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

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

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

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

560378
stoichiometry: 1.0
species: 761098
type: SpeciesReference

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

561071
persistant: true
initial value: true
type: Trigger

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

560316
stoichiometry: 1.0
species: 761098
type: SpeciesReference

560683
stoichiometry: 1.0
species: 761102
type: SpeciesReference

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

560451
stoichiometry: 1.0
species: 761101
type: SpeciesReference

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

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

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

560328
stoichiometry: 1.0
species: 761099
type: SpeciesReference

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

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

561107
persistant: true
initial value: true
type: Trigger

560927
stoichiometry: 1.0
species: 761108
type: SpeciesReference

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

560414
stoichiometry: 1.0
species: 761102
type: SpeciesReference

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

MODEL0911120000
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
parameter: 761179

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

560975
stoichiometry: 1.0
species: 761096
type: SpeciesReference

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

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

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

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

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

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

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

561035
persistant: true
initial value: true
type: Trigger

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

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

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

560634
stoichiometry: 1.0
species: 761107
type: SpeciesReference

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

560902
stoichiometry: 1.0
species: 761108
type: SpeciesReference

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

560695
stoichiometry: 1.0
species: 761099
type: SpeciesReference

560865
stoichiometry: 1.0
species: 761108
type: SpeciesReference

560573
stoichiometry: 1.0
species: 761104
type: SpeciesReference

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

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

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

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

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

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

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

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

560999
persistant: true
initial value: true
type: Trigger

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

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

560523
stoichiometry: 1.0
species: 761104
type: SpeciesReference

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

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

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

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

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

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

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

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

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

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

560560
stoichiometry: 1.0
species: 761101
type: SpeciesReference

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

560487
stoichiometry: 1.0
species: 761101
type: SpeciesReference

560951
stoichiometry: 1.0
species: 761105
type: SpeciesReference

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

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

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

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

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

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

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

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

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

560438
stoichiometry: 1.0
species: 761099
type: SpeciesReference

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

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

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

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

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

560535
stoichiometry: 1.0
species: 761102
type: SpeciesReference

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

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

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

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

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

560402
stoichiometry: 1.0
species: 761099
type: SpeciesReference

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

560353
stoichiometry: 1.0
species: 761102
type: SpeciesReference

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

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

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

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

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

560292
stoichiometry: 1.0
species: 761107
type: SpeciesReference

560499
stoichiometry: 1.0
species: 761104
type: SpeciesReference

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

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

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

560268
stoichiometry: 1.0
species: 761107
type: SpeciesReference

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

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

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

560756
stoichiometry: 1.0
species: 761098
type: SpeciesReference