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368722
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368329
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species: 368161
type: SpeciesReference

COPASI12
constant: true
value: 30.0
name: K4
type: Parameter

COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.9998844265
initial amount: NaN
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name: MK
type: Species

368784
value: 0.1
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368101
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369359
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369385
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species: COPASI2
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368637
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368649
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species: 368209
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368699
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name: k4
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368809
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species: 368185
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COPASI13
constant: true
value: 30.0
name: K5
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COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
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368149
constant: true
size: 1.0
spatial dimensions: 3.0
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368257
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species: 368161
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369372
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species: COPASI3
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368185
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368892
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species: COPASI3
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369012
value: 0.1
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368710
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368317
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species: 368173
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COPASI14
constant: true
value: 30.0
name: K6
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COPASI4
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initial concentration: 99.9999951844376
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COPASI29
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COPASI5
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initial concentration: 99.9999951844376
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COPASI15
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value: 30.0
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368173
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COPASI28
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COPASI6
constant: true
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368626
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368137
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kind: MOLE
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368940
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368245
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368964
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species: 368221
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COPASI7
constant: true
value: 30.0
name: K2
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COPASI16
constant: true
value: 30.0
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type: Parameter

COPASI21
name: 2
modifier: 368341
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type: Reaction
product: 368329
kinetic law: 368613
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MODEL1204280013
time units: 291235
reaction: COPASI22
function def: COPASI37
compartment: 368149
substance units: 368125
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_PSEQ_short_duration_signal)
parameter: COPASI10
species: 368185
is described by: http://identifiers.org/pubmed/22748295
name: 8
parameter: COPASI18
function def: COPASI38
function def: COPASI31
species: 368161
reaction: COPASI28
parameter: COPASI13
function def: COPASI32
area units: 061696
species: COPASI5
reaction: COPASI21
reaction: COPASI23
reaction: COPASI26
parameter: COPASI8
units def: 368125
species: 368245
notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_PSEQ_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…
parameter: COPASI17
function def: COPASI36
species: 368221
species: 368209
name: 2
parameter: COPASI12
function def: COPASI30
species: COPASI2
name: 3
name: 5
name: 1
function def: COPASI35
species: COPASI3
parameter: COPASI15
reaction: COPASI20
name: 10
units def: 368101
reaction: COPASI25
parameter: COPASI7
reaction: COPASI27
parameter: COPASI9
species: 368197
curated: false
name: 6
parameter: COPASI16
length unit: length
name: 7
function def: COPASI39
name: 9
parameter: COPASI11
species: 368233
parameter: COPASI6
species: 368173
function def: COPASI33
reaction: COPASI29
type: SBMLModel
name: 4
parameter: COPASI14
volume units: 368101
function def: COPASI34
species: COPASI4
reaction: COPASI24
event: COPASI19

COPASI11
constant: true
value: 30.0
name: K3
type: Parameter

369518
value: 0.1
name: k3
type: LocalParameter

369457
stoichiometry: 1.0
species: 368185
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369024
stoichiometry: 1.0
species: 368221
type: SpeciesReference

COPASI27
name: 9
modifier: 912438
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kinetic law: 369348
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type: Reaction
fast: false
modifier: 912450
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reversible: false
product: 369036
modifier: 912414

368305
value: 0.2
name: k1
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368125
unit: 368137
name: substance
type: SBMLUnitsDef

COPASI17
constant: true
value: 30.0
name: K9
type: Parameter

368161
constant: false
boundary condition: false
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initial concentration: 299.999971106626
initial amount: NaN
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name: MKKK
type: Species

COPASI8
constant: true
value: 30.0
name: Kse1
type: Parameter

COPASI26
modifier: 368988
fast: false
product: 368964
modifier: 912390
type: Reaction
modifier: 912378
kinetic law: 369000
reversible: false
reactant: 368952
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COPASI20
modifier: 912150
reactant: 368257
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product: 368269
name: 1
fast: false
type: Reaction
kinetic law: 368293
reversible: false
modifier: 368281

COPASI10
constant: true
value: 30.0
name: Kse3
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368197
constant: false
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initial concentration: 0.0
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name: MKK_P
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368952
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI9
constant: true
value: 30.0
name: Kse2
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COPASI18
constant: true
value: 30.0
name: K10
type: Parameter

368221
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
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name: MK_PP
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368796
stoichiometry: 1.0
species: 368197
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369036
stoichiometry: 1.0
species: COPASI3
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369445
value: 0.1
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COPASI25
modifier: 912354
reversible: false
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kinetic law: 368928
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reactant: 368880
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fast: false

COPASI23
reversible: false
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reactant: 368710
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name: 5
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kinetic law: 368772
product: 368722

368209
constant: false
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name: MKK_PP
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368269
stoichiometry: 1.0
species: 368173
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368113
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

COPASI19
event assignment: 369542
trigger: 369530
use values from trigger time: true
name: event_1
type: Event

COPASI22
modifier: 368674
fast: false
type: Reaction
modifier: 912210
reactant: 368637
modifier: 912234
modifier: 368662
kinetic law: 368687
name: 4
product: 368649
reversible: false
modifier: 912222

COPASI24
modifier: 912306
product: 368809
kinetic law: 368856
modifier: 912330
modifier: 368821
fast: false
modifier: 368844
reversible: false
type: Reaction
modifier: 912318
name: 6
reactant: 368796
modifier: 368832
modifier: 912294

368868
value: 0.1
name: k6
type: LocalParameter

369530
persistant: true
initial value: true
type: Trigger