MODEL1204280039
type: SBMLModel
name: 1
function def: COPASI28
units def: 362967
reaction: COPASI18
parameter: COPASI7
name: 10
reaction: COPASI23
function def: COPASI30
parameter: COPASI11
function def: COPASI33
name: 8
species: COPASI2
time units: 291235
name: 3
name: 5
units def: 362991
species: 363339
parameter: COPASI12
function def: COPASI26
species: 363363
species: 363039
function def: COPASI29
species: 363327
species: 363027
curated: false
reaction: COPASI19
parameter: COPASI8
function def: COPASI31
name: 7
area units: 061696
parameter: COPASI3
name: 9
reaction: COPASI24
reaction: COPASI16
reaction: COPASI25
parameter: COPASI14
function def: COPASI34
name: 2
volume units: 362967
species: 363087
function def: COPASI27
is described by: http://identifiers.org/pubmed/22748295
parameter: COPASI5
parameter: COPASI13
notes: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_QSS_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 [ MODEL1204…
reaction: COPASI20
name: 6
length unit: length
reaction: COPASI21
substance units: 362991
parameter: COPASI10
parameter: COPASI4
species: 363075
function def: COPASI32
function def: COPASI35
species: 363063
reaction: COPASI17
species: 363351
parameter: COPASI9
compartment: 363015
event: COPASI15
species: 363051
reaction: COPASI22
name: 4
name: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_QSS_PSEQ)
parameter: COPASI6

362967
type: SBMLUnitsDef
unit: 362979
name: volume

362979
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

COPASI18
type: Reaction
product: 363519
modifier: 044439
fast: false
reversible: false
modifier: 044463
modifier: 044451
name: 3
modifier: 363531
modifier: 363543
reactant: 363507
kinetic law: 363555

363519
type: SpeciesReference
stoichiometry: 1.0
species: 363063

363063
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 363015
name: MKK_P

363015
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

363039
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 363015
name: MKKK_P

363051
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 363015
name: MKK

363507
type: SpeciesReference
stoichiometry: 1.0
species: 363051

363567
type: LocalParameter
value: 0.01
name: k3

COPASI7
type: Parameter
constant: true
value: 26.2
name: K5

COPASI23
type: Reaction
modifier: 364426
modifier: 044727
modifier: 044715
kinetic law: 364450
modifier: 364438
product: 364414
reactant: 364402
fast: false
modifier: 044740
reversible: false
name: 8

363075
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 363015
name: MKK_PP

363087
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 363015
name: MK_P

364462
type: LocalParameter
value: 15.0
name: k7

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 363015
name: MK

364414
type: SpeciesReference
stoichiometry: 1.0
species: 363327

363327
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 363015
name: MK_PP

364402
type: SpeciesReference
stoichiometry: 1.0
species: 363087

COPASI11
type: Parameter
constant: true
value: 24.6
name: K9

362991
type: SBMLUnitsDef
unit: 363003
name: substance

363003
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

363339
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: 363015
name: P1

COPASI12
type: Parameter
constant: true
value: 108.6
name: K10

363363
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: 363015
name: Sig

363027
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999985553313
initial amount: NaN
in compartment: 363015
name: MKKK

COPASI19
type: Reaction
name: 4
modifier: 044487
modifier: 044475
modifier: 044499
modifier: 363834
product: 363591
reactant: 363579
fast: false
reversible: false
kinetic law: 363846
modifier: 363603

363591
type: SpeciesReference
stoichiometry: 1.0
species: 363075

363579
type: SpeciesReference
stoichiometry: 1.0
species: 363063

363858
type: LocalParameter
value: 15.0
name: k4

COPASI8
type: Parameter
constant: true
value: 108.6
name: K6

COPASI3
type: Parameter
constant: true
value: 100.0
name: K1

COPASI24
type: Reaction
fast: false
modifier: 364558
modifier: 364510
reversible: false
modifier: 044801
modifier: 364498
modifier: 364534
modifier: 044825
name: 9
modifier: 044789
kinetic law: 364570
modifier: 044765
modifier: 044752
modifier: 044777
modifier: 364522
modifier: 044813
reactant: 364474
modifier: 364546
product: 364486

363351
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: 363015
name: P2

364699
type: LocalParameter
value: 0.092
name: k9

364474
type: SpeciesReference
stoichiometry: 1.0
species: 363327

364486
type: SpeciesReference
stoichiometry: 1.0
species: 363087

COPASI16
type: Reaction
fast: false
product: 363387
modifier: 044378
kinetic law: 363411
modifier: 044390
modifier: 363399
reactant: 363375
reversible: false
name: 1

363387
type: SpeciesReference
stoichiometry: 1.0
species: 363039

363423
type: LocalParameter
value: 1.0
name: k1

363375
type: SpeciesReference
stoichiometry: 1.0
species: 363027

COPASI25
type: Reaction
modifier: 044898
reversible: false
reactant: 364711
modifier: 364772
modifier: 364748
modifier: 044837
product: 364723
modifier: 044886
modifier: 364760
modifier: 044850
fast: false
modifier: 364736
modifier: 044861
modifier: 364784
modifier: 044874
kinetic law: 364796
name: 10

364711
type: SpeciesReference
stoichiometry: 1.0
species: 363087

364723
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

364808
type: LocalParameter
value: 0.086
name: k10

COPASI14
type: Parameter
constant: true
value: 0.06
name: Kse2

COPASI5
type: Parameter
constant: true
value: 50.5
name: K3

COPASI13
type: Parameter
constant: true
value: 0.06
name: Kse1

COPASI20
type: Reaction
modifier: 363893
modifier: 363929
reactant: 363869
reversible: false
product: 363881
modifier: 044511
modifier: 044571
modifier: 044583
modifier: 044523
fast: false
kinetic law: 363965
modifier: 044535
name: 5
modifier: 363941
modifier: 044547
modifier: 363905
modifier: 363917
modifier: 363953
modifier: 044559

363869
type: SpeciesReference
stoichiometry: 1.0
species: 363075

363881
type: SpeciesReference
stoichiometry: 1.0
species: 363063

363978
type: LocalParameter
value: 0.092
name: k5

COPASI21
type: Reaction
kinetic law: 364085
reversible: false
product: 364001
modifier: 364013
fast: false
modifier: 364061
modifier: 364025
reactant: 363989
modifier: 044607
modifier: 044631
modifier: 044595
modifier: 044667
name: 6
modifier: 044643
modifier: 364037
modifier: 044619
modifier: 364049
modifier: 044655
modifier: 364073

364097
type: LocalParameter
value: 0.086
name: k6

364001
type: SpeciesReference
stoichiometry: 1.0
species: 363051

363989
type: SpeciesReference
stoichiometry: 1.0
species: 363063

COPASI10
type: Parameter
constant: true
value: 500.0
name: K8

COPASI4
type: Parameter
constant: true
value: 54.3
name: K2

COPASI17
type: Reaction
modifier: 044414
modifier: 044402
reversible: false
reactant: 363435
kinetic law: 363483
fast: false
name: 2
product: 363447
modifier: 363459
modifier: 363471
modifier: 044427

363435
type: SpeciesReference
stoichiometry: 1.0
species: 363039

363495
type: LocalParameter
value: 0.086
name: k2

363447
type: SpeciesReference
stoichiometry: 1.0
species: 363027

COPASI9
type: Parameter
constant: true
value: 50.5
name: K7

COPASI15
type: Event
event assignment: 364832
trigger: 364820
use values from trigger time: true
name: event_1

364820
type: Trigger
persistant: true
initial value: true

COPASI22
type: Reaction
modifier: 044691
modifier: 044703
kinetic law: 364378
modifier: 044679
modifier: 364354
fast: false
reversible: false
reactant: 364109
modifier: 364366
name: 7
product: 364121

364390
type: LocalParameter
value: 0.01
name: k7

364109
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

364121
type: SpeciesReference
stoichiometry: 1.0
species: 363087

COPASI6
type: Parameter
constant: true
value: 500.0
name: K4