COPASI25
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266194
value: 0.1
name: k4
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COPASI11
constant: true
value: 30.0
name: K5
type: Parameter

COPASI26
type: Reaction
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266328
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species: 265581
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265593
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name: MKK_P
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265569
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name: MKKK_P
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265641
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species: COPASI2
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265713
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species: COPASI2
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COPASI5
constant: false
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initial concentration: 99.9999951844376
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name: P1
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265617
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initial concentration: 0.0
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name: MK_PP
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266061
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species: 265581
type: SpeciesReference

COPASI27
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fast: false
product: 266785
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name: 8
modifier: 895592

COPASI24
fast: false
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266954
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

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

265557
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI6
constant: false
boundary condition: false
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initial concentration: 199.999990368875
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name: P3
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COPASI28
reversible: false
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kinetic law: 266915
reactant: 266850
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product: 266863
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MODEL1204280010
parameter: COPASI18
species: 265569
time units: 291235
name: 7
function def: COPASI32
function def: COPASI36
name: 6
is described by: http://identifiers.org/pubmed/22748295
function def: COPASI33
parameter: COPASI16
compartment: 265557
substance units: 265533
parameter: COPASI8
function def: COPASI37
species: COPASI3
reaction: COPASI21
name: 1
notes: Sarma2012 - Interaction topologies of MAPK cascade (M2_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…
species: COPASI6
name: 4
species: 265593
species: COPASI5
length unit: length
function def: COPASI38
name: Sarma2012 - Interaction topologies of MAPK cascade (M2_K1_USEQ_short_duration_signal)
parameter: COPASI11
species: 265617
reaction: COPASI26
function def: COPASI39
reaction: COPASI22
name: 9
reaction: COPASI28
species: COPASI2
parameter: COPASI14
parameter: COPASI9
name: 3
function def: COPASI34
species: COPASI4
name: 2
event: COPASI19
name: 5
species: 265629
species: 265581
parameter: COPASI13
reaction: COPASI27
units def: 265509
reaction: COPASI23
units def: 265533
reaction: COPASI24
function def: COPASI30
parameter: COPASI7
parameter: COPASI12
reaction: COPASI29
function def: COPASI31
parameter: COPASI15
function def: COPASI35
name: 8
parameter: COPASI17
species: 265605
reaction: COPASI20
type: SBMLModel
curated: false
reaction: COPASI25
volume units: 265509
area units: 061696
parameter: COPASI10
name: 10

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

266837
value: 0.1
name: k7
type: LocalParameter

COPASI23
name: 4
modifier: 266170
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reversible: false
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fast: false

COPASI8
constant: true
value: 30.0
name: K2
type: Parameter

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

266073
stoichiometry: 1.0
species: 265593
type: SpeciesReference

265689
value: 0.2
name: k1
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COPASI18
constant: true
value: 3.0E51
name: Kse2
type: Parameter

265701
stoichiometry: 1.0
species: 265569
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265629
constant: false
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name: Sig
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265545
exponent: 1.0
scale: -9
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266759
value: 0.1
name: k7
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COPASI29
fast: false
modifier: 895664
reversible: false
kinetic law: 267006
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name: 10
reactant: 266941
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modifier: 266993

COPASI12
constant: true
value: 30.0
name: K6
type: Parameter

COPASI22
modifier: 895326
type: Reaction
product: 266073
kinetic law: 266109
reversible: false
modifier: 895338
name: 3
reactant: 266061
fast: false
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266442
stoichiometry: 1.0
species: COPASI4
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COPASI9
constant: true
value: 30.0
name: K3
type: Parameter

COPASI19
event assignment: 267045
trigger: 267032
use values from trigger time: true
name: event_1
type: Event

266941
stoichiometry: 1.0
species: COPASI4
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266928
value: 0.1
name: k9
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266207
stoichiometry: 1.0
species: 265605
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266785
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species: 265617
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266772
stoichiometry: 1.0
species: COPASI4
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COPASI21
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kinetic law: 266035
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265533
unit: 265545
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266146
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species: 265605
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266850
stoichiometry: 1.0
species: 265617
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COPASI16
constant: true
value: 30.0
name: K10
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266219
stoichiometry: 1.0
species: 265593
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COPASI20
product: 265653
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reversible: false
name: 1
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265605
constant: false
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266429
stoichiometry: 1.0
species: COPASI3
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266316
stoichiometry: 1.0
species: 265593
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COPASI2
constant: false
boundary condition: false
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initial concentration: 299.999971106626
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in compartment: 265557
name: MKKK
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COPASI17
constant: true
value: 3.0E51
name: Kse1
type: Parameter

266863
stoichiometry: 1.0
species: COPASI4
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266134
stoichiometry: 1.0
species: 265593
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265521
exponent: 1.0
scale: -3
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kind: LITRE
type: SBMLUnit

267032
persistant: true
initial value: true
type: Trigger

266048
value: 0.01
name: k2
type: LocalParameter

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

266416
value: 0.1
name: k6
type: LocalParameter

265581
constant: false
boundary condition: false
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initial concentration: 1199.9998844265
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in compartment: 265557
name: MKK
type: Species

COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.9998844265
initial amount: NaN
in compartment: 265557
name: MK
type: Species

266303
value: 0.1
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267019
value: 0.1
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type: LocalParameter

266121
value: 0.1
name: k3
type: LocalParameter

265653
stoichiometry: 1.0
species: 265569
type: SpeciesReference

COPASI15
constant: true
value: 30.0
name: K9
type: Parameter

265509
unit: 265521
name: volume
type: SBMLUnitsDef

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