MODEL1204280016
type: SBMLModel
event: COPASI21
reaction: COPASI22
parameter: COPASI9
name: function_4_9_1
function def: 591896
name: function_4_3_1
reaction: COPASI30
parameter: COPASI12
name: function_4_1_1
reaction: COPASI31
curated: false
function def: 591921
parameter: COPASI13
function def: 591909
name: function_4_5_1
function def: 591848
time units: 291235
function def: 591872
name: function_4_10_1
function def: 591945
reaction: COPASI26
compartment: COPASI2
units def: 591969
parameter: COPASI20
species: COPASI4
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_PSEQ_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…
name: function_4_4_1
species: COPASI6
parameter: COPASI14
parameter: COPASI16
parameter: COPASI10
parameter: COPASI19
name: function_4_2_1
units def: 591993
parameter: COPASI17
reaction: COPASI23
name: function_4_8_1
reaction: COPASI24
area units: 061696
volume units: 591969
substance units: 591993
species: 592029
reaction: COPASI27
function def: 591860
compartment: COPASI3
species: 592017
function def: 591933
reaction: COPASI28
is described by: http://identifiers.org/pubmed/22748295
species: 592078
name: function_4_7_1
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_PSEQ_short_duration_signal)
parameter: COPASI8
function def: 591884
name: function_4_6_1
species: 592066
function def: 591957
length unit: length
species: 592054
parameter: COPASI11
reaction: COPASI25
species: 592042
parameter: COPASI7
species: 592090
species: 592102
parameter: COPASI18
parameter: COPASI15
reaction: COPASI29
species: COPASI5

COPASI21
type: Event
event assignment: 593158
trigger: 593146
use values from trigger time: true
name: event_1

592102
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.99999951844375
initial amount: NaN
in compartment: COPASI2
name: Sig

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

593146
type: Trigger
persistant: true
initial value: true

COPASI22
type: Reaction
reactant: 592114
name: 1
product: 592126
modifier: 930050
modifier: 930038
fast: false
kinetic law: 592150
reversible: false
modifier: 592138

592114
type: SpeciesReference
stoichiometry: 1.0
species: 592017

592017
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 300.0
initial amount: NaN
in compartment: COPASI2
name: MKKK

592126
type: SpeciesReference
stoichiometry: 1.0
species: 592029

592029
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

592162
type: LocalParameter
value: 0.2
name: k1

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

COPASI30
type: Reaction
fast: false
modifier: 592978
modifier: 930592
reactant: 592906
modifier: 592954
modifier: 592966
modifier: 592930
modifier: 930580
modifier: 930532
modifier: 592942
reversible: false
modifier: 930556
name: 9
kinetic law: 593002
modifier: 930544
modifier: 930519
modifier: 592990
product: 592918
modifier: 930568

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

592090
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

592906
type: SpeciesReference
stoichiometry: 1.0
species: 592090

592078
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

592042
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MKK

592066
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

592054
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

593014
type: LocalParameter
value: 0.1
name: k9b

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

592918
type: SpeciesReference
stoichiometry: 1.0
species: 592078

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

COPASI31
type: Reaction
kinetic law: 593122
modifier: 593050
modifier: 930677
modifier: 593062
modifier: 930616
modifier: 593098
modifier: 593110
product: 593038
modifier: 930665
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reversible: false
modifier: 930629
modifier: 930604
reactant: 593026
modifier: 930653
fast: false
name: 10
modifier: 593074
modifier: 593086

593134
type: LocalParameter
value: 0.1
name: k10b

593038
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

593026
type: SpeciesReference
stoichiometry: 1.0
species: 592078

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

COPASI26
type: Reaction
modifier: 930315
reactant: 592426
name: 5
modifier: 930303
modifier: 930291
modifier: 592510
modifier: 592486
modifier: 592474
product: 592438
modifier: 592534
reversible: false
modifier: 592522
kinetic law: 592558
modifier: 930279
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modifier: 592546
modifier: 592462
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modifier: 930255
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modifier: 930207
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fast: false
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modifier: 930231

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

592426
type: SpeciesReference
stoichiometry: 1.0
species: 592066

592438
type: SpeciesReference
stoichiometry: 1.0
species: 592054

592582
type: LocalParameter
value: 0.1
name: k5b

592570
type: LocalParameter
value: 0.1
name: k5a

591969
type: SBMLUnitsDef
unit: 591981
name: volume

591981
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

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

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

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

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

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

591993
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unit: 592005
name: substance

592005
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exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

COPASI17
type: Parameter
constant: true
value: 30.0
name: Kse1

COPASI23
type: Reaction
modifier: 592222
modifier: 592210
modifier: 930110
name: 2
reversible: false
reactant: 592174
modifier: 930074
modifier: 930086
product: 592186
modifier: 592234
modifier: 930122
modifier: 930062
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fast: false
kinetic law: 592258
modifier: 930098

592174
type: SpeciesReference
stoichiometry: 1.0
species: 592029

592186
type: SpeciesReference
stoichiometry: 1.0
species: 592017

592270
type: LocalParameter
value: 0.01
name: k2a

COPASI24
type: Reaction
modifier: 930134
modifier: 592306
reactant: 592282
fast: false
product: 592294
name: 3
modifier: 930158
modifier: 930146
modifier: 592318
kinetic law: 592330
reversible: false

592282
type: SpeciesReference
stoichiometry: 1.0
species: 592042

592294
type: SpeciesReference
stoichiometry: 1.0
species: 592054

592342
type: LocalParameter
value: 0.1
name: k3

COPASI27
type: Reaction
modifier: 930399
reactant: 592594
modifier: 592678
fast: false
modifier: 592714
modifier: 930423
modifier: 930387
modifier: 930327
name: 6
modifier: 592618
modifier: 930375
modifier: 930435
modifier: 930411
modifier: 592642
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modifier: 930351
modifier: 592690
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reversible: false
product: 592606
modifier: 592702
modifier: 592630
kinetic law: 592726
modifier: 930339
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592594
type: SpeciesReference
stoichiometry: 1.0
species: 592054

592606
type: SpeciesReference
stoichiometry: 1.0
species: 592042

592750
type: LocalParameter
value: 0.1
name: k6b

592738
type: LocalParameter
value: 0.1
name: k6a

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

COPASI28
type: Reaction
modifier: 592798
modifier: 592786
name: 7
reversible: false
modifier: 930471
product: 592774
kinetic law: 592810
fast: false
reactant: 592762
modifier: 930459
modifier: 930447

592774
type: SpeciesReference
stoichiometry: 1.0
species: 592078

592822
type: LocalParameter
value: 0.1
name: k7

592762
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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

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

COPASI25
type: Reaction
reversible: false
modifier: 930183
reactant: 592354
modifier: 592390
modifier: 592378
name: 4
kinetic law: 592402
modifier: 930195
fast: false
modifier: 930170
product: 592366

592354
type: SpeciesReference
stoichiometry: 1.0
species: 592054

592414
type: LocalParameter
value: 0.1
name: k4

592366
type: SpeciesReference
stoichiometry: 1.0
species: 592066

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

COPASI18
type: Parameter
constant: true
value: 30.0
name: Kse2

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

COPASI29
type: Reaction
modifier: 930495
modifier: 930483
fast: false
modifier: 930507
modifier: 592858
product: 592846
name: 8
kinetic law: 592882
reactant: 592834
modifier: 592870
reversible: false

592846
type: SpeciesReference
stoichiometry: 1.0
species: 592090

592894
type: LocalParameter
value: 0.1
name: k7

592834
type: SpeciesReference
stoichiometry: 1.0
species: 592078