MODEL1012090002
type: SBMLModel
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
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

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

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

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

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

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

952322
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: 227841
name: rA1dI1

952310
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

952298
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: 227841
name: rA1

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

952224
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: 227841
name: T21A1

952212
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: 227841
name: A1

952200
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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

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

953135
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

953123
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: 227841
name: RNaseH

953110
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

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

952742
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: 227841
name: RNAPT21

952730
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

952718
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: 227841
name: RNAP

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

952646
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: 227841
name: RNAPT21A1

952634
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

952622
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

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

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

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

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

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

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

952598
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: 227841
name: RNAPT12A2

952586
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: 227841
name: T12A2

952574
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

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

952490
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: 227841
name: A1dI1

952478
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

952466
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

952454
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

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

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

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

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

952922
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

952910
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

952898
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

952886
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

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

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

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

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

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

953086
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: 227841
name: RNaseHA2rI2

953074
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

953062
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

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

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

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

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

952370
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

952358
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

952346
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

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

952274
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

952262
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

952249
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

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

952802
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

952790
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

952778
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

952766
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

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

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

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

952984
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

952972
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

952960
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

952948
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

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

952862
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

952850
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

952838
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

952826
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

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

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

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

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

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

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

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

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

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

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

953183
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

953171
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

953159
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

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

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

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

952176
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

952163
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

952151
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

952694
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

952682
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

952670
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

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

952550
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

952538
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

952526
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

952514
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

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

952430
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

952418
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

952406
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

952394
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

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

953036
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

953023
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

953010
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

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

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

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