965458
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI23
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: T23A3
type: Species

COPASI80
kinetic law: 965290
product: 965278
reactant: 965266
reactant: 965254
fast: false
reversible: true
name: RNAPbinding1
type: Reaction

965096
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI43
constant: true
value: 1.0E8
name: kplusH
type: Parameter

COPASI70
constant: true
value: 0.62
name: ksminus2
type: Parameter

965157
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

965905
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI90
kinetic law: 965820
product: 965808
product: 965796
reactant: 965784
fast: false
reversible: false
name: RNaseHcat1
type: Reaction

COPASI63
constant: true
value: 4120.0
name: ksplus1
type: Parameter

965507
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

966181
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

965230
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI81
kinetic law: 965338
product: 965326
reactant: 965314
reactant: 965302
fast: false
reversible: true
name: RNAPbinding2
type: Reaction

964904
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

965483
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI22
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-7
initial amount: NaN
in compartment: 133252
name: T23
type: Species

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

COPASI62
constant: true
value: 1.0E-7
name: T23tot
type: Parameter

966037
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI71
constant: true
value: 6730.0
name: ksplus3
type: Parameter

965640
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI91
kinetic law: 965869
product: 965857
product: 965844
reactant: 965832
fast: false
reversible: false
name: RNaseHcat2
type: Reaction

964964
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

964892
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

965108
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

965832
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

COPASI31
constant: true
value: 5.0E-7
name: A3tot
type: Parameter

COPASI21
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNaseHA2rI2
type: Species

COPASI82
kinetic law: 965386
product: 965374
reactant: 965362
reactant: 965350
fast: false
reversible: true
name: RNAPbinding3
type: Reaction

COPASI51
constant: true
value: 0.02
name: kcatOFF12
type: Parameter

965145
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI61
constant: true
value: 0.02
name: kcatOFF31
type: Parameter

COPASI11
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: A1rI1
type: Species

965398
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI41
constant: true
value: 24000.0
name: kAI3
type: Parameter

965446
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

966097
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI20
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNaseHA1rI1
type: Species

COPASI30
constant: true
value: 5.0E-7
name: A1tot
type: Parameter

966049
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI50
constant: true
value: 0.08
name: kcatON12
type: Parameter

COPASI83
kinetic law: 965434
product: 965422
reactant: 965410
reactant: 965398
fast: false
reversible: true
name: RNAPbinding4
type: Reaction

965652
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI60
constant: true
value: 0.08
name: kcatON31
type: Parameter

965471
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI10
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: T31A1
type: Species

COPASI40
constant: true
value: 53000.0
name: kTAI12
type: Parameter

964952
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

965132
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

965941
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI27
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNaseHA3rI3
type: Species

COPASI13
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: A2rI2
type: Species

965857
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

965592
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI53
constant: true
value: 0.02
name: kcatOFF23
type: Parameter

COPASI67
constant: true
value: 7.6
name: kminusH3
type: Parameter

COPASI94
kinetic law: 966025
product: 966013
reactant: 966001
reactant: 965989
fast: false
reversible: true
name: RNAPbinding5
type: Reaction

COPASI12
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 133252
name: A3
type: Species

964940
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

965048
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI26
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: A3rI3
type: Species

966279
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

965808
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

966013
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

965748
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

965664
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI52
constant: true
value: 0.08
name: kcatON23
type: Parameter

MODEL1012090004
species: COPASI26
reaction: COPASI74
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.
type: SBMLModel
reaction: COPASI95
reaction: COPASI97
species: COPASI11
volume units: volume
reaction: COPASI77
reaction: COPASI79
parameter: COPASI41
parameter: COPASI45
compartment: 133252
parameter: COPASI62
species: COPASI5
parameter: COPASI64
parameter: COPASI28
reaction: COPASI83
parameter: COPASI68
reaction: COPASI85
parameter: COPASI48
species: COPASI17
parameter: COPASI50
parameter: COPASI52
species: COPASI15
parameter: COPASI56
parameter: COPASI36
parameter: COPASI38
parameter: COPASI55
curated: false
initial assignment: MODEL1012090004#
parameter: COPASI59
species: COPASI18
substance units: substance
reaction: COPASI88
reaction: COPASI96
reaction: COPASI94
species: COPASI27
reaction: COPASI76
species: COPASI23
species: COPASI7
species: COPASI21
area units: area
species: COPASI20
species: COPASI9
length unit: length
reaction: COPASI78
species: COPASI3
is described by: http://identifiers.org/pubmed/21283141
species: COPASI2
reaction: COPASI99
parameter: COPASI61
parameter: COPASI63
parameter: COPASI43
parameter: COPASI47
parameter: COPASI49
species: COPASI6
name: Kim2011_Oscillator_DetailedIII
parameter: COPASI31
parameter: COPASI33
parameter: COPASI71
parameter: COPASI35
reaction: COPASI80
reaction: COPASI82
species: COPASI12
parameter: COPASI66
species: COPASI25
species: COPASI24
reaction: COPASI87
reaction: COPASI91
reaction: COPASI89
species: COPASI19
reaction: COPASI93
parameter: COPASI54
reaction: COPASI73
parameter: COPASI58
reaction: COPASI75
species: COPASI8
species: COPASI10
time units: time

COPASI66
constant: true
value: 0.0
name: rI2init
type: Parameter

965760
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

965193
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI95
kinetic law: 966073
product: 966061
reactant: 966049
reactant: 966037
fast: false
reversible: true
name: RNAPbinding6
type: Reaction

COPASI15
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.0E-8
initial amount: NaN
in compartment: 133252
name: RNaseH
type: Species

965580
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

965736
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI25
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT31
type: Species

965688
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

965084
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

COPASI55
constant: true
value: 0.05
name: kcatH2
type: Parameter

COPASI92
kinetic law: 965917
product: 965905
reactant: 965893
reactant: 965881
fast: false
reversible: false
name: Activation3
type: Reaction

965422
stoichiometry: 1.0
species: COPASI25
type: SpeciesReference

COPASI65
constant: true
value: 7.5E-7
name: rI1init
type: Parameter

965844
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI14
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.5E-8
initial amount: NaN
in compartment: 133252
name: RNAP
type: Species

965410
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI24
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT31A1
type: Species

965036
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI54
constant: true
value: 0.05
name: kcatH1
type: Parameter

COPASI93
kinetic law: 965977
product: 965965
product: 965953
reactant: 965941
reactant: 965929
fast: false
reversible: false
name: Inhibition3
type: Reaction

964916
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

966121
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI64
constant: true
value: 0.83
name: ksminus1
type: Parameter

COPASI6
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: rI3
type: Species

COPASI78
kinetic law: 965181
product: 965169
product: 965157
reactant: 965145
reactant: 965132
fast: false
reversible: false
name: Inhibition1
type: Reaction

965784
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

965881
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI56
constant: true
value: 74000.0
name: kTA31
type: Parameter

COPASI88
kinetic law: 965724
product: 965712
reactant: 965700
reactant: 965688
fast: false
reversible: true
name: RNaseHbinding1
type: Reaction

COPASI17
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT12
type: Species

COPASI36
constant: true
value: 74000.0
name: kTA12
type: Parameter

966169
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI98
kinetic law: 966243
product: 966231
reactant: 966218
reactant: 966205
fast: false
reversible: true
name: RNaseHbinding3
type: Reaction

COPASI5
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 133252
name: A1
type: Species

COPASI79
kinetic law: 965242
product: 965230
product: 965217
reactant: 965205
reactant: 965193
fast: false
reversible: false
name: Inhibition2
type: Reaction

965326
stoichiometry: 1.0
species: COPASI24
type: SpeciesReference

COPASI89
kinetic law: 965772
product: 965760
reactant: 965748
reactant: 965736
fast: false
reversible: true
name: RNaseHbinding2
type: Reaction

966218
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

965350
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI57
constant: true
value: 53000.0
name: kTAI31
type: Parameter

965965
stoichiometry: 1.0
species: COPASI26
type: SpeciesReference

COPASI16
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT12A2
type: Species

COPASI37
constant: true
value: 24000.0
name: kAI1
type: Parameter

965712
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

COPASI99
kinetic law: 966291
product: 966279
product: 966267
reactant: 966255
fast: false
reversible: false
name: RNaseHcat3
type: Reaction

COPASI4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-7
initial amount: NaN
in compartment: 133252
name: T31
type: Species

965628
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI68
constant: true
value: 0.05
name: kcatH3
type: Parameter

964988
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI76
kinetic law: 965072
product: 965060
reactant: 965048
reactant: 965036
fast: false
reversible: false
name: Annihilation2
type: Reaction

966231
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

COPASI58
constant: true
value: 24.8
name: kminusON31
type: Parameter

965893
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

965278
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

965012
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI19
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT23
type: Species

COPASI3
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-7
initial amount: NaN
in compartment: 133252
name: A2
type: Species

COPASI29
constant: true
value: 1.0E-7
name: T31tot
type: Parameter

COPASI96
kinetic law: 966133
product: 966121
product: 966109
product: 966097
reactant: 966085
fast: false
reversible: false
name: RNAPcat5
type: Reaction

COPASI38
constant: true
value: 24000.0
name: kAI2
type: Parameter

COPASI48
constant: true
value: 7.6
name: kminusH1
type: Parameter

COPASI69
constant: true
value: 13100.0
name: ksplus2
type: Parameter

COPASI77
kinetic law: 965120
product: 965108
reactant: 965096
reactant: 965084
fast: false
reversible: false
name: Annihilation3
type: Reaction

965314
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI59
constant: true
value: 267.0
name: kminusOFF31
type: Parameter

966061
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI49
constant: true
value: 7.6
name: kminusH2
type: Parameter

133252
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI18
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: RNAPT23A3
type: Species

COPASI2
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E-7
initial amount: NaN
in compartment: 133252
name: T12
type: Species

COPASI28
constant: true
value: 1.0E-7
name: T12tot
type: Parameter

965953
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI39
constant: true
value: 53000.0
name: kTAI23
type: Parameter

965929
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI97
kinetic law: 966193
product: 966181
product: 966169
product: 966157
reactant: 966145
fast: false
reversible: false
name: RNAPcat6
type: Reaction

966145
stoichiometry: 1.0
species: COPASI25
type: SpeciesReference

COPASI74
kinetic law: 964976
product: 964964
reactant: 964952
reactant: 964940
fast: false
reversible: false
name: Activation2
type: Reaction

966205
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

965000
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

965567
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

966001
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI46
constant: true
value: 24.8
name: kminusON23
type: Parameter

966109
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

965266
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI32
constant: true
value: 5.0E-7
name: A2tot
type: Parameter

COPASI84
kinetic law: 965495
product: 965483
product: 965471
product: 965458
reactant: 965446
fast: false
reversible: false
name: RNAPcat1
type: Reaction

966267
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

965989
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

965217
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI85
kinetic law: 965555
product: 965543
product: 965531
product: 965519
reactant: 965507
fast: false
reversible: false
name: RNAPcat2
type: Reaction

965604
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI75
kinetic law: 965024
product: 965012
reactant: 965000
reactant: 964988
fast: false
reversible: false
name: Annihilation1
type: Reaction

965531
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI9
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: T12A2
type: Species

COPASI47
constant: true
value: 267.0
name: kminusOFF23
type: Parameter

COPASI33
constant: true
value: 7.5E-8
name: RNAPtot
type: Parameter

965060
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

965302
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

965374
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

COPASI86
kinetic law: 965616
product: 965604
product: 965592
product: 965580
reactant: 965567
fast: false
reversible: false
name: RNAPcat3
type: Reaction

966157
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI8
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 133252
name: rI2
type: Species

965254
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI72
constant: true
value: 0.59
name: ksminus3
type: Parameter

COPASI44
constant: true
value: 24.8
name: kminusON12
type: Parameter

966255
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

COPASI34
constant: true
value: 3.0E-8
name: RNaseHtot
type: Parameter

965796
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

966085
stoichiometry: 1.0
species: COPASI24
type: SpeciesReference

COPASI87
kinetic law: 965676
product: 965664
product: 965652
product: 965640
reactant: 965628
fast: false
reversible: false
name: RNAPcat4
type: Reaction

965543
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

965205
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

965519
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI7
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.5E-7
initial amount: NaN
in compartment: 133252
name: rI1
type: Species

965700
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI73
kinetic law: 964928
product: 964916
reactant: 964904
reactant: 964892
fast: false
reversible: false
name: Activation1
type: Reaction

965362
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI45
constant: true
value: 267.0
name: kminusOFF12
type: Parameter

965169
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

COPASI35
constant: true
value: 74000.0
name: kTA23
type: Parameter