BIOMD0000000410
type: SBMLModel
rule: 350615
name: Rate Law for Degradation
species: COPASI11
reaction: 350134
reaction: 350288
reaction: COPASI32
volume units: volume
species: 349940
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

COPASI11
type: Species
constant: false
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

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

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

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

539888
type: SpeciesReference
stoichiometry: 2.0
species: 349705

349705
type: Species
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
initial amount: NaN

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

539876
type: SpeciesReference
stoichiometry: 1.0
species: 349706

349706
type: Species
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

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

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

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

541691
type: SpeciesReference
stoichiometry: 1.0
species: 349959

349959
type: Species
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

541679
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI14
type: Species
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

541667
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI7
type: Species
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
has only substance units: false
initial concentration: 0.0

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

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

542027
type: SpeciesReference
stoichiometry: 3.0
species: 349902

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

542015
type: SpeciesReference
stoichiometry: 3.0
species: COPASI16

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

542003
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

COPASI8
type: Species
initial concentration: 0.0
has part: Q60979
is: SBO:0000296
constant: false
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

349940
type: Species
is version of: C00562
name: pSmad3_Smad4_Ski_n
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

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

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

539828
type: SpeciesReference
stoichiometry: 1.0
species: 349707

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

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

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

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

541595
type: SpeciesReference
stoichiometry: 1.0
species: 349959

541583
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

541571
type: SpeciesReference
stoichiometry: 1.0
species: 349940

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

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

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

541835
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

541823
type: SpeciesReference
stoichiometry: 3.0
species: COPASI11

541811
type: SpeciesReference
stoichiometry: 3.0
species: 349902

349910
type: Species
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
has part: Q60979

349907
type: Species
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
is version of: A2A5Z6
name: Smad7_Smurf2_n

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

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

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

541306
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI6
type: Species
is version of: A2A5Z6
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

538559
type: SBMLUnitsDef
unit: 538571
name: substance

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

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

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

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

539780
type: SpeciesReference
stoichiometry: 1.0
species: 349903

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

539768
type: SpeciesReference
stoichiometry: 1.0
species: 349711

349711
type: Species
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

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

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

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

541499
type: SpeciesReference
stoichiometry: 1.0
species: 349959

541487
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

541474
type: SpeciesReference
stoichiometry: 1.0
species: 349931

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

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

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

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

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

540693
type: SpeciesReference
stoichiometry: 1.0
species: 349914

349914
type: Species
has part: P97471
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

540681
type: SpeciesReference
stoichiometry: 2.0
species: COPASI13

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

540669
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

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

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

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

540813
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

540801
type: SpeciesReference
stoichiometry: 1.0
species: 349838

349838
type: Species
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
initial concentration: 0.0
is version of: C00562
has part: Q60979

349773
type: Species
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
is version of: C00562
has only substance units: false

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

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

541246
type: SpeciesReference
stoichiometry: 1.0
species: 349710

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

541234
type: SpeciesReference
stoichiometry: 1.0
species: 349805

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

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

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

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

541402
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

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

541390
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

541378
type: SpeciesReference
stoichiometry: 1.0
species: 349914

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

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

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

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

540020
type: SpeciesReference
stoichiometry: 1.0
species: 349711

540008
type: SpeciesReference
stoichiometry: 1.0
species: 349716

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

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

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

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

540741
type: SpeciesReference
stoichiometry: 1.0
species: 349931

540729
type: SpeciesReference
stoichiometry: 2.0
species: COPASI11

540717
type: SpeciesReference
stoichiometry: 1.0
species: 349914

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

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

540597
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

540585
type: SpeciesReference
stoichiometry: 1.0
species: 349769

349769
type: Species
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

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

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

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

539527
type: SpeciesReference
stoichiometry: 1.0
species: 349712

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

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

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

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

541150
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

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

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

540873
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

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

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

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

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

539960
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

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

540104
type: SpeciesReference
stoichiometry: 1.0
species: 349711

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

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

538790
type: SpeciesReference
stoichiometry: 1.0
species: 349869

349869
type: Species
initial amount: NaN
has part: P97471
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

538778
type: SpeciesReference
stoichiometry: 2.0
species: 349902

538766
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

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

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

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

540513
type: SpeciesReference
stoichiometry: 1.0
species: 349770

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

540501
type: SpeciesReference
stoichiometry: 1.0
species: 349766

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

540489
type: SpeciesReference
stoichiometry: 1.0
species: 349712

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

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

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

541078
type: SpeciesReference
stoichiometry: 1.0
species: 349789

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

541066
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

541054
type: SpeciesReference
stoichiometry: 1.0
species: 349766

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

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

539912
type: SpeciesReference
stoichiometry: 1.0
species: 349711

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

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

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

540428
type: SpeciesReference
stoichiometry: 1.0
species: 349911

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

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

542075
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

542063
type: SpeciesReference
stoichiometry: 3.0
species: COPASI16

542051
type: SpeciesReference
stoichiometry: 1.0
species: 349838

349749
type: Species
constant: false
in compartment: 349703
has part: O35253
name: Rec_Smad7
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

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

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

539852
type: SpeciesReference
stoichiometry: 1.0
species: 349705

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

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

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

539623
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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

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

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

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

540332
type: SpeciesReference
stoichiometry: 1.0
species: 349769

540320
type: SpeciesReference
stoichiometry: 1.0
species: 349766

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

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

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

541883
type: SpeciesReference
stoichiometry: 1.0
species: 349838

541871
type: SpeciesReference
stoichiometry: 3.0
species: COPASI11

541859
type: SpeciesReference
stoichiometry: 3.0
species: COPASI13

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

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

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

539804
type: SpeciesReference
stoichiometry: 1.0
species: 349710

538535
type: SBMLUnitsDef
unit: 538547
name: time

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

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

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

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

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

540260
type: SpeciesReference
stoichiometry: 1.0
species: 349943

540248
type: SpeciesReference
stoichiometry: 1.0
species: 349914

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

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

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

539479
type: SpeciesReference
stoichiometry: 1.0
species: 349749

539467
type: SpeciesReference
stoichiometry: 1.0
species: 349710

539455
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

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

COPASI9
type: Species
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
is: SBO:0000252

540837
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

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

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

541282
type: SpeciesReference
stoichiometry: 1.0
species: 349805

541270
type: SpeciesReference
stoichiometry: 1.0
species: 349939

349939
type: Species
has part: A2A5Z6
has part: O35253
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

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

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

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

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

539744
type: SpeciesReference
stoichiometry: 1.0
species: 349910

539732
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

539720
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

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

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

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

538693
type: SpeciesReference
stoichiometry: 1.0
species: 349886

538681
type: SpeciesReference
stoichiometry: 2.0
species: COPASI11

538669
type: SpeciesReference
stoichiometry: 1.0
species: 349869

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

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

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

540188
type: SpeciesReference
stoichiometry: 1.0
species: 349766

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

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

540645
type: SpeciesReference
stoichiometry: 1.0
species: 349773

540633
type: SpeciesReference
stoichiometry: 2.0
species: 349769

540621
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

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

539395
type: SpeciesReference
stoichiometry: 1.0
species: 349748

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

539383
type: SpeciesReference
stoichiometry: 1.0
species: 349907

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

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

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

539563
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

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

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

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

541210
type: SpeciesReference
stoichiometry: 1.0
species: 349940

541198
type: SpeciesReference
stoichiometry: 2.0
species: 349932

541186
type: SpeciesReference
stoichiometry: 1.0
species: 349914

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

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

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

540909
type: SpeciesReference
stoichiometry: 1.0
species: 349932

540897
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

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

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

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

540140
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

540128
type: SpeciesReference
stoichiometry: 1.0
species: 349765

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

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

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

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

538826
type: SpeciesReference
stoichiometry: 1.0
species: 349903

538814
type: SpeciesReference
stoichiometry: 1.0
species: 349902

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

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

540561
type: SpeciesReference
stoichiometry: 2.0
species: 349903

540549
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

540537
type: SpeciesReference
stoichiometry: 1.0
species: 349915

349915
type: Species
has part: Q62432
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

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

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

539321
type: SpeciesReference
stoichiometry: 1.0
species: 349869

539309
type: SpeciesReference
stoichiometry: 1.0
species: 349732

349732
type: Species
is: SBO:0000296
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

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

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

538608
type: SpeciesReference
stoichiometry: 2.0
species: 349911

538596
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

538584
type: SpeciesReference
stoichiometry: 1.0
species: 349943

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

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

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

541126
type: SpeciesReference
stoichiometry: 1.0
species: 349939

541114
type: SpeciesReference
stoichiometry: 1.0
species: 349906

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

541102
type: SpeciesReference
stoichiometry: 1.0
species: 349936

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

349822
type: Species
has only substance units: false
has part: Q62432
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

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

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

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

540465
type: SpeciesReference
stoichiometry: 1.0
species: 349911

540452
type: SpeciesReference
stoichiometry: 1.0
species: 349766

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

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

539248
type: SpeciesReference
stoichiometry: 1.0
species: 349732

539236
type: SpeciesReference
stoichiometry: 2.0
species: 349716

539224
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

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

541030
type: SpeciesReference
stoichiometry: 1.0
species: 349935

541018
type: SpeciesReference
stoichiometry: 1.0
species: 349932

541006
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

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

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

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

542111
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

542099
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

ORG:
  orgname: Biological and Neural Computation Group, Science and Technology Research Institute, University of Hertfordshire, College Lane, Hatfield, Hertfordshire, United Kingdom
n:
  given: Katja
  family: Wegner

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

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

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

539660
type: SpeciesReference
stoichiometry: 1.0
species: 349765

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

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

540392
type: SpeciesReference
stoichiometry: 1.0
species: 349712

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

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

540368
type: SpeciesReference
stoichiometry: 1.0
species: 349770

540380
type: SpeciesReference
stoichiometry: 1.0
species: 349769

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

539127
type: SpeciesReference
stoichiometry: 1.0
species: 349715

349715
type: Species
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

539139
type: SpeciesReference
stoichiometry: 1.0
species: 349716

539151
type: SpeciesReference
stoichiometry: 1.0
species: 349712

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

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

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

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

541955
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

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

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

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

540296
type: SpeciesReference
stoichiometry: 1.0
species: 349911

540284
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

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

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

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

539055
type: SpeciesReference
stoichiometry: 1.0
species: 349715

539043
type: SpeciesReference
stoichiometry: 1.0
species: 349711

539031
type: SpeciesReference
stoichiometry: 1.0
species: 349712

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

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

540969
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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

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

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

540224
type: SpeciesReference
stoichiometry: 1.0
species: 349766

540212
type: SpeciesReference
stoichiometry: 1.0
species: 349769

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

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

538947
type: SpeciesReference
stoichiometry: 1.0
species: 349706

538935
type: SpeciesReference
stoichiometry: 2.0
species: 349705

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

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

539431
type: SpeciesReference
stoichiometry: 1.0
species: 349710

539419
type: SpeciesReference
stoichiometry: 1.0
species: 349748

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

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

539696
type: SpeciesReference
stoichiometry: 1.0
species: 349707

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

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

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

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

540933
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

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

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

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

538644
type: SpeciesReference
stoichiometry: 1.0
species: 349915

538632
type: SpeciesReference
stoichiometry: 1.0
species: 349869

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

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

540164
type: SpeciesReference
stoichiometry: 1.0
species: 349766

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

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

538862
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

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

538850
type: SpeciesReference
stoichiometry: 1.0
species: 349903

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

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

538742
type: SpeciesReference
stoichiometry: 3.0
species: 349902

538730
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

538718
type: SpeciesReference
stoichiometry: 3.0
species: COPASI12

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

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

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

539358
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

539345
type: SpeciesReference
stoichiometry: 1.0
species: 349906

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

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

541907
type: SpeciesReference
stoichiometry: 1.0
species: 349869

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

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

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

541739
type: SpeciesReference
stoichiometry: 1.0
species: 349959

541727
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

541715
type: SpeciesReference
stoichiometry: 1.0
species: 349935

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

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

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

539284
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

539272
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

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

541643
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

541631
type: SpeciesReference
stoichiometry: 2.0
species: 349932

541619
type: SpeciesReference
stoichiometry: 1.0
species: 349869

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

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

539200
type: SpeciesReference
stoichiometry: 1.0
species: 349902

539188
type: SpeciesReference
stoichiometry: 1.0
species: 349716

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

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

541979
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

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

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

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

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

541547
type: SpeciesReference
stoichiometry: 1.0
species: 349959

541535
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

541523
type: SpeciesReference
stoichiometry: 1.0
species: 349886

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

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

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

539091
type: SpeciesReference
stoichiometry: 1.0
species: 349716

539079
type: SpeciesReference
stoichiometry: 1.0
species: 349711

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

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

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

541354
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

541342
type: SpeciesReference
stoichiometry: 1.0
species: 349936

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

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

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

541450
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

541438
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

541426
type: SpeciesReference
stoichiometry: 1.0
species: 349869

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

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

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

540777
type: SpeciesReference
stoichiometry: 1.0
species: 349914

540765
type: SpeciesReference
stoichiometry: 1.0
species: 349773

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

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

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

539007
type: SpeciesReference
stoichiometry: 1.0
species: 349710

538995
type: SpeciesReference
stoichiometry: 2.0
species: 349707

538983
type: SpeciesReference
stoichiometry: 1.0
species: 349706

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

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

540044
type: SpeciesReference
stoichiometry: 1.0
species: 349765

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

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

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

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

539984
type: SpeciesReference
stoichiometry: 1.0
species: 349712

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

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

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

538911
type: SpeciesReference
stoichiometry: 1.0
species: 349907

538899
type: SpeciesReference
stoichiometry: 1.0
species: 349906

538887
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

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

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

539503
type: SpeciesReference
stoichiometry: 1.0
species: 349705

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

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

539936
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

541931
type: SpeciesReference
stoichiometry: 1.0
species: 349914

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

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

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

541787
type: SpeciesReference
stoichiometry: 1.0
species: 349822

541775
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

541763
type: SpeciesReference
stoichiometry: 1.0
species: 349711

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

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

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

540080
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

540068
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

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

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