source: Promot/trunk/promot/kb/testsuite/mdl/hynne.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-variable
8  :class "var-rate"
9  :super-classes ("variable")
10  :value "100.0d0"
11  :minimum "0.0d0"
12  :maximum "100000.0d0"
13  :unit "1/h")
14
15
16(define-variable
17  :class "concentration"
18  :super-classes ("variable")
19  :unit "mol/l")
20
21
22(define-variable
23  :class "molar-flux"
24  :super-classes ("variable")
25  :minimum "0.0d0"
26  :maximum "1000.0d0"
27  :unit "mol/s")
28
29
30(define-variable
31  :class "mass"
32  :super-classes ("variable")
33  :minimum "0.0d0"
34  :maximum "10000.0d0"
35  :unit "mol")
36
37
38(define-variable
39  :class "scaling-parameter"
40  :super-classes ("variable")
41  :documentation "parameter to perform manual numeric scaling of rate-laws
42  etc. for optimization. It is marked as a help-variable to eventually
43remove it by the equation-optimizer in Promot."
44  :system-theoretic "help"
45  :value "1.0d0")
46
47
48(define-variable
49  :class "kinetic-parameter"
50  :super-classes ("variable")
51  :system-theoretic "real-parameter")
52
53
54(define-variable
55  :class "stoichiometry"
56  :super-classes ("variable")
57  :documentation "Don't know what is the best solution, but these parameters
58  should not be changed by the user during simulation, therefore I consider them
59  as helps, which means they can be optimized away."
60  :system-theoretic "help"
61  :value "1.0d0"
62  :unit "1")
63
64
65(define-variable
66  :class "volume"
67  :super-classes ("variable")
68  :minimum "0.0d0"
69  :maximum "10.0d0"
70  :unit "l")
71
72
73(define-variable
74  :class "var-output"
75  :super-classes ("variable")
76  :system-theoretic "output")
77
78
79(define-module
80  :class "sbml-model"
81  :super-classes ("module"))
82
83
84(define-variable
85  :class "var-input"
86  :super-classes ("variable")
87  :system-theoretic "input")
88
89
90(define-module
91  :class "compartment"
92  :super-classes ("module")
93  :variables
94  (("v"
95    :is-a "volume"
96    :system-theoretic "real-parameter"
97    :value "1.0d0")))
98
99
100(define-module
101  :class "reaction"
102  :super-classes ("library")
103  :documentation "Superclass containing all reaction definitions.")
104
105
106(define-module
107  :class "structure"
108  :super-classes ("reaction")
109  :documentation "Superclass containing all possible reaction structures."
110  :variables
111  (("r")))
112
113
114(define-terminal
115  :class "tsig"
116  :super-classes ("terminal")
117  :icon "icons/term_concentration_in.gif"
118  :link-color "green"
119  :variables
120  (("c"
121    :is-a "concentration"
122    :system-theoretic "state"
123    :value "0.0d0")))
124
125
126(define-terminal
127  :class "tflux"
128  :super-classes ("tsig")
129  :icon "icons/term_react_blue.gif"
130  :link-color "blue"
131  :variables
132  (("r"
133    :is-a "molar-flux"
134    :system-theoretic "state"
135    :positive-vector-direction "out"
136    :value "0.0d0")))
137
138
139(define-module
140  :class "s-2-1"
141  :super-classes ("structure")
142  :terminals
143  (("t_p1"
144    :is-a "tflux"
145    :geometry-side "right"
146    :geometry-position "0.5")
147   ("t_r1"
148    :is-a "tflux"
149    :geometry-side "left"
150    :geometry-position "0.33333334")
151   ("t_r2"
152    :is-a "tflux"
153    :geometry-side "left"
154    :geometry-position "0.6666667"))
155  :variables
156  (("gamma_p1"
157    :is-a "stoichiometry"
158    :value "1.0d0")
159   ("gamma_r1"
160    :is-a "stoichiometry"
161    :value "-1.0d0")
162   ("gamma_r2"
163    :is-a "stoichiometry"
164    :value "-1.0d0"))
165  :equations
166  (("e_p1"
167    :relation "t_p1.r == gamma_p1*r")
168   ("e_r1"
169    :relation "t_r1.r == gamma_r1*r")
170   ("e_r2"
171    :relation "t_r2.r == gamma_r2*r")))
172
173
174(define-variable
175  :class "reaction-rate"
176  :super-classes ("molar-flux")
177  :unit "mol/s")
178
179
180(define-module
181  :class "kinetics"
182  :super-classes ("reaction")
183  :documentation "Superclass containing all kinetics."
184  :variables
185  (("r"
186    :is-a "reaction-rate"
187    :documentation "reaction-rate"
188    :system-theoretic "help"
189    :report "lumped"
190    :unit "umol/g_dw/h")
191   ("skal"
192    :is-a "scaling-parameter")))
193
194
195(define-terminal
196  :class "tvol"
197  :super-classes ("terminal")
198  :link-color "yellow"
199  :variables
200  (("v"
201    :is-a "volume"
202    :system-theoretic "state")))
203
204
205(define-module
206  :class "kin-2-1_0_1_k20"
207  :super-classes ("s-2-1" "kinetics")
208  :icon "icons/rev_l"
209  :terminals
210  (("t_c1"
211    :is-a "tvol"
212    :geometry-side "bottom"
213    :geometry-position "0.5"))
214  :variables
215  (("k20"
216    :is-a "kinetic-parameter")))
217
218
219(define-module
220  :class "s-1-1"
221  :super-classes ("structure")
222  :terminals
223  (("t_p1"
224    :is-a "tflux"
225    :geometry-side "right"
226    :geometry-position "0.5")
227   ("t_r1"
228    :is-a "tflux"
229    :geometry-side "left"
230    :geometry-position "0.5"))
231  :variables
232  (("gamma_p1"
233    :is-a "stoichiometry"
234    :value "1.0d0")
235   ("gamma_r1"
236    :is-a "stoichiometry"
237    :value "-1.0d0"))
238  :equations
239  (("e_p1"
240    :relation "t_p1.r == gamma_p1*r")
241   ("e_r1"
242    :relation "t_r1.r == gamma_r1*r")))
243
244
245(define-module
246  :class "kin-1-1_0_1_k0"
247  :super-classes ("s-1-1" "kinetics")
248  :icon "icons/rev_l"
249  :terminals
250  (("t_c1"
251    :is-a "tvol"
252    :geometry-side "bottom"
253    :geometry-position "0.5"))
254  :variables
255  (("k0"
256    :is-a "kinetic-parameter")))
257
258
259(define-module
260  :class "kin-1-1_1_2_2glc_p2_k2ig6p_k2iig6p_v2r1c7f"
261  :super-classes ("s-1-1" "kinetics")
262  :icon "icons/rev_l"
263  :terminals
264  (("t_c1"
265    :is-a "tvol"
266    :geometry-side "bottom"
267    :geometry-position "0.33333334")
268   ("t_c2"
269    :is-a "tvol"
270    :geometry-side "bottom"
271    :geometry-position "0.6666667")
272   ("t_m1"
273    :is-a "tsig"
274    :geometry-side "top"
275    :geometry-position "0.5"))
276  :variables
277  (("k2glc"
278    :is-a "kinetic-parameter")
279   ("k2ig6p"
280    :is-a "kinetic-parameter")
281   ("k2iig6p"
282    :is-a "kinetic-parameter")
283   ("p2"
284    :is-a "kinetic-parameter")
285   ("v2f"
286    :is-a "kinetic-parameter")
287   ("v2r"
288    :is-a "kinetic-parameter")
289   ("yvol"
290    :is-a "kinetic-parameter")))
291
292
293(define-module
294  :class "kin-1-1_0_2_k16_yvol"
295  :super-classes ("s-1-1" "kinetics")
296  :icon "icons/rev_l"
297  :terminals
298  (("t_c1"
299    :is-a "tvol"
300    :geometry-side "bottom"
301    :geometry-position "0.33333334")
302   ("t_c2"
303    :is-a "tvol"
304    :geometry-side "bottom"
305    :geometry-position "0.6666667"))
306  :variables
307  (("k16"
308    :is-a "kinetic-parameter")
309   ("yvol"
310    :is-a "kinetic-parameter")))
311
312
313(define-module
314  :class "kin-1-1_0_2_k13_yvol"
315  :super-classes ("s-1-1" "kinetics")
316  :icon "icons/rev_l"
317  :terminals
318  (("t_c1"
319    :is-a "tvol"
320    :geometry-side "bottom"
321    :geometry-position "0.33333334")
322   ("t_c2"
323    :is-a "tvol"
324    :geometry-side "bottom"
325    :geometry-position "0.6666667"))
326  :variables
327  (("k13"
328    :is-a "kinetic-parameter")
329   ("yvol"
330    :is-a "kinetic-parameter")))
331
332
333(define-module
334  :class "kin-1-1_0_2_k18_yvol"
335  :super-classes ("s-1-1" "kinetics")
336  :icon "icons/rev_l"
337  :terminals
338  (("t_c1"
339    :is-a "tvol"
340    :geometry-side "bottom"
341    :geometry-position "0.33333334")
342   ("t_c2"
343    :is-a "tvol"
344    :geometry-side "bottom"
345    :geometry-position "0.6666667"))
346  :variables
347  (("k18"
348    :is-a "kinetic-parameter")
349   ("yvol"
350    :is-a "kinetic-parameter")))
351
352
353(define-module
354  :class "dyn-adapter"
355  :super-classes ("library")
356  :documentation "Superclass containing adapters. Useful for instance for propagating terminals already connected to other elements.")
357
358
359(define-module
360  :class "adapter-vol"
361  :super-classes ("dyn-adapter"))
362
363
364(define-module
365  :class "adapter-volume-pop"
366  :super-classes ("adapter-vol")
367  :parent-type "compartment"
368  :documentation "exports one tvol as volume out of parent"
369  :properties
370  (("abstract"
371    :value "no"))
372  :icon "icons/adapter.gif"
373  :terminals
374  (("out"
375    :is-a "tvol"
376    :geometry-side "RIGHT"
377    :variables
378    (("v"
379      :is-eq-to "parent.v"))))
380  :variables
381  (("v"
382    :is-eq-to "parent.v")))
383
384
385(define-module
386  :class "compartment-out"
387  :super-classes ("compartment")
388  :terminals
389  (("out"
390    :is-a "tvol"
391    :geometry-side "bottom"
392    :variables
393    (("v"
394      :is-eq-to "parent.v")))))
395
396
397(define-module
398  :class "kin-1-1_0_1__k7gap_v7r_k7eq199b"
399  :super-classes ("s-1-1" "kinetics")
400  :icon "icons/rev_l"
401  :terminals
402  (("t_c1"
403    :is-a "tvol"
404    :geometry-side "bottom"
405    :geometry-position "0.5"))
406  :variables
407  (("k7dhap"
408    :is-a "kinetic-parameter")
409   ("k7eq"
410    :is-a "kinetic-parameter")
411   ("k7gap"
412    :is-a "kinetic-parameter")
413   ("v7f"
414    :is-a "kinetic-parameter")
415   ("v7r"
416    :is-a "kinetic-parameter")))
417
418
419(define-module
420  :class "kin-2-1_0_1_k22"
421  :super-classes ("s-2-1" "kinetics")
422  :icon "icons/rev_l"
423  :terminals
424  (("t_c1"
425    :is-a "tvol"
426    :geometry-side "bottom"
427    :geometry-position "0.5"))
428  :variables
429  (("k22"
430    :is-a "kinetic-parameter")))
431
432
433(define-module
434  :class "s-2-2"
435  :super-classes ("structure")
436  :terminals
437  (("t_p1"
438    :is-a "tflux"
439    :geometry-side "right"
440    :geometry-position "0.33333334")
441   ("t_p2"
442    :is-a "tflux"
443    :geometry-side "right"
444    :geometry-position "0.6666667")
445   ("t_r1"
446    :is-a "tflux"
447    :geometry-side "left"
448    :geometry-position "0.33333334")
449   ("t_r2"
450    :is-a "tflux"
451    :geometry-side "left"
452    :geometry-position "0.6666667"))
453  :variables
454  (("gamma_p1"
455    :is-a "stoichiometry"
456    :value "1.0d0")
457   ("gamma_p2"
458    :is-a "stoichiometry"
459    :value "1.0d0")
460   ("gamma_r1"
461    :is-a "stoichiometry"
462    :value "-1.0d0")
463   ("gamma_r2"
464    :is-a "stoichiometry"
465    :value "-1.0d0"))
466  :equations
467  (("e_p1"
468    :relation "t_p1.r == gamma_p1*r")
469   ("e_p2"
470    :relation "t_p2.r == gamma_p2*r")
471   ("e_r1"
472    :relation "t_r1.r == gamma_r1*r")
473   ("e_r2"
474    :relation "t_r2.r == gamma_r2*r")))
475
476
477(define-module
478  :class "kin-2-2_0_1_v10m_k10pep_k10adp"
479  :super-classes ("s-2-2" "kinetics")
480  :icon "icons/rev_l"
481  :terminals
482  (("t_c1"
483    :is-a "tvol"
484    :geometry-side "bottom"
485    :geometry-position "0.5"))
486  :variables
487  (("k10adp"
488    :is-a "kinetic-parameter")
489   ("k10pep"
490    :is-a "kinetic-parameter")
491   ("v10m"
492    :is-a "kinetic-parameter")))
493
494
495(define-module
496  :class "kin-1-1_0_1_k4f6p_v4r_k4eqnpd"
497  :super-classes ("s-1-1" "kinetics")
498  :icon "icons/rev_l"
499  :terminals
500  (("t_c1"
501    :is-a "tvol"
502    :geometry-side "bottom"
503    :geometry-position "0.5"))
504  :variables
505  (("k4eq"
506    :is-a "kinetic-parameter")
507   ("k4f6p"
508    :is-a "kinetic-parameter")
509   ("k4g6p"
510    :is-a "kinetic-parameter")
511   ("v4f"
512    :is-a "kinetic-parameter")
513   ("v4r"
514    :is-a "kinetic-parameter")))
515
516
517(define-module
518  :class "kin-2-2_1_1_v5m_k5_kappa5"
519  :super-classes ("s-2-2" "kinetics")
520  :icon "icons/rev_l"
521  :terminals
522  (("t_c1"
523    :is-a "tvol"
524    :geometry-side "bottom"
525    :geometry-position "0.5")
526   ("t_m1"
527    :is-a "tsig"
528    :geometry-side "top"
529    :geometry-position "0.5"))
530  :variables
531  (("k5"
532    :is-a "kinetic-parameter")
533   ("kappa5"
534    :is-a "kinetic-parameter")
535   ("v5m"
536    :is-a "kinetic-parameter")))
537
538
539(define-module
540  :class "kin-1-1_0_1_v11m_k11"
541  :super-classes ("s-1-1" "kinetics")
542  :icon "icons/rev_l"
543  :terminals
544  (("t_c1"
545    :is-a "tvol"
546    :geometry-side "bottom"
547    :geometry-position "0.5"))
548  :variables
549  (("k11"
550    :is-a "kinetic-parameter")
551   ("v11m"
552    :is-a "kinetic-parameter")))
553
554
555(define-module
556  :class "kin-2-2_0_1_k9f_k9r"
557  :super-classes ("s-2-2" "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  :variables
565  (("k9f"
566    :is-a "kinetic-parameter")
567   ("k9r"
568    :is-a "kinetic-parameter")))
569
570
571(define-module
572  :class "kin-2-2_0_1_ap_k15inadh_k15inad_k15nadhifc"
573  :super-classes ("s-2-2" "kinetics")
574  :icon "icons/rev_l"
575  :terminals
576  (("t_c1"
577    :is-a "tvol"
578    :geometry-side "bottom"
579    :geometry-position "0.5"))
580  :variables
581  (("k15dhap"
582    :is-a "kinetic-parameter")
583   ("k15inad"
584    :is-a "kinetic-parameter")
585   ("k15inadh"
586    :is-a "kinetic-parameter")
587   ("k15nadh"
588    :is-a "kinetic-parameter")
589   ("v15m"
590    :is-a "kinetic-parameter")))
591
592
593(define-module
594  :class "kin-2-2_0_1__k3atp_k3glc1949"
595  :super-classes ("s-2-2" "kinetics")
596  :icon "icons/rev_l"
597  :terminals
598  (("t_c1"
599    :is-a "tvol"
600    :geometry-side "bottom"
601    :geometry-position "0.5"))
602  :variables
603  (("k3atp"
604    :is-a "kinetic-parameter")
605   ("k3dglc"
606    :is-a "kinetic-parameter")
607   ("k3glc"
608    :is-a "kinetic-parameter")
609   ("v3m"
610    :is-a "kinetic-parameter")))
611
612
613(define-module
614  :class "kin-2-2_0_1_k8nad_k8bpg_k8nadh_v8r_k8eq155b"
615  :super-classes ("s-2-2" "kinetics")
616  :icon "icons/rev_l"
617  :terminals
618  (("t_c1"
619    :is-a "tvol"
620    :geometry-side "bottom"
621    :geometry-position "0.5"))
622  :variables
623  (("k8bpg"
624    :is-a "kinetic-parameter")
625   ("k8eq"
626    :is-a "kinetic-parameter")
627   ("k8gap"
628    :is-a "kinetic-parameter")
629   ("k8nad"
630    :is-a "kinetic-parameter")
631   ("k8nadh"
632    :is-a "kinetic-parameter")
633   ("v8f"
634    :is-a "kinetic-parameter")
635   ("v8r"
636    :is-a "kinetic-parameter")))
637
638
639(define-module
640  :class "kin-1-1_0_1_k23"
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  (("k23"
650    :is-a "kinetic-parameter")))
651
652
653(define-module
654  :class "s-1-2"
655  :super-classes ("structure")
656  :terminals
657  (("t_p1"
658    :is-a "tflux"
659    :geometry-side "right"
660    :geometry-position "0.33333334")
661   ("t_p2"
662    :is-a "tflux"
663    :geometry-side "right"
664    :geometry-position "0.6666667")
665   ("t_r1"
666    :is-a "tflux"
667    :geometry-side "left"
668    :geometry-position "0.5"))
669  :variables
670  (("gamma_p1"
671    :is-a "stoichiometry"
672    :value "1.0d0")
673   ("gamma_p2"
674    :is-a "stoichiometry"
675    :value "1.0d0")
676   ("gamma_r1"
677    :is-a "stoichiometry"
678    :value "-1.0d0"))
679  :equations
680  (("e_p1"
681    :relation "t_p1.r == gamma_p1*r")
682   ("e_p2"
683    :relation "t_p2.r == gamma_p2*r")
684   ("e_r1"
685    :relation "t_r1.r == gamma_r1*r")))
686
687
688(define-module
689  :class "kin-1-2_0_1_k6dhap_k6eq_ratio6_k6gap_k6igapf7a"
690  :super-classes ("s-1-2" "kinetics")
691  :icon "icons/rev_l"
692  :terminals
693  (("t_c1"
694    :is-a "tvol"
695    :geometry-side "bottom"
696    :geometry-position "0.5"))
697  :variables
698  (("k6dhap"
699    :is-a "kinetic-parameter")
700   ("k6eq"
701    :is-a "kinetic-parameter")
702   ("k6fbp"
703    :is-a "kinetic-parameter")
704   ("k6gap"
705    :is-a "kinetic-parameter")
706   ("k6igap"
707    :is-a "kinetic-parameter")
708   ("ratio6"
709    :is-a "kinetic-parameter")
710   ("v6f"
711    :is-a "kinetic-parameter")))
712
713
714(define-module
715  :class "kin-2-1_0_1_k24f_k24r"
716  :super-classes ("s-2-1" "kinetics")
717  :icon "icons/rev_l"
718  :terminals
719  (("t_c1"
720    :is-a "tvol"
721    :geometry-side "bottom"
722    :geometry-position "0.5"))
723  :variables
724  (("k24f"
725    :is-a "kinetic-parameter")
726   ("k24r"
727    :is-a "kinetic-parameter")))
728
729
730(define-module
731  :class "kin-2-2_0_1_v12m_k12nadh_k12aca"
732  :super-classes ("s-2-2" "kinetics")
733  :icon "icons/rev_l"
734  :terminals
735  (("t_c1"
736    :is-a "tvol"
737    :geometry-side "bottom"
738    :geometry-position "0.5"))
739  :variables
740  (("k12aca"
741    :is-a "kinetic-parameter")
742   ("k12nadh"
743    :is-a "kinetic-parameter")
744   ("v12m"
745    :is-a "kinetic-parameter")))
746
747
748(define-variable
749  :class "var-rate-out"
750  :super-classes ("var-rate" "var-output")
751  :absolute-error "1.0d-8")
752
753
754(define-variable
755  :class "var-concentration"
756  :super-classes ("concentration")
757  :value "1.0d-4"
758  :minimum "0.0d0"
759  :maximum "10.0d0")
760
761
762(define-variable
763  :class "var-concentration-out"
764  :super-classes ("var-concentration" "var-output")
765  :absolute-error "1.0d-8")
766
767
768(define-variable
769  :class "var-state-concentration-out"
770  :super-classes ("var-concentration-out")
771  :system-theoretic "output")
772
773
774(define-variable
775  :class "var-rate-in"
776  :super-classes ("var-rate" "var-input")
777  :absolute-error "1.0d-8")
778
779
780(define-terminal
781  :class "term-storage-flux"
782  :super-classes ("terminal")
783  :documentation "Terminal for a flux in a storage."
784  :icon "icons/term_stor_blue.gif"
785  :link-color "blue"
786  :variables
787  (("c"
788    :is-a "var-concentration-out")
789   ("r"
790    :is-a "var-rate-in"
791    :positive-vector-direction "in"
792    :unit "umol/g_dw/h")))
793
794
795(define-variable
796  :class "var-concentration-in"
797  :super-classes ("var-concentration" "var-input")
798  :absolute-error "1.0d-8")
799
800
801(define-terminal
802  :class "term-reaction-flux"
803  :super-classes ("terminal")
804  :documentation "Terminal for a flux in a reaction."
805  :icon "icons/term_react_blue.gif"
806  :link-color "blue"
807  :variables
808  (("c"
809    :is-a "var-concentration-in"
810    :unit "umol/g_dw")
811   ("r"
812    :is-a "var-rate-out"
813    :positive-vector-direction "out"
814    :unit "umol/g_dw/h")))
815
816
817(define-module
818  :class "adapter-flux"
819  :super-classes ("dyn-adapter")
820  :documentation "Flux -> Flux"
821  :properties
822  (("abstract"
823    :value "no"))
824  :icon "icons/adapter.gif"
825  :terminals
826  (("in"
827    :is-a "term-reaction-flux"
828    :geometry-side "LEFT"
829    :geometry-position "0.47333333"
830    :variables
831    (("r"
832      :is-eq-to "parent.r")))
833   ("out"
834    :is-a "term-storage-flux"
835    :geometry-side "RIGHT"
836    :geometry-position "0.47333333"
837    :variables
838    (("c"
839      :is-eq-to "parent.c"))))
840  :variables
841  (("c"
842    :is-a "var-state-concentration-out")
843   ("r"
844    :is-a "var-rate-out"
845    :positive-vector-direction "out"
846    :value "0.0d0"))
847  :equations
848  (("hurg"
849    :relation "c == in.c")
850   ("rate"
851    :relation "r == out.r")))
852
853
854(define-module
855  :class "help"
856  :super-classes ("library")
857  :documentation "Superclass containing accessories for making basic operations on signals or converting terminals.")
858
859
860(define-module
861  :class "term-conv"
862  :super-classes ("help")
863  :documentation "Superclass containing elements for converting different terminal types.")
864
865
866(define-terminal
867  :class "term-concentration-out"
868  :super-classes ("terminal")
869  :documentation "Output terminal for a concentration (signal)"
870  :icon "icons/term_concentration_out.gif"
871  :link-color "green"
872  :variables
873  (("c"
874    :is-a "var-concentration-out"
875    :unit "umol/g_dw")))
876
877
878(define-module
879  :class "cf2co"
880  :super-classes ("term-conv")
881  :documentation "Flux -> Signal. Converts a cf-term to a co-term ."
882  :properties
883  (("abstract"
884    :value "no"))
885  :icon "icons/adapter"
886  :terminals
887  (("cf"
888    :is-a "term-reaction-flux"
889    :geometry-side "LEFT"
890    :geometry-position "0.52666664"
891    :variables
892    (("c"
893      :is-eq-to "parent.c")))
894   ("co"
895    :is-a "term-concentration-out"
896    :geometry-side "RIGHT"
897    :geometry-position "0.52666664"))
898  :variables
899  (("c"
900    :is-a "var-concentration-in"))
901  :equations
902  (("free"
903    :relation "co.c == c")
904   ("rate"
905    :relation "cf.r == 0.0d0")))
906
907
908(define-module
909  :class "storage"
910  :super-classes ("library")
911  :documentation "Superclass for species in the network.")
912
913
914(define-module
915  :class "species"
916  :super-classes ("storage")
917  :documentation "Constant species"
918  :icon "icons/species"
919  :parameters
920  (("cf.r"
921    :positive-vector-direction "in"
922    :value "0.0d0"))
923  :terminals
924  (("cf"
925    :is-a "tflux"
926    :variables
927    (("c"
928      :is-eq-to "parent.c"))))
929  :variables
930  (("c"
931    :is-a "concentration"
932    :system-theoretic "help"
933    :report "lumped"
934    :value "n/v")
935   ("n"
936    :is-a "mass"
937    :system-theoretic "real-parameter")
938   ("v"
939    :is-eq-to "parent.v")))
940
941
942(define-module
943  :class "speciesv"
944  :super-classes ("species")
945  :documentation "Species with molar balance, defined by connected reactions.
946Concentration calculated using surrounding compartment"
947  :icon "icons/speciesv"
948  :parameters
949  (("n"
950    :system-theoretic "state"))
951  :equations
952  (("balc"
953    :relation ":diff<t> n == cf.r")))
954
955
956(define-module
957  :class "hynne2001_glycolysis-cytosol"
958  :super-classes ("compartment-out")
959  :rdf-annotation ((:name "BQB_IS_VERSION_OF" :resources
960                    ("urn:miriam:obo.go:GO%3A0005829")))
961  :geometry-width "976"
962  :geometry-height "1154"
963  :parameters
964  (("aca.c"
965    :label "Acetaldehyde"
966    :model-name "ACA")
967   ("aca.n"
968    :value "1.48153d0*v")
969   ("adp.c"
970    :label "ADP"
971    :model-name "ADP")
972   ("adp.n"
973    :value "1.5d0*v")
974   ("amp.c"
975    :label "AMP"
976    :model-name "AMP")
977   ("amp.n"
978    :value "0.33d0*v")
979   ("atp.c"
980    :label "ATP"
981    :model-name "ATP")
982   ("atp.n"
983    :value "2.1d0*v")
984   ("bpg.c"
985    :label "1,3-Bisphosphoglycerate"
986    :model-name "BPG")
987   ("bpg.n"
988    :value "2.7d-4*v")
989   ("dhap.c"
990    :label "Dihydroxyacetone phosphate"
991    :model-name "DHAP")
992   ("dhap.n"
993    :value "2.95d0*v")
994   ("etoh.c"
995    :model-name "EtOH")
996   ("etoh.n"
997    :value "19.2379d0*v")
998   ("f6p.c"
999    :label "Fructose-6-Phosphate"
1000    :model-name "F6P")
1001   ("f6p.n"
1002    :value "0.49d0*v")
1003   ("fbp.c"
1004    :label "Fructose 1,6-bisphosphate"
1005    :model-name "FBP")
1006   ("fbp.n"
1007    :value "4.64d0*v")
1008   ("g6p.c"
1009    :label "Glucose-6-Phosphate"
1010    :model-name "G6P")
1011   ("g6p.n"
1012    :value "4.2d0*v")
1013   ("gap.c"
1014    :label "Glyceraldehyde 3-phosphate"
1015    :model-name "GAP")
1016   ("gap.n"
1017    :value "0.115d0*v")
1018   ("glc.c"
1019    :label "Cytosolic glucose"
1020    :model-name "Glc")
1021   ("glc.n"
1022    :value "0.573074d0*v")
1023   ("glyc.c"
1024    :label "Glycerol"
1025    :model-name "Glyc")
1026   ("glyc.n"
1027    :value "4.196d0*v")
1028   ("nad.c"
1029    :label "NAD"
1030    :model-name "NAD")
1031   ("nad.n"
1032    :value "0.65d0*v")
1033   ("nadh.c"
1034    :label "NADH"
1035    :model-name "NADH")
1036   ("nadh.n"
1037    :value "0.33d0*v")
1038   ("pep.c"
1039    :label "Phosphoenolpyruvate"
1040    :model-name "PEP")
1041   ("pep.n"
1042    :value "0.04d0*v")
1043   ("pyr.c"
1044    :label "Pyruvate"
1045    :model-name "Pyr")
1046   ("pyr.n"
1047    :value "8.7d0*v")
1048   ("v"
1049    :value "1.0d0"
1050    :model-name "cytosol")
1051   ("vadh.k12aca"
1052    :value "0.71d0")
1053   ("vadh.k12nadh"
1054    :value "0.1d0")
1055   ("vadh.r"
1056    :label "Alcohol dehydrogenase"
1057    :value "v12m*t_r2.c*t_r1.c/((k12nadh+t_r1.c)*(k12aca+t_r2.c))*t_c1.v"
1058    :model-name "vADH")
1059   ("vadh.v12m"
1060    :value "89.8023d0")
1061   ("vak.gamma_p1"
1062    :value "2.0d0")
1063   ("vak.k24f"
1064    :value "432.9d0")
1065   ("vak.k24r"
1066    :value "133.333d0")
1067   ("vak.r"
1068    :label "Adenylate kinase"
1069    :value "t_c1.v*(k24f*t_r2.c*t_r1.c-k24r*t_p1.c ^ 2)"
1070    :model-name "vAK")
1071   ("vald.k6dhap"
1072    :value "2.0d0")
1073   ("vald.k6eq"
1074    :value "0.081d0")
1075   ("vald.k6fbp"
1076    :value "0.3d0")
1077   ("vald.k6gap"
1078    :value "4.0d0")
1079   ("vald.k6igap"
1080    :value "10.0d0")
1081   ("vald.r"
1082    :label "Aldolase"
1083    :value "t_c1.v*(v6f*t_r1.c/(k6fbp+t_r1.c+t_p1.c*k6dhap*v6f/(k6eq*v6f*ratio6)+t_p2.c*k6gap*v6f/(k6eq*v6f*ratio6)+t_r1.c*t_p1.c/k6igap+t_p1.c*t_p2.c*v6f/(k6eq*v6f*ratio6))-v6f*t_p1.c*t_p2.c/k6eq/(k6fbp+t_r1.c+t_p1.c*k6dhap*v6f/(k6eq*v6f*ratio6)+t_p2.c*k6gap*v6f/(k6eq*v6f*ratio6)+t_r1.c*t_p1.c/k6igap+t_p1.c*t_p2.c*v6f/(k6eq*v6f*ratio6)))"
1084    :model-name "vALD")
1085   ("vald.ratio6"
1086    :value "5.0d0")
1087   ("vald.v6f"
1088    :value "2207.82d0")
1089   ("vconsum.k23"
1090    :value "3.2076d0")
1091   ("vconsum.r"
1092    :label "ATP consumption"
1093    :value "t_c1.v*k23*t_r1.c"
1094    :model-name "vconsum")
1095   ("vgapdh.k8bpg"
1096    :value "0.01d0")
1097   ("vgapdh.k8eq"
1098    :value "0.0055d0")
1099   ("vgapdh.k8gap"
1100    :value "0.6d0")
1101   ("vgapdh.k8nad"
1102    :value "0.1d0")
1103   ("vgapdh.k8nadh"
1104    :value "0.06d0")
1105   ("vgapdh.r"
1106    :label "Glyceraldehyde 3-phosphate dehydrogenase"
1107    :value "t_c1.v*(v8f*t_r1.c*t_r2.c/k8gap/k8nad/((1+t_r1.c/k8gap+t_p2.c/k8bpg)*(1+t_r2.c/k8nad+t_p1.c/k8nadh))-v8r*t_p2.c*t_p1.c/k8eq/k8gap/k8nad/((1+t_r1.c/k8gap+t_p2.c/k8bpg)*(1+t_r2.c/k8nad+t_p1.c/k8nadh)))"
1108    :model-name "vGAPDH")
1109   ("vgapdh.v8f"
1110    :value "833.858d0")
1111   ("vgapdh.v8r"
1112    :value "833.858d0")
1113   ("vhk.k3atp"
1114    :value "0.1d0")
1115   ("vhk.k3dglc"
1116    :value "0.37d0")
1117   ("vhk.k3glc"
1118    :value "0.0d0")
1119   ("vhk.r"
1120    :label "Hexokinase"
1121    :value "t_c1.v*v3m*t_r1.c*t_r2.c/(k3dglc*k3atp+k3glc*t_r1.c+k3atp*t_r2.c+t_r2.c*t_r1.c)"
1122    :model-name "vHK")
1123   ("vhk.v3m"
1124    :value "51.7547d0")
1125   ("vlpglyc.k15dhap"
1126    :value "25.0d0")
1127   ("vlpglyc.k15inad"
1128    :value "0.13d0")
1129   ("vlpglyc.k15inadh"
1130    :value "0.034d0")
1131   ("vlpglyc.k15nadh"
1132    :value "0.13d0")
1133   ("vlpglyc.r"
1134    :label "Glycerol synthesis"
1135    :value "v15m*t_r1.c/(k15dhap*(1+k15inadh/t_r2.c*(1+t_p2.c/k15inad))+t_r1.c*(1+k15nadh/t_r2.c*(1+t_p2.c/k15inad)))*t_c1.v"
1136    :model-name "vlpGlyc")
1137   ("vlpglyc.v15m"
1138    :value "81.4797d0")
1139   ("vlppep.k9f"
1140    :value "443866.0d0")
1141   ("vlppep.k9r"
1142    :value "1528.62d0")
1143   ("vlppep.r"
1144    :label "Phosphoenolpyruvate synthesis"
1145    :value "t_c1.v*(k9f*t_r1.c*t_r2.c-k9r*t_p1.c*t_p2.c)"
1146    :model-name "vlpPEP")
1147   ("vpdc.k11"
1148    :value "0.3d0")
1149   ("vpdc.r"
1150    :label "Pyruvate decarboxylase"
1151    :value "v11m*t_r1.c/(k11+t_r1.c)*t_c1.v"
1152    :model-name "vPDC")
1153   ("vpdc.v11m"
1154    :value "53.1328d0")
1155   ("vpfk.k5"
1156    :value "0.021d0")
1157   ("vpfk.kappa5"
1158    :value "0.15d0")
1159   ("vpfk.r"
1160    :label "Phosphofructokinase"
1161    :value "v5m*t_r1.c ^ 2/(k5*(1+t_r2.c/t_m1.c*kappa5*t_r2.c/t_m1.c)+t_r1.c ^ 2)*t_c1.v"
1162    :model-name "vPFK")
1163   ("vpfk.v5m"
1164    :value "45.4327d0")
1165   ("vpgi.k4eq"
1166    :value "0.13d0")
1167   ("vpgi.k4f6p"
1168    :value "0.15d0")
1169   ("vpgi.k4g6p"
1170    :value "0.8d0")
1171   ("vpgi.r"
1172    :label "Phosphoglucoisomerase"
1173    :value "t_c1.v*(v4f*t_r1.c/(k4g6p+t_r1.c+k4g6p/k4f6p*t_p1.c)-t_p1.c/k4eq*v4r/(k4g6p+t_r1.c+k4g6p/k4f6p*t_p1.c))"
1174    :model-name "vPGI")
1175   ("vpgi.v4f"
1176    :value "496.042d0")
1177   ("vpgi.v4r"
1178    :value "496.042d0")
1179   ("vpk.k10adp"
1180    :value "0.17d0")
1181   ("vpk.k10pep"
1182    :value "0.2d0")
1183   ("vpk.r"
1184    :label "Pyruvate kinase"
1185    :value "v10m*t_r1.c*t_r2.c/((k10pep+t_r2.c)*(k10adp+t_r1.c))*t_c1.v"
1186    :model-name "vPK")
1187   ("vpk.v10m"
1188    :value "343.096d0")
1189   ("vstorage.k22"
1190    :value "2.25932d0")
1191   ("vstorage.r"
1192    :label "Storage"
1193    :value "t_c1.v*k22*t_r1.c*t_r2.c"
1194    :model-name "vstorage")
1195   ("vtim.k7dhap"
1196    :value "1.23d0")
1197   ("vtim.k7eq"
1198    :value "0.055d0")
1199   ("vtim.k7gap"
1200    :value "1.27d0")
1201   ("vtim.r"
1202    :label "Triosephosphate isomerase"
1203    :value "t_c1.v*(v7f*t_r1.c/(k7dhap+t_r1.c+k7dhap/k7gap*t_p1.c)-t_p1.c/k7eq*v7r/(k7dhap+t_r1.c+k7dhap/k7gap*t_p1.c))"
1204    :model-name "vTIM")
1205   ("vtim.v7f"
1206    :value "116.365d0")
1207   ("vtim.v7r"
1208    :value "116.365d0"))
1209  :terminals
1210  (("out"
1211    :geometry-side "TOP"
1212    :geometry-position "0.07530738")
1213   ("t_aca"
1214    :is-eq-to "fa_aca.out"
1215    :geometry-side "BOTTOM"
1216    :geometry-position "0.92469263")
1217   ("t_etoh"
1218    :is-eq-to "fa_etoh.out"
1219    :geometry-side "LEFT"
1220    :geometry-position "0.22487001")
1221   ("t_g6p"
1222    :is-eq-to "fa_g6p.out"
1223    :geometry-side "BOTTOM"
1224    :geometry-position "0.321209")
1225   ("t_glc"
1226    :is-eq-to "fa_glc.out"
1227    :geometry-side "RIGHT"
1228    :geometry-position "0.92504334")
1229   ("t_glyc"
1230    :is-eq-to "fa_glyc.out"
1231    :geometry-side "BOTTOM"
1232    :geometry-position "0.92469263"))
1233  :modules
1234  (("aca"
1235    :is-a "speciesv"
1236    :rdf-annotation ((:name "BQB_IS" :resources
1237                      ("urn:miriam:obo.chebi:CHEBI%3A15343"
1238                       "urn:miriam:kegg.compound:C00084")))
1239    :geometry-x "723"
1240    :geometry-y "237")
1241   ("adp"
1242    :is-a "speciesv"
1243    :rdf-annotation ((:name "BQB_IS" :resources
1244                      ("urn:miriam:obo.chebi:CHEBI%3A16761"
1245                       "urn:miriam:kegg.compound:C00008")))
1246    :geometry-x "685"
1247    :geometry-y "786")
1248   ("amp"
1249    :is-a "speciesv"
1250    :rdf-annotation ((:name "BQB_IS" :resources
1251                      ("urn:miriam:obo.chebi:CHEBI%3A16027"
1252                       "urn:miriam:kegg.compound:C00020")))
1253    :geometry-x "888"
1254    :geometry-y "772")
1255   ("atp"
1256    :is-a "speciesv"
1257    :rdf-annotation ((:name "BQB_IS" :resources
1258                      ("urn:miriam:obo.chebi:CHEBI%3A15422"
1259                       "urn:miriam:kegg.compound:C00002")))
1260    :geometry-x "735"
1261    :geometry-y "649")
1262   ("bpg"
1263    :is-a "speciesv"
1264    :rdf-annotation ((:name "BQB_IS" :resources
1265                      ("urn:miriam:obo.chebi:CHEBI%3A16001"
1266                       "urn:miriam:kegg.compound:C00236")))
1267    :geometry-x "544"
1268    :geometry-y "345")
1269   ("ca_amp"
1270    :is-a "cf2co"
1271    :geometry-x "716"
1272    :geometry-y "741")
1273   ("dhap"
1274    :is-a "speciesv"
1275    :rdf-annotation ((:name "BQB_IS" :resources
1276                      ("urn:miriam:obo.chebi:CHEBI%3A16108"
1277                       "urn:miriam:kegg.compound:C00111")))
1278    :geometry-x "165"
1279    :geometry-y "502")
1280   ("etoh"
1281    :is-a "speciesv"
1282    :rdf-annotation ((:name "BQB_IS" :resources
1283                      ("urn:miriam:obo.chebi:CHEBI%3A16236"
1284                       "urn:miriam:kegg.compound:C00469")))
1285    :geometry-x "125"
1286    :geometry-y "278")
1287   ("f6p"
1288    :is-a "speciesv"
1289    :rdf-annotation ((:name "BQB_IS" :resources
1290                      ("urn:miriam:obo.chebi:CHEBI%3A20935"
1291                       "urn:miriam:kegg.compound:C00085")))
1292    :geometry-x "642"
1293    :geometry-y "937")
1294   ("fa_aca"
1295    :is-a "adapter-flux"
1296    :geometry-x "796"
1297    :geometry-y "261")
1298   ("fa_etoh"
1299    :is-a "adapter-flux"
1300    :geometry-x "65"
1301    :geometry-y "340")
1302   ("fa_g6p"
1303    :is-a "adapter-flux"
1304    :geometry-x "272"
1305    :geometry-y "893")
1306   ("fa_glc"
1307    :is-a "adapter-flux"
1308    :geometry-x "481"
1309    :geometry-y "1073")
1310   ("fa_glyc"
1311    :is-a "adapter-flux"
1312    :geometry-x "447"
1313    :geometry-y "78")
1314   ("fbp"
1315    :is-a "speciesv"
1316    :rdf-annotation ((:name "BQB_IS" :resources
1317                      ("urn:miriam:obo.chebi:CHEBI%3A16905"
1318                       "urn:miriam:kegg.compound:C00354")))
1319    :geometry-x "254"
1320    :geometry-y "768")
1321   ("g6p"
1322    :is-a "speciesv"
1323    :rdf-annotation ((:name "BQB_IS" :resources
1324                      ("urn:miriam:obo.chebi:CHEBI%3A15954"
1325                       "urn:miriam:kegg.compound:C00092")))
1326    :geometry-x "371"
1327    :geometry-y "898")
1328   ("gap"
1329    :is-a "speciesv"
1330    :rdf-annotation ((:name "BQB_IS" :resources
1331                      ("urn:miriam:obo.chebi:CHEBI%3A29052"
1332                       "urn:miriam:kegg.compound:C00118")))
1333    :geometry-x "167"
1334    :geometry-y "604")
1335   ("glc"
1336    :is-a "speciesv"
1337    :rdf-annotation ((:name "BQB_IS" :resources
1338                      ("urn:miriam:obo.chebi:CHEBI%3A17234"
1339                       "urn:miriam:kegg.compound:C00293")))
1340    :geometry-x "418"
1341    :geometry-y "1055")
1342   ("glyc"
1343    :is-a "speciesv"
1344    :rdf-annotation ((:name "BQB_IS" :resources
1345                      ("urn:miriam:obo.chebi:CHEBI%3A17754"
1346                       "urn:miriam:kegg.compound:C00116")))
1347    :geometry-x "379"
1348    :geometry-y "96")
1349   ("nad"
1350    :is-a "speciesv"
1351    :rdf-annotation ((:name "BQB_IS" :resources
1352                      ("urn:miriam:obo.chebi:CHEBI%3A15846"
1353                       "urn:miriam:kegg.compound:C00003")))
1354    :geometry-x "349"
1355    :geometry-y "253")
1356   ("nadh"
1357    :is-a "speciesv"
1358    :rdf-annotation ((:name "BQB_IS" :resources
1359                      ("urn:miriam:obo.chebi:CHEBI%3A16908"
1360                       "urn:miriam:kegg.compound:C00004")))
1361    :geometry-x "260"
1362    :geometry-y "286")
1363   ("pep"
1364    :is-a "speciesv"
1365    :rdf-annotation ((:name "BQB_IS" :resources
1366                      ("urn:miriam:obo.chebi:CHEBI%3A26055"
1367                       "urn:miriam:kegg.compound:C00074")))
1368    :geometry-x "747"
1369    :geometry-y "429")
1370   ("pyr"
1371    :is-a "speciesv"
1372    :rdf-annotation ((:name "BQB_IS" :resources
1373                      ("urn:miriam:obo.chebi:CHEBI%3A32816"
1374                       "urn:miriam:kegg.compound:C00022")))
1375    :geometry-x "853"
1376    :geometry-y "462")
1377   ("va"
1378    :is-a "adapter-volume-pop"
1379    :geometry-x "435"
1380    :geometry-y "564")
1381   ("vadh"
1382    :is-a "kin-2-2_0_1_v12m_k12nadh_k12aca"
1383    :geometry-x "404"
1384    :geometry-y "373")
1385   ("vak"
1386    :is-a "kin-2-1_0_1_k24f_k24r"
1387    :geometry-x "653"
1388    :geometry-y "677")
1389   ("vald"
1390    :is-a "kin-1-2_0_1_k6dhap_k6eq_ratio6_k6gap_k6igapf7a"
1391    :geometry-x "314"
1392    :geometry-y "607")
1393   ("vconsum"
1394    :is-a "kin-1-1_0_1_k23"
1395    :geometry-x "545"
1396    :geometry-y "634")
1397   ("vgapdh"
1398    :is-a "kin-2-2_0_1_k8nad_k8bpg_k8nadh_v8r_k8eq155b"
1399    :geometry-x "374"
1400    :geometry-y "455")
1401   ("vhk"
1402    :is-a "kin-2-2_0_1__k3atp_k3glc1949"
1403    :geometry-x "499"
1404    :geometry-y "757")
1405   ("vlpglyc"
1406    :is-a "kin-2-2_0_1_ap_k15inadh_k15inad_k15nadhifc"
1407    :geometry-x "354"
1408    :geometry-y "394")
1409   ("vlppep"
1410    :is-a "kin-2-2_0_1_k9f_k9r"
1411    :geometry-x "562"
1412    :geometry-y "561")
1413   ("vpdc"
1414    :is-a "kin-1-1_0_1_v11m_k11"
1415    :geometry-x "659"
1416    :geometry-y "432")
1417   ("vpfk"
1418    :is-a "kin-2-2_1_1_v5m_k5_kappa5"
1419    :geometry-x "560"
1420    :geometry-y "730")
1421   ("vpgi"
1422    :is-a "kin-1-1_0_1_k4f6p_v4r_k4eqnpd"
1423    :geometry-x "480"
1424    :geometry-y "803")
1425   ("vpk"
1426    :is-a "kin-2-2_0_1_v10m_k10pep_k10adp"
1427    :geometry-x "626"
1428    :geometry-y "574")
1429   ("vstorage"
1430    :is-a "kin-2-1_0_1_k22"
1431    :geometry-x "505"
1432    :geometry-y "694")
1433   ("vtim"
1434    :is-a "kin-1-1_0_1__k7gap_v7r_k7eq199b"
1435    :geometry-x "324"
1436    :geometry-y "554"))
1437  :links
1438  (("cl_amp"
1439    :terminals ("ca_amp.co" "vpfk.t_m1"))
1440   ("fl_aca"
1441    :terminals ("aca.cf" "vpdc.t_p1" "vadh.t_r2" "fa_aca.in")
1442    :nodes (("667" "315"))
1443    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1444   ("fl_adp"
1445    :terminals ("adp.cf" "vhk.t_p2" "vpfk.t_p2" "vlppep.t_r2"
1446                "vpk.t_r1" "vstorage.t_p1" "vconsum.t_p1" "vak.t_p1")
1447    :nodes (("592" "688"))
1448    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1449            ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil)))
1450   ("fl_amp"
1451    :terminals ("amp.cf" "ca_amp.cf" "vak.t_r2")
1452    :nodes (("779" "749"))
1453    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1454   ("fl_atp"
1455    :terminals ("atp.cf" "vhk.t_r1" "vpfk.t_r2" "vlppep.t_p2"
1456                "vpk.t_p2" "vstorage.t_r1" "vconsum.t_r1" "vak.t_r1")
1457    :nodes (("582" "661"))
1458    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1459            ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil)))
1460   ("fl_bpg"
1461    :terminals ("bpg.cf" "vgapdh.t_p2" "vlppep.t_r1")
1462    :nodes (("492" "443"))
1463    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1464   ("fl_dhap"
1465    :terminals ("dhap.cf" "vald.t_p2" "vtim.t_r1" "vlpglyc.t_r1")
1466    :nodes (("260" "508"))
1467    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1468   ("fl_etoh"
1469    :terminals ("etoh.cf" "vadh.t_p2" "fa_etoh.in")
1470    :nodes (("166" "335"))
1471    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1472   ("fl_f6p"
1473    :terminals ("f6p.cf" "vpgi.t_p1" "vpfk.t_r1")
1474    :nodes (("568" "853"))
1475    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1476   ("fl_fbp"
1477    :terminals ("fbp.cf" "vpfk.t_p1" "vald.t_r1")
1478    :nodes (("336" "715"))
1479    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1480   ("fl_g6p"
1481    :terminals ("g6p.cf" "fa_g6p.in" "vhk.t_p1" "vpgi.t_r1"
1482                "vstorage.t_r2")
1483    :nodes (("406" "824"))
1484    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1485            ("4" "-1" nil)))
1486   ("fl_gap"
1487    :terminals ("gap.cf" "vald.t_p1" "vtim.t_p1" "vgapdh.t_r1")
1488    :nodes (("267" "560"))
1489    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1490   ("fl_glc"
1491    :terminals ("glc.cf" "fa_glc.in" "vhk.t_r2")
1492    :nodes (("451" "990"))
1493    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1494   ("fl_glyc"
1495    :terminals ("glyc.cf" "vlpglyc.t_p1" "fa_glyc.in")
1496    :nodes (("395" "172"))
1497    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1498   ("fl_nad"
1499    :terminals ("nad.cf" "vgapdh.t_r2" "vadh.t_p1" "vlpglyc.t_p2")
1500    :nodes (("359" "348"))
1501    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1502   ("fl_nadh"
1503    :terminals ("nadh.cf" "vgapdh.t_p1" "vadh.t_r1" "vlpglyc.t_r2")
1504    :nodes (("313" "364"))
1505    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1506   ("fl_pep"
1507    :terminals ("pep.cf" "vlppep.t_p1" "vpk.t_r2")
1508    :nodes (("644" "504"))
1509    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1510   ("fl_pyr"
1511    :terminals ("pyr.cf" "vpk.t_p1" "vpdc.t_r1")
1512    :nodes (("735" "485"))
1513    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1514   ("vl_cytosol"
1515    :terminals ("va.out" "vhk.t_c1" "vpgi.t_c1" "vpfk.t_c1" "vald.t_c1"
1516                "vtim.t_c1" "vgapdh.t_c1" "vlppep.t_c1" "vpk.t_c1"
1517                "vpdc.t_c1" "vadh.t_c1" "vlpglyc.t_c1" "vstorage.t_c1"
1518                "vconsum.t_c1" "vak.t_c1")
1519    :nodes (("485" "608"))
1520    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1521            ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil)
1522            ("8" "-1" nil) ("9" "-1" nil) ("10" "-1" nil)
1523            ("11" "-1" nil) ("12" "-1" nil) ("13" "-1" nil)
1524            ("14" "-1" nil)))))
1525
1526
1527(define-module
1528  :class "hynne2001_glycolysis-extracellular"
1529  :super-classes ("compartment")
1530  :rdf-annotation ((:name "BQB_IS_VERSION_OF" :resources
1531                    ("urn:miriam:obo.go:GO%3A0005576")))
1532  :geometry-width "850"
1533  :geometry-height "741"
1534  :parameters
1535  (("acax.c"
1536    :label "Extracellular acetaldehyde"
1537    :model-name "ACAX")
1538   ("acax.n"
1539    :value "1.28836d0*v")
1540   ("cnx.c"
1541    :label "Extracellular cyanide"
1542    :model-name "CNX")
1543   ("cnx.n"
1544    :value "5.20358d0*v")
1545   ("cnx0.c"
1546    :label "Mixed flow cyanide "
1547    :model-name "CNX0")
1548   ("cnx0.n"
1549    :value "5.6d0*v")
1550   ("etohx.c"
1551    :label "Extracellular ethanol"
1552    :model-name "EtOHX")
1553   ("etohx.n"
1554    :value "16.4514d0*v")
1555   ("glcx.c"
1556    :label "Extracellular glucose"
1557    :model-name "GlcX")
1558   ("glcx.n"
1559    :value "6.7d0*v")
1560   ("glcx0.c"
1561    :label "Mixed flow glucose"
1562    :model-name "GlcX0")
1563   ("glcx0.n"
1564    :value "24.0d0*v")
1565   ("glycx.c"
1566    :label "Extracellular glycerol"
1567    :model-name "GlycX")
1568   ("glycx.n"
1569    :value "1.68478d0*v")
1570   ("p.c"
1571    :model-name "P")
1572   ("p.n"
1573    :value "0.0d0")
1574   ("v"
1575    :value "1.0d0"
1576    :model-name "extracellular")
1577   ("vdifaca.gamma_r1"
1578    :value "-59.0d0")
1579   ("vdifaca.k18"
1580    :value "24.7d0")
1581   ("vdifaca.r"
1582    :label "Acetaldehyde out"
1583    :value "k18/yvol*(t_c2.v*t_r1.c-t_c1.v*t_p1.c)"
1584    :model-name "vdifACA")
1585   ("vdifaca.yvol"
1586    :value "59.0d0")
1587   ("vdifetoh.gamma_r1"
1588    :value "-59.0d0")
1589   ("vdifetoh.k13"
1590    :value "16.72d0")
1591   ("vdifetoh.r"
1592    :label "Ethanol out"
1593    :value "k13/yvol*(t_c2.v*t_r1.c-t_c1.v*t_p1.c)"
1594    :model-name "vdifEtOH")
1595   ("vdifetoh.yvol"
1596    :value "59.0d0")
1597   ("vdifglyc.gamma_r1"
1598    :value "-59.0d0")
1599   ("vdifglyc.k16"
1600    :value "1.9d0")
1601   ("vdifglyc.r"
1602    :label "Glycerol out"
1603    :value "k16/yvol*(t_c2.v*t_r1.c-t_c1.v*t_p1.c)"
1604    :model-name "vdifGlyc")
1605   ("vdifglyc.yvol"
1606    :value "59.0d0")
1607   ("vglctrans.gamma_p1"
1608    :value "59.0d0")
1609   ("vglctrans.k2glc"
1610    :value "1.7d0")
1611   ("vglctrans.k2ig6p"
1612    :value "1.2d0")
1613   ("vglctrans.k2iig6p"
1614    :value "7.2d0")
1615   ("vglctrans.p2"
1616    :value "1.0d0")
1617   ("vglctrans.r"
1618    :label "Glucose uptake"
1619    :value "t_c2.v*v2f/yvol*t_r1.c/k2glc/(1+t_r1.c/k2glc+(t_r1.c/k2glc*p2+1)/(t_p1.c/k2glc*p2+1)*(1+t_p1.c/k2glc+t_m1.c/k2ig6p+t_p1.c*t_m1.c/(k2glc*k2iig6p)))-t_c1.v*v2r/yvol*t_p1.c/k2glc/(1+t_p1.c/k2glc+(t_p1.c/k2glc*p2+1)/(t_r1.c/k2glc*p2+1)*(1+t_r1.c/k2glc)+t_m1.c/k2ig6p+t_p1.c*t_m1.c/(k2glc*k2iig6p))"
1620    :model-name "vGlcTrans")
1621   ("vglctrans.v2f"
1622    :value "1014.96d0")
1623   ("vglctrans.v2r"
1624    :value "1014.96d0")
1625   ("vglctrans.yvol"
1626    :value "59.0d0")
1627   ("vincn.k0"
1628    :value "0.048d0")
1629   ("vincn.r"
1630    :label "Cyanide flow"
1631    :value "t_c1.v*k0*(t_r1.c-t_p1.c)"
1632    :model-name "vinCN")
1633   ("vinglc.k0"
1634    :value "0.048d0")
1635   ("vinglc.r"
1636    :label "Glucose Mixed flow to extracellular medium"
1637    :value "t_c1.v*k0*(t_r1.c-t_p1.c)"
1638    :model-name "vinGlc")
1639   ("vlacto.k20"
1640    :value "0.00283828d0")
1641   ("vlacto.r"
1642    :label "Cyanide-Acetaldehyde flow"
1643    :value "t_c1.v*k20*t_r2.c*t_r1.c"
1644    :model-name "vlacto")
1645   ("voutaca.k0"
1646    :value "0.048d0")
1647   ("voutaca.r"
1648    :label "Acetaldehyde flow"
1649    :value "t_c1.v*k0*t_r1.c"
1650    :model-name "voutACA")
1651   ("voutetoh.k0"
1652    :value "0.048d0")
1653   ("voutetoh.r"
1654    :label "Ethanol flow"
1655    :value "t_c1.v*k0*t_r1.c"
1656    :model-name "voutEtOH")
1657   ("voutglyc.k0"
1658    :value "0.048d0")
1659   ("voutglyc.r"
1660    :label "Glycerol flow"
1661    :value "t_c1.v*k0*t_r1.c"
1662    :model-name "voutGlyc"))
1663  :modules
1664  (("acax"
1665    :is-a "speciesv"
1666    :rdf-annotation ((:name "BQB_IS" :resources
1667                      ("urn:miriam:obo.chebi:CHEBI%3A15343"
1668                       "urn:miriam:kegg.compound:C00084")))
1669    :geometry-x "529"
1670    :geometry-y "160")
1671   ("ca_g6p"
1672    :is-a "cf2co"
1673    :geometry-x "138"
1674    :geometry-y "427")
1675   ("cnx"
1676    :is-a "speciesv"
1677    :rdf-annotation ((:name "BQB_IS" :resources
1678                      ("urn:miriam:obo.chebi:CHEBI%3A17514"
1679                       "urn:miriam:kegg.compound:C00177")))
1680    :geometry-x "762"
1681    :geometry-y "312")
1682   ("cnx0"
1683    :is-a "species"
1684    :rdf-annotation ((:name "BQB_IS" :resources
1685                      ("urn:miriam:obo.chebi:CHEBI%3A17514"
1686                       "urn:miriam:kegg.compound:C00177")))
1687    :geometry-x "704"
1688    :geometry-y "475")
1689   ("cytosol"
1690    :is-a "hynne2001_glycolysis-cytosol"
1691    :geometry-x "152"
1692    :geometry-y "303")
1693   ("etohx"
1694    :is-a "speciesv"
1695    :rdf-annotation ((:name "BQB_IS" :resources
1696                      ("urn:miriam:obo.chebi:CHEBI%3A16236"
1697                       "urn:miriam:kegg.compound:C000469")))
1698    :geometry-x "295"
1699    :geometry-y "88")
1700   ("glcx"
1701    :is-a "speciesv"
1702    :rdf-annotation ((:name "BQB_IS" :resources
1703                      ("urn:miriam:obo.chebi:CHEBI%3A17234"
1704                       "urn:miriam:kegg.compound:C00293")))
1705    :geometry-x "135"
1706    :geometry-y "615")
1707   ("glcx0"
1708    :is-a "species"
1709    :rdf-annotation ((:name "BQB_IS" :resources
1710                      ("urn:miriam:obo.chebi:CHEBI%3A17234"
1711                       "urn:miriam:kegg.compound:C00293")))
1712    :geometry-x "253"
1713    :geometry-y "658")
1714   ("glycx"
1715    :is-a "speciesv"
1716    :rdf-annotation ((:name "BQB_IS" :resources
1717                      ("urn:miriam:obo.chebi:CHEBI%3A17754"
1718                       "urn:miriam:kegg.compound:C00116")))
1719    :geometry-x "485"
1720    :geometry-y "633")
1721   ("p"
1722    :is-a "species"
1723    :geometry-x "608"
1724    :geometry-y "348")
1725   ("va"
1726    :is-a "adapter-volume-pop"
1727    :geometry-x "407"
1728    :geometry-y "459")
1729   ("vdifaca"
1730    :is-a "kin-1-1_0_2_k18_yvol"
1731    :geometry-x "340"
1732    :geometry-y "342")
1733   ("vdifetoh"
1734    :is-a "kin-1-1_0_2_k13_yvol"
1735    :geometry-x "285"
1736    :geometry-y "258")
1737   ("vdifglyc"
1738    :is-a "kin-1-1_0_2_k16_yvol"
1739    :geometry-x "337"
1740    :geometry-y "440")
1741   ("vglctrans"
1742    :is-a "kin-1-1_1_2_2glc_p2_k2ig6p_k2iig6p_v2r1c7f"
1743    :geometry-x "235"
1744    :geometry-y "444")
1745   ("vincn"
1746    :is-a "kin-1-1_0_1_k0"
1747    :geometry-x "620"
1748    :geometry-y "423")
1749   ("vinglc"
1750    :is-a "kin-1-1_0_1_k0"
1751    :geometry-x "262"
1752    :geometry-y "565")
1753   ("vlacto"
1754    :is-a "kin-2-1_0_1_k20"
1755    :geometry-x "537"
1756    :geometry-y "311")
1757   ("voutaca"
1758    :is-a "kin-1-1_0_1_k0"
1759    :geometry-x "456"
1760    :geometry-y "322")
1761   ("voutetoh"
1762    :is-a "kin-1-1_0_1_k0"
1763    :geometry-x "396"
1764    :geometry-y "279")
1765   ("voutglyc"
1766    :is-a "kin-1-1_0_1_k0"
1767    :geometry-x "467"
1768    :geometry-y "450"))
1769  :links
1770  (("cl_g6p"
1771    :terminals ("ca_g6p.co" "vglctrans.t_m1"))
1772   ("fl_aca"
1773    :terminals ("cytosol.t_aca" "vdifaca.t_r1"))
1774   ("fl_acax"
1775    :terminals ("acax.cf" "vdifaca.t_p1" "voutaca.t_r1" "vlacto.t_r2")
1776    :nodes (("467" "260"))
1777    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))
1778   ("fl_cnx"
1779    :terminals ("cnx.cf" "vlacto.t_r1" "vincn.t_p1")
1780    :nodes (("662" "338"))
1781    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1782   ("fl_cnx0"
1783    :terminals ("cnx0.cf" "vincn.t_r1"))
1784   ("fl_etoh"
1785    :terminals ("cytosol.t_etoh" "vdifetoh.t_r1"))
1786   ("fl_etohx"
1787    :terminals ("etohx.cf" "vdifetoh.t_p1" "voutetoh.t_r1")
1788    :nodes (("301" "180"))
1789    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1790   ("fl_g6p"
1791    :terminals ("cytosol.t_g6p" "ca_g6p.cf"))
1792   ("fl_glc"
1793    :terminals ("cytosol.t_glc" "vglctrans.t_p1"))
1794   ("fl_glcx"
1795    :terminals ("glcx.cf" "vinglc.t_p1" "vglctrans.t_r1")
1796    :nodes (("187" "553"))
1797    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1798   ("fl_glcx0"
1799    :terminals ("glcx0.cf" "vinglc.t_r1"))
1800   ("fl_glyc"
1801    :terminals ("cytosol.t_glyc" "vdifglyc.t_r1"))
1802   ("fl_glycx"
1803    :terminals ("glycx.cf" "vdifglyc.t_p1" "voutglyc.t_r1")
1804    :nodes (("431" "539"))
1805    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))
1806   ("fl_p"
1807    :terminals ("p.cf" "voutetoh.t_p1" "voutglyc.t_p1" "voutaca.t_p1"
1808                "vlacto.t_p1")
1809    :nodes (("510" "355"))
1810    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1811            ("4" "-1" nil)))
1812   ("vl_cytosol"
1813    :terminals ("cytosol.out" "vglctrans.t_c1" "vdifetoh.t_c2"
1814                "vdifglyc.t_c2" "vdifaca.t_c2")
1815    :nodes (("263" "353"))
1816    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1817            ("4" "-1" nil)))
1818   ("vl_extracellular"
1819    :terminals ("va.out" "vinglc.t_c1" "vglctrans.t_c2" "vdifetoh.t_c1"
1820                "voutetoh.t_c1" "vdifglyc.t_c1" "voutglyc.t_c1"
1821                "vdifaca.t_c1" "voutaca.t_c1" "vlacto.t_c1"
1822                "vincn.t_c1")
1823    :nodes (("391" "403"))
1824    :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)
1825            ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil)
1826            ("8" "-1" nil) ("9" "-1" nil) ("10" "-1" nil)))))
1827
1828
1829(define-module
1830  :class "hynne2001_glycolysis"
1831  :super-classes ("sbml-model")
1832  :documentation "
1833      <body xmlns=\"http://www.w3.org/1999/xhtml\">
1834        <p align=\"right\"> The model reproduces Fig 6 of the paper. The stoichiometry and rate of reactions involving uptake of metabolites from extracellular medium have been changed corresponding to Yvol (ratio of extracellular volume to cytosolic volume) mentioned in the publication. The extracellular and cytosolic compartments have been set to 1. Concentration of extracellular glucose, GlcX, is set to 6.7 according to the equation for cellular glucose uptake rate in Table 7 of the paper. The model was successfully tested on MathSBML and Jarnac</p>
1835        <p align=\"right\">
1836          <font color=\"#FFFFFF\">.</font>
1837        </p>
1838        <p align=\"right\">
1839          <font color=\"#FFFFFF\">.</font>
1840        </p>
1841        <p align=\"right\">
1842          <font color=\"#FFFFFF\">.</font>
1843        </p>
1844        <p align=\"left\">
1845          <font face=\"Arial, Helvetica, sans-serif\">
1846            <b>
1847              <a href=\"http://www.sbml.org/\">SBML</a> level 2 code generated for the JWS Online project by Jacky Snoep using
1848         
1849             
1850             
1851              <a href=\"http://pysces.sourceforge.net/\">PySCeS</a>
1852              <br></br>
1853Run this model online at
1854         
1855             
1856             
1857              <a href=\"http://jjj.biochem.sun.ac.za/\">http://jjj.biochem.sun.ac.za</a>
1858              <br></br>
1859To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004)
1860         
1861             
1862             
1863              <a href=\"http://bioinformatics.oupjournals.org/cgi/content/abstract/20/13/2143\">Web-based
1864modelling using JWS Online</a>, Bioinformatics, 20:2143-2144
1865 </b>
1866            </font>
1867          </p>
1868          <p align=\"right\">
1869            <font color=\"#FFFFFF\">.</font>
1870          </p>
1871          <p align=\"right\">
1872            <font color=\"#FFFFFF\">.</font>
1873          </p>
1874          <p align=\"right\">
1875            <font color=\"#FFFFFF\">.</font>
1876          </p>
1877          <p align=\"right\">
1878            <font color=\"#FFFFFF\">.</font>
1879          </p>
1880          <p align=\"right\">
1881            <font color=\"#FFFFFF\">.</font>
1882          </p>
1883          <p align=\"right\">
1884            <font color=\"#FFFFFF\">.</font>
1885          </p>
1886          <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>
1887        </p>
1888      </body>
1889    "
1890  :rdf-annotation ((:name "BQM_IS" :resources
1891                    ("urn:miriam:biomodels.db:BIOMD0000000061"))
1892                   (:name "BQM_IS_DESCRIBED_BY" :resources
1893                    ("urn:miriam:pubmed:11744196"))
1894                   (:name "BQB_IS_HOMOLOG_TO" :resources
1895                    ("urn:miriam:reactome:REACT_1383"))
1896                   (:name "BQB_IS_VERSION_OF" :resources
1897                    ("urn:miriam:obo.go:GO%3A0006096"))
1898                   (:name "BQB_IS" :resources
1899                    ("urn:miriam:taxonomy:4932"
1900                     "urn:miriam:kegg.pathway:sce00010")))
1901  :geometry-width "290"
1902  :geometry-height "286"
1903  :modules
1904  (("extracellular"
1905    :is-a "hynne2001_glycolysis-extracellular"
1906    :geometry-x "140"
1907    :geometry-y "147")))
1908
1909
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