysis-rules"
2457    :geometry-x "120"
2458    :geometry-y "184"))
2459  :links
2460  (("cl_adp"
2461    :terminals ("ca_adp.co" "rules.t_adp"))
2462   ("cl_amp"
2463    :terminals ("ca_amp.co" "rules.t_amp"))
2464   ("cl_atp"
2465    :terminals ("ca_atp.co" "rules.t_atp"))
2466   ("cl_p"
2467    :terminals ("ca_p.co" "rules.t_p"))
2468   ("cl_sum_p"
2469    :terminals ("ca_sum_p.co" "rules.t_sum_p"))
2470   ("fl_adp"
2471    :terminals ("extracellular.t_adp" "ca_adp.cf"))
2472   ("fl_amp"
2473    :terminals ("extracellular.t_amp" "ca_amp.cf"))
2474   ("fl_atp"
2475    :terminals ("extracellular.t_atp" "ca_atp.cf"))
2476   ("fl_p"
2477    :terminals ("extracellular.t_p" "ca_p.cf"))
2478   ("fl_sum_p"
2479    :terminals ("extracellular.t_sum_p" "ca_sum_p.cf")))
2480  :variables
2481  (("cipfkatp"
2482    :is-a "sbml-parameter"
2483    :system-theoretic "real-parameter"
2484    :value "100.0d0"
2485    :model-name "cipfkatp")
2486   ("cpfkamp"
2487    :is-a "sbml-parameter"
2488    :system-theoretic "real-parameter"
2489    :value "0.0845d0"
2490    :model-name "cpfkamp")
2491   ("cpfkatp"
2492    :is-a "sbml-parameter"
2493    :system-theoretic "real-parameter"
2494    :value "3.0d0"
2495    :model-name "cpfkatp")
2496   ("cpfkf16bp"
2497    :is-a "sbml-parameter"
2498    :system-theoretic "real-parameter"
2499    :value "0.397d0"
2500    :model-name "cpfkf16bp")
2501   ("cpfkf26bp"
2502    :is-a "sbml-parameter"
2503    :system-theoretic "real-parameter"
2504    :value "0.0174d0"
2505    :model-name "cpfkf26bp")
2506   ("gr"
2507    :is-a "sbml-parameter"
2508    :system-theoretic "real-parameter"
2509    :value "5.12d0"
2510    :model-name "gr")
2511   ("keqak"
2512    :label "AK eq constant"
2513    :is-a "sbml-parameter"
2514    :system-theoretic "real-parameter"
2515    :value "0.45d0"
2516    :model-name "keqak")
2517   ("keqtpi"
2518    :label "TPI eq constant"
2519    :is-a "sbml-parameter"
2520    :system-theoretic "real-parameter"
2521    :value "0.045d0"
2522    :model-name "keqtpi")
2523   ("kipfkatp"
2524    :is-a "sbml-parameter"
2525    :system-theoretic "real-parameter"
2526    :value "0.65d0"
2527    :model-name "kipfkatp")
2528   ("kmpfkatp"
2529    :is-a "sbml-parameter"
2530    :system-theoretic "real-parameter"
2531    :value "0.71d0"
2532    :model-name "kmpfkatp")
2533   ("kmpfkf6p"
2534    :is-a "sbml-parameter"
2535    :system-theoretic "real-parameter"
2536    :value "0.1d0"
2537    :model-name "kmpfkf6p")
2538   ("kpfkamp"
2539    :is-a "sbml-parameter"
2540    :system-theoretic "real-parameter"
2541    :value "0.0995d0"
2542    :model-name "kpfkamp")
2543   ("kpfkf16bp"
2544    :is-a "sbml-parameter"
2545    :system-theoretic "real-parameter"
2546    :value "0.111d0"
2547    :model-name "kpfkf16bp")
2548   ("kpfkf26bp"
2549    :is-a "sbml-parameter"
2550    :system-theoretic "real-parameter"
2551    :value "6.82d-4"
2552    :model-name "kpfkf26bp")
2553   ("lzero"
2554    :is-a "sbml-parameter"
2555    :system-theoretic "real-parameter"
2556    :value "0.66d0"
2557    :model-name "lzero")))
2558
2559
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