COPASI15
constant: true
value: 24.3
name: K9b
type: Parameter

302075
value: 0.01
name: k7
type: LocalParameter

301331
initial concentration: 0.0
has only substance units: false
is version of: P27361
type: Species
is version of: C00562
boundary condition: false
constant: false
name: MK_P
in compartment: COPASI2
initial amount: NaN

301439
stoichiometry: 1.0
species: 301271
type: SpeciesReference

COPASI14
constant: true
value: 500.0
name: K8
type: Parameter

301523
value: 0.086
name: k2a
type: LocalParameter

301595
value: 0.01
name: k3
type: LocalParameter

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

301223
unit: 301235
name: volume
type: SBMLUnitsDef

302087
stoichiometry: 1.0
species: 301331
type: SpeciesReference

301427
stoichiometry: 1.0
species: 301283
type: SpeciesReference

301295
is version of: Q02750
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MKK
type: Species

COPASI16
constant: true
value: 108.6
name: K10b
type: Parameter

BIOMD0000000432
function def: COPASI34
reaction: COPASI23
parameter: COPASI8
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_QSS_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-MODEL1204280040). 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_USE…
parameter: COPASI20
length unit: 844677
function def: COPASI40
compartment: COPASI3
reaction: COPASI26
name: 1
reaction: COPASI29
function def: COPASI31
species: COPASI5
is described by: http://identifiers.org/pubmed/22748295
function def: COPASI32
function def: COPASI38
name: 7
parameter: COPASI12
parameter: COPASI16
name: 6
parameter: COPASI19
species: COPASI4
reaction: COPASI21
units def: 301247
species: 301343
reaction: COPASI30
curated: true
function def: COPASI35
species: 301355
species: 301319
occurs in: http://identifiers.org/taxonomy/131567
species: 301331
function def: COPASI36
creator:
  ORG:
    orgname: National Centre for Cell Science
  n:
    given: Uddipan
    family: Sarma
reaction: COPASI24
reaction: COPASI27
time units: 844725
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_QSS_USEQ)
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
name: 5
parameter: COPASI9
species: 301271
function def: COPASI33
parameter: COPASI10
name: 10
parameter: COPASI13
name: 4
parameter: COPASI14
modified:
  W3 CDTF: Fri Dec 14 14:17:17 GMT 2012
parameter: COPASI17
function def: COPASI39
type: SBMLModel
substance units: 301247
is version of: GO:0000165
volume units: 301223
parameter: COPASI7
reaction: COPASI22
reaction: COPASI25
function def: COPASI37
species: 301295
species: COPASI6
species: 301283
units def: 301223
compartment: COPASI2
reaction: COPASI28
name: 3
parameter: COPASI11
name: 2
parameter: COPASI15
species: 301307
name: 9
created:
  W3 CDTF: Fri Nov 23 16:17:24 GMT 2012
is: MODEL1204280036
parameter: COPASI18
name: 8
area units: 844749

COPASI19
constant: true
value: 24.3
name: K5b
type: Parameter

302147
value: 15.0
name: k7
type: LocalParameter

302099
stoichiometry: 1.0
species: 301343
type: SpeciesReference

302291
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

301355
is version of: P61225
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: COPASI2
name: Sig
type: Species

COPASI9
constant: true
value: 50.5
name: K3
type: Parameter

COPASI29
product: 302171
reversible: false
name: 9
modifier: 302207
modifier: 441619
modifier: 302195
modifier: 441655
type: Reaction
modifier: 302243
modifier: 441679
modifier: 302219
modifier: 441631
kinetic law: 302255
fast: false
modifier: 441667
modifier: 441607
modifier: 302183
is version of: GO:0016311
modifier: 441643
reactant: 302159
modifier: 302231

301691
stoichiometry: 1.0
species: 301307
type: SpeciesReference

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

301667
value: 15.0
name: k4
type: LocalParameter

COPASI28
reversible: false
reactant: 302087
type: Reaction
modifier: 441571
modifier: 302111
kinetic law: 302135
modifier: 441583
modifier: 302123
is version of: GO:0016310
name: 8
modifier: 441595
fast: false
product: 302099

301415
value: 1.0
name: k1
type: LocalParameter

301283
is version of: P04049
boundary condition: false
initial amount: NaN
in compartment: COPASI2
constant: false
type: Species
initial concentration: 0.0
has only substance units: false
is version of: C00562
name: MKKK_P

302159
stoichiometry: 1.0
species: 301343
type: SpeciesReference

301343
is version of: P27361
is version of: C00562
boundary condition: false
constant: false
has only substance units: false
initial concentration: 0.0
in compartment: COPASI2
type: Species
name: MK_PP
initial amount: NaN

COPASI27
kinetic law: 302063
modifier: 302039
type: Reaction
modifier: 441547
product: 302027
fast: false
modifier: 441535
is version of: GO:0016310
modifier: 302051
name: 7
reversible: false
reactant: 302015
modifier: 441559

301991
value: 0.086
name: k6a
type: LocalParameter

301319
is version of: C00562
boundary condition: false
initial amount: NaN
constant: false
type: Species
is version of: Q02750
in compartment: COPASI2
name: MKK_PP
initial concentration: 0.0
has only substance units: false

301679
stoichiometry: 1.0
species: 301319
type: SpeciesReference

301271
is version of: P04049
constant: false
boundary condition: false
has only substance units: false
initial concentration: 300.0
initial amount: NaN
in compartment: COPASI2
name: MKKK
type: Species

COPASI26
modifier: 441475
modifier: 441463
modifier: 301919
modifier: 301907
product: 301859
modifier: 441451
reactant: 301847
modifier: 301871
modifier: 301883
modifier: 301967
type: Reaction
name: 6
reversible: false
modifier: 301955
modifier: 301943
modifier: 441439
modifier: 441427
fast: false
modifier: 301931
modifier: 441415
modifier: 441499
is version of: GO:0016311
modifier: 441487
modifier: 441523
modifier: 441511
kinetic law: 301979
modifier: 301895

301307
is version of: Q02750
constant: false
in compartment: COPASI2
is version of: C00562
has only substance units: false
boundary condition: false
initial amount: NaN
name: MKK_P
initial concentration: 0.0
type: Species

COPASI25
modifier: 301751
modifier: 441307
modifier: 301715
modifier: 441343
modifier: 441331
kinetic law: 301811
fast: false
reactant: 301679
type: Reaction
modifier: 441403
modifier: 441391
modifier: 301799
modifier: 301787
modifier: 441379
modifier: 301775
modifier: 301703
modifier: 301763
modifier: 441367
modifier: 441295
modifier: 441319
modifier: 301739
is version of: GO:0016311
name: 5
reversible: false
product: 301691
modifier: 301727
modifier: 441355

COPASI5
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: COPASI2
name: P1
type: Species

301859
stoichiometry: 1.0
species: 301295
type: SpeciesReference

COPASI24
reversible: false
modifier: 441271
name: 4
modifier: 301631
modifier: 301643
type: Reaction
reactant: 301607
is version of: GO:0016310
kinetic law: 301655
fast: false
product: 301619
modifier: 441259
modifier: 441283

302003
value: 0.086
name: k6b
type: LocalParameter

301823
value: 0.092
name: k5a
type: LocalParameter

COPASI6
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: COPASI2
name: P2
type: Species

301247
unit: 301259
name: substance
type: SBMLUnitsDef

COPASI23
modifier: 441247
reactant: 301535
modifier: 441235
fast: false
modifier: 441223
kinetic law: 301583
product: 301547
modifier: 301559
type: Reaction
is version of: GO:0016310
modifier: 301571
name: 3
reversible: false

301847
stoichiometry: 1.0
species: 301307
type: SpeciesReference

COPASI7
constant: true
value: 100.0
name: K1
type: Parameter

COPASI22
modifier: 441211
fast: false
modifier: 301487
modifier: 301463
modifier: 441151
modifier: 441199
reversible: false
name: 2
product: 301439
type: Reaction
modifier: 301499
modifier: 441187
modifier: 441163
modifier: 301475
kinetic law: 301511
reactant: 301427
modifier: 301451
modifier: 441175
is version of: GO:0016311

301235
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

COPASI8
constant: true
value: 54.3
name: K2a
type: Parameter

302267
value: 0.092
name: k9b
type: LocalParameter

301835
value: 0.092
name: k5b
type: LocalParameter

301535
stoichiometry: 1.0
species: 301295
type: SpeciesReference

COPASI21
modifier: 301391
reactant: 301367
kinetic law: 301403
modifier: 441139
reversible: false
type: Reaction
product: 301379
is version of: GO:0016310
fast: false
modifier: 441127
name: 1

302387
value: 0.086
name: k10b
type: LocalParameter

COPASI11
constant: true
value: 24.3
name: K5a
type: Parameter

302171
stoichiometry: 1.0
species: 301331
type: SpeciesReference

COPASI30
modifier: 302363
product: 302291
type: Reaction
name: 10
modifier: 441727
modifier: 441691
modifier: 441751
modifier: 441703
is version of: GO:0016311
modifier: 302351
fast: false
modifier: 302303
modifier: 302327
kinetic law: 302375
modifier: 441739
modifier: 441763
modifier: 441715
reactant: 302279
reversible: false
modifier: 302339
modifier: 302315

COPASI20
constant: true
value: 108.6
name: K6b
type: Parameter

302279
stoichiometry: 1.0
species: 301331
type: SpeciesReference

302027
stoichiometry: 1.0
species: 301331
type: SpeciesReference

301367
stoichiometry: 1.0
species: 301271
type: SpeciesReference

301619
stoichiometry: 1.0
species: 301319
type: SpeciesReference

COPASI10
constant: true
value: 500.0
name: K4
type: Parameter

COPASI2
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

301547
stoichiometry: 1.0
species: 301307
type: SpeciesReference

COPASI13
constant: true
value: 50.5
name: K7
type: Parameter

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

301259
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

301607
stoichiometry: 1.0
species: 301307
type: SpeciesReference

COPASI12
constant: true
value: 108.6
name: K6a
type: Parameter

302015
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

301379
stoichiometry: 1.0
species: 301283
type: SpeciesReference

COPASI4
is version of: P27361
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MK
type: Species