MODEL1012090003
type: SBMLModel
parameter: COPASI39
parameter: COPASI60
parameter: COPASI33
parameter: COPASI53
parameter: COPASI57
reaction: COPASI80
parameter: COPASI41
parameter: COPASI45
parameter: COPASI31
parameter: COPASI36
reaction: COPASI74
reaction: COPASI85
reaction: COPASI65
reaction: COPASI62
volume units: volume
parameter: COPASI43
parameter: COPASI37
length unit: length
parameter: COPASI29
parameter: COPASI26
species: COPASI6
reaction: COPASI79
name: Kim2011_Oscillator_DetailedII
reaction: COPASI72
species: COPASI22
species: COPASI3
reaction: COPASI67
parameter: COPASI49
parameter: COPASI38
species: COPASI4
reaction: COPASI73
species: COPASI20
parameter: COPASI52
parameter: COPASI56
species: COPASI15
parameter: COPASI40
parameter: COPASI44
parameter: COPASI30
reaction: COPASI76
parameter: COPASI54
reaction: COPASI84
reaction: COPASI64
curated: false
reaction: COPASI83
parameter: COPASI42
parameter: COPASI28
species: COPASI8
parameter: COPASI35
reaction: COPASI78
species: COPASI24
species: COPASI5
species: COPASI11
reaction: COPASI69
species: COPASI7
area units: area
reaction: COPASI66
parameter: COPASI48
species: COPASI19
parameter: COPASI47
species: COPASI23
species: COPASI2
species: COPASI16
reaction: COPASI87
reaction: COPASI71
parameter: COPASI50
species: COPASI17
species: COPASI21
parameter: COPASI61
parameter: COPASI32
species: COPASI14
compartment: 116968
reaction: COPASI77
parameter: COPASI51
parameter: COPASI55
reaction: COPASI81
time units: time
reaction: COPASI82
species: COPASI12
parameter: COPASI34

COPASI39
type: Parameter
constant: true
value: 140000.0
name: kTAI12

COPASI60
type: Parameter
constant: true
value: 0.002
name: kcatOFF11

COPASI33
type: Parameter
constant: true
value: 74000.0
name: kTA21

COPASI53
type: Parameter
constant: true
value: 0.05
name: kcatH1

COPASI57
type: Parameter
constant: true
value: 24.7
name: kminusON11

COPASI80
type: Reaction
kinetic law: 959116
product: 959104
product: 959092
reactant: 959080
fast: false
reversible: false
name: RNaseHcat1

959104
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI6
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-6
initial amount: NaN
in compartment: 116968
name: dI1

116968
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

959092
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI15
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.5E-8
initial amount: NaN
in compartment: 116968
name: RNaseH

959080
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

COPASI20
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNaseHrA1dI1

COPASI41
type: Parameter
constant: true
value: 1.0E8
name: kplus

COPASI45
type: Parameter
constant: true
value: 24.7
name: kminusON21

COPASI31
type: Parameter
constant: true
value: 1.25E-7
name: RNAPtot

COPASI36
type: Parameter
constant: true
value: 24000.0
name: krAI1

COPASI74
type: Reaction
kinetic law: 958791
product: 958779
product: 958766
product: 958753
reactant: 958741
fast: false
reversible: false
name: RNAPcat1

958779
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI7
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: rA1

958766
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI9
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: T12A2

958753
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI14
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.25E-7
initial amount: NaN
in compartment: 116968
name: RNAP

958741
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

COPASI16
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNAPT12A2

COPASI85
type: Reaction
kinetic law: 959370
product: 959358
reactant: 959346
reactant: 959333
fast: false
reversible: true
name: RNAPbinding6

959358
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25

COPASI25
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNAPT11

959346
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

COPASI22
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.0E-8
initial amount: NaN
in compartment: 116968
name: T11

959333
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI65
type: Reaction
kinetic law: 958305
product: 958293
reactant: 958281
reactant: 958269
fast: false
reversible: false
name: Annihilation2

958293
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

COPASI12
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: rA1dI1

958281
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

958269
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI62
type: Reaction
kinetic law: 958160
product: 958148
reactant: 958136
reactant: 958123
fast: false
reversible: false
name: Activation1

958148
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

958136
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 116968
name: A2

958123
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4.5E-8
initial amount: NaN
in compartment: 116968
name: T12

COPASI43
type: Parameter
constant: true
value: 6.8
name: kminusON12

COPASI37
type: Parameter
constant: true
value: 31000.0
name: kAI2

COPASI29
type: Parameter
constant: true
value: 1.0E-6
name: dI1tot

COPASI26
type: Parameter
constant: true
value: 4.5E-8
name: T12tot

COPASI79
type: Reaction
kinetic law: 959068
product: 959056
reactant: 959044
reactant: 959032
fast: false
reversible: true
name: RNaseHbinding2

959056
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI21
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNaseHA2rI2

959044
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

COPASI13
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: A2rI2

959032
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI72
type: Reaction
kinetic law: 958680
product: 958668
reactant: 958656
reactant: 958644
fast: false
reversible: true
name: RNAPbinding3

958668
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI17
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNAPT12

958656
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

958644
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI67
type: Reaction
kinetic law: 958413
product: 958401
product: 958389
reactant: 958377
reactant: 958365
fast: false
reversible: false
name: Inhibition1

958401
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

958389
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

958377
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

COPASI8
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: rI2

958365
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI49
type: Parameter
constant: true
value: 0.05
name: kcatON12

COPASI38
type: Parameter
constant: true
value: 28000.0
name: kTAI21

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 116968
name: T21

COPASI73
type: Reaction
kinetic law: 958729
product: 958717
reactant: 958704
reactant: 958692
fast: false
reversible: true
name: RNAPbinding4

958717
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

COPASI19
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNAPT21

958704
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

958692
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI52
type: Parameter
constant: true
value: 0.02
name: kcatOFF21

COPASI56
type: Parameter
constant: true
value: 28000.0
name: kTAI11

COPASI40
type: Parameter
constant: true
value: 28000.0
name: kAIrA1

COPASI44
type: Parameter
constant: true
value: 262.0
name: kminusOFF12

COPASI30
type: Parameter
constant: true
value: 5.0E-7
name: A2tot

COPASI76
type: Reaction
kinetic law: 958912
product: 958900
product: 958888
product: 958875
reactant: 958863
fast: false
reversible: false
name: RNAPcat3

958900
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

958888
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

958875
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

958863
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI54
type: Parameter
constant: true
value: 0.24
name: kcatH2

COPASI84
type: Reaction
kinetic law: 959321
product: 959309
reactant: 959297
reactant: 959285
fast: false
reversible: true
name: RNAPbinding5

959309
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

COPASI24
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNAPT11A1

959297
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

COPASI23
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: T11A1

959285
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI64
type: Reaction
kinetic law: 958257
product: 958245
reactant: 958233
reactant: 958221
fast: false
reversible: false
name: Annihilation1

958245
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

COPASI11
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: A1dI1

958233
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

958221
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI5
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 116968
name: A1

COPASI83
type: Reaction
kinetic law: 959273
product: 959261
product: 959248
reactant: 959236
reactant: 959224
fast: false
reversible: false
name: Inhibition3

959261
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

959248
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

959236
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

959224
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

COPASI42
type: Parameter
constant: true
value: 1.0E8
name: kplusH

COPASI28
type: Parameter
constant: true
value: 2.5E-7
name: A1tot

COPASI35
type: Parameter
constant: true
value: 53000.0
name: kAI1

COPASI78
type: Reaction
kinetic law: 959020
product: 959008
reactant: 958996
reactant: 958984
fast: false
reversible: true
name: RNaseHbinding1

959008
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

958996
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

958984
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI69
type: Reaction
kinetic law: 958535
product: 958523
product: 958511
reactant: 958499
reactant: 958486
fast: false
reversible: false
name: Release

958523
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

958511
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

958499
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

958486
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI66
type: Reaction
kinetic law: 958353
product: 958341
reactant: 958329
reactant: 958317
fast: false
reversible: false
name: Annihilation3

958341
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

958329
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

958317
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI48
type: Parameter
constant: true
value: 1.6
name: kminusH2

COPASI47
type: Parameter
constant: true
value: 7.6
name: kminusH1

COPASI87
type: Reaction
kinetic law: 959490
product: 959478
product: 959466
product: 959454
reactant: 959442
fast: false
reversible: false
name: RNAPcat6

959478
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

959466
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

959454
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

959442
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25

COPASI71
type: Reaction
kinetic law: 958632
product: 958620
reactant: 958608
reactant: 958596
fast: false
reversible: true
name: RNAPbinding2

958620
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI18
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: RNAPT21A1

958608
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

COPASI10
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 116968
name: T21A1

958596
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI50
type: Parameter
constant: true
value: 0.002
name: kcatOFF12

COPASI61
type: Parameter
constant: true
value: 3.0E-8
name: T11tot

COPASI32
type: Parameter
constant: true
value: 1.5E-8
name: RNaseHtot

COPASI77
type: Reaction
kinetic law: 958972
product: 958960
product: 958948
product: 958936
reactant: 958924
fast: false
reversible: false
name: RNAPcat4

958960
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

958948
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

958936
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

958924
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

COPASI51
type: Parameter
constant: true
value: 0.08
name: kcatON21

COPASI55
type: Parameter
constant: true
value: 74000.0
name: kTA11

COPASI81
type: Reaction
kinetic law: 959164
product: 959152
product: 959140
reactant: 959128
fast: false
reversible: false
name: RNaseHcat2

959152
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

959140
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

959128
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI82
type: Reaction
kinetic law: 959212
product: 959200
reactant: 959188
reactant: 959176
fast: false
reversible: false
name: Activation3

959200
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

959188
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

959176
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

COPASI34
type: Parameter
constant: true
value: 14000.0
name: kTA12

COPASI75
type: Reaction
kinetic law: 958851
product: 958839
product: 958827
product: 958815
reactant: 958803
fast: false
reversible: false
name: RNAPcat2

958839
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

958827
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

958815
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

958803
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI58
type: Parameter
constant: true
value: 267.0
name: kminusOFF11

COPASI63
type: Reaction
kinetic law: 958209
product: 958196
reactant: 958184
reactant: 958172
fast: false
reversible: false
name: Activation2

958196
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

958184
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

958172
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI68
type: Reaction
kinetic law: 958474
product: 958462
product: 958449
reactant: 958437
reactant: 958425
fast: false
reversible: false
name: Inhibition2

958462
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

958449
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

958437
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

958425
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

COPASI46
type: Parameter
constant: true
value: 267.0
name: kminusOFF21

COPASI27
type: Parameter
constant: true
value: 2.5E-7
name: T21tot

COPASI59
type: Parameter
constant: true
value: 0.05
name: kcatON11

COPASI86
type: Reaction
kinetic law: 959430
product: 959418
product: 959406
product: 959394
reactant: 959382
fast: false
reversible: false
name: RNAPcat5

959418
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

959406
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

959394
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

959382
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

COPASI70
type: Reaction
kinetic law: 958584
product: 958572
reactant: 958560
reactant: 958547
fast: false
reversible: true
name: RNAPbinding1

958572
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

958560
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

958547
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14