COPASI29
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337449
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COPASI5
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initial concentration: 100.0
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COPASI15
constant: true
value: 24.6
name: K9
type: Parameter

COPASI21
modifier: 039132
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fast: false
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reversible: false
name: 2
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337754
value: 0.092
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336557
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

337375
stoichiometry: 1.0
species: COPASI3
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337074
value: 0.092
name: k5
type: LocalParameter

336118
unit: 336130
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336473
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336202
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336142
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MODEL1204280038
reaction: COPASI23
species: 336178
time units: 291235
function def: COPASI30
reaction: COPASI28
species: COPASI5
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length unit: length
notes: Sarma2012 - Interaction topologies of MAPK cascade (M2_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…
parameter: COPASI11
reaction: COPASI25
reaction: COPASI27
function def: COPASI34
name: 10
function def: COPASI37
type: SBMLModel
parameter: COPASI10
area units: 061696
name: 4
parameter: COPASI9
species: 336473
species: 336190
parameter: COPASI18
parameter: COPASI12
species: 336461
function def: COPASI31
units def: 336142
species: COPASI4
parameter: COPASI13
name: 1
parameter: COPASI15
reaction: COPASI20
event: COPASI19
reaction: COPASI29
compartment: 336166
is described by: http://identifiers.org/pubmed/22748295
name: 8
curated: false
function def: COPASI35
name: Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_QSS_PSEQ)
name: 9
name: 3
name: 5
function def: COPASI38
reaction: COPASI22
species: COPASI3
units def: 336118
parameter: COPASI14
reaction: COPASI21
function def: COPASI32
species: COPASI6
name: 7
species: 336214
function def: COPASI33
volume units: 336118
reaction: COPASI24
species: 336202
reaction: COPASI26
name: 2
substance units: 336142
parameter: COPASI7
function def: COPASI36
function def: COPASI39
parameter: COPASI16
parameter: COPASI8
parameter: COPASI17
species: COPASI2

COPASI4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 336166
name: MK_P
type: Species

COPASI14
constant: true
value: 500.0
name: K8
type: Parameter

337992
persistant: true
initial value: true
type: Trigger

COPASI28
name: 9
modifier: 039449
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kinetic law: 337742
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reversible: false
fast: false
modifier: 337718
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COPASI20
modifier: 039048
type: Reaction
product: 336497
modifier: 039060
name: 1
reactant: 336485
kinetic law: 336521
fast: false
reversible: false
modifier: 336509

336894
value: 0.01
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336918
stoichiometry: 1.0
species: 336214
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336178
constant: false
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336190
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
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name: MKK
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337838
value: 0.086
name: k10
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337670
value: 15.0
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type: LocalParameter

COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 336166
name: MK
type: Species

COPASI13
constant: true
value: 50.5
name: K7
type: Parameter

337437
value: 0.01
name: k7
type: LocalParameter

337461
stoichiometry: 1.0
species: 336461
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COPASI23
modifier: 039180
modifier: 336930
reactant: 336906
product: 336918
type: Reaction
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kinetic law: 336954
fast: false
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reversible: false
name: 4
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336641
value: 0.086
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336130
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

336461
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336545
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336906
stoichiometry: 1.0
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COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999985553313
initial amount: NaN
in compartment: 336166
name: MKKK
type: Species

COPASI12
constant: true
value: 108.6
name: K6
type: Parameter

COPASI22
name: 3
kinetic law: 336882
fast: false
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reversible: false
reactant: 336653
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product: 336665
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337388
stoichiometry: 1.0
species: COPASI4
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COPASI11
constant: true
value: 26.6
name: K5
type: Parameter

336497
stoichiometry: 1.0
species: 336178
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336653
stoichiometry: 1.0
species: 336190
type: SpeciesReference

COPASI19
event assignment: 338005
trigger: 337992
use values from trigger time: true
name: event_1
type: Event

COPASI8
constant: true
value: 54.3
name: K2
type: Parameter

COPASI25
modifier: 039350
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reactant: 337086
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337778
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336154
exponent: 1.0
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337694
stoichiometry: 1.0
species: COPASI4
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COPASI10
constant: true
value: 500.0
name: K4
type: Parameter

COPASI9
constant: true
value: 50.5
name: K3
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336966
value: 15.0
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COPASI24
modifier: 039254
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reversible: false
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name: 5
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COPASI18
constant: true
value: 0.06
name: Kse2
type: Parameter

336665
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336214
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336485
stoichiometry: 1.0
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337363
value: 0.086
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COPASI17
constant: true
value: 0.06
name: Kse1
type: Parameter

336533
value: 1.0
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COPASI6
constant: false
boundary condition: false
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initial concentration: 200.0
initial amount: NaN
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name: P3
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COPASI27
name: 8
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kinetic law: 337658
reversible: false
product: 337461
type: Reaction
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reactant: 337449
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337278
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species: 336190
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336990
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337086
stoichiometry: 1.0
species: 336202
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337682
stoichiometry: 1.0
species: 336461
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337766
stoichiometry: 1.0
species: COPASI4
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336166
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

336978
stoichiometry: 1.0
species: 336214
type: SpeciesReference

COPASI16
constant: true
value: 108.6
name: K10
type: Parameter

COPASI7
constant: true
value: 100.0
name: K1
type: Parameter

COPASI26
product: 337388
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reversible: false
kinetic law: 337425
modifier: 039362
reactant: 337375
fast: false
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type: Reaction
modifier: 337401
name: 7