COPASI6
constant: true
value: 500.0
name: K4
type: Parameter

363051
constant: false
boundary condition: false
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initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 363015
name: MKK
type: Species

COPASI11
constant: true
value: 24.6
name: K9
type: Parameter

COPASI21
kinetic law: 364085
reversible: false
product: 364001
modifier: 364013
fast: false
modifier: 364061
modifier: 364025
reactant: 363989
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name: 6
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364414
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362991
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362979
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

364097
value: 0.086
name: k6
type: LocalParameter

COPASI5
constant: true
value: 50.5
name: K3
type: Parameter

364808
value: 0.086
name: k10
type: LocalParameter

COPASI10
constant: true
value: 500.0
name: K8
type: Parameter

363387
stoichiometry: 1.0
species: 363039
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363039
constant: false
boundary condition: false
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initial concentration: 0.0
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name: MKKK_P
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COPASI20
modifier: 363893
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reversible: false
product: 363881
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fast: false
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364820
persistant: true
initial value: true
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363435
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species: 363039
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363591
stoichiometry: 1.0
species: 363075
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364699
value: 0.092
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363579
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species: 363063
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363519
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species: 363063
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364402
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species: 363087
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COPASI8
constant: true
value: 108.6
name: K6
type: Parameter

MODEL1204280039
name: 1
function def: COPASI28
units def: 362967
reaction: COPASI18
parameter: COPASI7
name: 10
reaction: COPASI23
function def: COPASI30
parameter: COPASI11
function def: COPASI33
name: 8
species: COPASI2
time units: 291235
name: 3
name: 5
units def: 362991
species: 363339
parameter: COPASI12
function def: COPASI26
species: 363363
species: 363039
function def: COPASI29
species: 363327
species: 363027
curated: false
reaction: COPASI19
parameter: COPASI8
function def: COPASI31
type: SBMLModel
name: 7
area units: 061696
parameter: COPASI3
name: 9
reaction: COPASI24
reaction: COPASI16
reaction: COPASI25
parameter: COPASI14
function def: COPASI34
name: 2
volume units: 362967
species: 363087
function def: COPASI27
is described by: http://identifiers.org/pubmed/22748295
parameter: COPASI5
parameter: COPASI13
notes: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_QSS_PSEQ) 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…
reaction: COPASI20
name: 6
length unit: length
reaction: COPASI21
substance units: 362991
parameter: COPASI10
parameter: COPASI4
species: 363075
function def: COPASI32
function def: COPASI35
species: 363063
reaction: COPASI17
species: 363351
parameter: COPASI9
compartment: 363015
event: COPASI15
species: 363051
reaction: COPASI22
name: 4
name: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_QSS_PSEQ)
parameter: COPASI6

363063
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 363015
name: MKK_P
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364462
value: 15.0
name: k7
type: LocalParameter

COPASI13
constant: true
value: 0.06
name: Kse1
type: Parameter

363339
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
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in compartment: 363015
name: P1
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COPASI7
constant: true
value: 26.2
name: K5
type: Parameter

363027
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999985553313
initial amount: NaN
in compartment: 363015
name: MKKK
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363423
value: 1.0
name: k1
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363881
stoichiometry: 1.0
species: 363063
type: SpeciesReference

COPASI12
constant: true
value: 108.6
name: K10
type: Parameter

363869
stoichiometry: 1.0
species: 363075
type: SpeciesReference

363495
value: 0.086
name: k2
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363858
value: 15.0
name: k4
type: LocalParameter

COPASI25
modifier: 044898
reversible: false
reactant: 364711
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fast: false
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kinetic law: 364796
name: 10

363351
constant: false
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initial concentration: 200.0
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363075
constant: false
boundary condition: false
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initial concentration: 0.0
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364001
stoichiometry: 1.0
species: 363051
type: SpeciesReference

COPASI15
event assignment: 364832
trigger: 364820
use values from trigger time: true
name: event_1
type: Event

COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 363015
name: MK
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363507
stoichiometry: 1.0
species: 363051
type: SpeciesReference

COPASI9
constant: true
value: 50.5
name: K7
type: Parameter

COPASI24
fast: false
modifier: 364558
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reversible: false
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364474
stoichiometry: 1.0
species: 363327
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364109
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

364711
stoichiometry: 1.0
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363363
constant: false
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name: Sig
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363327
constant: false
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364121
stoichiometry: 1.0
species: 363087
type: SpeciesReference

COPASI14
constant: true
value: 0.06
name: Kse2
type: Parameter

363015
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

363567
value: 0.01
name: k3
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COPASI23
modifier: 364426
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fast: false
modifier: 044740
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name: 8

362967
unit: 362979
name: volume
type: SBMLUnitsDef

364390
value: 0.01
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363447
stoichiometry: 1.0
species: 363027
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COPASI4
constant: true
value: 54.3
name: K2
type: Parameter

COPASI17
modifier: 044414
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reversible: false
reactant: 363435
kinetic law: 363483
fast: false
name: 2
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363989
stoichiometry: 1.0
species: 363063
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COPASI18
product: 363519
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fast: false
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name: 3
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363087
constant: false
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name: MK_P
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363978
value: 0.092
name: k5
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COPASI22
modifier: 044691
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kinetic law: 364378
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fast: false
reversible: false
reactant: 364109
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name: 7
type: Reaction
product: 364121

364723
stoichiometry: 1.0
species: COPASI2
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363375
stoichiometry: 1.0
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363003
exponent: 1.0
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364486
stoichiometry: 1.0
species: 363087
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COPASI3
constant: true
value: 100.0
name: K1
type: Parameter

COPASI19
name: 4
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reversible: false
kinetic law: 363846
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COPASI16
fast: false
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type: Reaction
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kinetic law: 363411
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reversible: false
name: 1