COPASI13
constant: true
value: 24.3
name: K5
type: Parameter

208452
stoichiometry: 1.0
species: 208305
type: SpeciesReference

208933
stoichiometry: 1.0
species: 208318
type: SpeciesReference

COPASI27
modifier: 209321
modifier: 209297
product: 209285
kinetic law: 209333
reactant: 209272
fast: false
modifier: 209309
type: Reaction
name: 9
modifier: 017164
modifier: 017200
modifier: 017188
modifier: 017176
reversible: false

208659
stoichiometry: 1.0
species: 208343
type: SpeciesReference

208791
value: 0.092
name: k5
type: LocalParameter

COPASI12
constant: true
value: 500.0
name: K4
type: Parameter

209017
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

208145
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

COPASI26
modifier: 209236
reversible: false
type: Reaction
modifier: 017140
fast: false
kinetic law: 209248
modifier: 209224
reactant: 209077
name: 8
modifier: 017128
modifier: 017152
product: 209212

COPASI9
constant: true
value: 3.0E51
name: Kse2
type: Parameter

209285
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

209345
value: 0.092
name: k9
type: LocalParameter

208318
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 208157
name: MKK
type: Species

209212
stoichiometry: 1.0
species: 208355
type: SpeciesReference

208379
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: 208157
name: Sig
type: Species

209272
stoichiometry: 1.0
species: 208355
type: SpeciesReference

COPASI11
constant: true
value: 50.5
name: K3
type: Parameter

208440
value: 1.0
name: k1
type: LocalParameter

COPASI29
type: Reaction
product: 209577
modifier: 017261
modifier: 209601
modifier: 017285
reversible: false
modifier: 017273
fast: false
modifier: 209589
reactant: 209565
name: 3
kinetic law: 209613

COPASI8
constant: true
value: 3.0E51
name: Kse1
type: Parameter

COPASI21
reversible: false
name: 2
modifier: 016935
type: Reaction
modifier: 208488
kinetic law: 208622
modifier: 208476
product: 208464
modifier: 016923
modifier: 016947
reactant: 208452
fast: false

208707
value: 15.0
name: k4
type: LocalParameter

209577
stoichiometry: 1.0
species: 208330
type: SpeciesReference

208731
stoichiometry: 1.0
species: 208330
type: SpeciesReference

208647
stoichiometry: 1.0
species: 208330
type: SpeciesReference

COPASI19
event assignment: 209649
trigger: 209637
use values from trigger time: true
name: event_1
type: Event

209357
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI10
constant: true
value: 3.0E51
name: Kse3
type: Parameter

208157
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI28
type: Reaction
modifier: 209516
modifier: 209529
modifier: 017212
reversible: false
reactant: 209357
product: 209369
modifier: 209381
modifier: 017236
modifier: 017224
fast: false
name: 10
kinetic law: 209541
modifier: 017249

COPASI7
constant: true
value: 54.3
name: K2
type: Parameter

COPASI6
constant: true
value: 100.0
name: K1
type: Parameter

COPASI20
modifier: 016899
name: 1
kinetic law: 208428
type: Reaction
reversible: false
product: 208404
modifier: 208416
reactant: 208392
modifier: 016911
fast: false

COPASI18
constant: true
value: 108.6
name: K10
type: Parameter

208635
value: 0.086
name: k2
type: LocalParameter

209565
stoichiometry: 1.0
species: 208318
type: SpeciesReference

208343
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MKK_PP
type: Species

208719
stoichiometry: 1.0
species: 208343
type: SpeciesReference

208121
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

COPASI17
constant: true
value: 24.3
name: K9
type: Parameter

209260
value: 15.0
name: k7
type: LocalParameter

COPASI5
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: 208157
name: P2
type: Species

COPASI23
modifier: 017007
modifier: 208755
kinetic law: 208779
name: 5
type: Reaction
modifier: 208743
modifier: 017019
product: 208731
modifier: 208767
reactant: 208719
modifier: 016995
modifier: 017031
fast: false
reversible: false

209637
persistant: true
initial value: true
type: Trigger

208355
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MK_PP
type: Species

MODEL1204280033
function def: COPASI30
species: 208355
parameter: COPASI6
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K2_QSS_USEQ)
name: 7
units def: 208133
volume units: 208109
reaction: COPASI25
parameter: COPASI15
name: 6
parameter: COPASI11
name: 9
species: 208169
function def: COPASI35
name: 4
function def: COPASI36
species: COPASI3
length unit: length
parameter: COPASI7
species: 208379
reaction: COPASI26
substance units: 208133
type: SBMLModel
units def: 208109
function def: COPASI31
parameter: COPASI18
reaction: COPASI24
function def: COPASI32
area units: 061696
name: 3
species: 208330
species: 208318
event: COPASI19
reaction: COPASI21
parameter: COPASI16
name: 2
parameter: COPASI12
time units: 291235
name: 10
parameter: COPASI8
name: 5
species: 208305
function def: COPASI37
is described by: http://identifiers.org/pubmed/22748295
reaction: COPASI27
function def: COPASI38
curated: false
reaction: COPASI29
reaction: COPASI22
notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_K2_QSS_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 [ MODEL1204…
compartment: 208157
function def: COPASI33
parameter: COPASI14
parameter: COPASI17
reaction: COPASI20
name: 8
parameter: COPASI10
parameter: COPASI13
function def: COPASI34
species: 208343
species: COPASI2
species: COPASI5
parameter: COPASI9
name: 1
function def: COPASI39
species: COPASI4
reaction: COPASI28
species: 208367
reaction: COPASI23

208169
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999985553313
initial amount: NaN
in compartment: 208157
name: MKKK
type: Species

COPASI16
constant: true
value: 500.0
name: K8
type: Parameter

209369
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: 208157
name: P1
type: Species

COPASI22
reversible: false
name: 4
fast: false
kinetic law: 208695
modifier: 016971
modifier: 208683
type: Reaction
modifier: 208671
modifier: 016959
product: 208659
reactant: 208647
modifier: 016983

208330
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MKK_P
type: Species

208993
value: 0.086
name: k6
type: LocalParameter

209553
value: 0.086
name: k10
type: LocalParameter

209065
value: 0.01
name: k7
type: LocalParameter

COPASI15
constant: true
value: 50.5
name: K7
type: Parameter

COPASI25
type: Reaction
fast: false
modifier: 017104
reactant: 209005
modifier: 209029
modifier: 209041
reversible: false
kinetic law: 209053
modifier: 017116
name: 7
product: 209017
modifier: 017092

COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MK_P
type: Species

208464
stoichiometry: 1.0
species: 208169
type: SpeciesReference

208133
unit: 208145
name: substance
type: SBMLUnitsDef

208367
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: 208157
name: P3
type: Species

208392
stoichiometry: 1.0
species: 208169
type: SpeciesReference

209077
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

209625
value: 0.01
name: k3
type: LocalParameter

208109
unit: 208121
name: volume
type: SBMLUnitsDef

COPASI14
constant: true
value: 108.6
name: K6
type: Parameter

208305
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MKKK_P
type: Species

COPASI24
modifier: 017080
fast: false
type: Reaction
modifier: 208945
product: 208933
reversible: false
modifier: 208969
modifier: 017068
name: 6
modifier: 017056
modifier: 017043
kinetic law: 208981
reactant: 208921
modifier: 208957

209005
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

208404
stoichiometry: 1.0
species: 208305
type: SpeciesReference

COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 208157
name: MK
type: Species

208921
stoichiometry: 1.0
species: 208330
type: SpeciesReference