COPASI11
constant: true
value: 30.0
name: K5
type: Parameter

039421
value: 0.1
name: k6
type: LocalParameter

038881
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 038821
name: MK_PP
type: Species

MODEL1204280006
type: SBMLModel
time units: 291235
species: 038893
length unit: length
units def: 038797
function def: COPASI37
function def: COPASI35
area units: 061696
name: 4
function def: COPASI31
reaction: COPASI21
compartment: 038821
parameter: COPASI11
species: COPASI2
name: 6
reaction: COPASI23
parameter: COPASI8
reaction: COPASI27
units def: 038773
name: 5
species: COPASI6
reaction: COPASI25
parameter: COPASI16
reaction: COPASI22
function def: COPASI38
function def: COPASI36
name: 3
species: COPASI4
name: 10
function def: COPASI32
parameter: COPASI14
parameter: COPASI13
name: 8
name: 9
name: 1
curated: false
reaction: COPASI24
reaction: COPASI28
is described by: http://identifiers.org/pubmed/22748295
species: 038881
parameter: COPASI9
reaction: COPASI26
function def: COPASI29
notes: Sarma2012 - Interaction topologies of MAPK cascade (M2_K1_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 [ MODEL12042800…
function def: COPASI33
species: COPASI5
reaction: COPASI19
volume units: 038773
name: Sarma2012 - Interaction topologies of MAPK cascade (M2_K1_PSEQ)
parameter: COPASI15
name: 2
species: COPASI3
species: 038869
function def: COPASI34
parameter: COPASI10
function def: COPASI30
species: 038857
name: 7
parameter: COPASI18
species: 038845
parameter: COPASI17
reaction: COPASI20
substance units: 038797
species: 038833
parameter: COPASI7
parameter: COPASI12

COPASI19
type: Reaction
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kinetic law: 038941
fast: false
product: 038917
reversible: false
reactant: 038905
modifier: 872799
name: 1

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

COPASI20
modifier: 872859
product: 038977
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fast: false
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reversible: false
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kinetic law: 039049
name: 2
reactant: 038965
modifier: 039001
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type: Reaction

COPASI28
fast: false
reversible: false
product: 039673
modifier: 039685
type: Reaction
modifier: 039709
reactant: 039661
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modifier: 873258
modifier: 873234
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kinetic law: 039721
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modifier: 873246

038857
constant: false
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initial concentration: 0.0
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name: MKK_P
type: Species

039145
stoichiometry: 1.0
species: 038857
type: SpeciesReference

039061
value: 0.01
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038785
exponent: 1.0
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kind: LITRE
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038953
value: 0.2
name: k1
type: LocalParameter

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

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

039337
stoichiometry: 1.0
species: 038845
type: SpeciesReference

COPASI27
reactant: 039577
kinetic law: 039637
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name: 9
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fast: false
type: Reaction
modifier: 039613
product: 039589
reversible: false
modifier: 873210

039205
value: 0.1
name: k4
type: LocalParameter

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

COPASI6
constant: false
boundary condition: false
has only substance units: false
initial concentration: 199.999990368875
initial amount: NaN
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name: P3
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039577
stoichiometry: 1.0
species: 038881
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038845
constant: false
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COPASI26
modifier: 873162
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reversible: false
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reactant: 039505
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fast: false
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COPASI10
constant: true
value: 30.0
name: K4
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039661
stoichiometry: 1.0
species: COPASI4
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039157
stoichiometry: 1.0
species: 038869
type: SpeciesReference

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

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

039325
stoichiometry: 1.0
species: 038857
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038917
stoichiometry: 1.0
species: 038833
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038965
stoichiometry: 1.0
species: 038833
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COPASI25
kinetic law: 039481
reversible: false
modifier: 873100
name: 7
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fast: false
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reactant: 039433
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type: Reaction

038797
unit: 038809
name: substance
type: SBMLUnitsDef

038977
stoichiometry: 1.0
species: COPASI2
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COPASI15
constant: true
value: 30.0
name: K9
type: Parameter

COPASI24
modifier: 873064
reversible: false
reactant: 039325
kinetic law: 039409
product: 039337
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type: Reaction
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039445
stoichiometry: 1.0
species: COPASI4
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039589
stoichiometry: 1.0
species: COPASI4
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039085
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species: 038857
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038773
unit: 038785
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species: 038881
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COPASI4
constant: false
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initial concentration: 0.0
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038905
stoichiometry: 1.0
species: COPASI2
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COPASI23
modifier: 039265
name: 5
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modifier: 872968
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fast: false
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reversible: false
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kinetic law: 039301
type: Reaction
product: 039229
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COPASI16
constant: true
value: 30.0
name: K10
type: Parameter

038833
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 038821
name: MKKK_P
type: Species

039313
value: 0.1
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value: 0.1
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038893
constant: false
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039493
value: 0.1
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039673
stoichiometry: 1.0
species: COPASI3
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COPASI5
constant: false
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initial concentration: 99.9999951844376
initial amount: NaN
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COPASI13
constant: true
value: 30.0
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038869
constant: false
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initial concentration: 0.0
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039073
stoichiometry: 1.0
species: 038845
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039505
stoichiometry: 1.0
species: COPASI4
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038809
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

COPASI22
type: Reaction
modifier: 872920
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fast: false
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reversible: false
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name: 4

COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999971106626
initial amount: NaN
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name: MKKK
type: Species

038821
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI14
constant: true
value: 30.0
name: K8
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039565
value: 0.1
name: k7
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039733
value: 0.1
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039433
stoichiometry: 1.0
species: COPASI3
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039133
value: 0.1
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039217
stoichiometry: 1.0
species: 038869
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COPASI21
modifier: 872884
reversible: false
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name: 3
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COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.9998844265
initial amount: NaN
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name: MK
type: Species