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name: k10b
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COPASI31
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reversible: false
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has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MKK
type: Species

MODEL1204280004
name: 8
parameter: COPASI14
reaction: COPASI29
type: SBMLModel
reaction: COPASI27
species: 926938
reaction: COPASI22
parameter: COPASI7
units def: 926878
parameter: COPASI20
parameter: COPASI12
function def: COPASI45
reaction: COPASI30
volume units: 926854
compartment: COPASI3
units def: 926854
parameter: COPASI9
reaction: COPASI26
species: 926950
name: 2
parameter: COPASI16
species: 926962
name: 9
name: 3
name: 5
parameter: COPASI19
substance units: 926878
name: 10
curated: false
parameter: COPASI11
reaction: COPASI24
time units: 291235
function def: COPASI44
species: COPASI4
function def: COPASI48
species: 926914
species: COPASI5
name: 6
function def: COPASI42
function def: COPASI49
name: 1
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_USEQ)
parameter: COPASI8
function def: COPASI51
reaction: COPASI25
name: 7
is described by: http://identifiers.org/pubmed/22748295
parameter: COPASI17
parameter: COPASI13
parameter: COPASI15
reaction: COPASI28
species: 926926
parameter: COPASI18
area units: 061696
length unit: length
name: 4
parameter: COPASI10
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_USEQ) 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 [ MODEL12042800…
reaction: COPASI23
species: 926902
compartment: COPASI2
function def: COPASI46
species: 926974
function def: COPASI50
function def: COPASI43
reaction: COPASI31
function def: COPASI47
species: 926986
species: COPASI6

COPASI28
reactant: 927646
product: 927658
type: Reaction
reversible: false
fast: false
modifier: 861744
name: 7
modifier: 927682
modifier: 861768
kinetic law: 927694
modifier: 927670
modifier: 861756

927622
value: 0.1
name: k6a
type: LocalParameter

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

926950
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

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

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

927166
stoichiometry: 1.0
species: 926926
type: SpeciesReference

927466
value: 0.1
name: k5b
type: LocalParameter

COPASI27
modifier: 861696
modifier: 861636
name: 6
modifier: 927574
modifier: 861720
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reversible: false
modifier: 861660
fast: false
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kinetic law: 927610
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type: Reaction
reactant: 927478
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product: 927490

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

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

927910
stoichiometry: 1.0
species: 926962
type: SpeciesReference

927490
stoichiometry: 1.0
species: 926926
type: SpeciesReference

COPASI26
modifier: 861540
modifier: 861588
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reversible: false
modifier: 861504
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type: Reaction
fast: false
modifier: 861516
modifier: 861576
name: 5
modifier: 927334
reactant: 927310
kinetic law: 927442
modifier: 927370
product: 927322

926962
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

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

927634
value: 0.1
name: k6b
type: LocalParameter

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

COPASI30
modifier: 861816
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reactant: 927790
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fast: false
product: 927802
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type: Reaction
name: 9
kinetic law: 927886
reversible: false
modifier: 927838

927154
value: 0.01
name: k2a
type: LocalParameter

COPASI25
reversible: false
kinetic law: 927286
name: 4
fast: false
modifier: 861468
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product: 927250
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type: Reaction
modifier: 861492
reactant: 927238

927922
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI15
constant: true
value: 30.0
name: K9b
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

927478
stoichiometry: 1.0
species: 926938
type: SpeciesReference

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

926974
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

927646
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

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

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

COPASI24
fast: false
modifier: 861444
reactant: 927166
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kinetic law: 927214
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name: 3
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reversible: false

927010
stoichiometry: 1.0
species: 926914
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926902
constant: false
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initial concentration: 300.0
initial amount: NaN
in compartment: COPASI2
name: MKKK
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COPASI2
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

926938
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
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in compartment: COPASI2
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926890
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

927790
stoichiometry: 1.0
species: 926974
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926878
unit: 926890
name: substance
type: SBMLUnitsDef

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

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stoichiometry: 1.0
species: 926950
type: SpeciesReference

927718
stoichiometry: 1.0
species: 926962
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927322
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927238
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COPASI23
modifier: 927106
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modifier: 861360
name: 2
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fast: false
reactant: 927058

927058
stoichiometry: 1.0
species: 926914
type: SpeciesReference

927778
value: 0.1
name: k7
type: LocalParameter

COPASI29
reversible: false
modifier: 927754
modifier: 861804
kinetic law: 927766
product: 927730
modifier: 861780
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modifier: 927742
type: Reaction
name: 8
fast: false
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927070
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species: 926902
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926986
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.99999951844375
initial amount: NaN
in compartment: COPASI2
name: Sig
type: Species

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

927658
stoichiometry: 1.0
species: 926962
type: SpeciesReference

927730
stoichiometry: 1.0
species: 926974
type: SpeciesReference

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

926914
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

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

926854
unit: 926866
name: volume
type: SBMLUnitsDef

927298
value: 0.1
name: k4
type: LocalParameter

927178
stoichiometry: 1.0
species: 926938
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COPASI22
reactant: 926998
modifier: 861348
kinetic law: 927034
fast: false
name: 1
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reversible: false
type: Reaction
modifier: 927022
modifier: 861336

927802
stoichiometry: 1.0
species: 926962
type: SpeciesReference

927706
value: 0.1
name: k7
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value: 0.1
name: k5a
type: LocalParameter

926866
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

927226
value: 0.1
name: k3
type: LocalParameter

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

927046
value: 0.2
name: k1
type: LocalParameter

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

926998
stoichiometry: 1.0
species: 926902
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927310
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species: 926950
type: SpeciesReference