COPASI11
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: A1dI1
type: Species

952454
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

952984
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI39
constant: true
value: 6.8
name: kminusON12
type: Parameter

COPASI25
constant: true
value: 1.0E-6
name: dI1tot
type: Parameter

COPASI8
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: rI2
type: Species

952358
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI58
kinetic law: 952562
product: 952550
product: 952538
reactant: 952526
reactant: 952514
fast: false
reversible: false
name: Release
type: Reaction

COPASI44
constant: true
value: 1.6
name: kminusH2
type: Parameter

COPASI64
kinetic law: 952874
product: 952862
product: 952850
product: 952838
reactant: 952826
fast: false
reversible: false
name: RNAPcat2
type: Reaction

COPASI63
kinetic law: 952814
product: 952802
product: 952790
product: 952778
reactant: 952766
fast: false
reversible: false
name: RNAPcat1
type: Reaction

952718
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

952802
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

953123
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI19
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: RNAPT21
type: Species

953086
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

COPASI31
constant: true
value: 53000.0
name: kAI1
type: Parameter

952310
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI10
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: T21A1
type: Species

COPASI38
constant: true
value: 1.0E8
name: kplusH
type: Parameter

952886
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

953159
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

COPASI24
constant: true
value: 2.5E-7
name: A1tot
type: Parameter

COPASI7
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: rA1
type: Species

COPASI59
kinetic law: 952610
product: 952598
reactant: 952586
reactant: 952574
fast: false
reversible: true
name: RNAPbinding1
type: Reaction

COPASI45
constant: true
value: 0.05
name: kcatON12
type: Parameter

COPASI62
kinetic law: 952754
product: 952742
reactant: 952730
reactant: 952718
fast: false
reversible: true
name: RNAPbinding4
type: Reaction

952200
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

952418
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI65
kinetic law: 952935
product: 952922
product: 952910
product: 952898
reactant: 952886
fast: false
reversible: false
name: RNAPcat3
type: Reaction

COPASI6
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-6
initial amount: NaN
in compartment: 227841
name: dI1
type: Species

952622
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI18
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: RNAPT21A1
type: Species

952586
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

952370
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

952163
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

953171
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI30
constant: true
value: 14000.0
name: kTA12
type: Parameter

952790
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI37
constant: true
value: 1.0E8
name: kplus
type: Parameter

COPASI56
kinetic law: 952442
product: 952430
product: 952418
reactant: 952406
reactant: 952394
fast: false
reversible: false
name: Inhibition1
type: Reaction

952346
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

952406
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

952948
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI46
constant: true
value: 0.002
name: kcatOFF12
type: Parameter

952274
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

952466
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI27
constant: true
value: 1.25E-7
name: RNAPtot
type: Parameter

952972
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI5
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 227841
name: A1
type: Species

952766
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI66
kinetic law: 952997
product: 952984
product: 952972
product: 952960
reactant: 952948
fast: false
reversible: false
name: RNAPcat4
type: Reaction

953023
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

953074
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

COPASI61
kinetic law: 952706
product: 952694
reactant: 952682
reactant: 952670
fast: false
reversible: true
name: RNAPbinding3
type: Reaction

COPASI17
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: RNAPT12
type: Species

MODEL1012090002
species: COPASI6
species: COPASI20
area units: area
parameter: COPASI30
reaction: COPASI54
reaction: COPASI52
reaction: COPASI69
compartment: 227841
reaction: COPASI62
reaction: COPASI60
notes: This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
species: COPASI19
species: COPASI17
parameter: COPASI29
parameter: COPASI40
name: Kim2011_Oscillator_DetailedI
parameter: COPASI35
species: COPASI3
reaction: COPASI59
reaction: COPASI57
parameter: COPASI22
parameter: COPASI32
parameter: COPASI38
time units: time
species: COPASI9
reaction: COPASI65
parameter: COPASI47
initial assignment: MODEL1012090002#
parameter: COPASI45
species: COPASI13
species: COPASI11
species: COPASI8
reaction: COPASI68
parameter: COPASI48
parameter: COPASI25
parameter: COPASI31
reaction: COPASI55
species: COPASI4
species: COPASI21
species: COPASI5
parameter: COPASI28
reaction: COPASI53
volume units: volume
is described by: http://identifiers.org/pubmed/21283141
species: COPASI18
species: COPASI16
reaction: COPASI63
parameter: COPASI43
parameter: COPASI41
species: COPASI15
reaction: COPASI66
reaction: COPASI64
parameter: COPASI46
parameter: COPASI23
parameter: COPASI33
parameter: COPASI39
type: SBMLModel
species: COPASI12
species: COPASI10
parameter: COPASI26
parameter: COPASI36
parameter: COPASI24
species: COPASI7
parameter: COPASI49
parameter: COPASI42
reaction: COPASI70
parameter: COPASI50
species: COPASI2
parameter: COPASI34
reaction: COPASI51
species: COPASI14
reaction: COPASI61
reaction: COPASI58
substance units: substance
reaction: COPASI56
reaction: COPASI67
curated: false
length unit: length
parameter: COPASI44
parameter: COPASI27

COPASI51
kinetic law: 952188
product: 952176
reactant: 952163
reactant: 952151
fast: false
reversible: false
name: Activation1
type: Reaction

953135
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI36
constant: true
value: 28000.0
name: kAIrA1
type: Parameter

COPASI47
constant: true
value: 0.08
name: kcatON21
type: Parameter

COPASI57
kinetic law: 952502
product: 952490
product: 952478
reactant: 952466
reactant: 952454
fast: false
reversible: false
name: Inhibition2
type: Reaction

COPASI60
kinetic law: 952658
product: 952646
reactant: 952634
reactant: 952622
fast: false
reversible: true
name: RNAPbinding2
type: Reaction

952538
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI26
constant: true
value: 5.0E-7
name: A2tot
type: Parameter

952598
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 227841
name: T21
type: Species

COPASI67
kinetic law: 953049
product: 953036
reactant: 953023
reactant: 953010
fast: false
reversible: true
name: RNaseHbinding1
type: Reaction

COPASI50
constant: true
value: 0.24
name: kcatH2
type: Parameter

952634
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

227841
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI16
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: RNAPT12A2
type: Species

COPASI70
kinetic law: 953195
product: 953183
product: 953171
reactant: 953159
fast: false
reversible: false
name: RNaseHcat2
type: Reaction

952646
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI40
constant: true
value: 262.0
name: kminusOFF12
type: Parameter

952550
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

COPASI29
constant: true
value: 74000.0
name: kTA21
type: Parameter

COPASI54
kinetic law: 952334
product: 952322
reactant: 952310
reactant: 952298
fast: false
reversible: false
name: Annihilation2
type: Reaction

953062
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.2E-7
initial amount: NaN
in compartment: 227841
name: T12
type: Species

952224
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

952730
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI35
constant: true
value: 140000.0
name: kTAI12
type: Parameter

952490
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

952262
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

952960
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI15
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.5E-8
initial amount: NaN
in compartment: 227841
name: RNaseH
type: Species

COPASI48
constant: true
value: 0.02
name: kcatOFF21
type: Parameter

952826
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

952176
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

952430
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

COPASI68
kinetic law: 953098
product: 953086
reactant: 953074
reactant: 953062
fast: false
reversible: true
name: RNaseHbinding2
type: Reaction

COPASI21
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: RNaseHA2rI2
type: Species

952850
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI28
constant: true
value: 1.5E-8
name: RNaseHtot
type: Parameter

COPASI41
constant: true
value: 24.7
name: kminusON21
type: Parameter

COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 227841
name: A2
type: Species

COPASI55
kinetic law: 952382
product: 952370
reactant: 952358
reactant: 952346
fast: false
reversible: false
name: Annihilation3
type: Reaction

952778
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

953036
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

952910
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI69
kinetic law: 953147
product: 953135
product: 953123
reactant: 953110
fast: false
reversible: false
name: RNaseHcat1
type: Reaction

952478
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI34
constant: true
value: 28000.0
name: kTAI21
type: Parameter

COPASI14
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.25E-7
initial amount: NaN
in compartment: 227841
name: RNAP
type: Species

952670
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

952526
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI20
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: RNaseHrA1dI1
type: Species

COPASI49
constant: true
value: 0.05
name: kcatH1
type: Parameter

952151
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

952212
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI42
constant: true
value: 267.0
name: kminusOFF21
type: Parameter

952742
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI52
kinetic law: 952237
product: 952224
reactant: 952212
reactant: 952200
fast: false
reversible: false
name: Activation2
type: Reaction

952694
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

952394
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

952838
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI33
constant: true
value: 31000.0
name: kAI2
type: Parameter

952862
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI23
constant: true
value: 2.5E-7
name: T21tot
type: Parameter

953183
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI13
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: A2rI2
type: Species

COPASI43
constant: true
value: 7.6
name: kminusH1
type: Parameter

952249
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

952922
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI9
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: T12A2
type: Species

COPASI53
kinetic law: 952286
product: 952274
reactant: 952262
reactant: 952249
fast: false
reversible: false
name: Annihilation1
type: Reaction

952574
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

953110
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

953010
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

952322
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

COPASI32
constant: true
value: 24000.0
name: krAI1
type: Parameter

952898
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI22
constant: true
value: 1.2E-7
name: T12tot
type: Parameter

952298
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

952682
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI12
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 227841
name: rA1dI1
type: Species

952514
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference