MODEL1204280004
type: SBMLModel
name: 8
parameter: COPASI14
reaction: COPASI29
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

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

COPASI29
type: Reaction
reversible: false
modifier: 927754
modifier: 861804
kinetic law: 927766
product: 927730
modifier: 861780
modifier: 861792
modifier: 927742
name: 8
fast: false
reactant: 927718

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MK

COPASI2
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

927778
type: LocalParameter
value: 0.1
name: k7

927730
type: SpeciesReference
stoichiometry: 1.0
species: 926974

926974
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MK_PP

926950
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MKK_PP

926962
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MK_P

927718
type: SpeciesReference
stoichiometry: 1.0
species: 926962

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

926938
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MKK_P

926902
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 300.0
initial amount: NaN
in compartment: COPASI2
name: MKKK

926914
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: MKKK_P

926926
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MKK

COPASI6
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: COPASI2
name: P2

COPASI5
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: COPASI2
name: P1

927634
type: LocalParameter
value: 0.1
name: k6b

927622
type: LocalParameter
value: 0.1
name: k6a

927478
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species: 926938

927490
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species: 926926

COPASI22
type: Reaction
reactant: 926998
modifier: 861348
kinetic law: 927034
fast: false
name: 1
product: 927010
reversible: false
modifier: 927022
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926998
type: SpeciesReference
stoichiometry: 1.0
species: 926902

926986
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.99999951844375
initial amount: NaN
in compartment: COPASI2
name: Sig

927046
type: LocalParameter
value: 0.2
name: k1

927010
type: SpeciesReference
stoichiometry: 1.0
species: 926914

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

926878
type: SBMLUnitsDef
unit: 926890
name: substance

926890
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

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

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

COPASI30
type: Reaction
modifier: 861816
modifier: 861876
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reactant: 927790
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fast: false
product: 927802
modifier: 861840
name: 9
kinetic law: 927886
reversible: false
modifier: 927838

927790
type: SpeciesReference
stoichiometry: 1.0
species: 926974

927802
type: SpeciesReference
stoichiometry: 1.0
species: 926962

927898
type: LocalParameter
value: 0.1
name: k9b

926854
type: SBMLUnitsDef
unit: 926866
name: volume

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

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

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

COPASI26
type: Reaction
modifier: 861540
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reversible: false
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fast: false
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name: 5
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kinetic law: 927442
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927310
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927466
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927454
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927322
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species: 926938

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

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

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

COPASI24
type: Reaction
fast: false
modifier: 861444
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product: 927178
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kinetic law: 927214
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name: 3
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reversible: false

927166
type: SpeciesReference
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927178
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stoichiometry: 1.0
species: 926938

927226
type: LocalParameter
value: 0.1
name: k3

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

COPASI25
type: Reaction
reversible: false
kinetic law: 927286
name: 4
fast: false
modifier: 861468
modifier: 861480
modifier: 927274
product: 927250
modifier: 927262
modifier: 861492
reactant: 927238

927298
type: LocalParameter
value: 0.1
name: k4

927250
type: SpeciesReference
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927238
type: SpeciesReference
stoichiometry: 1.0
species: 926938

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

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

COPASI15
type: Parameter
constant: true
value: 30.0
name: K9b

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

927646
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

927658
type: SpeciesReference
stoichiometry: 1.0
species: 926962

927706
type: LocalParameter
value: 0.1
name: k7

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

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

COPASI23
type: Reaction
modifier: 927106
modifier: 861384
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modifier: 861408
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modifier: 927130
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reversible: false
modifier: 927082
modifier: 861360
name: 2
kinetic law: 927142
fast: false
reactant: 927058

927070
type: SpeciesReference
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927154
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value: 0.01
name: k2a

927058
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species: 926914

COPASI31
type: Reaction
modifier: 927958
reversible: false
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product: 927922
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kinetic law: 928006
fast: false
modifier: 861912
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927922
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

927910
type: SpeciesReference
stoichiometry: 1.0
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928018
type: LocalParameter
value: 0.1
name: k10b