MODEL0911120000
type: SBMLModel
parameter: 761202
parameter: 761175
parameter: 761200
parameter: 761220
rule: 761168
rule: 761159
species: 761098
reaction: 761111
name: Sorokina2009_PhyA_FHL_ON_OFF_9h
parameter: 761199
parameter: 761203
compartment: 761093
area units: area
event: 761147
parameter: 761226
parameter: 761236
parameter: 761185
reaction: 761118
parameter: 761187
species: 761096
parameter: 761193
reaction: 761117
reaction: 761127
parameter: 761208
parameter: 761218
reaction: 761135
reaction: 761133
parameter: 761227
parameter: 761172
parameter: 761211
parameter: 761221
parameter: 761170
rule: 761166
parameter: 761190
rule: 761157
reaction: 761114
reaction: 761112
species: 761099
compartment: 761094
parameter: 761230
reaction: 761109
event: 761146
curated: false
reaction: 761129
parameter: 761196
parameter: 761178
parameter: 761188
rule: 761162
rule: 761163
rule: 761153
species: 761108
parameter: 761209
parameter: 761229
substance units: 556541
parameter: 761214
parameter: 761224
parameter: 761173
parameter: 761212
parameter: 761232
rule: 761165
parameter: 761181
parameter: 761191
rule: 761156
reaction: 761115
parameter: 761206
reaction: 761123
reaction: 761121
parameter: 761205
parameter: 761215
time units: 552468
species: 761105
reaction: 761120
reaction: 761130
notes: Final version obtained by merging of the PhyA_FHL model with On_OFF 9h long experiment 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.
event: 761149
species: 761104
species: 761102
compartment: 761095
parameter: 761197

761202
type: Parameter
notes: optimizedvalue
constant: true
value: 10.0013
name: RLU

761175
type: Parameter
constant: true
value: 99.9996024453186
name: Pool_PIF3

761200
type: Parameter
constant: true
value: 1900000.0
name: Km

761220
type: Parameter
constant: false
value: 0.0
name: kLUC

761098
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: Pfr_GBD_c

761093
type: Compartment
constant: true
size: 1.0E-4
spatial dimensions: 3.0
name: colony

761111
type: Reaction
kinetic law: 560304
reactant: 560292
fast: false
reversible: false
name: LUCdeg

560292
type: SpeciesReference
stoichiometry: 1.0
species: 761107

761107
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 1.0
in compartment: 761093
name: nLUC

761199
type: Parameter
constant: true
value: 499.790308377165
name: k_cat

761203
type: Parameter
constant: true
value: 0.0
name: RLU_a

761147
type: Event
event assignment: 561059
delay: 561047
trigger: 561035
use values from trigger time: true
name: StateChange_2

761105
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: RL

561035
type: Trigger
persistant: true
initial value: true

761226
type: Parameter
constant: false
value: 0.0
name: rnaCopies

761236
type: Parameter
constant: false
value: 0.0
name: LuM

761185
type: Parameter
constant: true
value: 1.04620770351146
name: g_Luc

761118
type: Reaction
kinetic law: 560475
modifier: 560463
product: 560451
reactant: 560438
fast: false
reversible: false
name: Pfr_PIF3cplx

761104
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: Pr_PIF3

560451
type: SpeciesReference
stoichiometry: 1.0
species: 761101

761101
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: Pfr_PIF3

560438
type: SpeciesReference
stoichiometry: 1.0
species: 761099

761099
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: Pfr_GBD_f

761187
type: Parameter
constant: true
value: 29.4081640279003
name: n_Luc

761096
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: FRL

761193
type: Parameter
constant: true
value: 0.001701
name: Ki_FR

761117
type: Reaction
kinetic law: 560426
product: 560414
reactant: 560402
fast: false
reversible: false
name: Darkrev_f

560414
type: SpeciesReference
stoichiometry: 1.0
species: 761102

761102
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 761093
name: Pr_GBD_f

560402
type: SpeciesReference
stoichiometry: 1.0
species: 761099

761127
type: Reaction
modifier: 560793
fast: false
modifier: 560841
name: Phyact_c
product: 560756
reversible: true
modifier: 560805
modifier: 560768
modifier: 560780
kinetic law: 560853
modifier: 560817
modifier: 560829

761108
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 1.0
in compartment: 761093
name: nLuc

560756
type: SpeciesReference
stoichiometry: 1.0
species: 761098

761208
type: Parameter
constant: true
value: 7.0E-14
name: vCell

761218
type: Parameter
constant: true
value: 0.00646
name: m_S

761135
type: Reaction
kinetic law: 560987
product: 560975
fast: false
reversible: false
name: farRedLight

560975
type: SpeciesReference
stoichiometry: 1.0
species: 761096

761133
type: Reaction
kinetic law: 560963
product: 560951
fast: false
reversible: false
name: redLight

560951
type: SpeciesReference
stoichiometry: 1.0
species: 761105

761227
type: Parameter
constant: false
value: 0.0
name: lucCopies

761172
type: Parameter
constant: true
value: 3.0
name: mLUC

761211
type: Parameter
constant: true
value: 43.6
name: coefnM

761221
type: Parameter
constant: false
value: 0.0
name: kLuc

761170
type: Parameter
constant: true
value: 0.457713413019138
name: Kbase

761190
type: Parameter
constant: true
value: 3.553E-5
name: Ka_FR

761114
type: Reaction
kinetic law: 560365
reactant: 560353
fast: false
reversible: false
name: Pr_GBDtrs

560353
type: SpeciesReference
stoichiometry: 1.0
species: 761102

761112
type: Reaction
kinetic law: 560341
product: 560328
reactant: 560316
fast: false
reversible: false
name: Pfr_GBDtrs

560328
type: SpeciesReference
stoichiometry: 1.0
species: 761099

560316
type: SpeciesReference
stoichiometry: 1.0
species: 761098

761094
type: Compartment
constant: true
size: 0.02
spatial dimensions: 3.0
name: gel

761230
type: Parameter
constant: false
value: 0.0
name: Pr_GBD_c

761109
type: Reaction
kinetic law: 560280
product: 560268
fast: false
reversible: false
name: LUCtrnbasic

560268
type: SpeciesReference
stoichiometry: 1.0
species: 761107

761146
type: Event
event assignment: 561023
delay: 561011
trigger: 560999
use values from trigger time: true
name: StateChange_1

560999
type: Trigger
persistant: true
initial value: true

761129
type: Reaction
kinetic law: 560890
modifier: 560877
product: 560865
fast: false
reversible: false
name: Luctrl

560865
type: SpeciesReference
stoichiometry: 1.0
species: 761108

761196
type: Parameter
constant: true
value: 0.0
name: m_Luc1

761178
type: Parameter
constant: true
value: 0.0118460853656881
name: K2

761188
type: Parameter
constant: true
value: 0.004953
name: Ka_R

761209
type: Parameter
constant: true
value: 6.23E23
name: Navogadro

761229
type: Parameter
constant: false
value: 0.0
name: PhyCopies

761214
type: Parameter
constant: true
value: 1.9092E-5
name: r0

761224
type: Parameter
constant: false
value: 0.0
name: LUC

761173
type: Parameter
constant: true
value: 40.0
name: Pool_Phy

761212
type: Parameter
constant: true
value: -0.023956
name: D

761232
type: Parameter
constant: false
value: 0.0
name: PIF3_GAD

761181
type: Parameter
constant: true
value: 0.0310929101712517
name: K_dis

761191
type: Parameter
constant: true
value: 7.439E-4
name: Ki_R

761115
type: Reaction
kinetic law: 560390
reactant: 560378
fast: false
reversible: false
name: Darkrev_c

560378
type: SpeciesReference
stoichiometry: 1.0
species: 761098

761206
type: Parameter
constant: true
value: 8.173E-5
name: Ki_560

761123
type: Reaction
modifier: 560597
reactant: 560560
modifier: 560585
product: 560573
name: Pfr_PIF3_fcon
modifier: 560610
reversible: false
fast: false
kinetic law: 560622

560560
type: SpeciesReference
stoichiometry: 1.0
species: 761101

560573
type: SpeciesReference
stoichiometry: 1.0
species: 761104

761121
type: Reaction
kinetic law: 560548
product: 560535
reactant: 560523
fast: false
reversible: false
name: Pr_PIF3diss

560535
type: SpeciesReference
stoichiometry: 1.0
species: 761102

560523
type: SpeciesReference
stoichiometry: 1.0
species: 761104

761205
type: Parameter
constant: true
value: 3.988E-4
name: Ka_560

761215
type: Parameter
constant: true
value: 0.33707
name: A

761120
type: Reaction
kinetic law: 560511
product: 560499
reactant: 560487
fast: false
reversible: false
name: Darkrev_cplx

560499
type: SpeciesReference
stoichiometry: 1.0
species: 761104

560487
type: SpeciesReference
stoichiometry: 1.0
species: 761101

761130
type: Reaction
kinetic law: 560915
reactant: 560902
fast: false
reversible: false
name: Lucdeg

560902
type: SpeciesReference
stoichiometry: 1.0
species: 761108

761149
type: Event
event assignment: 561095
delay: 561083
trigger: 561071
use values from trigger time: true
name: StateChange_3

561071
type: Trigger
persistant: true
initial value: true

761095
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: default

761197
type: Parameter
constant: true
value: 0.793942683910748
name: m_Luc

761179
type: Parameter
constant: true
value: 9.99870580247869
name: K3

761235
type: Parameter
constant: false
value: 0.0
name: R_a

761184
type: Parameter
constant: true
value: 2.0
name: a_Luc

761176
type: Parameter
constant: true
value: 1.5
name: K1

761223
type: Parameter
constant: false
value: 0.0
name: Luc

761194
type: Parameter
constant: true
value: 10.0005909042167
name: p_Luc

761233
type: Parameter
constant: false
value: 0.0
name: Scyt

761182
type: Parameter
constant: true
value: 0.204771607516236
name: K_rev

761126
type: Reaction
kinetic law: 560744
name: Phyact_f
reactant: 560683
modifier: 560720
fast: false
modifier: 560732
product: 560695
reversible: true
modifier: 560707

560683
type: SpeciesReference
stoichiometry: 1.0
species: 761102

560695
type: SpeciesReference
stoichiometry: 1.0
species: 761099

761217
type: Parameter
constant: true
value: 0.5705
name: B

761124
type: Reaction
kinetic law: 560671
modifier: 560659
modifier: 560647
product: 560634
fast: false
reversible: false
name: LUCtrnind

560634
type: SpeciesReference
stoichiometry: 1.0
species: 761107

761132
type: Reaction
kinetic law: 560939
reactant: 560927
fast: false
reversible: false
name: LucSdeg

560927
type: SpeciesReference
stoichiometry: 1.0
species: 761108

761150
type: Event
event assignment: 561132
delay: 561119
trigger: 561107
use values from trigger time: true
name: StateChange_4

561107
type: Trigger
persistant: true
initial value: true