MODEL1005050000
type: SBMLModel
species: 145464
parameter: 145628
parameter: 145555
parameter: 145646
species: 145452
reaction: 145480
parameter: 145562
parameter: 145618
reaction: 145509
parameter: 145570
parameter: 145558
parameter: 145561
reaction: 145470
parameter: 145574
parameter: 145565
reaction: 145491
parameter: 145637
reaction: 145482
parameter: 145655
reaction: 145501
notes: This a model from the article: Prediction of photoperiodic regulators from quantitative gene circuit models. Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ Cell 2009 Dec; 139(6): 1170-9 20005809 , Abstract: Photoperiod sensors allow physiological adaptation to the changing seasons. The prevalent hypothesis is that day length perception is mediated through coupling of an endogenous rhythm with an external light signal. Sufficient molecular data are available to test this quantitatively in plants, though not yet in mammals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their light-sensitive proteins are thought to form an external coincidence sensor. Here, we model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, our models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modeling makes this complexity explicit and may thus contribute to crop improvement. Note: There are four models described in the paper. This model corresponds to model 3 (which is a combination of model 1 and model 2). The SBML file is redeveloped from Kevin S This model is same as BIOMD0000000055 , but with revised light function. 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…
parameter: 145649
parameter: 145567
parameter: 145630
reaction: 145498
reaction: 145513
reaction: 145489
species: 145461
species: 145455
parameter: 145591
parameter: 145551
parameter: 145607
parameter: 145579
parameter: 145642
parameter: 145582
parameter: 145595
parameter: 145550
parameter: 145586
parameter: 145594
parameter: 145658
parameter: 145600
name: Salazar2009_PhotoperiodicRegulation
parameter: 145598
parameter: 145588
parameter: 145651
parameter: 145556
reaction: 145519
parameter: 145619
reaction: 145485
parameter: 145571
reaction: 145476
reaction: 145471
length unit: 335510
parameter: 145603
parameter: 145621
parameter: 145612
reaction: 145503
reaction: 145488
species: 145449
reaction: 145483
volume units: 950046
parameter: 145609
parameter: 145606
area units: area
parameter: 145624
name: lightFunction
parameter: 145559
species: 145453
is described by: http://identifiers.org/pubmed/20005809
parameter: 145577
parameter: 145640
parameter: 145580
parameter: 145568
parameter: 145631
reaction: 145494
species: 145468
parameter: 145552
parameter: 145592
reaction: 145521

145464
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.4
initial amount: NaN
in compartment: 145445
name: cXn

145445
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

145628
type: Parameter
constant: true
value: 0.1347
name: m13

145555
type: Parameter
constant: true
value: 1.5283
name: m1

145646
type: Parameter
constant: true
value: 0.0
name: phase

145452
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.539
initial amount: NaN
in compartment: 145445
name: cLm

145480
type: Reaction
kinetic law: 184305
modifier: 184293
modifier: 184281
product: 184269
fast: false
reversible: false
name: one14

145468
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.013
initial amount: NaN
in compartment: 145445
name: cYn

145453
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0855
initial amount: NaN
in compartment: 145445
name: cLn

184269
type: SpeciesReference
stoichiometry: 1.0
species: 145458

145458
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.456
initial amount: NaN
in compartment: 145445
name: cTm

145562
type: Parameter
constant: true
value: 20.44
name: m2

145618
type: Parameter
constant: true
value: 1.0237
name: f

145509
type: Reaction
kinetic law: 184923
product: 184911
reactant: 184899
fast: false
reversible: false
name: one22

184911
type: SpeciesReference
stoichiometry: 1.0
species: 145468

184899
type: SpeciesReference
stoichiometry: 1.0
species: 145465

145465
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.004
initial amount: NaN
in compartment: 145445
name: cYc

145570
type: Parameter
constant: true
value: 1.0258
name: b

145558
type: Parameter
constant: true
value: 0.8295
name: p1

145561
type: Parameter
constant: true
value: 0.1687
name: r2

145470
type: Reaction
kinetic law: 184075
modifier: 184063
product: 184051
fast: false
reversible: false
name: two11

184051
type: SpeciesReference
stoichiometry: 1.0
species: 145452

145574
type: Parameter
constant: true
value: 1.0258
name: c

145565
type: Parameter
constant: true
value: 3.6888
name: m3

145491
type: Reaction
kinetic law: 184524
modifier: 184512
product: 184500
fast: false
reversible: false
name: one17

145459
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.4
initial amount: NaN
in compartment: 145445
name: cTn

184500
type: SpeciesReference
stoichiometry: 1.0
species: 145462

145462
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.08
initial amount: NaN
in compartment: 145445
name: cXm

145637
type: Parameter
constant: true
value: 1.0
name: q3

145482
type: Reaction
kinetic law: 184329
reactant: 184317
fast: false
reversible: false
name: two14

184317
type: SpeciesReference
stoichiometry: 1.0
species: 145458

145655
type: Parameter
constant: true
value: 2.0976
name: kCOp

145501
type: Reaction
kinetic law: 184766
modifier: 184754
modifier: 184742
modifier: 184730
product: 184717
fast: false
reversible: false
name: one20

145455
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.835
initial amount: NaN
in compartment: 145445
name: cPn

184717
type: SpeciesReference
stoichiometry: 1.0
species: 145467

145467
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.037
initial amount: NaN
in compartment: 145445
name: cYm

145649
type: Parameter
constant: true
value: 8.0
name: two11_Fch_0

145567
type: Parameter
constant: true
value: 1.2765
name: k3

145630
type: Parameter
constant: true
value: 1.8258
name: k11

145498
type: Reaction
kinetic law: 184681
product: 184669
reactant: 184656
fast: false
reversible: false
name: one19

184669
type: SpeciesReference
stoichiometry: 1.0
species: 145464

184656
type: SpeciesReference
stoichiometry: 1.0
species: 145461

145461
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.34
initial amount: NaN
in compartment: 145445
name: cXc

145513
type: Reaction
kinetic law: 184996
reactant: 184984
fast: false
reversible: false
name: two23

184984
type: SpeciesReference
stoichiometry: 1.0
species: 145455

145489
type: Reaction
kinetic law: 184488
reactant: 184476
fast: false
reversible: false
name: three16

184476
type: SpeciesReference
stoichiometry: 1.0
species: 145459

145591
type: Parameter
constant: true
value: 0.4033
name: k6

145551
type: Parameter
constant: true
value: 5.1694
name: n1

145607
type: Parameter
constant: true
value: 3.3442
name: m11

145579
type: Parameter
constant: true
value: 4.324
name: p2

145642
type: Parameter
constant: true
value: 0.0
name: lightOffset

145582
type: Parameter
constant: true
value: 2.1509
name: r4

145595
type: Parameter
constant: true
value: 0.538811228
name: g4

145550
type: Parameter
constant: true
value: 2.4514
name: q1

145586
type: Parameter
constant: true
value: 2.7454
name: k5

145594
type: Parameter
constant: true
value: 1.4422
name: d

145658
type: Parameter
constant: true
value: 7.3533
name: kCOFT

145600
type: Parameter
constant: true
value: 2.147
name: p3

145598
type: Parameter
constant: true
value: 6.5585
name: k7

145588
type: Parameter
constant: true
value: 0.0492
name: m7

145651
type: Parameter
constant: true
value: 8.0
name: four12_Fch_0

145556
type: Parameter
constant: true
value: 1.817
name: k1

145519
type: Reaction
kinetic law: 185116
modifier: 185104
product: 185092
fast: false
reversible: false
name: FTinductionbyCOp

145447
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145445
name: cCOp

185092
type: SpeciesReference
stoichiometry: 1.0
species: 145449

145449
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145445
name: cFTm

145619
type: Parameter
constant: true
value: 3.6064
name: e

145485
type: Reaction
kinetic law: 184403
product: 184391
reactant: 184378
fast: false
reversible: false
name: three15

184391
type: SpeciesReference
stoichiometry: 1.0
species: 145456

145456
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 8.7
initial amount: NaN
in compartment: 145445
name: cTc

184378
type: SpeciesReference
stoichiometry: 1.0
species: 145459

145571
type: Parameter
constant: true
value: 0.036805783
name: g2

145476
type: Reaction
kinetic law: 184196
reactant: 184184
fast: false
reversible: false
name: four12

184184
type: SpeciesReference
stoichiometry: 1.0
species: 145450

145450
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.015
initial amount: NaN
in compartment: 145445
name: cLc

145471
type: Reaction
kinetic law: 184099
reactant: 184087
fast: false
reversible: false
name: three11

184087
type: SpeciesReference
stoichiometry: 1.0
species: 145452

145603
type: Parameter
constant: true
value: 3.3017
name: r6

145621
type: Parameter
constant: true
value: 4.297
name: m12

145612
type: Parameter
constant: true
value: 0.0857
name: n4

145503
type: Reaction
kinetic law: 184790
reactant: 184778
fast: false
reversible: false
name: two20

184778
type: SpeciesReference
stoichiometry: 1.0
species: 145467

145488
type: Reaction
kinetic law: 184464
product: 184452
reactant: 184440
fast: false
reversible: false
name: one16

184452
type: SpeciesReference
stoichiometry: 1.0
species: 145459

184440
type: SpeciesReference
stoichiometry: 1.0
species: 145456

145483
type: Reaction
kinetic law: 184366
modifier: 184353
product: 184341
fast: false
reversible: false
name: one15

184341
type: SpeciesReference
stoichiometry: 1.0
species: 145456

145609
type: Parameter
constant: true
value: 17.1111
name: k9

145606
type: Parameter
constant: true
value: 0.6632
name: k8

145624
type: Parameter
constant: true
value: 0.2485
name: p4

145559
type: Parameter
constant: true
value: 16.8363
name: r1

145577
type: Parameter
constant: true
value: 2.5734
name: k4

145640
type: Parameter
constant: true
value: 1.0
name: lightAmplitude

145580
type: Parameter
constant: true
value: 0.3166
name: r3

145568
type: Parameter
constant: true
value: 3.0087
name: n2

145631
type: Parameter
constant: true
value: 0.6114
name: m14

145494
type: Reaction
kinetic law: 184584
modifier: 184572
product: 184560
fast: false
reversible: false
name: one18

184560
type: SpeciesReference
stoichiometry: 1.0
species: 145461

145552
type: Parameter
constant: true
value: 3.3064
name: a

145592
type: Parameter
constant: true
value: 0.2431
name: n3

145521
type: Reaction
kinetic law: 185140
reactant: 185128
fast: false
reversible: false
name: FTmdegradation

185128
type: SpeciesReference
stoichiometry: 1.0
species: 145449

145583
type: Parameter
constant: true
value: 0.0013
name: m5

145515
type: Reaction
kinetic law: 185020
reactant: 185008
fast: false
reversible: false
name: three23

185008
type: SpeciesReference
stoichiometry: 1.0
species: 145455

145615
type: Parameter
constant: true
value: 1.17803247
name: g5

145506
type: Reaction
kinetic law: 184863
product: 184851
reactant: 184839
fast: false
reversible: false
name: three21

184851
type: SpeciesReference
stoichiometry: 1.0
species: 145465

184839
type: SpeciesReference
stoichiometry: 1.0
species: 145468

145633
type: Parameter
constant: true
value: 1.8066
name: k12

145601
type: Parameter
constant: true
value: 1.0352
name: r5

145627
type: Parameter
constant: true
value: 0.2002
name: r8

145518
type: Reaction
kinetic law: 185080
reactant: 185068
fast: false
reversible: false
name: COpdegradation

185068
type: SpeciesReference
stoichiometry: 1.0
species: 145447

145645
type: Parameter
constant: true
value: 8.0
name: photoPeriod

145661
type: Parameter
constant: true
value: 5.3925
name: kFT

145589
type: Parameter
constant: true
value: 4.0424
name: m8

145652
type: Parameter
constant: true
value: 1.1452
name: vCOm

145474
type: Reaction
kinetic law: 184172
product: 184160
reactant: 184148
fast: false
reversible: false
name: three12

184160
type: SpeciesReference
stoichiometry: 1.0
species: 145450

184148
type: SpeciesReference
stoichiometry: 1.0
species: 145453

145660
type: Parameter
constant: true
value: 1.8674
name: vFT

145573
type: Parameter
constant: true
value: 0.26593318
name: g3

145564
type: Parameter
constant: true
value: 1.5644
name: k2

145473
type: Reaction
kinetic law: 184135
modifier: 184123
product: 184111
fast: false
reversible: false
name: one12

184111
type: SpeciesReference
stoichiometry: 1.0
species: 145450

145610
type: Parameter
constant: true
value: 2.40178
name: q2

145510
type: Reaction
kinetic law: 184947
reactant: 184935
fast: false
reversible: false
name: three22

184935
type: SpeciesReference
stoichiometry: 1.0
species: 145468

145486
type: Reaction
kinetic law: 184428
reactant: 184415
fast: false
reversible: false
name: four15

184415
type: SpeciesReference
stoichiometry: 1.0
species: 145456

145636
type: Parameter
constant: true
value: 1.2
name: k13

145477
type: Reaction
kinetic law: 184232
product: 184220
reactant: 184208
fast: false
reversible: false
name: one13

184220
type: SpeciesReference
stoichiometry: 1.0
species: 145453

184208
type: SpeciesReference
stoichiometry: 1.0
species: 145450

145469
type: Reaction
kinetic law: 184039
modifier: 184027
product: 184015
fast: false
reversible: false
name: one11

184015
type: SpeciesReference
stoichiometry: 1.0
species: 145452

145654
type: Parameter
constant: true
value: 9.2242
name: vCOp

145604
type: Parameter
constant: true
value: 0.2179
name: m10

145576
type: Parameter
constant: true
value: 3.8231
name: m4

145500
type: Reaction
kinetic law: 184705
reactant: 184693
fast: false
reversible: false
name: three19

184693
type: SpeciesReference
stoichiometry: 1.0
species: 145464

145622
type: Parameter
constant: true
value: 1.7303
name: k10

145613
type: Parameter
constant: true
value: 0.1649
name: n5

145648
type: Parameter
constant: true
value: 0.0416666667
name: twilightPeriod

145639
type: Parameter
constant: true
value: 1.2
name: m15

145497
type: Reaction
kinetic law: 184644
reactant: 184632
fast: false
reversible: false
name: four18

184632
type: SpeciesReference
stoichiometry: 1.0
species: 145461

145657
type: Parameter
constant: true
value: 0.6683
name: vCOFT

145512
type: Reaction
kinetic law: 184971
product: 184959
fast: false
reversible: false
name: one23

184959
type: SpeciesReference
stoichiometry: 1.0
species: 145455

145492
type: Reaction
kinetic law: 184548
reactant: 184536
fast: false
reversible: false
name: two17

184536
type: SpeciesReference
stoichiometry: 1.0
species: 145462

145479
type: Reaction
kinetic law: 184257
reactant: 184244
fast: false
reversible: false
name: three13

184244
type: SpeciesReference
stoichiometry: 1.0
species: 145453

145504
type: Reaction
kinetic law: 184827
modifier: 184815
product: 184802
fast: false
reversible: false
name: one21

184802
type: SpeciesReference
stoichiometry: 1.0
species: 145465

145495
type: Reaction
kinetic law: 184620
product: 184608
reactant: 184596
fast: false
reversible: false
name: three18

184608
type: SpeciesReference
stoichiometry: 1.0
species: 145461

184596
type: SpeciesReference
stoichiometry: 1.0
species: 145464

145585
type: Parameter
constant: true
value: 3.1741
name: m6

145553
type: Parameter
constant: true
value: 0.876738488
name: g1

145625
type: Parameter
constant: true
value: 2.2123
name: r7

145597
type: Parameter
constant: true
value: 10.1132
name: m9

145516
type: Reaction
kinetic law: 185056
modifier: 185044
product: 185032
fast: false
reversible: false
name: COpistranslatedfromCOmthatisassumedtobeequaltocTn

185032
type: SpeciesReference
stoichiometry: 1.0
species: 145447

145616
type: Parameter
constant: true
value: 0.064455137
name: g6

145643
type: Parameter
constant: true
value: 24.0
name: cyclePeriod

145507
type: Reaction
kinetic law: 184887
reactant: 184875
fast: false
reversible: false
name: four21

184875
type: SpeciesReference
stoichiometry: 1.0
species: 145465

145634
type: Parameter
constant: true
value: 0.5
name: p5