COPASI87
kinetic law: 973181
product: 973168
reactant: 973155
reactant: 973142
fast: false
reversible: true
name: RNaseHbinding2
type: Reaction

COPASI4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 153431
name: T21
type: Species

COPASI26
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: sI2
type: Species

973505
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

973793
stoichiometry: 1.0
species: COPASI28
type: SpeciesReference

972926
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI46
constant: true
value: 1.0E8
name: kplusH
type: Parameter

COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 153431
name: A2
type: Species

COPASI15
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.75E-8
initial amount: NaN
in compartment: 153431
name: RNaseH
type: Species

COPASI67
constant: true
value: 0.032
name: ksminus
type: Parameter

COPASI86
kinetic law: 973129
product: 973116
reactant: 973103
reactant: 973090
fast: false
reversible: true
name: RNaseHbinding1
type: Reaction

973116
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

973445
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972239
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI27
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: A2sI2
type: Species

COPASI5
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5E-7
initial amount: NaN
in compartment: 153431
name: A1
type: Species

972323
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI47
constant: true
value: 11.3
name: kminusON12
type: Parameter

973241
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

COPASI14
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.25E-7
initial amount: NaN
in compartment: 153431
name: RNAP
type: Species

972720
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI66
constant: true
value: 192000.0
name: ksplus
type: Parameter

COPASI89
kinetic law: 973277
product: 973265
product: 973253
reactant: 973241
fast: false
reversible: false
name: RNaseHcat2
type: Reaction

COPASI38
constant: true
value: 4630.0
name: kTA12
type: Parameter

COPASI28
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T12A2sI2
type: Species

973517
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

972648
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972938
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI99
kinetic law: 973805
product: 973793
reactant: 973781
reactant: 973769
fast: false
reversible: true
name: sI2binding2
type: Reaction

COPASI79
kinetic law: 972732
product: 972720
reactant: 972708
reactant: 972696
fast: false
reversible: true
name: RNAPbinding2
type: Reaction

COPASI48
constant: true
value: 161.0
name: kminusOFF12
type: Parameter

COPASI17
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT12
type: Species

972588
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI58
constant: true
value: 0.062
name: kcatH2
type: Parameter

COPASI69
constant: true
value: 5.5E-7
name: rI2init
type: Parameter

COPASI29
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT12A2sI2
type: Species

973733
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

972227
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI88
kinetic law: 973229
product: 973217
product: 973205
reactant: 973193
fast: false
reversible: false
name: RNaseHcat1
type: Reaction

973745
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

COPASI98
kinetic law: 973757
product: 973745
reactant: 973733
reactant: 973721
fast: false
reversible: true
name: sI2binding1
type: Reaction

COPASI39
constant: true
value: 10000.0
name: kAI1
type: Parameter

973457
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

973253
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: 153431
name: T12
type: Species

COPASI49
constant: true
value: 11.8
name: kminusON21
type: Parameter

COPASI78
kinetic law: 972684
product: 972672
reactant: 972660
reactant: 972648
fast: false
reversible: true
name: RNAPbinding1
type: Reaction

973301
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

972251
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI59
constant: true
value: 74000.0
name: kTA11
type: Parameter

COPASI16
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT12A2
type: Species

972528
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI68
constant: true
value: 8.0E-7
name: rA1init
type: Parameter

972552
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI22
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T11
type: Species

COPASI8
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.5E-7
initial amount: NaN
in compartment: 153431
name: rI2
type: Species

973409
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI61
constant: true
value: 24.7
name: kminusON11
type: Parameter

COPASI63
constant: true
value: 0.05
name: kcatON11
type: Parameter

973469
stoichiometry: 1.0
species: COPASI25
type: SpeciesReference

COPASI36
constant: true
value: 1.75E-8
name: RNaseHtot
type: Parameter

972744
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI11
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: A1dI1
type: Species

153431
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

MODEL1012090005
species: COPASI16
reaction: COPASI77
reaction: COPASI79
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.
parameter: COPASI32
parameter: COPASI34
parameter: COPASI36
parameter: COPASI55
reaction: COPASI100
parameter: COPASI57
parameter: COPASI59
parameter: COPASI64
parameter: COPASI43
reaction: COPASI74
substance units: substance
parameter: COPASI47
reaction: COPASI81
species: COPASI3
reaction: COPASI83
parameter: COPASI67
parameter: COPASI69
parameter: COPASI60
species: COPASI22
parameter: COPASI52
species: COPASI24
reaction: COPASI88
name: Kim2011_Oscillator_ExtendedI
reaction: COPASI71
type: SBMLModel
parameter: COPASI40
reaction: COPASI97
curated: false
species: COPASI4
parameter: COPASI31
parameter: COPASI35
reaction: COPASI92
reaction: COPASI94
area units: area
reaction: COPASI76
is described by: http://identifiers.org/pubmed/21283141
species: COPASI26
species: COPASI28
species: COPASI11
species: COPASI10
reaction: COPASI99
species: COPASI13
parameter: COPASI54
parameter: COPASI51
species: COPASI19
species: COPASI18
parameter: COPASI58
parameter: COPASI38
initial assignment: MODEL1012090005#
reaction: COPASI87
parameter: COPASI42
species: COPASI23
parameter: COPASI39
species: COPASI6
reaction: COPASI80
parameter: COPASI46
species: COPASI25
species: COPASI8
reaction: COPASI82
parameter: COPASI66
parameter: COPASI63
parameter: COPASI45
parameter: COPASI68
parameter: COPASI49
reaction: COPASI85
reaction: COPASI91
species: COPASI20
species: COPASI5
reaction: COPASI93
reaction: COPASI73
length unit: length
species: COPASI15
species: COPASI14
species: COPASI17
reaction: COPASI75
compartment: 153431

COPASI77
kinetic law: 972637
product: 972624
product: 972612
reactant: 972600
reactant: 972588
fast: false
reversible: false
name: Release
type: Reaction

973397
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972818
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

973168
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

972902
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

972540
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

973565
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI9
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T12A2
type: Species

COPASI23
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T11A1
type: Species

COPASI60
constant: true
value: 28000.0
name: kTAI11
type: Parameter

COPASI62
constant: true
value: 267.0
name: kminusOFF11
type: Parameter

COPASI37
constant: true
value: 60400.0
name: kTA21
type: Parameter

COPASI10
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: T21A1
type: Species

COPASI76
kinetic law: 972576
product: 972564
product: 972552
reactant: 972540
reactant: 972528
fast: false
reversible: false
name: Inhibition2
type: Reaction

972467
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

973205
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI24
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT11A1
type: Species

COPASI6
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-6
initial amount: NaN
in compartment: 153431
name: dI1
type: Species

972564
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI34
constant: true
value: 5.0E-7
name: A2tot
type: Parameter

972479
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI65
constant: true
value: 0.0
name: T11tot
type: Parameter

COPASI13
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: A2rI2
type: Species

972914
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972793
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972756
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

973721
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

973103
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

COPASI75
kinetic law: 972516
product: 972504
product: 972492
reactant: 972479
reactant: 972467
fast: false
reversible: false
name: Inhibition1
type: Reaction

COPASI74
kinetic law: 972455
product: 972443
reactant: 972431
reactant: 972419
fast: false
reversible: false
name: Annihilation3
type: Reaction

COPASI7
constant: false
boundary condition: false
has only substance units: false
initial concentration: 8.0E-7
initial amount: NaN
in compartment: 153431
name: rA1
type: Species

COPASI25
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT11
type: Species

972842
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI35
constant: true
value: 1.25E-7
name: RNAPtot
type: Parameter

972275
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

973553
stoichiometry: 1.0
species: COPASI25
type: SpeciesReference

972504
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

973217
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI64
constant: true
value: 0.002
name: kcatOFF11
type: Parameter

973769
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI12
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: rA1dI1
type: Species

973155
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

973889
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

972443
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

COPASI90
kinetic law: 973325
product: 973313
reactant: 973301
reactant: 973289
fast: false
reversible: false
name: Activation3
type: Reaction

973051
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

972419
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI32
constant: true
value: 2.5E-7
name: A1tot
type: Parameter

COPASI70
kinetic law: 972263
product: 972251
reactant: 972239
reactant: 972227
fast: false
reversible: false
name: Activation1
type: Reaction

972287
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

973661
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

COPASI52
constant: true
value: 5.5
name: kminusH2
type: Parameter

972866
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI84
kinetic law: 973012
product: 973000
product: 972988
product: 972975
reactant: 972963
fast: false
reversible: false
name: RNAPcat3
type: Reaction

973577
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

973637
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

972768
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

972371
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI53
constant: true
value: 0.081
name: kcatON12
type: Parameter

COPASI91
kinetic law: 973385
product: 973373
product: 973361
reactant: 973349
reactant: 973337
fast: false
reversible: false
name: Inhibition3
type: Reaction

973038
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

973193
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

COPASI33
constant: true
value: 1.0E-6
name: dI1tot
type: Parameter

COPASI71
kinetic law: 972311
product: 972299
reactant: 972287
reactant: 972275
fast: false
reversible: false
name: Activation2
type: Reaction

973000
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI85
kinetic law: 973077
product: 973064
product: 973051
product: 973038
reactant: 973025
fast: false
reversible: false
name: RNAPcat4
type: Reaction

973361
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI30
constant: true
value: 1.2E-7
name: T12tot
type: Parameter

COPASI92
kinetic law: 973433
product: 973421
reactant: 973409
reactant: 973397
fast: false
reversible: true
name: RNAPbinding5
type: Reaction

973877
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

973265
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

972805
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI50
constant: true
value: 48.0
name: kminusOFF21
type: Parameter

COPASI72
kinetic law: 972359
product: 972347
reactant: 972335
reactant: 972323
fast: false
reversible: false
name: Annihilation1
type: Reaction

973589
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

972708
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI20
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNaseHrA1dI1
type: Species

973090
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

973673
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972299
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

972854
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI40
constant: true
value: 42700.0
name: krAI1
type: Parameter

COPASI82
kinetic law: 972890
product: 972878
product: 972866
product: 972854
reactant: 972842
fast: false
reversible: false
name: RNAPcat1
type: Reaction

COPASI101
kinetic law: 973913
product: 973901
product: 973889
reactant: 973877
reactant: 973865
fast: false
reversible: false
name: sI2annihilation
type: Reaction

972383
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

972600
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI93
kinetic law: 973481
product: 973469
reactant: 973457
reactant: 973445
fast: false
reversible: true
name: RNAPbinding6
type: Reaction

COPASI51
constant: true
value: 4.4
name: kminusH1
type: Parameter

COPASI73
kinetic law: 972407
product: 972395
reactant: 972383
reactant: 972371
fast: false
reversible: false
name: Annihilation2
type: Reaction

COPASI31
constant: true
value: 2.5E-7
name: T21tot
type: Parameter

COPASI21
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNaseHA2rI2
type: Species

973865
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

COPASI83
kinetic law: 972950
product: 972938
product: 972926
product: 972914
reactant: 972902
fast: false
reversible: false
name: RNAPcat2
type: Reaction

COPASI41
constant: true
value: 42800.0
name: kAI2
type: Parameter

COPASI100
kinetic law: 973853
product: 973841
reactant: 973829
reactant: 973817
fast: false
reversible: false
name: sI2activation
type: Reaction

COPASI56
constant: true
value: 0.0024
name: kcatOFF21
type: Parameter

973685
stoichiometry: 1.0
species: COPASI28
type: SpeciesReference

COPASI94
kinetic law: 973541
product: 973529
product: 973517
product: 973505
reactant: 973493
fast: false
reversible: false
name: RNAPcat5
type: Reaction

973901
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

COPASI42
constant: true
value: 10300.0
name: kTAI21
type: Parameter

COPASI18
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT21A1
type: Species

973817
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

973025
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

972492
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI80
kinetic law: 972780
product: 972768
reactant: 972756
reactant: 972744
fast: false
reversible: true
name: RNAPbinding3
type: Reaction

972672
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

973337
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI95
kinetic law: 973601
product: 973589
product: 973577
product: 973565
reactant: 973553
fast: false
reversible: false
name: RNAPcat6
type: Reaction

972963
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

COPASI57
constant: true
value: 0.024
name: kcatH1
type: Parameter

972988
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI43
constant: true
value: 22300.0
name: kTAI12
type: Parameter

COPASI19
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 153431
name: RNAPT21
type: Species

973064
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

973613
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI81
kinetic law: 972830
product: 972818
reactant: 972805
reactant: 972793
fast: false
reversible: true
name: RNAPbinding4
type: Reaction

972395
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

972612
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

973529
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI96
kinetic law: 973649
product: 973637
reactant: 973625
reactant: 973613
fast: false
reversible: true
name: RNAPbinding7
type: Reaction

973313
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI54
constant: true
value: 0.0018
name: kcatOFF12
type: Parameter

973829
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

973697
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI44
constant: true
value: 79600.0
name: kAIrA1
type: Parameter

972878
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

972660
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

972431
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

973841
stoichiometry: 1.0
species: COPASI28
type: SpeciesReference

973421
stoichiometry: 1.0
species: COPASI24
type: SpeciesReference

972335
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

973289
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

972696
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI55
constant: true
value: 0.026
name: kcatON21
type: Parameter

972347
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI45
constant: true
value: 1.0E8
name: kplus
type: Parameter

973349
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

973493
stoichiometry: 1.0
species: COPASI24
type: SpeciesReference

973373
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

972975
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

972624
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

973142
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

973781
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

973625
stoichiometry: 1.0
species: COPASI28
type: SpeciesReference

COPASI97
kinetic law: 973709
product: 973697
product: 973685
product: 973673
reactant: 973661
fast: false
reversible: false
name: RNAPcat7
type: Reaction