349914
has part: P97471
type: Species
is version of: C00562
has only substance units: false
is: SBO:0000296
name: pSmad3_Smad4_n
initial amount: NaN
in compartment: 349704
boundary condition: false
constant: false
has part: Q05CN3
initial concentration: 0.0

538730
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

539696
stoichiometry: 1.0
species: 349707
type: SpeciesReference

350054
kinetic law: 539443
reactant: 539431
reactant: 539419
is version of: GO:0009056
fast: false
reversible: false
name: Rec_degrad1
type: Reaction

541487
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

349705
has only substance units: false
constant: false
name: TGF_RII
initial concentration: 0.0
is version of: Q62312
in compartment: 349703
boundary condition: false
is: SBO:0000252
type: Species
initial amount: NaN

540332
stoichiometry: 1.0
species: 349769
type: SpeciesReference

350468
is: SBO:0000156
value: 0.05288
name: k2
type: LocalParameter

539732
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

540681
stoichiometry: 2.0
species: COPASI13
type: SpeciesReference

542099
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

350451
is: SBO:0000153
value: 8.69
name: k1
type: LocalParameter

540392
stoichiometry: 1.0
species: 349712
type: SpeciesReference

350127
kinetic law: 539816
reactant: 539804
is version of: GO:0009056
fast: false
reversible: false
name: Rec_degrad
type: Reaction

350252
kinetic law: 541222
product: 541210
reactant: 541198
reactant: 541186
is version of: GO:0006461
fast: false
reversible: true
name: Smad_inhibComp3Ski
type: Reaction

COPASI3
type: Species
is version of: O35253
in compartment: 349703
initial concentration: 0.0
is: SBO:0000252
boundary condition: false
has only substance units: false
name: Smad7_c
initial amount: NaN
constant: false

350441
is: SBO:0000153
value: 0.156
name: k1
type: LocalParameter

349915
has part: Q62432
type: Species
has part: P97471
in compartment: 349704
is: SBO:0000296
initial amount: NaN
has only substance units: false
boundary condition: false
initial concentration: 0.0
name: Smad4_Smad2_n
constant: false

350479
is: SBO:0000009
value: 0.01183
name: v
type: LocalParameter

349704
is version of: GO:0005634
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus
type: Compartment

350469
is: SBO:0000153
value: 0.156
name: k1
type: LocalParameter

350045
kinetic law: 539260
product: 539248
reactant: 539236
reactant: 539224
is version of: GO:0006461
fast: false
reversible: false
name: Smad_compCyt2
type: Reaction

350703
is: SBO:0000196
constant: true
value: 0.01
name: TGFbeta
type: Parameter

539780
stoichiometry: 1.0
species: 349903
type: SpeciesReference

541078
stoichiometry: 1.0
species: 349789
type: SpeciesReference

540633
stoichiometry: 2.0
species: 349769
type: SpeciesReference

539309
stoichiometry: 1.0
species: 349732
type: SpeciesReference

350325
kinetic law: 541943
reactant: 541931
is version of: GO:0009056
fast: false
reversible: false
name: Samd3-comp-degrad
type: Reaction

350440
is: SBO:0000337
value: 1000.0
name: k1
type: LocalParameter

349935
type: Species
has only substance units: false
is: SBO:0000252
initial concentration: 0.0
in compartment: 349704
constant: false
initial amount: NaN
has part: P97471
boundary condition: false
name: Smad4_Ski_n

540080
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

541643
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

539936
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI4
is: SBO:0000252
has only substance units: false
is version of: A2A5Z6
initial amount: NaN
in compartment: 349703
constant: false
initial concentration: 0.0
type: Species
name: Smurf2_c
boundary condition: false

538718
stoichiometry: 3.0
species: COPASI12
type: SpeciesReference

541499
stoichiometry: 1.0
species: 349959
type: SpeciesReference

539720
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

540693
stoichiometry: 1.0
species: 349914
type: SpeciesReference

349703
is version of: GO:0005737
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

350042
kinetic law: 539212
product: 539200
reactant: 539188
is version of: GO:0006810
fast: false
reversible: false
name: Smad2-P_transp
type: Reaction

350466
is: SBO:0000009
value: 0.0125
name: v
type: LocalParameter

350453
is: SBO:0000009
value: 0.00146
name: v
type: LocalParameter

540296
stoichiometry: 1.0
species: 349911
type: SpeciesReference

540380
stoichiometry: 1.0
species: 349769
type: SpeciesReference

349932
in compartment: 349704
is version of: Q60698
has only substance units: false
constant: false
boundary condition: false
initial concentration: 0.0
type: Species
initial amount: NaN
name: Ski_n
is: SBO:0000252

540969
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI5
is version of: Q60698
constant: false
boundary condition: false
type: Species
in compartment: 349703
has only substance units: false
initial concentration: 0.0
is: SBO:0000252
initial amount: NaN
name: Ski_c

350715
constant: false
value: 0.0
name: allSmad2
type: Parameter

350057
kinetic law: 539491
product: 539479
reactant: 539467
reactant: 539455
is version of: GO:0006461
fast: false
reversible: true
name: Rec_inhib
type: Reaction

538899
stoichiometry: 1.0
species: 349906
type: SpeciesReference

540128
stoichiometry: 1.0
species: 349765
type: SpeciesReference

350467
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

539284
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

350169
kinetic law: 540272
product: 540260
reactant: 540248
is version of: GO:0016311
fast: false
reversible: false
name: Smad3_dephospNuc
type: Reaction

350452
is: SBO:0000156
value: 0.01
name: k2
type: LocalParameter

540621
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

350255
kinetic law: 541258
reactant: 541246
reactant: 541234
is version of: GO:0009056
fast: false
reversible: false
name: Rec_degrad2
type: Reaction

COPASI6
is version of: A2A5Z6
type: Species
has only substance units: false
name: Smurf1_c
is: SBO:0000252
initial amount: NaN
boundary condition: false
in compartment: 349703
initial concentration: 0.0
constant: false

350050
kinetic law: 539370
product: 539358
reactant: 539345
is version of: GO:0006810
fast: false
reversible: true
name: Smad7_transp
type: Reaction

542075
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

349769
constant: false
initial concentration: 0.0
has only substance units: false
initial amount: NaN
boundary condition: false
is version of: C00562
in compartment: 349703
is version of: Q05CN3
name: pSmad3_c
is: SBO:0000252
type: Species

350718
constant: false
value: 0.0
name: allSmad4
type: Parameter

540428
stoichiometry: 1.0
species: 349911
type: SpeciesReference

350508
is: SBO:0000186
value: 3.51
name: V
type: LocalParameter

538608
stoichiometry: 2.0
species: 349911
type: SpeciesReference

349910
name: Smad4_SnoN_n
is: SBO:0000296
has only substance units: false
in compartment: 349704
initial concentration: 0.0
has part: P97471
constant: false
initial amount: NaN
boundary condition: false
type: Species
has part: Q60979

350276
kinetic law: 541414
product: 541402
reactant: 541390
reactant: 541378
is version of: GO:0010843
fast: false
reversible: true
name: Smad3-freePromot
type: Reaction

349715
in compartment: 349703
name: Smad2_SARA
is: SBO:0000296
boundary condition: false
constant: false
has part: Q62432
initial concentration: 0.0
has only substance units: false
has part: A9XB08
initial amount: NaN
type: Species

350030
kinetic law: 538923
product: 538911
reactant: 538899
reactant: 538887
is version of: GO:0006461
fast: false
reversible: true
name: Smad7-Smurf2
type: Reaction

350256
kinetic law: 541294
product: 541282
reactant: 541270
is version of: GO:0006810
fast: false
reversible: true
name: Smad7-Smurf1_transp
type: Reaction

349749
constant: false
in compartment: 349703
has part: O35253
name: Rec_Smad7
type: Species
has only substance units: false
initial amount: NaN
is: SBO:0000296
has part: P04202
boundary condition: false
initial concentration: 0.0
has part: Q64729
has part: Q62312

350041
reactant: 539127
product: 539139
is version of: GO:0016310
type: Reaction
name: Smad2_phosphSARA
product: 539151
modifier: 539164
reversible: false
fast: false
kinetic law: 539176

350408
is: SBO:0000027
value: 40.0
name: Km
type: LocalParameter

350247
kinetic law: 541090
product: 541078
reactant: 541066
reactant: 541054
is version of: GO:0006461
fast: false
reversible: true
name: Smad3-Ski_cyt
type: Reaction

349789
has only substance units: false
has part: Q60698
is: SBO:0000296
has part: Q05CN3
in compartment: 349703
name: Smad3_Ski_c
type: Species
initial concentration: 0.0
initial amount: NaN
constant: false
boundary condition: false

541306
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

349911
type: Species
in compartment: 349704
initial concentration: 0.0
is: SBO:0000252
has only substance units: false
boundary condition: false
is version of: Q05CN3
constant: false
name: Smad3_n
initial amount: NaN

349939
has part: A2A5Z6
has part: O35253
type: Species
is: SBO:0000296
initial amount: NaN
name: Smad7_Smurf1_n
boundary condition: false
constant: false
in compartment: 349704
has only substance units: false
initial concentration: 0.0

541054
stoichiometry: 1.0
species: 349766
type: SpeciesReference

539272
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

541619
stoichiometry: 1.0
species: 349869
type: SpeciesReference

349748
constant: false
has part: O35253
boundary condition: false
initial concentration: 0.0
type: Species
initial amount: NaN
has only substance units: false
has part: A2A5Z6
name: Smad7_Smurf2_c
is: SBO:0000296
in compartment: 349703

350139
kinetic law: 539972
reactant: 539960
is version of: GO:0009056
fast: false
reversible: false
name: Smad4_degrad
type: Reaction

349707
boundary condition: false
has only substance units: false
is version of: Q64729
name: TGF_RI
type: Species
is: SBO:0000252
in compartment: 349703
initial amount: NaN
initial concentration: 0.0
constant: false

349838
name: pSmad3_SnoN_n
has only substance units: false
in compartment: 349703
boundary condition: false
has part: Q05CN3
initial amount: NaN
constant: false
is: SBO:0000296
type: Species
initial concentration: 0.0
is version of: C00562
has part: Q60979

541571
stoichiometry: 1.0
species: 349940
type: SpeciesReference

350706
constant: false
value: 0.0
name: allSnoN
type: Parameter

349936
is version of: A2A5Z6
boundary condition: false
constant: false
initial amount: NaN
name: Smurf1_n
type: Species
initial concentration: 0.0
in compartment: 349704
is: SBO:0000252
has only substance units: false

540368
stoichiometry: 1.0
species: 349770
type: SpeciesReference

350324
kinetic law: 541919
reactant: 541907
is version of: GO:0009056
fast: false
reversible: false
name: Smad2-comp-degrad
type: Reaction

539419
stoichiometry: 1.0
species: 349748
type: SpeciesReference

538790
stoichiometry: 1.0
species: 349869
type: SpeciesReference

538742
stoichiometry: 3.0
species: 349902
type: SpeciesReference

350244
kinetic law: 541042
product: 541030
reactant: 541018
reactant: 541006
is version of: GO:0006461
fast: false
reversible: true
name: Smad4-Ski
type: Reaction

539503
stoichiometry: 1.0
species: 349705
type: SpeciesReference

350509
is: SBO:0000025
value: 1000.0
name: k
type: LocalParameter

541631
stoichiometry: 2.0
species: 349932
type: SpeciesReference

539660
stoichiometry: 1.0
species: 349765
type: SpeciesReference

350406
is: SBO:0000282
value: 0.0492
name: k1
type: LocalParameter

349706
initial amount: NaN
constant: false
has only substance units: false
in compartment: 349703
has part: P04202
initial concentration: 0.0
has part: Q62312
boundary condition: false
name: TGFbeta_TGF_RII
is: SBO:0000296
type: Species

541066
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

349766
boundary condition: false
name: Smad3_c
in compartment: 349703
type: Species
is: SBO:0000252
has only substance units: false
constant: false
is version of: Q05CN3
initial amount: NaN
initial concentration: 0.0

350279
kinetic law: 541462
product: 541450
reactant: 541438
reactant: 541426
is version of: GO:0010843
fast: false
reversible: true
name: Smad2-freePromot
type: Reaction

350159
kinetic law: 540092
product: 540080
reactant: 540068
is version of: GO:0006810
fast: false
reversible: true
name: Smurf2_transp
type: Reaction

350053
kinetic law: 539407
product: 539395
reactant: 539383
is version of: GO:0006810
fast: false
reversible: true
name: Smad7-Smurf2_transp
type: Reaction

541150
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

350519
is: SBO:0000282
value: 0.0492
name: k1
type: LocalParameter

350259
kinetic law: 541330
modifier: 541318
reactant: 541306
is version of: GO:0009056
fast: false
reversible: false
name: Smurf1_degrad
type: Reaction

COPASI2
type: Species
has only substance units: false
is: SBO:0000252
initial concentration: 0.0
in compartment: 349703
boundary condition: false
initial amount: NaN
name: Smad4_c
constant: false
is version of: P97471

350033
kinetic law: 538971
modifier: 538959
product: 538947
reactant: 538935
is version of: GO:0006461
fast: false
reversible: false
name: Rec_comp1
type: Reaction

349716
constant: false
in compartment: 349703
is version of: Q62432
boundary condition: false
initial amount: NaN
is version of: C00562
has only substance units: false
type: Species
initial concentration: 0.0
name: pSmad2_c
is: SBO:0000252

W3 CDTF: Tue Mar 27 14:41:12 BST 2012

350549
is: SBO:0000156
value: 0.0022
name: k1
type: LocalParameter

350460
is: SBO:0000156
value: 0.1
name: k1
type: LocalParameter

541715
stoichiometry: 1.0
species: 349935
type: SpeciesReference

350538
is: SBO:0000356
value: 0.05
name: k1
type: LocalParameter

350470
is: SBO:0000156
value: 0.336
name: k2
type: LocalParameter

BIOMD0000000410
rule: 350615
name: Rate Law for Degradation
species: COPASI11
reaction: 350134
reaction: 350288
volume units: volume
species: 349940
reaction: COPASI32
rule: 350612
reaction: 350130
reaction: 350284
name: Constant flux (irreversible)
reaction: COPASI28
species: 349910
species: 349907
reaction: 350259
substance units: 538559
reaction: 350126
reaction: 350280
species: 349903
parameter: 350718
species: 349886
reaction: 350189
reaction: COPASI24
species: 349773
reaction: 350255
species: 349805
reaction: 350276
species: 349911
function def: COPASI37
reaction: 350143
reaction: 350190
species: 349706
reaction: 350185
reaction: COPASI20
reaction: 350251
reaction: 350225
parameter: 350709
reaction: 350139
name: Henri-Michaelis-Menten (irreversible)
rule: 350605
reaction: 350160
reaction: 350027
reaction: 350181
is: MODEL1202090000
reaction: 350247
species: 349716
reaction: 350135
parameter: 350706
reaction: 350177
name: Wegner2012_TGFbetaSignalling_FeedbackLoops
notes: This model is from the article: Dynamics and feedback loops in the transforming growth factor β signaling pathway. Wegner K, Bachmann A, Schad JU, Lucarelli P, Sahle S, Nickel P, Meyer C, Klingmüller U, Dooley S, Kummer U. Biophys Chem. 2012 Jan 5. 22284904 , Abstract: Transforming growth factor β (TGF-β) ligands activate a signaling cascade with multiple cell context dependent outcomes. Disruption or disturbance leads to variant clinical disorders. To develop strategies for disease intervention, delineation of the pathway in further detail is required. Current theoretical models of this pathway describe production and degradation of signal mediating proteins and signal transduction from the cell surface into the nucleus, whereas feedback loops have not exhaustively been included. In this study we present a mathematical model to determine the relevance of feedback regulators (Arkadia, Smad7, Smurf1, Smurf2, SnoN and Ski) on TGF-β target gene expression and the potential to initiate stable oscillations within a realistic parameter space. We employed massive sampling of the parameters space to pinpoint crucial players for potential oscillations as well as transcriptional product levels. We identified Smad7 and Smurf2 with the highest impact on the dynamics. Based on these findings, we conducted preliminary time course experiments. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
function def: COPASI39
reaction: COPASI33
species: COPASI13
species: 349749
species: COPASI6
reaction: 350131
reaction: 350105
reaction: 350173
reaction: COPASI29
species: 349932
reaction: 350127
species: COPASI14
units def: 538535
species: 349943
compartment: 349704
species: 349711
reaction: 350169
reaction: 350057
reaction: COPASI25
reaction: 350256
parameter: 350724
species: COPASI8
reaction: 350123
rule: 350616
species: COPASI3
reaction: 350011
parameter: 350715
reaction: 350165

350524
is: SBO:0000337
value: 255.068
name: k1
type: LocalParameter

349886
has only substance units: false
is: SBO:0000296
has part: P97471
name: pSmad2_Smad4_SnoN_n
initial amount: NaN
type: Species
initial concentration: 0.0
has part: Q62432
in compartment: 349704
constant: false
is version of: C00562
has part: Q60979
boundary condition: false

349765
is version of: Q60979
in compartment: 349703
type: Species
initial amount: NaN
constant: false
is: SBO:0000252
has only substance units: false
name: SnoN_c
boundary condition: false
initial concentration: 0.0

350449
is: SBO:0000356
value: 1900.0
name: k1
type: LocalParameter

350421
is: SBO:0000153
value: 2.9
name: k1
type: LocalParameter

350431
is: SBO:0000025
value: 1000.0
name: k
type: LocalParameter

541787
stoichiometry: 1.0
species: 349822
type: SpeciesReference

541030
stoichiometry: 1.0
species: 349935
type: SpeciesReference

350518
is: SBO:0000156
value: 0.1
name: k2
type: LocalParameter

539467
stoichiometry: 1.0
species: 349710
type: SpeciesReference

350461
is: SBO:0000153
value: 2.28E-4
name: k
type: LocalParameter

541871
stoichiometry: 3.0
species: COPASI11
type: SpeciesReference

538778
stoichiometry: 2.0
species: 349902
type: SpeciesReference

538862
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

541102
stoichiometry: 1.0
species: 349936
type: SpeciesReference

350499
is: SBO:0000356
value: 0.2
name: k1
type: LocalParameter

350448
is: SBO:0000156
value: 0.01
name: k2
type: LocalParameter

350503
is: SBO:0000186
value: 2.34
name: V
type: LocalParameter

542051
stoichiometry: 1.0
species: 349838
type: SpeciesReference

539395
stoichiometry: 1.0
species: 349748
type: SpeciesReference

350430
is: SBO:0000156
value: 0.1
name: k2
type: LocalParameter

350517
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

540260
stoichiometry: 1.0
species: 349943
type: SpeciesReference

350138
kinetic law: 539948
product: 539936
is version of: GO:0006412
fast: false
reversible: false
name: fluxSmad4
type: Reaction

350547
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

540669
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

350536
is: SBO:0000156
value: 5.5E-4
name: k1
type: LocalParameter

350135
kinetic law: 539924
product: 539912
is version of: GO:0006412
fast: false
reversible: false
name: fluxSmad2
type: Reaction

350472
is: SBO:0000356
value: 0.027778
name: k1
type: LocalParameter

541727
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

350526
is: SBO:0000156
value: 1.6
name: k2
type: LocalParameter

541390
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI30
kinetic law: 541967
product: 541955
is version of: GO:0006412
fast: false
reversible: false
name: fluxArkadia
type: Reaction

541775
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

539479
stoichiometry: 1.0
species: 349749
type: SpeciesReference

350447
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

350516
is: SBO:0000156
value: 0.336
name: k2
type: LocalParameter

350248
kinetic law: 541138
product: 541126
reactant: 541114
reactant: 541102
is version of: GO:0006461
fast: false
reversible: true
name: Smad7-Smurf1
type: Reaction

539527
stoichiometry: 1.0
species: 349712
type: SpeciesReference

538850
stoichiometry: 1.0
species: 349903
type: SpeciesReference

350535
is: SBO:0000153
value: 2.0E-5
name: k
type: LocalParameter

350548
is: SBO:0000153
value: 1.0E-4
name: k
type: LocalParameter

539852
stoichiometry: 1.0
species: 349705
type: SpeciesReference

350525
is: SBO:0000153
value: 1.6
name: k1
type: LocalParameter

350473
is: SBO:0000356
value: 0.027778
name: k1
type: LocalParameter

540212
stoichiometry: 1.0
species: 349769
type: SpeciesReference

540873
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

538766
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI31
kinetic law: 541991
reactant: 541979
is version of: GO:0009056
fast: false
reversible: false
name: Arkadia_deg
type: Reaction

350288
kinetic law: 541703
product: 541691
reactant: 541679
reactant: 541667
is version of: GO:0010843
fast: false
reversible: true
name: Smad2-Ski-gene
type: Reaction

350446
is: SBO:0000156
value: 0.01
name: k2
type: LocalParameter

350505
is: SBO:0000027
value: 0.53
name: Km
type: LocalParameter

350487
is: SBO:0000153
value: 0.2333
name: k1
type: LocalParameter

539127
stoichiometry: 1.0
species: 349715
type: SpeciesReference

350193
kinetic law: 540789
product: 540777
reactant: 540765
is version of: GO:0006810
fast: false
reversible: false
name: Smad_compTransp3
type: Reaction

350515
is: SBO:0000153
value: 0.156
name: k1
type: LocalParameter

542063
stoichiometry: 3.0
species: COPASI16
type: SpeciesReference

350432
is: SBO:0000027
value: 0.0318
name: km
type: LocalParameter

350474
is: SBO:0000356
value: 0.027778
name: k1
type: LocalParameter

540008
stoichiometry: 1.0
species: 349716
type: SpeciesReference

COPASI7
is version of: C00562
initial amount: NaN
boundary condition: false
has part: Q60698
name: pSmad2_Smad4_Ski_n
is: SBO:0000296
has part: Q62432
has part: P97471
in compartment: 349703
constant: false
type: Species
has only substance units: false
initial concentration: 0.0

350143
kinetic law: 540032
product: 540020
reactant: 540008
is version of: GO:0016311
fast: false
reversible: false
name: Smad2_dephospCyt
type: Reaction

350425
is: SBO:0000153
value: 0.03333
name: k1
type: LocalParameter

541186
stoichiometry: 1.0
species: 349914
type: SpeciesReference

349959
is: SBO:0000252
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 349704
name: inactivePromoters
type: Species

350455
is: SBO:0000156
value: 0.031
name: k1
type: LocalParameter

350590
is: SBO:0000156
value: 1.0
name: k2
type: LocalParameter

350464
is: SBO:0000156
value: 5.5E-4
name: k1
type: LocalParameter

541667
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

541763
stoichiometry: 1.0
species: 349711
type: SpeciesReference

350514
is: SBO:0000356
value: 0.2
name: k1
type: LocalParameter

350484
is: SBO:0000186
value: 0.53
name: V
type: LocalParameter

541739
stoichiometry: 1.0
species: 349959
type: SpeciesReference

350445
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

349805
name: Smad7_Smurf1_c
boundary condition: false
in compartment: 349703
initial amount: NaN
has part: O35253
type: Species
has part: A2A5Z6
initial concentration: 0.0
is: SBO:0000296
constant: false
has only substance units: false

350123
kinetic law: 539756
product: 539744
reactant: 539732
reactant: 539720
is version of: GO:0006461
fast: false
reversible: true
name: Smad4-SnoN
type: Reaction

350500
is: SBO:0000027
value: 3.51
name: Km
type: LocalParameter

538887
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

COPASI8
initial concentration: 0.0
has part: Q60979
is: SBO:0000296
constant: false
type: Species
has only substance units: false
boundary condition: false
has part: Q62432
is version of: C00562
initial amount: NaN
in compartment: 349703
name: pSmad2_SnoN_n

541907
stoichiometry: 1.0
species: 349869
type: SpeciesReference

540933
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

350527
is: SBO:0000337
value: 0.16
name: k1
type: LocalParameter

350444
is: SBO:0000009
value: 0.16
name: k1
type: LocalParameter

539888
stoichiometry: 2.0
species: 349705
type: SpeciesReference

350454
is: SBO:0000153
value: 1.0E-4
name: k
type: LocalParameter

350134
kinetic law: 539900
product: 539888
reactant: 539876
is version of: GO:0006461
fast: false
reversible: false
name: Rec_recycl
type: Reaction

350434
is: SBO:0000025
value: 3.51
name: k
type: LocalParameter

540284
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

538547
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

538814
stoichiometry: 1.0
species: 349902
type: SpeciesReference

349770
has part: Q05CN3
initial amount: NaN
initial concentration: 0.0
type: Species
boundary condition: false
is: SBO:0000296
constant: false
in compartment: 349703
has only substance units: false
name: Smad3_SARA
has part: A9XB08

540224
stoichiometry: 1.0
species: 349766
type: SpeciesReference

350485
is: SBO:0000356
value: 0.232
name: k1
type: LocalParameter

541126
stoichiometry: 1.0
species: 349939
type: SpeciesReference

541679
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

350423
is: SBO:0000337
value: 9.45
name: k
type: LocalParameter

539455
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

350476
is: SBO:0000009
value: 0.03333
name: k1
type: LocalParameter

540645
stoichiometry: 1.0
species: 349773
type: SpeciesReference

350131
kinetic law: 539864
reactant: 539852
is version of: GO:0009056
fast: false
reversible: false
name: RecII_degrad
type: Reaction

350437
is: SBO:0000027
value: 0.53
name: km
type: LocalParameter

541198
stoichiometry: 2.0
species: 349932
type: SpeciesReference

350462
is: SBO:0000156
value: 0.0285
name: k1
type: LocalParameter

350457
is: SBO:0000153
value: 1.0E-4
name: k
type: LocalParameter

350512
is: SBO:0000027
value: 0.53
name: km
type: LocalParameter

350482
is: SBO:0000356
value: 0.065
name: k1
type: LocalParameter

349773
has part: P97471
initial concentration: 0.0
initial amount: NaN
constant: false
is: SBO:0000296
has part: Q05CN3
boundary condition: false
name: pSmad3_Smad4_c
in compartment: 349703
type: Species
is version of: C00562
has only substance units: false

350190
kinetic law: 540753
product: 540741
reactant: 540729
reactant: 540717
is version of: GO:0006461
fast: false
reversible: true
name: Smad_inhibComp3SnoN
type: Reaction

COPASI9
initial amount: NaN
is version of: Q99ML9
initial concentration: 0.0
name: Arkadia_c
has only substance units: false
in compartment: 349703
boundary condition: false
constant: false
type: Species
is: SBO:0000252

350712
constant: false
value: 0.0
name: allSmurf2
type: Parameter

350502
is: SBO:0000027
value: 40.0
name: Km
type: LocalParameter

350496
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

350442
is: SBO:0000156
value: 0.156
name: k2
type: LocalParameter

350477
is: SBO:0000009
value: 0.0156
name: v
type: LocalParameter

350529
is: SBO:0000356
value: 0.232
name: k1
type: LocalParameter

350126
kinetic law: 539792
product: 539780
reactant: 539768
is version of: GO:0006810
fast: false
reversible: true
name: Smad2_transp
type: Reaction

350539
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

350463
is: SBO:0000153
value: 2.0E-5
name: k
type: LocalParameter

539876
stoichiometry: 1.0
species: 349706
type: SpeciesReference

540320
stoichiometry: 1.0
species: 349766
type: SpeciesReference

350483
is: SBO:0000027
value: 3.51
name: Km
type: LocalParameter

538559
unit: 538571
name: substance
type: SBMLUnitsDef

350511
is: SBO:0000025
value: 3.51
name: k
type: LocalParameter

541114
stoichiometry: 1.0
species: 349906
type: SpeciesReference

350422
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

540897
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

350501
is: SBO:0000186
value: 0.53
name: V
type: LocalParameter

538826
stoichiometry: 1.0
species: 349903
type: SpeciesReference

350497
is: SBO:0000009
value: 0.04528
name: v
type: LocalParameter

542027
stoichiometry: 3.0
species: 349902
type: SpeciesReference

350292
kinetic law: 541799
product: 541787
reactant: 541775
reactant: 541763
is version of: GO:0006461
fast: false
reversible: true
name: Smad2-Ski_cyt
type: Reaction

350564
is: SBO:0000153
value: 0.463
name: k1
type: LocalParameter

539383
stoichiometry: 1.0
species: 349907
type: SpeciesReference

350721
constant: false
value: 0.0
name: allPSmad3
type: Parameter

350541
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

541955
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

350491
is: SBO:0000356
value: 0.2
name: k1
type: LocalParameter

COPASI25
kinetic law: 540861
modifier: 540849
reactant: 540837
is version of: GO:0009056
fast: false
reversible: false
name: Smad7_degrad
type: Reaction

350554
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

350130
kinetic law: 539840
reactant: 539828
is version of: GO:0009056
fast: false
reversible: false
name: RecI_degrad
type: Reaction

540140
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

350521
is: SBO:0000009
value: 16.6
name: k1
type: LocalParameter

538995
stoichiometry: 2.0
species: 349707
type: SpeciesReference

COPASI11
constant: false
type: Species
initial concentration: 0.0
boundary condition: false
is version of: Q60979
initial amount: NaN
has only substance units: false
is: SBO:0000252
name: SnoN_n
in compartment: 349704

541859
stoichiometry: 3.0
species: COPASI13
type: SpeciesReference

350416
is: SBO:0000337
value: 255.068
name: k1
type: LocalParameter

540597
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

538596
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

538644
stoichiometry: 1.0
species: 349915
type: SpeciesReference

350480
is: SBO:0000356
value: 0.1266
name: k1
type: LocalParameter

350283
kinetic law: 541559
product: 541547
reactant: 541535
reactant: 541523
fast: false
reversible: true
name: Smad2-SnoN-gene
type: Reaction

350563
is: SBO:0000156
value: 0.102
name: k2
type: LocalParameter

539248
stoichiometry: 1.0
species: 349732
type: SpeciesReference

350542
is: SBO:0000156
value: 0.1
name: k2
type: LocalParameter

350553
is: SBO:0000356
value: 1900.0
name: k1
type: LocalParameter

350490
is: SBO:0000156
value: 1.8056
name: k2
type: LocalParameter

350522
is: SBO:0000337
value: 1000.0
name: k1
type: LocalParameter

COPASI24
kinetic law: 540825
product: 540813
reactant: 540801
is version of: GO:0009056
fast: false
reversible: false
name: SnoN_degrad3
type: Reaction

350170
kinetic law: 540308
product: 540296
reactant: 540284
is version of: GO:0016311
fast: false
reversible: false
name: Smad3_dephospNuc2
type: Reaction

COPASI10
is: SBO:0000252
name: Smad4_n
constant: false
type: Species
in compartment: 349704
is version of: P97471
initial concentration: 0.0
initial amount: NaN
boundary condition: false
has only substance units: false

540549
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

539431
stoichiometry: 1.0
species: 349710
type: SpeciesReference

350594
is: SBO:0000356
value: 0.005
name: k1
type: LocalParameter

350417
is: SBO:0000027
value: 0.53
name: Km
type: LocalParameter

539744
stoichiometry: 1.0
species: 349910
type: SpeciesReference

350493
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

350181
kinetic law: 540525
product: 540513
reactant: 540501
reactant: 540489
is version of: GO:0006461
fast: false
reversible: true
name: SARA-comp3
type: Reaction

539139
stoichiometry: 1.0
species: 349716
type: SpeciesReference

542015
stoichiometry: 3.0
species: COPASI16
type: SpeciesReference

350280
kinetic law: 541511
product: 541499
reactant: 541487
reactant: 541474
is version of: GO:0010843
fast: false
reversible: true
name: Smad3-SnoN-freePromot
type: Reaction

COPASI27
kinetic law: 541366
product: 541354
reactant: 541342
is version of: GO:0006810
fast: false
reversible: true
name: Smurf1_transp
type: Reaction

539345
stoichiometry: 1.0
species: 349906
type: SpeciesReference

350428
is: SBO:0000156
value: 0.03333
name: k2
type: LocalParameter

541234
stoichiometry: 1.0
species: 349805
type: SpeciesReference

538632
stoichiometry: 1.0
species: 349869
type: SpeciesReference

350414
is: SBO:0000356
value: 0.232
name: k1
type: LocalParameter

538983
stoichiometry: 1.0
species: 349706
type: SpeciesReference

350142
kinetic law: 539996
reactant: 539984
is version of: GO:0009056
fast: false
reversible: false
name: SARA_degrad
type: Reaction

350591
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

540068
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

541474
stoichiometry: 1.0
species: 349931
type: SpeciesReference

350530
is: SBO:0000356
value: 0.1
name: k1
type: LocalParameter

539188
stoichiometry: 1.0
species: 349716
type: SpeciesReference

350724
constant: false
value: 0.0
name: allSmad3
type: Parameter

350182
kinetic law: 540573
product: 540561
product: 540549
reactant: 540537
is version of: GO:0006461
fast: false
reversible: false
name: Smad_dissoc2
type: Reaction

350565
is: SBO:0000156
value: 0.102
name: k2
type: LocalParameter

COPASI26
kinetic law: 540993
modifier: 540981
reactant: 540969
is version of: GO:0009056
fast: false
reversible: false
name: Smurf2_degrad
type: Reaction

350551
is: SBO:0000156
value: 1.6
name: k2
type: LocalParameter

350579
is: SBO:0000156
value: 1.6
name: k2
type: LocalParameter

350540
is: SBO:0000156
value: 0.05288
name: k2
type: LocalParameter

350429
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

540741
stoichiometry: 1.0
species: 349931
type: SpeciesReference

350510
is: SBO:0000027
value: 0.0318
name: km
type: LocalParameter

540537
stoichiometry: 1.0
species: 349915
type: SpeciesReference

350592
is: SBO:0000156
value: 1.0
name: k2
type: LocalParameter

541931
stoichiometry: 1.0
species: 349914
type: SpeciesReference

540909
stoichiometry: 1.0
species: 349932
type: SpeciesReference

541246
stoichiometry: 1.0
species: 349710
type: SpeciesReference

350225
kinetic law: 540885
reactant: 540873
is version of: GO:0009056
fast: false
reversible: false
name: Ski_degrad
type: Reaction

COPASI21
reversible: false
name: fluxSmad7
kinetic law: 539611
fast: false
product: 539563
type: Reaction
modifier: 539587
is version of: GO:0006412
modifier: 539575
modifier: 539599

350588
is: SBO:0000156
value: 0.1
name: k2
type: LocalParameter

538947
stoichiometry: 1.0
species: 349706
type: SpeciesReference

542003
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI15
boundary condition: false
initial amount: NaN
type: Species
constant: false
initial concentration: 0.0
has only substance units: false
in compartment: 349704
is version of: CCO:U0000003
name: geneProduct
is: SBO:0000236

350597
is: SBO:0000009
value: 2.0E-5
name: v
type: LocalParameter

349907
initial amount: NaN
is version of: O35253
in compartment: 349704
constant: false
initial concentration: 0.0
has only substance units: false
is: SBO:0000296
boundary condition: false
type: Species
is version of: A2A5Z6
name: Smad7_Smurf2_n

541883
stoichiometry: 1.0
species: 349838
type: SpeciesReference

350558
is: SBO:0000153
value: 0.05
name: k1
type: LocalParameter

538669
stoichiometry: 1.0
species: 349869
type: SpeciesReference

539768
stoichiometry: 1.0
species: 349711
type: SpeciesReference

COPASI20
kinetic law: 539551
modifier: 539539
product: 539527
is version of: GO:0006412
fast: false
reversible: false
name: fluxSara
type: Reaction

COPASI34
kinetic law: 542123
product: 542111
reactant: 542099
is version of: GO:0006810
fast: false
reversible: true
name: transArkadia
type: Reaction

350287
kinetic law: 541655
product: 541643
reactant: 541631
reactant: 541619
is version of: GO:0006461
fast: false
reversible: true
name: Smad_inhibComp2Ski
type: Reaction

350532
is: SBO:0000356
value: 0.232
name: k1
type: LocalParameter

COPASI14
is: SBO:0000252
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0999999951844375
initial amount: NaN
in compartment: 349704
name: freePromoters
type: Species

540813
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

350598
is: SBO:0000356
value: 0.1
name: k1
type: LocalParameter

541535
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

350567
is: SBO:0000153
value: 0.2
name: k1
type: LocalParameter

350011
kinetic law: 538706
product: 538693
reactant: 538681
reactant: 538669
is version of: GO:0006461
fast: false
reversible: true
name: Smad_inhibComp2SnoN
type: Reaction

349906
type: Species
in compartment: 349704
is: SBO:0000252
initial amount: NaN
initial concentration: 0.0
name: Smad7_n
boundary condition: false
constant: false
is version of: O35253
has only substance units: false

540729
stoichiometry: 2.0
species: COPASI11
type: SpeciesReference

539224
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

540248
stoichiometry: 1.0
species: 349914
type: SpeciesReference

349822
has only substance units: false
has part: Q62432
type: Species
is: SBO:0000296
name: Smad2_Ski_c
boundary condition: false
has part: Q60698
initial concentration: 0.0
initial amount: NaN
constant: false
in compartment: 349703

COPASI23
kinetic law: 540056
reactant: 540044
is version of: GO:0009056
fast: false
reversible: false
name: SnoN_degrad
type: Reaction

COPASI33
kinetic law: 542087
product: 542075
reactant: 542063
reactant: 542051
is version of: GO:0009056
fast: false
reversible: false
name: SnoN-deg3
type: Reaction

541342
stoichiometry: 1.0
species: 349936
type: SpeciesReference

542111
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

540044
stoichiometry: 1.0
species: 349765
type: SpeciesReference

350438
is: SBO:0000009
value: 16.6
name: k1
type: LocalParameter

350227
kinetic law: 540957
modifier: 540945
product: 540933
is version of: GO:0006412
fast: false
reversible: false
name: fluxSki
type: Reaction

350284
kinetic law: 541607
product: 541595
reactant: 541583
reactant: 541571
is version of: GO:0010843
fast: false
reversible: true
name: Smad3-Ski-freePromot
type: Reaction

350595
is: SBO:0000356
value: 0.005
name: k1
type: LocalParameter

350533
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

COPASI13
is version of: Q05CN3
boundary condition: false
is: SBO:0000252
type: Species
initial amount: NaN
has only substance units: false
initial concentration: 0.0
constant: false
in compartment: 349704
name: pSmad3_n
is version of: C00562

350418
is: SBO:0000186
value: 3.51
name: V
type: LocalParameter

539031
stoichiometry: 1.0
species: 349712
type: SpeciesReference

350576
is: SBO:0000153
value: 1.6
name: k1
type: LocalParameter

350556
is: SBO:0000356
value: 0.5
name: k1
type: LocalParameter

539321
stoichiometry: 1.0
species: 349869
type: SpeciesReference

540765
stoichiometry: 1.0
species: 349773
type: SpeciesReference

COPASI32
kinetic law: 542039
product: 542027
reactant: 542015
reactant: 542003
is version of: GO:0009056
fast: false
reversible: false
name: SnoN-deg2
type: Reaction

350589
is: SBO:0000153
value: 1.0
name: k1
type: LocalParameter

540452
stoichiometry: 1.0
species: 349766
type: SpeciesReference

COPASI22
kinetic law: 539708
product: 539696
is version of: GO:0032800
fast: false
reversible: false
name: fluxRecI
type: Reaction

350226
kinetic law: 540921
product: 540909
reactant: 540897
is version of: GO:0006810
fast: false
reversible: true
name: Ski_trans
type: Reaction

540717
stoichiometry: 1.0
species: 349914
type: SpeciesReference

540513
stoichiometry: 1.0
species: 349770
type: SpeciesReference

350419
is: SBO:0000356
value: 0.2
name: k1
type: LocalParameter

COPASI12
is version of: A2A5Z6
initial concentration: 0.0
in compartment: 349704
name: Smurf2_n
is: SBO:0000252
type: Species
initial amount: NaN
has only substance units: false
constant: false
boundary condition: false

350534
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

539236
stoichiometry: 2.0
species: 349716
type: SpeciesReference

350544
is: SBO:0000153
value: 2.9
name: k1
type: LocalParameter

350730
constant: false
value: 0.0
name: allSmad4nuc
type: Parameter

541450
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

350555
is: SBO:0000156
value: 0.01
name: k2
type: LocalParameter

541547
stoichiometry: 1.0
species: 349959
type: SpeciesReference

540801
stoichiometry: 1.0
species: 349838
type: SpeciesReference

350602
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

540837
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

350574
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

539079
stoichiometry: 1.0
species: 349711
type: SpeciesReference

540501
stoichiometry: 1.0
species: 349766
type: SpeciesReference

COPASI19
kinetic law: 539515
product: 539503
is version of: GO:0032800
fast: false
reversible: false
name: fluxRecII
type: Reaction

539200
stoichiometry: 1.0
species: 349902
type: SpeciesReference

350177
kinetic law: 540440
reactant: 540428
is version of: GO:0009056
fast: false
reversible: false
name: Smad3_degrad
type: Reaction

540104
stoichiometry: 1.0
species: 349711
type: SpeciesReference

540777
stoichiometry: 1.0
species: 349914
type: SpeciesReference

349903
name: Smad2_n
constant: false
type: Species
has part: Q62432
in compartment: 349704
boundary condition: false
is: SBO:0000252
initial amount: NaN
has only substance units: false
initial concentration: 0.0

539563
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

539043
stoichiometry: 1.0
species: 349711
type: SpeciesReference

350603
is: SBO:0000156
value: 0.1
name: k2
type: LocalParameter

350573
is: SBO:0000153
value: 0.2
name: k1
type: LocalParameter

539804
stoichiometry: 1.0
species: 349710
type: SpeciesReference

541006
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

350160
kinetic law: 540116
reactant: 540104
is version of: GO:0009056
fast: false
reversible: false
name: Smad2_cyt_degrad
type: Reaction

541811
stoichiometry: 3.0
species: 349902
type: SpeciesReference

350034
kinetic law: 539019
product: 539007
reactant: 538995
reactant: 538983
is version of: GO:0006461
fast: false
reversible: true
name: Rec_comp2
type: Reaction

350583
is: SBO:0000156
value: 0.1
name: k2
type: LocalParameter

COPASI18
kinetic law: 538754
product: 538742
reactant: 538730
reactant: 538718
is version of: GO:0009056
fast: false
reversible: false
name: SnoN_degrad2
type: Reaction

541426
stoichiometry: 1.0
species: 349869
type: SpeciesReference

541354
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

350178
kinetic law: 540477
product: 540465
reactant: 540452
is version of: GO:0006810
fast: false
reversible: true
name: Smad3_transp
type: Reaction

349902
initial amount: NaN
has part: Q62432
in compartment: 349704
has only substance units: false
boundary condition: false
name: pSmad2_n
constant: false
type: Species
is version of: C00562
initial concentration: 0.0
is: SBO:0000252

540188
stoichiometry: 1.0
species: 349766
type: SpeciesReference

350572
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

350037
kinetic law: 539067
product: 539055
reactant: 539043
reactant: 539031
is version of: GO:0006461
fast: false
reversible: true
name: SARA-comp2
type: Reaction

COPASI17
kinetic law: 538620
product: 538608
product: 538596
reactant: 538584
is version of: GO:0043241
fast: false
reversible: false
name: Smad_dissoc3
type: Reaction

541523
stoichiometry: 1.0
species: 349886
type: SpeciesReference

350161
kinetic law: 540152
product: 540140
reactant: 540128
is version of: GO:0006810
fast: false
reversible: true
name: SnoN_trans
type: Reaction

350709
constant: false
value: 0.0
name: allSmad7
type: Parameter

350599
is: SBO:0000356
value: 0.1
name: k1
type: LocalParameter

349931
is version of: C00562
name: pSmad3_Smad4_SnoN_n
has only substance units: false
has part: Q60979
has part: P97471
constant: false
type: Species
is: SBO:0000296
initial amount: NaN
initial concentration: 0.0
boundary condition: false
in compartment: 349704

350189
kinetic law: 540705
product: 540693
reactant: 540681
reactant: 540669
is version of: GO:0006461
fast: false
reversible: false
name: Smad_compNuc3
type: Reaction

350162
kinetic law: 540176
product: 540164
is version of: GO:0006412
fast: false
reversible: false
name: fluxSmad3
type: Reaction

541018
stoichiometry: 1.0
species: 349932
type: SpeciesReference

539984
stoichiometry: 1.0
species: 349712
type: SpeciesReference

350601
is: SBO:0000356
value: 0.1
name: k1
type: LocalParameter

350571
is: SBO:0000153
value: 0.2
name: k1
type: LocalParameter

COPASI16
type: Species
in compartment: 349704
boundary condition: false
constant: false
is version of: Q99ML9
initial concentration: 0.0
has only substance units: false
is: SBO:0000252
initial amount: NaN
name: Arkadia_n

539055
stoichiometry: 1.0
species: 349715
type: SpeciesReference

350585
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

539007
stoichiometry: 1.0
species: 349710
type: SpeciesReference

539151
stoichiometry: 1.0
species: 349712
type: SpeciesReference

540020
stoichiometry: 1.0
species: 349711
type: SpeciesReference

540561
stoichiometry: 2.0
species: 349903
type: SpeciesReference

538693
stoichiometry: 1.0
species: 349886
type: SpeciesReference

538935
stoichiometry: 2.0
species: 349705
type: SpeciesReference

540465
stoichiometry: 1.0
species: 349911
type: SpeciesReference

541438
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

539623
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

349943
is: SBO:0000296
has part: Q05CN3
has only substance units: false
initial amount: NaN
has part: P97471
boundary condition: false
in compartment: 349704
type: Species
name: Smad4_Smad3_n
initial concentration: 0.0
constant: false

538535
unit: 538547
name: time
type: SBMLUnitsDef

349732
is: SBO:0000296
type: Species
initial amount: NaN
initial concentration: 0.0
has only substance units: false
has part: Q62432
in compartment: 349703
name: pSmad2_Smad4_c
boundary condition: false
constant: false
has part: P97471
is version of: C00562

350580
is: SBO:0000153
value: 0.2
name: k1
type: LocalParameter

350570
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

350106
kinetic law: 539684
modifier: 539672
product: 539660
is version of: GO:0006412
fast: false
reversible: false
name: fluxSnoN
type: Reaction

350049
kinetic law: 539333
product: 539321
reactant: 539309
is version of: GO:0006810
fast: false
reversible: false
name: Smad_compTransp2
type: Reaction

350550
is: SBO:0000153
value: 1.6
name: k1
type: LocalParameter

COPASI29
kinetic law: 541895
product: 541883
reactant: 541871
reactant: 541859
is version of: GO:0006461
fast: false
reversible: true
name: Smad3-Snon
type: Reaction

349712
is homolog to: A9XB08
is: SBO:0000252
initial amount: NaN
boundary condition: false
in compartment: 349703
name: SARA
has only substance units: false
type: Species
constant: false
initial concentration: 0.0

539358
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

350029
kinetic law: 538875
reactant: 538862
reactant: 538850
is version of: GO:0009056
fast: false
reversible: false
name: Smad2_degrad
type: Reaction

350412
is: SBO:0000153
value: 1.6
name: k1
type: LocalParameter

541282
stoichiometry: 1.0
species: 349805
type: SpeciesReference

350173
kinetic law: 540356
modifier: 540344
product: 540332
reactant: 540320
is version of: GO:0016310
fast: false
reversible: false
name: Smad3_phosph
type: Reaction

350008
kinetic law: 538656
product: 538644
reactant: 538632
is version of: GO:0016311
fast: false
reversible: false
name: Smad2_dephosphNuc
type: Reaction

540164
stoichiometry: 1.0
species: 349766
type: SpeciesReference

541378
stoichiometry: 1.0
species: 349914
type: SpeciesReference

541835
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

538681
stoichiometry: 2.0
species: COPASI11
type: SpeciesReference

350105
kinetic law: 539648
modifier: 539636
product: 539623
is version of: GO:0006412
fast: false
reversible: false
name: fluxSmurf2
type: Reaction

COPASI28
kinetic law: 541847
product: 541835
reactant: 541823
reactant: 541811
is version of: GO:0006461
fast: false
reversible: true
name: Smad2-Snon
type: Reaction

539828
stoichiometry: 1.0
species: 349707
type: SpeciesReference

541595
stoichiometry: 1.0
species: 349959
type: SpeciesReference

538571
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

350028
kinetic law: 538838
product: 538826
reactant: 538814
is version of: GO:0016311
fast: false
reversible: false
name: Smad2_dephosphNuc2
type: Reaction

350413
is: SBO:0000156
value: 1.6
name: k2
type: LocalParameter

350038
kinetic law: 539115
modifier: 539103
product: 539091
reactant: 539079
is version of: GO:0016310
fast: false
reversible: false
name: Smad2_phosph
type: Reaction

350174
reversible: false
product: 540392
fast: false
is version of: GO:0016310
modifier: 540404
kinetic law: 540416
reactant: 540368
product: 540380
type: Reaction
name: Smad3_phosphSARA

541979
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

541691
stoichiometry: 1.0
species: 349959
type: SpeciesReference

541402
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

539091
stoichiometry: 1.0
species: 349716
type: SpeciesReference

350251
kinetic law: 541174
modifier: 541162
product: 541150
is version of: GO:0006412
fast: false
reversible: false
name: fluxSmurf1
type: Reaction

350582
is: SBO:0000153
value: 0.1
name: k1
type: LocalParameter

349869
initial amount: NaN
has part: P97471
type: Species
is: SBO:0000296
boundary condition: false
in compartment: 349704
constant: false
has part: Q62432
name: pSmad2_Smad4_n
is version of: C00562
has only substance units: false
initial concentration: 0.0

350165
kinetic law: 540200
reactant: 540188
is version of: GO:0009056
fast: false
reversible: false
name: Smad3_cyt_degrad
type: Reaction

539912
stoichiometry: 1.0
species: 349711
type: SpeciesReference

350185
kinetic law: 540609
product: 540597
reactant: 540585
is version of: GO:0006810
fast: false
reversible: false
name: Smad3-P-transp
type: Reaction

350027
kinetic law: 538802
product: 538790
reactant: 538778
reactant: 538766
is version of: GO:0006461
fast: false
reversible: false
name: Smad_compNuc2
type: Reaction

349710
is version of: CHEBI:26523
in compartment: 349703
is: SBO:0000247
type: Species
constant: false
initial amount: NaN
boundary condition: false
name: Rec_active
has only substance units: false
initial concentration: 0.0

350727
constant: false
value: 0.0
name: allSmad4cyt
type: Parameter

350562
is: SBO:0000153
value: 0.463
name: k1
type: LocalParameter

541270
stoichiometry: 1.0
species: 349939
type: SpeciesReference

350581
is: SBO:0000156
value: 0.2
name: k2
type: LocalParameter

540489
stoichiometry: 1.0
species: 349712
type: SpeciesReference

540585
stoichiometry: 1.0
species: 349769
type: SpeciesReference

541210
stoichiometry: 1.0
species: 349940
type: SpeciesReference

538584
stoichiometry: 1.0
species: 349943
type: SpeciesReference

538911
stoichiometry: 1.0
species: 349907
type: SpeciesReference

349940
is version of: C00562
name: pSmad3_Smad4_Ski_n
type: Species
has part: Q60698
has part: Q05CN3
initial concentration: 0.0
boundary condition: false
has part: P97471
in compartment: 349704
constant: false
is: SBO:0000296
has only substance units: false
initial amount: NaN

350411
is: SBO:0000186
value: 2.34
name: V
type: LocalParameter

350166
kinetic law: 540236
product: 540224
reactant: 540212
is version of: GO:0016311
fast: false
reversible: false
name: Smad3_dephospCyt
type: Reaction

541823
stoichiometry: 3.0
species: COPASI11
type: SpeciesReference

539960
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

350186
kinetic law: 540657
product: 540645
reactant: 540633
reactant: 540621
is version of: GO:0006461
fast: false
reversible: false
name: Smad_compCyt3
type: Reaction

541583
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

350046
kinetic law: 539297
product: 539284
reactant: 539272
is version of: GO:0006810
fast: false
reversible: true
name: Smad4_transp
type: Reaction

349711
name: Smad2_c
boundary condition: false
constant: false
is version of: Q62432
in compartment: 349703
is: SBO:0000252
initial amount: NaN
has only substance units: false
initial concentration: 0.0
type: Species

350561
is: SBO:0000156
value: 3.0
name: k2
type: LocalParameter

350291
kinetic law: 541751
product: 541739
reactant: 541727
reactant: 541715
is version of: GO:0010843
fast: false
reversible: true
name: Smad4-freePromot
type: Reaction

W3 CDTF: Fri Feb 10 11:45:56 GMT 2012

orgname: Biological and Neural Computation Group, Science and Technology Research Institute, University of Hertfordshire, College Lane, Hatfield, Hertfordshire, United Kingdom

ORG:
  orgname: Molecular Alcohol Research in Gastroentorology, Department of Medicine II, Universitätsmedizin Mannheim, University of Heidelberg, Mannheim, Germany
n:
  given: Anastasia
  family: Bachmann

given: Katja
family: Wegner

orgname: EMBL-EBI

given: Vijayalakshmi
family: Chelliah