BIOMD0000000444
type: SBMLModel
reaction: COPASI11
species: 173809
name: 21
reaction: COPASI14
function def: 173698
species: 173821
name: function_4_5_1
function def: 173673
function def: 173621
species: 173905
parameter: COPASI7
area units: area
reaction: COPASI16
name: Sarma2012 - Oscillations in MAPK cascade (S2n)
name: function_4_9_1
name: function_4_3_1
reaction: COPASI28
species: 173857
function def: COPASI34
species: 173845
reaction: COPASI19
reaction: COPASI22
name: function_4_2_1
name: function_4_4_1
notes: Sarma2012 - Oscillations in MAPK cascade (S2n) Two plausible designs (S1 and S2) of coupled positive and negative feedback loops of MAPK cascade has been described in this paper. Further these models were extended to S1n and S2n, to incorporate the nuclear-cytoplasmic translocation of the MK layer components of the cascade. This model corresponds to model S2n that comprises negative feedback from MK-PP to MKK-PP layer coupled to positive feedback from MK-PP to MKKK-PP layer, with the inclusion of nuclear-cytoplasmic translocation. This model is described in the article: Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. Sarma U, Ghosh I. BMC Res Notes. 2012 Jun 13;5:287. Abstract: BACKGROUND: Feedback loops, both positive and negative are embedded in the Mitogen Activated Protein Kinase (MAPK) cascade. In the three layer MAPK cascade, both feedback loops originate from the terminal layer and their sites of action are either of the two upstream layers. Recent studies have shown that the cascade uses coupled positive and negative feedback loops in generating oscillations. Two plausible designs of coupled positive and negative feedback loops can be elucidated from the literature; in one design the positive feedback precedes the negative feedback in the direction of signal flow and vice-versa in another. But it remains unexplored how the two designs contribute towards triggering oscillations in MAPK cascade. Thus it is also not known how amplitude, frequency, robustness or nature (analogous/digital) of the oscillations would be shaped by these two designs. RESULTS: We built two models of MAPK cascade that exhibited oscillations as function of two underlying designs of coupled positive and negative feedback loops. Frequency, amplitude and nature (digital/analogous) of oscillations were found to be differentially determined by each design. It was observed that the positive feedback emerging from an oscillating M…
reaction: COPASI12
species: 173785
function def: 173609
reaction: COPASI9
species: 173773
curated: true
reaction: COPASI25
function def: 173634
species: 173917
species: COPASI6
compartment: COPASI2
is: MODEL1112190007
function def: 173660
species: COPASI5
function def: COPASI31
is: GO:0000165
species: 173893
species: 173881
units def: 173711
reaction: COPASI20
reaction: COPASI17
reaction: COPASI8
species: 173797
length unit: length
reaction: COPASI10
reaction: COPASI29
function def: COPASI30
name: function_4_6_1
name: function_4_10_1
reaction: COPASI23
reaction: COPASI26
function def: COPASI35
reaction: COPASI13
volume units: 173711
species: 173869
function def: 173686
name: 22
units def: 173737
name: function_4_8_1
name: function_4_7_1
is: http://identifiers.org/taxonomy/131567
name: function_4_1_1
name: 11
name: 12
function def: COPASI32
is described by: http://identifiers.org/pubmed/22694947
function def: 173596
species: 173761
reaction: COPASI15
reaction: COPASI18
function def: COPASI33
name: 15
species: COPASI4
time units: time

COPASI11
type: Reaction
fast: false
is version of: GO:0016310
reversible: false
product: 174253
reactant: 174241
kinetic law: 174289
name: 7
modifier: 091071
modifier: 091047
modifier: 174265
modifier: 091059
modifier: 174277

173821
type: Species
name: M_P
initial concentration: 0.0
is version of: P28482
in compartment: COPASI2
has only substance units: false
initial amount: NaN
is version of: C00562
constant: false
boundary condition: false

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

173809
type: Species
is version of: P28482
constant: false
boundary condition: false
has only substance units: false
initial concentration: 999.999903688753
initial amount: NaN
in compartment: COPASI2
name: M

173797
type: Species
constant: false
boundary condition: false
is version of: C00562
initial concentration: 0.0
initial amount: NaN
name: MKK_PP
has only substance units: false
in compartment: COPASI2
is version of: Q02750

174253
type: SpeciesReference
stoichiometry: 1.0
species: 173821

174241
type: SpeciesReference
stoichiometry: 1.0
species: 173809

174313
type: LocalParameter
value: 0.1
name: k7

174301
type: LocalParameter
value: 20.0
name: K7

COPASI14
type: Reaction
reversible: false
reactant: 174481
modifier: 174517
modifier: 091144
modifier: 174505
modifier: 091170
is version of: GO:0016311
name: 5
kinetic law: 174529
product: 174493
fast: false
modifier: 091157

174481
type: SpeciesReference
stoichiometry: 1.0
species: 173797

173785
type: Species
is version of: Q02750
name: MKK_P
in compartment: COPASI2
initial concentration: 0.0
boundary condition: false
is version of: C00562
initial amount: NaN
constant: false
has only substance units: false

173857
type: Species
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 499.999951844377
initial amount: NaN
in compartment: COPASI2
name: P2

174553
type: LocalParameter
value: 0.02
name: k5

174541
type: LocalParameter
value: 20.0
name: K5

174493
type: SpeciesReference
stoichiometry: 1.0
species: 173785

173905
type: Species
constant: false
in compartment: COPASI2
is version of: P28482
initial concentration: 0.0
initial amount: NaN
occurs in: GO:0005634
has only substance units: false
boundary condition: false
name: M_n

COPASI7
type: Parameter
constant: true
value: 0.022
name: k13

COPASI16
type: Reaction
modifier: 091242
modifier: 174674
reversible: false
modifier: 091230
modifier: 091218
fast: false
name: 9
modifier: 174686
is version of: GO:0016311
kinetic law: 174710
product: 174662
reactant: 174650
modifier: 174698

173833
type: Species
is version of: C00562
in compartment: COPASI2
constant: false
boundary condition: false
name: M_PP
has only substance units: false
initial amount: NaN
initial concentration: 0.0
is version of: P28482

173869
type: Species
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 499.999975922188
initial amount: NaN
in compartment: COPASI2
name: P3

174734
type: LocalParameter
value: 0.02
name: k9

174722
type: LocalParameter
value: 20.0
name: K9

174662
type: SpeciesReference
stoichiometry: 1.0
species: 173821

174650
type: SpeciesReference
stoichiometry: 1.0
species: 173833

COPASI28
type: Reaction
modifier: 175383
fast: false
reactant: 175359
modifier: 175395
reversible: false
product: 175371
kinetic law: 175407
name: 21
modifier: 091460
is version of: GO:0016311
modifier: 091472
modifier: 091485

COPASI6
type: Species
boundary condition: false
name: P3_n
initial concentration: 0.0
occurs in: GO:0005634
in compartment: COPASI2
constant: false
initial amount: NaN
has only substance units: false
is version of: P51452

175359
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI4
type: Species
is version of: C00562
initial concentration: 0.0
is version of: P28482
in compartment: COPASI2
has only substance units: false
occurs in: GO:0005634
name: M_PP_n
constant: false
boundary condition: false
initial amount: NaN

173917
type: Species
in compartment: COPASI2
name: M_P_n
boundary condition: false
occurs in: GO:0005634
has only substance units: false
is version of: C00562
initial amount: NaN
constant: false
is version of: P28482
initial concentration: 0.0

175371
type: SpeciesReference
stoichiometry: 1.0
species: 173917

175443
type: LocalParameter
value: 87.0
name: K21i

175431
type: LocalParameter
value: 10300.0
name: K21

175419
type: LocalParameter
value: 0.68
name: k21

173845
type: Species
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 99.9999903688752
initial amount: NaN
in compartment: COPASI2
name: P1

COPASI19
type: Reaction
is version of: GO:0009299
kinetic law: 174926
modifier: 091315
product: 174902
fast: false
reversible: false
name: 12
modifier: 174914

174962
type: LocalParameter
value: 169.0
name: K12

174950
type: LocalParameter
value: 3.97
name: n12

174938
type: LocalParameter
value: 29.24
name: V12

174902
type: SpeciesReference
stoichiometry: 1.0
species: 173881

173881
type: Species
constant: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
is: SBO:0000311
encodes: P51452
name: PreP3_mRNA
occurs in: GO:0005634
has only substance units: false
boundary condition: false

COPASI22
type: Reaction
product: 175058
is version of: GO:0002181
modifier: 091351
fast: false
kinetic law: 175082
modifier: 175070
name: 15
reversible: false

175058
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI5
type: Species
occurs in: GO:0005737
boundary condition: false
initial concentration: 0.0
has only substance units: false
is version of: P51452
constant: false
initial amount: NaN
name: P3_c
in compartment: COPASI2

173893
type: Species
initial concentration: 0.0
name: P3mRNA
constant: false
in compartment: COPASI2
initial amount: NaN
is: SBO:0000312
encodes: P51452
occurs in: GO:0005634
has only substance units: false
boundary condition: false

175095
type: LocalParameter
value: 0.0012
name: k15

COPASI12
type: Reaction
modifier: 174349
reactant: 174325
modifier: 091096
fast: false
name: 8
reversible: false
kinetic law: 174373
modifier: 174361
product: 174337
is version of: GO:0016310
modifier: 091108
modifier: 091083

174325
type: SpeciesReference
stoichiometry: 1.0
species: 173821

174397
type: LocalParameter
value: 0.1
name: k8

174385
type: LocalParameter
value: 20.0
name: K8

174337
type: SpeciesReference
stoichiometry: 1.0
species: 173833

COPASI9
type: Reaction
modifier: 090951
kinetic law: 174085
fast: false
modifier: 174049
reactant: 174025
modifier: 090987
is version of: GO:0016310
modifier: 174073
name: 3
modifier: 090963
modifier: 174061
modifier: 090975
product: 174037
reversible: false

173773
type: Species
is version of: P04049
name: MKKK_P
in compartment: COPASI2
initial concentration: 0.0
boundary condition: false
is version of: C00562
initial amount: NaN
constant: false
has only substance units: false

174121
type: LocalParameter
value: 0.1
name: k3

174109
type: LocalParameter
value: 9.0
name: KI

174097
type: LocalParameter
value: 20.0
name: K3

174025
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI3
type: Species
is version of: Q02750
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3999.9998073775
initial amount: NaN
in compartment: COPASI2
name: MKK

174037
type: SpeciesReference
stoichiometry: 1.0
species: 173785

COPASI25
type: Reaction
kinetic law: 175215
modifier: 091399
reactant: 175203
is version of: GO:0006406
fast: false
reversible: false
name: 18

175227
type: LocalParameter
value: 2.5E-4
name: k1

175203
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

173711
type: SBMLUnitsDef
unit: 173724
name: volume

173724
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

COPASI20
type: Reaction
product: 174986
reactant: 174974
kinetic law: 174998
fast: false
is version of: GO:0006397
modifier: 091327
reversible: false
name: 13

174986
type: SpeciesReference
stoichiometry: 1.0
species: 173893

174974
type: SpeciesReference
stoichiometry: 1.0
species: 173881

175010
type: LocalParameter
value: 0.022
name: k1

COPASI17
type: Reaction
modifier: 091266
modifier: 091279
reactant: 174746
modifier: 174770
fast: false
product: 174758
is version of: GO:0016311
modifier: 174782
reversible: false
modifier: 174794
modifier: 091254
name: 10
kinetic law: 174806

174746
type: SpeciesReference
stoichiometry: 1.0
species: 173821

174758
type: SpeciesReference
stoichiometry: 1.0
species: 173809

174830
type: LocalParameter
value: 0.02
name: k10

174818
type: LocalParameter
value: 20.0
name: K10

COPASI8
type: Reaction
modifier: 173953
name: 1
modifier: 090927
kinetic law: 173965
modifier: 090939
reversible: false
product: 173941
reactant: 173929
is version of: GO:0016310
fast: false

173761
type: Species
is version of: P04049
constant: false
boundary condition: false
has only substance units: false
initial concentration: 999.999903688753
initial amount: NaN
in compartment: COPASI2
name: MKKK

174013
type: LocalParameter
value: 6.0
name: V1

174001
type: LocalParameter
value: 500.0
name: Ka

173989
type: LocalParameter
value: 15.0
name: K1

173977
type: LocalParameter
value: 100.0
name: A

173941
type: SpeciesReference
stoichiometry: 1.0
species: 173773

173929
type: SpeciesReference
stoichiometry: 1.0
species: 173761

COPASI10
type: Reaction
modifier: 091023
modifier: 090999
kinetic law: 174193
product: 174145
fast: false
reversible: false
modifier: 091035
modifier: 091011
modifier: 174181
name: 4
reactant: 174133
is version of: GO:0016310
modifier: 174157
modifier: 174169

174229
type: LocalParameter
value: 0.1
name: k4

174217
type: LocalParameter
value: 9.0
name: KI

174205
type: LocalParameter
value: 20.0
name: K4

174145
type: SpeciesReference
stoichiometry: 1.0
species: 173797

174133
type: SpeciesReference
stoichiometry: 1.0
species: 173785

COPASI29
type: Reaction
modifier: 175491
modifier: 175479
modifier: 091509
fast: false
modifier: 091521
reactant: 175455
name: 22
reversible: false
is version of: GO:0016311
kinetic law: 175503
product: 175467
modifier: 091497

175455
type: SpeciesReference
stoichiometry: 1.0
species: 173917

175539
type: LocalParameter
value: 10300.0
name: K22i

175527
type: LocalParameter
value: 87.0
name: K22

175515
type: LocalParameter
value: 0.31
name: k22

175467
type: SpeciesReference
stoichiometry: 1.0
species: 173905

COPASI23
type: Reaction
reactant: 175107
modifier: 091363
reversible: true
modifier: 091375
fast: false
name: 16
kinetic law: 175131
product: 175119
is version of: GO:0051169

175107
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

175155
type: LocalParameter
value: 15.4
name: k2

175143
type: LocalParameter
value: 22.56
name: k1

175119
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI26
type: Reaction
modifier: 091411
reversible: true
is version of: GO:0051169
name: 19
reactant: 175239
kinetic law: 175263
modifier: 091424
fast: false
product: 175251

175239
type: SpeciesReference
stoichiometry: 1.0
species: 173809

175287
type: LocalParameter
value: 2.86
name: k2

175275
type: LocalParameter
value: 10.34
name: k1

175251
type: SpeciesReference
stoichiometry: 1.0
species: 173905

COPASI13
type: Reaction
name: 2
kinetic law: 174445
modifier: 091120
modifier: 091132
reactant: 174409
fast: false
modifier: 174433
product: 174421
reversible: false
is version of: GO:0016311

174469
type: LocalParameter
value: 0.1
name: k2

174457
type: LocalParameter
value: 100.0
name: K2

174409
type: SpeciesReference
stoichiometry: 1.0
species: 173773

174421
type: SpeciesReference
stoichiometry: 1.0
species: 173761

173737
type: SBMLUnitsDef
unit: 173749
name: substance

173749
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

COPASI15
type: Reaction
fast: false
modifier: 091206
product: 174577
modifier: 091194
modifier: 174601
reactant: 174565
modifier: 174589
kinetic law: 174614
is version of: GO:0016311
name: 6
reversible: false
modifier: 091182

174577
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

174565
type: SpeciesReference
stoichiometry: 1.0
species: 173785

174638
type: LocalParameter
value: 0.02
name: k6

174626
type: LocalParameter
value: 20.0
name: K6

COPASI18
type: Reaction
reversible: true
modifier: 091291
kinetic law: 174866
modifier: 091303
is version of: GO:0051169
fast: false
reactant: 174842
product: 174854
name: 11

174890
type: LocalParameter
value: 2.86
name: k11b

174878
type: LocalParameter
value: 10.34
name: k11f

174842
type: SpeciesReference
stoichiometry: 1.0
species: 173833

174854
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI27
type: Reaction
fast: false
reactant: 175299
product: 175311
kinetic law: 175323
modifier: 091436
name: 20
reversible: true
is version of: GO:0051169
modifier: 091448

175299
type: SpeciesReference
stoichiometry: 1.0
species: 173821

175311
type: SpeciesReference
stoichiometry: 1.0
species: 173917

175347
type: LocalParameter
value: 2.86
name: k2

175335
type: LocalParameter
value: 10.34
name: k1

COPASI21
type: Reaction
kinetic law: 175034
modifier: 091339
reactant: 175022
is version of: GO:0006406
fast: false
reversible: false
name: 14

175046
type: LocalParameter
value: 0.0078
name: k1

175022
type: SpeciesReference
stoichiometry: 1.0
species: 173893

COPASI24
type: Reaction
kinetic law: 175179
modifier: 091387
reactant: 175167
is version of: GO:0051169
fast: false
reversible: false
name: 17

175191
type: LocalParameter
value: 2.5E-4
name: k1

175167
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

W3 CDTF: Mon Mar 18 14:07:51 GMT 2013

W3 CDTF: Wed May 22 14:50:32 BST 2013

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

ORG:
  orgname: EMBL-EBI
n:
  given: Nick
  family: Juty

ORG:
  orgname: National Centre for Cell Science
n:
  given: Uddipan
  family: Sarma