COPASI35
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386206
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385331
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384803
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COPASI25
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385535
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385139
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COPASI34
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386092
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386305
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385151
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384875
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COPASI24
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type: Species
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name: MK_P2
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BIOMD0000000430
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_USEQ)
parameter: COPASI28
reaction: COPASI33
species: 384743
reaction: COPASI34
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_USEQ) The paper presents the various interaction topologies between the kinases and phosphatases of MAPK cascade. They are represented as M1, M2, M3 and M4. The kinases of the cascades are MKKK, MKK and MK, and Phos1, Phos2 and Phos3 are phosphatases of the system. All three kinases in a M1 type network have specific phosphatases Phos1, Phos2 and Phos3 for the dephosphorylation process. In a M2 type system, kinases MKKK and MKK are dephosphorylated by Phos1 and MK is dephosphorylated by Phos2. The architecture of system like M3 is such that MKKK gets dephosphorylated by Phos1, whereas Phos2 dephosphorylates both MKK and MK. Finally, the MAPK cascade exhibiting more complex design of interaction such as M4 is such that MKKK and MKK are dephosphorylated by Phos1 whereas MKK and MK are dephosphorylated by Phos2. In addition, as it is plausible that the kinases can sequester their respective phosphatases by binding to them, this is considered in the design of the systems (PSEQ-sequestrated system; USEQ-Unsequestrated system). The robustness of different interaction designs of the systems is checked, considering both MichaelisMenten type kinetics (K1) and elementary mass action kinetics (K2). In the living systems, the MAPK cascade transmit both short and long duration signals where short duration signals trigger proliferation and long duration signals trigger cell differentiation. These signal variants are considered to interpret the systems behaviour. It is also tested how the robustness and signal response behaviour of K2 models are affected when K2 assumes quasi steady state (QSS). The combinations of the above variants resulted in 40 models (MODEL1204280001-40). All these 40 models are available from BioModels Database . Models that correspond to type M4 with mass-action kinetics K2, in four condition 1) USEQ [ MODEL1204280020 - M4_K2_USEQ], 2) PSEQ [ MODEL1204280024 - M4_K2_PSEQ], 3) QSS_USEQ [ MODEL12042800…
is version of: GO:0000165
species: COPASI7
species: COPASI15
units def: 384682
area units: 844749
reaction: COPASI51
reaction: COPASI39
reaction: COPASI43
length unit: 844677
created:
  W3 CDTF: Fri Nov 23 15:47:02 GMT 2012
reaction: COPASI52
reaction: COPASI42
species: COPASI4
species: COPASI22
species: COPASI25
type: SBMLModel
species: COPASI19
reaction: COPASI49
modified:
  W3 CDTF: Fri Dec 14 14:23:41 GMT 2012
species: COPASI12
volume units: 384682
reaction: COPASI48
species: COPASI2
compartment: 384730
reaction: COPASI31
curated: true
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
occurs in: http://identifiers.org/taxonomy/131567
reaction: COPASI32
creator:
  ORG:
    orgname: National Centre for Cell Science
  n:
    given: Uddipan
    family: Sarma
species: COPASI8
species: COPASI26
reaction: COPASI37
reaction: COPASI41
reaction: COPASI29
substance units: 384706
reaction: COPASI50
reaction: COPASI40
reaction: COPASI38
species: COPASI23
species: COPASI16
species: COPASI20
reaction: COPASI55
reaction: COPASI47
units def: 384706
reaction: COPASI56
reaction: COPASI46
species: COPASI10
species: COPASI5
species: COPASI13
time units: 844725
species: COPASI21
reaction: COPASI30
species: COPASI27
reaction: COPASI35
reaction: COPASI36
is described by: http://identifiers.org/pubmed/22748295
is: MODEL1204280020
species: COPASI14
species: COPASI9
species: COPASI17
reaction: COPASI53
reaction: COPASI45
reaction: COPASI54
species: COPASI11
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species: COPASI6
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385991
stoichiometry: 1.0
species: COPASI18
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386244
stoichiometry: 1.0
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386269
stoichiometry: 1.0
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value: 0.01
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386343
stoichiometry: 1.0
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385547
value: 1.0
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385091
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI37
product: 385307
kinetic law: 385319
type: Reaction
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name: 23
reversible: true
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fast: false
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modifier: 618909
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385965
stoichiometry: 1.0
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386440
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384815
value: 1.0
name: k2
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COPASI23
has only substance units: false
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constant: false
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type: Species
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name: MK-P_P2
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386231
value: 0.086
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385811
value: 1.0
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385739
value: 0.092
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type: LocalParameter

COPASI36
modifier: 618885
reversible: false
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fast: false
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name: 22
product: 385247

385427
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384718
exponent: 1.0
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stoichiometry: 1.0
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COPASI22
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constant: false
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name: MK-PP_P2
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384911
stoichiometry: 1.0
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value: 1.0
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386030
value: 1.0
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385559
stoichiometry: 1.0
species: COPASI12
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COPASI39
is version of: GO:0016310
modifier: 618969
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fast: false
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reactant: 385427
name: 7

386591
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385355
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stoichiometry: 1.0
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COPASI49
reactant: 386105
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name: 3
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reversible: true

COPASI29
fast: false
kinetic law: 384791
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name: 15
modifier: 618705
product: 384779
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reactant: 384755
reversible: true
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386466
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385583
stoichiometry: 1.0
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COPASI28
constant: true
value: 0.0
name: quantity_1
type: Parameter

385367
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384899
stoichiometry: 1.0
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value: 0.045
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value: 1.0
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386367
value: 0.092
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384947
value: 1.0
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COPASI38
modifier: 618933
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384706
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COPASI2
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constant: false
boundary condition: false
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name: MK
type: Species

COPASI48
product: 386055
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product: 386067
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modifier: 619197
kinetic law: 386079
reversible: false
name: 2

COPASI27
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name: MKK_P1

385715
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385643
stoichiometry: 1.0
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stoichiometry: 1.0
species: COPASI5
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COPASI47
name: 1
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fast: false
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reversible: true
type: Reaction
is version of: GO:0006461
product: 385991

385343
value: 0.0
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385901
stoichiometry: 1.0
species: COPASI8
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384935
value: 0.032
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COPASI26
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name: MKK-P_P1

385403
value: 0.02
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385379
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385163
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384887
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COPASI46
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fast: false
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kinetic law: 385926
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reversible: true

385307
stoichiometry: 1.0
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385978
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stoichiometry: 1.0
species: COPASI17
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COPASI45
product: 385849
name: 13_P2
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reversible: false
type: Reaction
kinetic law: 385862
fast: false

384743
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COPASI6
name: MK-P_MKK-PP
has part: Q02750
initial concentration: 0.0
initial amount: NaN
boundary condition: false
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type: Species
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COPASI55
product: 386529
type: Reaction
reversible: true
kinetic law: 386554
modifier: 619365
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product: 386541
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name: 14_P1
fast: false

385619
stoichiometry: 1.0
species: COPASI3
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385031
stoichiometry: 1.0
species: COPASI14
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384959
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI14
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
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name: P2
type: Species

385007
value: 15.0
name: k1
type: LocalParameter

385667
value: 0.045
name: k1
type: LocalParameter

COPASI44
reactant: 385751
modifier: 619089
name: 12_P2
fast: false
kinetic law: 385787
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type: Reaction
is version of: GO:0006461
reversible: true
reactant: 385763

386181
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

COPASI54
modifier: 619341
name: 13_P1
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fast: false
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kinetic law: 386491
product: 386479
reactant: 386453

COPASI5
boundary condition: false
has only substance units: false
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name: MK-P
initial amount: NaN
constant: false
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is version of: C00562
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type: Species

384682
unit: 384694
name: volume
type: SBMLUnitsDef

385283
stoichiometry: 1.0
species: COPASI24
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386055
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

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is version of: C00562
has only substance units: false
initial amount: NaN
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name: MKK-P_P2
constant: false
type: Species
has version: Q02750
boundary condition: false
in compartment: 384730

COPASI43
product: 385703
modifier: 619065
is version of: GO:0016311
is version of: GO:0043241
kinetic law: 385727
reversible: false
reactant: 385691
product: 385715
name: 11_P2
fast: false
type: Reaction

385199
value: 0.01
name: k1
type: LocalParameter

COPASI18
in compartment: 384730
type: Species
has part: P04049
boundary condition: false
has only substance units: false
name: MKKK_Sig
has part: P61225
constant: false
initial amount: NaN
initial concentration: 0.0

385607
value: 15.0
name: k1
type: LocalParameter

COPASI4
has part: Q02750
initial concentration: 0.0
name: MK_MKK-PP
boundary condition: false
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constant: false
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type: Species
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386017
value: 0.02
name: k1
type: LocalParameter

COPASI16
type: Species
initial concentration: 0.0
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boundary condition: false
name: MKK_P2
in compartment: 384730
constant: false

385751
stoichiometry: 1.0
species: COPASI11
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385043
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

385571
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI19
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constant: false
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initial concentration: 10.0
initial amount: NaN
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name: Sig
type: Species

384694
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

385451
stoichiometry: 1.0
species: COPASI9
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385019
stoichiometry: 1.0
species: COPASI7
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385679
value: 1.0
name: k2
type: LocalParameter

COPASI3
type: Species
has only substance units: false
boundary condition: false
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name: MKK-PP
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initial amount: NaN
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initial concentration: 0.0

COPASI42
reactant: 385631
kinetic law: 385655
reversible: true
modifier: 619041
name: 10_P2
modifier: 619029
is version of: GO:0006461
fast: false
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modifier: 619053
product: 385643
type: Reaction

384730
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI56
product: 386604
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type: Reaction
kinetic law: 386629
reversible: true
name: 5
fast: false
product: 386616
reactant: 386591
modifier: 619401
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modifier: 619389

386067
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species: COPASI19
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COPASI17
is version of: P04049
constant: false
boundary condition: false
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initial concentration: 300.0
initial amount: NaN
in compartment: 384730
name: MKKK
type: Species

385271
value: 0.086
name: k1
type: LocalParameter

COPASI41
reactant: 385559
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product: 385571
fast: false
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name: 9
modifier: 619017
type: Reaction
kinetic law: 385595
product: 385583

385247
stoichiometry: 1.0
species: COPASI14
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385211
value: 1.0
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384767
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species: COPASI3
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386479
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species: COPASI21
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386256
stoichiometry: 1.0
species: COPASI21
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COPASI51
name: 10_P1
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reactant: 386256
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reversible: true
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386654
value: 0.0
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COPASI10
has only substance units: false
initial concentration: 0.0
boundary condition: false
in compartment: 384730
initial amount: NaN
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name: MKK_MKKK-P
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type: Species

386529
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species: COPASI8
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COPASI31
reversible: true
reactant: 384887
modifier: 618765
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name: 17
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kinetic law: 384923
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product: 384911

COPASI21
is version of: P51452
constant: false
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initial concentration: 100.0
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name: P1
type: Species

386380
stoichiometry: 1.0
species: COPASI11
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385499
stoichiometry: 1.0
species: COPASI9
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384851
stoichiometry: 1.0
species: COPASI3
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species: COPASI14
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COPASI40
modifier: 619005
product: 385511
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name: 8
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reactant: 385499
fast: false
type: Reaction
kinetic law: 385523
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386428
value: 0.01
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386131
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species: COPASI20
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COPASI9
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name: MKKK-P
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386578
value: 0.0
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COPASI50
modifier: 619245
fast: false
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name: 4
kinetic law: 386219
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COPASI11
boundary condition: false
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name: MKK-P
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type: Species
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386604
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species: COPASI17
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COPASI30
is version of: GO:0016310
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is version of: GO:0043241
modifier: 618741
reversible: false
fast: false
name: 16
product: 384839
type: Reaction
product: 384851
kinetic law: 384863

384839
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI20
name: MKKK-P_P1
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has only substance units: false
in compartment: 384730
constant: false
initial concentration: 0.0
initial amount: NaN
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type: Species

385487
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI8
is version of: Q02750
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1200.0
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in compartment: 384730
name: MKK
type: Species

COPASI53
modifier: 619305
type: Reaction
modifier: 619329
modifier: 619317
fast: false
is version of: GO:0006461
reversible: true
reactant: 386380
name: 12_P1
kinetic law: 386416
product: 386404
reactant: 386392

385223
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

385775
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

385888
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

386105
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

385235
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

386392
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

386404
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

386156
value: 0.02
name: k1
type: LocalParameter

COPASI12
is version of: C00562
has part: P04049
has only substance units: false
initial amount: NaN
constant: false
name: MKK-P_MKKK-P
initial concentration: 0.0
boundary condition: false
in compartment: 384730
has part: Q02750
type: Species

386642
value: 0.0
name: k1
type: LocalParameter

COPASI33
reactant: 385031
is version of: GO:0006461
fast: false
type: Reaction
modifier: 618825
product: 385043
reactant: 385019
modifier: 618801
name: 19
modifier: 618813
reversible: true
kinetic law: 385055

384755
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

386503
value: 0.086
name: k1
type: LocalParameter

COPASI7
is version of: C00562
type: Species
initial concentration: 0.0
in compartment: 384730
is version of: P27361
initial amount: NaN
name: MK-PP
constant: false
has only substance units: false
boundary condition: false

386118
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

386566
value: 0.0
name: k1
type: LocalParameter

386043
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI52
reactant: 386318
is version of: GO:0016311
fast: false
name: 11_P1
type: Reaction
product: 386330
kinetic law: 386355
product: 386343
reversible: false
modifier: 619293
is version of: GO:0043241

385295
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

386330
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

384827
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

385703
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

386293
value: 0.045
name: k1
type: LocalParameter

385475
value: 0.01
name: k1
type: LocalParameter

COPASI13
initial concentration: 0.0
boundary condition: false
in compartment: 384730
has part: P51452
has only substance units: false
name: MKK-PP_P2
initial amount: NaN
constant: false
has part: Q02750
type: Species
is version of: C00562

385939
value: 0.0
name: k1
type: LocalParameter

385511
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

386516
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

COPASI32
product: 384971
is version of: GO:0043241
is version of: GO:0016310
product: 384983
modifier: 618789
type: Reaction
reactant: 384959
kinetic law: 384995
reversible: false
name: 18
fast: false

386541
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

386616
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference