COPASI22
reversible: false
product: 365440
modifier: 905844
fast: false
reactant: 365428
kinetic law: 365464
type: Reaction
modifier: 365452
name: 1
modifier: 905832

COPASI12
constant: true
value: 30.0
name: K6a
type: Parameter

COPASI23
modifier: 905892
modifier: 365548
modifier: 905856
modifier: 365560
name: 2
product: 365500
reversible: false
modifier: 365512
modifier: 905880
modifier: 365536
type: Reaction
modifier: 905904
fast: false
reactant: 365488
modifier: 905868
modifier: 365524
kinetic law: 365572
modifier: 905916

COPASI13
constant: true
value: 30.0
name: K7
type: Parameter

365476
value: 0.2
name: k1
type: LocalParameter

COPASI9
constant: true
value: 30.0
name: K3
type: Parameter

COPASI24
modifier: 905928
name: 3
modifier: 365620
fast: false
reversible: false
modifier: 905952
kinetic law: 365644
product: 365608
type: Reaction
modifier: 365632
modifier: 905940
reactant: 365596

COPASI10
constant: true
value: 30.0
name: K4
type: Parameter

366340
stoichiometry: 1.0
species: 365392
type: SpeciesReference

365392
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MK_P
type: Species

COPASI8
constant: true
value: 30.0
name: K2a
type: Parameter

366328
value: 0.1
name: k9b
type: LocalParameter

COPASI25
name: 4
modifier: 905988
modifier: 905964
reactant: 365668
modifier: 365704
type: Reaction
modifier: 905976
fast: false
reversible: false
modifier: 365692
kinetic law: 365716
product: 365680

365728
value: 0.1
name: k4
type: LocalParameter

COPASI11
constant: true
value: 30.0
name: K5a
type: Parameter

365320
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

366352
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI26
modifier: 906024
modifier: 906084
product: 365752
reactant: 365740
modifier: 906072
modifier: 906036
name: 5
modifier: 365824
modifier: 365800
modifier: 906096
modifier: 365764
modifier: 365788
modifier: 906048
modifier: 365860
modifier: 365848
modifier: 365836
modifier: 365776
modifier: 365812
modifier: 906108
kinetic law: 365872
reversible: false
modifier: 906012
modifier: 906000
type: Reaction
modifier: 906060
fast: false

COPASI16
constant: true
value: 30.0
name: K10b
type: Parameter

365656
value: 0.1
name: k3
type: LocalParameter

366076
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

366160
stoichiometry: 1.0
species: 365404
type: SpeciesReference

COPASI27
modifier: 365956
reversible: false
modifier: 906205
modifier: 365992
modifier: 906181
fast: false
modifier: 365944
modifier: 365968
modifier: 906229
modifier: 906145
name: 6
modifier: 906169
modifier: 906133
type: Reaction
modifier: 906157
kinetic law: 366040
modifier: 366028
modifier: 366016
modifier: 366004
product: 365920
modifier: 906193
modifier: 906217
modifier: 906120
modifier: 365980
reactant: 365908
modifier: 365932

COPASI17
constant: true
value: 3.0E51
name: Kse1
type: Parameter

366208
value: 0.1
name: k7
type: LocalParameter

365332
constant: false
boundary condition: false
has only substance units: false
initial concentration: 300.0
initial amount: NaN
in compartment: COPASI2
name: MKKK
type: Species

COPASI14
constant: true
value: 30.0
name: K8
type: Parameter

COPASI28
modifier: 366100
kinetic law: 366124
reactant: 366076
name: 7
modifier: 906266
modifier: 366112
type: Reaction
modifier: 906241
fast: false
product: 366088
reversible: false
modifier: 906254

366088
stoichiometry: 1.0
species: 365392
type: SpeciesReference

COPASI29
name: 8
modifier: 366184
fast: false
reactant: 366148
reversible: false
product: 366160
type: Reaction
modifier: 906290
kinetic law: 366196
modifier: 906278
modifier: 366172
modifier: 906302

365344
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MKKK_P
type: Species

365308
unit: 365320
name: substance
type: SBMLUnitsDef

365440
stoichiometry: 1.0
species: 365344
type: SpeciesReference

366460
persistant: true
initial value: true
type: Trigger

COPASI15
constant: true
value: 30.0
name: K9b
type: Parameter

366448
value: 0.1
name: k10b
type: LocalParameter

365404
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MK_PP
type: Species

365356
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MKK
type: Species

366052
value: 0.1
name: k6a
type: LocalParameter

COPASI2
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

365752
stoichiometry: 1.0
species: 365368
type: SpeciesReference

365500
stoichiometry: 1.0
species: 365332
type: SpeciesReference

365368
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MKK_P
type: Species

COPASI19
constant: true
value: 30.0
name: K5b
type: Parameter

365416
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.99999951844375
initial amount: NaN
in compartment: COPASI2
name: Sig
type: Species

365380
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MKK_PP
type: Species

366064
value: 0.1
name: k6b
type: LocalParameter

365596
stoichiometry: 1.0
species: 365356
type: SpeciesReference

365668
stoichiometry: 1.0
species: 365368
type: SpeciesReference

365740
stoichiometry: 1.0
species: 365380
type: SpeciesReference

365680
stoichiometry: 1.0
species: 365380
type: SpeciesReference

COPASI18
constant: true
value: 3.0E51
name: Kse2
type: Parameter

MODEL1204280012
is described by: http://identifiers.org/pubmed/22748295
substance units: 365308
reaction: COPASI24
species: 365368
length unit: length
name: function_4_6_1
species: COPASI5
parameter: COPASI18
parameter: COPASI20
parameter: COPASI9
compartment: COPASI2
species: 365380
species: 365344
reaction: COPASI31
area units: 061696
function def: 365164
function def: 365212
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_USEQ_short_duration_signal)
reaction: COPASI27
function def: 365200
parameter: COPASI16
reaction: COPASI23
parameter: COPASI10
function def: 365188
parameter: COPASI7
parameter: COPASI12
name: function_4_7_1
function def: 365236
function def: 365176
parameter: COPASI19
function def: 365224
species: 365404
species: 365356
event: COPASI21
parameter: COPASI8
reaction: COPASI30
parameter: COPASI14
species: 365332
parameter: COPASI15
volume units: 365284
parameter: COPASI11
reaction: COPASI26
units def: 365284
reaction: COPASI22
reaction: COPASI29
name: function_4_4_1
reaction: COPASI25
species: COPASI4
function def: 365248
name: function_4_2_1
name: function_4_9_1
name: function_4_3_1
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_USEQ_short_duration_signal) 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) QS…
type: SBMLModel
species: COPASI6
name: function_4_8_1
compartment: COPASI3
name: function_4_1_1
curated: false
function def: 365272
function def: 365260
name: function_4_5_1
units def: 365308
time units: 291235
species: 365392
parameter: COPASI17
name: function_4_10_1
parameter: COPASI13
reaction: COPASI28
species: 365416

COPASI5
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: COPASI2
name: P1
type: Species

365920
stoichiometry: 1.0
species: 365356
type: SpeciesReference

365428
stoichiometry: 1.0
species: 365332
type: SpeciesReference

COPASI6
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: COPASI2
name: P2
type: Species

COPASI30
modifier: 366244
product: 366232
modifier: 906375
modifier: 906326
reversible: false
modifier: 906363
modifier: 366304
modifier: 906338
name: 9
type: Reaction
modifier: 366292
modifier: 366256
reactant: 366220
kinetic law: 366316
modifier: 906314
modifier: 366268
modifier: 366280
fast: false
modifier: 906387
modifier: 906351

365296
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

365584
value: 0.01
name: k2a
type: LocalParameter

366148
stoichiometry: 1.0
species: 365392
type: SpeciesReference

366220
stoichiometry: 1.0
species: 365404
type: SpeciesReference

COPASI31
modifier: 366424
modifier: 906435
reversible: false
reactant: 366340
modifier: 906411
modifier: 906447
product: 366352
modifier: 366400
modifier: 366388
modifier: 906399
fast: false
modifier: 906423
kinetic law: 366436
modifier: 906471
modifier: 366364
type: Reaction
name: 10
modifier: 366376
modifier: 906459
modifier: 366412

COPASI7
constant: true
value: 30.0
name: K1
type: Parameter

365884
value: 0.1
name: k5a
type: LocalParameter

COPASI3
constant: true
size: 1.0
spatial dimensions: 3.0
name: No Name
type: Compartment

365608
stoichiometry: 1.0
species: 365368
type: SpeciesReference

365488
stoichiometry: 1.0
species: 365344
type: SpeciesReference

COPASI20
constant: true
value: 30.0
name: K6b
type: Parameter

COPASI4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MK
type: Species

365908
stoichiometry: 1.0
species: 365368
type: SpeciesReference

366232
stoichiometry: 1.0
species: 365392
type: SpeciesReference

366136
value: 0.1
name: k7
type: LocalParameter

365896
value: 0.1
name: k5b
type: LocalParameter

365284
unit: 365296
name: volume
type: SBMLUnitsDef

COPASI21
event assignment: 366472
trigger: 366460
use values from trigger time: true
name: event_1
type: Event