BIOMD0000000422
type: SBMLModel
parameter: tGA4off
species: s2
parameter: muGA20ox
reaction: CDMT00076
notes: This model is from the article: Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Middleton AM , Úbeda-Tomás S , Griffiths J , Holman T , Hedden P , Thomas SG , Phillips AL , Holdsworth MJ , Bennett MJ , King JR, Owen MR Proc. Natl. Acad. Sci. U.S.A. 2012 May; 109(19): 7571-6 22523240 , Abstract: The hormone gibberellin (GA) is a key regulator of plant growth. Many of the components of the gibberellin signal transduction [e.g., GIBBERELLIN INSENSITIVE DWARF 1 (GID1) and DELLA], biosynthesis [e.g., GA 20-oxidase (GA20ox) and GA3ox], and deactivation pathways have been identified. Gibberellin binds its receptor, GID1, to form a complex that mediates the degradation of DELLA proteins. In this way, gibberellin relieves DELLA-dependent growth repression. However, gibberellin regulates expression of GID1, GA20ox, and GA3ox, and there is also evidence that it regulates DELLA expression. In this paper, we use integrated mathematical modeling and experiments to understand how these feedback loops interact to control gibberellin signaling. Model simulations are in good agreement with in vitro data on the signal transduction and biosynthesis pathways and in vivo data on the expression levels of gibberellin-responsive genes. We find that GA-GID1 interactions are characterized by two timescales (because of a lid on GID1 that can open and close slowly relative to GA-GID1 binding and dissociation). Furthermore, the model accurately predicts the response to exogenous gibberellin after a number of chemical and genetic perturbations. Finally, we investigate the role of the various feedback loops in gibberellin signaling. We find that regulation of GA20ox transcription plays a significant role in both modulating the level of endogenous gibberellin and generating overshoots after the removal of exogenous gibberellin. Moreover, although the contribution of other individual feedback loops seems relatively small, GID1 and DELLA transcriptional…
species: s69
is: MODEL1206190000
reaction: re31
reaction: re22
parameter: muDELLA
reaction: re30
species: s32
species: s39
reaction: re34
species: s16
reaction: re16
reaction: re29
is: http://identifiers.org/taxonomy/3701
species: s26
species: s1
species: s40
reaction: re37
reaction: re4
species: s34
species: s22
parameter: muGID
reaction: re43
units def: volume
reaction: re42
reaction: re46
parameter: Pmem
species: s68
volume units: volume
units def: substance
parameter: omegaGA12ga13
species: s25
species: s5
species: s30
species: s31
reaction: re10
reaction: re32
species: s71
reaction: re23
species: s45
species: s15
species: s7
reaction: re27
curated: true
event: AddGA4
reaction: re35
reaction: re13
reaction: re2
reaction: re26
species: s33
units def: length
reaction: re17
reaction: CDMT00094
reaction: re39
parameter: omegaGA4
species: s11
reaction: CDMT00089
reaction: re5
reaction: re38
reaction: CDMT00097
reaction: re9
rule: CDMT00018
species: s29
reaction: re40
reaction: re8
species: s67
reaction: re44
species: s36
event: RemoveGA4
species: s24
units def: time
species: s70
species: s3
species: s41
species: s42

tGA4off
type: Parameter
constant: true
units: substance
value: 620.0
name: tGA4off

substance
type: SBMLUnitsDef
unit: CDMT00071
name: substance

CDMT00071
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

s2
type: Species
is version of: Q9MAA7
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GID

default
type: Compartment
is version of: GO:0005623
constant: true
units: volume
size: 1.0
spatial dimensions: 3.0

volume
type: SBMLUnitsDef
unit: CDMT00072
name: volume

CDMT00072
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

muGA20ox
type: Parameter
constant: true
units: substance
value: 0.047770755070625
name: muGA20ox

CDMT00076
type: Reaction
kinetic law: CDMT00139
modifier: 351410
modifier: CDMT00079
product: CDMT00078
reactant: CDMT00077
fast: false
reversible: false
name: ga20ox transcription (activated by DELLA)

thetaGA20ox
type: LocalParameter
units: substance
value: 0.6383
name: thetaGA20ox

s16
type: Species
is version of: Q9LQT8
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: DELLA

CDMT00078
type: SpeciesReference
stoichiometry: 1.0
species: s39

s39
type: Species
is version of: ath:AT4G25420
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: ga20ox

CDMT00077
type: SpeciesReference
stoichiometry: 1.0
species: s11

s11
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: ga20ox_source

s69
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: sa7_degraded

re31
type: Reaction
kinetic law: CDMT00135
modifier: 351362
modifier: CDMT00061
product: CDMT00060
reactant: CDMT00059
fast: false
reversible: false
name: della translation

deltaDELLA
type: LocalParameter
units: substance
value: 5.27749140286577E-4
name: deltaDELLA

s40
type: Species
is version of: Q9LQT8
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: della

CDMT00060
type: SpeciesReference
stoichiometry: 1.0
species: s16

CDMT00059
type: SpeciesReference
stoichiometry: 1.0
species: s7

s7
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: DELLA_source

re22
type: Reaction
kinetic law: CDMT00131
modifier: 351314
product: CDMT00051
product: CDMT00050
reactant: CDMT00049
fast: false
reversible: false
name: GA9.GA3ox dissociation

kd9
type: LocalParameter
units: substance
value: 0.008827838388125
name: kd9

s29
type: Species
initial amount: 0.01
has part: ath:AT4G21690
in compartment: default
has part: CHEBI:29605
constant: false
initial concentration: NaN
name: GA9-GA3ox
boundary condition: false
has only substance units: true

CDMT00051
type: SpeciesReference
stoichiometry: 1.0
species: s28

s28
type: Species
is version of: ath:AT4G21690
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA3ox

CDMT00050
type: SpeciesReference
stoichiometry: 1.0
species: s26

s26
type: Species
is version of: CHEBI:29605
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA9

CDMT00049
type: SpeciesReference
stoichiometry: 1.0
species: s29

muDELLA
type: Parameter
constant: true
units: substance
value: 0.070794578438414
name: muDELLA

re30
type: Reaction
kinetic law: CDMT00142
modifier: 351446
modifier: CDMT00088
product: CDMT00087
reactant: CDMT00086
fast: false
reversible: false
name: ga3ox transcription (activated by DELLA)

thetaGA3ox
type: LocalParameter
units: substance
value: 0.0082
name: thetaGA3ox

CDMT00087
type: SpeciesReference
stoichiometry: 1.0
species: s41

s41
type: Species
is version of: ath:AT4G21690
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: ga3ox

CDMT00086
type: SpeciesReference
stoichiometry: 1.0
species: s35

s35
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: ga3ox_source

s32
type: Species
initial amount: 0.01
in compartment: default
name: GA12-GA20ox
has only substance units: true
boundary condition: false
has part: ath:AT4G25420
has part: CHEBI:30088
constant: false
initial concentration: NaN

re34
type: Reaction
kinetic law: CDMT00137
modifier: 351386
modifier: CDMT00067
product: CDMT00066
reactant: CDMT00065
fast: false
reversible: false
name: ga3ox translation

deltaGA3ox
type: LocalParameter
units: substance
value: 0.019299031437811
name: deltaGA3ox

CDMT00066
type: SpeciesReference
stoichiometry: 1.0
species: s28

CDMT00065
type: SpeciesReference
stoichiometry: 1.0
species: s5

s5
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: GA3ox_source

re16
type: Reaction
kinetic law: CDMT00127
reactant: CDMT00037
reactant: CDMT00038
reversible: false
modifier: 351253
fast: false
product: CDMT00039
modifier: 351241
name: GA24-GA20ox association

ka24
type: LocalParameter
units: substance
value: 3099.18915892587
name: ka24

CDMT00037
type: SpeciesReference
stoichiometry: 1.0
species: s25

s25
type: Species
is version of: CHEBI:32906
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA24

CDMT00038
type: SpeciesReference
stoichiometry: 1.0
species: s27

s27
type: Species
is version of: ath:AT4G25420
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA20ox

CDMT00039
type: SpeciesReference
stoichiometry: 1.0
species: s30

s30
type: Species
boundary condition: false
has part: ath:AT4G25420
name: GA24-GA20ox
initial amount: 0.01
constant: false
in compartment: default
initial concentration: NaN
has part: CHEBI:32906
has only substance units: true

re29
type: Reaction
kinetic law: CDMT00141
modifier: 351434
modifier: CDMT00085
product: CDMT00084
reactant: CDMT00083
fast: false
reversible: false
name: della transcription (repressed by DELLA)

thetaDELLA
type: LocalParameter
units: substance
value: 0.01
name: thetaDELLA

CDMT00084
type: SpeciesReference
stoichiometry: 1.0
species: s40

CDMT00083
type: SpeciesReference
stoichiometry: 1.0
species: s34

s34
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: della_source

s1
type: Species
is version of: CHEBI:32902
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA4

re37
type: Reaction
kinetic law: CDMT00148
modifier: 351518
product: CDMT00104
reactant: CDMT00103
fast: false
reversible: false
name: GID decay

gammaGID
type: LocalParameter
units: substance
value: 3.514
name: gammaGID

CDMT00104
type: SpeciesReference
stoichiometry: 1.0
species: s33

s33
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: GID_source

CDMT00103
type: SpeciesReference
stoichiometry: 1.0
species: s2

re4
type: Reaction
modifier: 351099
reactant: CDMT00009
fast: false
product: CDMT00010
kinetic law: CDMT00117
modifier: 351087
reactant: CDMT00008
reversible: false
name: GA4.GID-DELLA1 association

CDMT00009
type: SpeciesReference
stoichiometry: 1.0
species: s16

CDMT00010
type: SpeciesReference
stoichiometry: 1.0
species: s45

s45
type: Species
initial concentration: NaN
name: GA4-GID-DELLA1
constant: false
has only substance units: true
has part: Q9LQT8
has part: CHEBI:32902
initial amount: 0.01
in compartment: default
boundary condition: false
has part: Q9MAA7

ua1
type: LocalParameter
units: substance
value: 10.0
name: ua1

s62
type: Species
has only substance units: true
has part: Q9MAA7
has part: CHEBI:32902
initial amount: 0.01
constant: false
in compartment: default
initial concentration: NaN
name: GA4-GID-closed
boundary condition: false

CDMT00008
type: SpeciesReference
stoichiometry: 1.0
species: s62

s22
type: Species
is version of: Q9LQT8
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: DELLA_U

muGID
type: Parameter
constant: true
units: substance
value: 0.045708818961487
name: muGID

re43
type: Reaction
kinetic law: CDMT00158
modifier: 351590
product: CDMT00157
reactant: CDMT00156
fast: false
reversible: false
name: degradation of GA15

s24
type: Species
is version of: CHEBI:29590
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA15

CDMT00157
type: SpeciesReference
stoichiometry: 1.0
species: s68

s68
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: sa6_degraded

CDMT00156
type: SpeciesReference
stoichiometry: 1.0
species: s24

re42
type: Reaction
kinetic law: CDMT00155
modifier: 351578
product: CDMT00154
reactant: CDMT00153
fast: false
reversible: false
name: degradation of GA12

s23
type: Species
is version of: CHEBI:30088
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: GA12

CDMT00154
type: SpeciesReference
stoichiometry: 1.0
species: s67

s67
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: sa5_degraded

CDMT00153
type: SpeciesReference
stoichiometry: 1.0
species: s23

re46
type: Reaction
kinetic law: CDMT00167
modifier: 351626
product: CDMT00166
reactant: CDMT00165
fast: false
reversible: false
name: degradation of GA4

B1
type: LocalParameter
units: substance
value: 3.9795E-4
name: B1

CDMT00166
type: SpeciesReference
stoichiometry: 1.0
species: s71

s71
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: sa1_degraded

CDMT00165
type: SpeciesReference
stoichiometry: 1.0
species: s1

Pmem
type: Parameter
constant: true
units: substance
value: 2.66664
name: Pmem

omegaGA12ga13
type: Parameter
constant: true
units: substance
value: 0.006602803853512
name: omegaGA12ga13

s31
type: Species
constant: false
name: GA15-GA20ox
has only substance units: true
boundary condition: false
has part: ath:AT4G25420
initial amount: 0.01
initial concentration: NaN
has part: CHEBI:29590
in compartment: default

re10
type: Reaction
kinetic law: CDMT00122
modifier: 351164
product: CDMT00024
product: CDMT00023
reactant: CDMT00022
fast: false
reversible: false
name: GA12.GA20ox dissociation

kd12
type: LocalParameter
units: substance
value: 2.67298621993027
name: kd12

CDMT00024
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00023
type: SpeciesReference
stoichiometry: 1.0
species: s23

CDMT00022
type: SpeciesReference
stoichiometry: 1.0
species: s32

re32
type: Reaction
kinetic law: CDMT00144
modifier: 351470
product: CDMT00093
reactant: CDMT00092
fast: false
reversible: false
name: gid decay

s42
type: Species
is version of: Q9MAA7
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.01
in compartment: default
name: gid

CDMT00093
type: SpeciesReference
stoichiometry: 1.0
species: s15

s15
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: gid_source

CDMT00092
type: SpeciesReference
stoichiometry: 1.0
species: s42

re23
type: Reaction
kinetic law: CDMT00132
modifier: 351326
product: CDMT00054
product: CDMT00053
reactant: CDMT00052
fast: false
reversible: false
name: GA4 production

km9
type: LocalParameter
units: substance
value: 763.777072066507
name: km9

CDMT00054
type: SpeciesReference
stoichiometry: 1.0
species: s1

CDMT00053
type: SpeciesReference
stoichiometry: 1.0
species: s28

CDMT00052
type: SpeciesReference
stoichiometry: 1.0
species: s29

re27
type: Reaction
kinetic law: CDMT00134
modifier: 351350
product: CDMT00058
reactant: CDMT00057
fast: false
reversible: false
name: GA4.GID-Closed lid opening

http://identifiers.org/biomodels.db/BIOMD0000000422#p
type: LocalParameter
units: substance
value: 0.077624711662869
name: p

CDMT00058
type: SpeciesReference
stoichiometry: 1.0
species: s65

s65
type: Species
name: GA4-GID
has only substance units: true
initial concentration: NaN
initial amount: 0.01
has part: Q9MAA7
constant: false
in compartment: default
has part: CHEBI:32902
boundary condition: false

CDMT00057
type: SpeciesReference
stoichiometry: 1.0
species: s62

AddGA4
type: Event
event assignment: CDMT00170
trigger: CDMT00168
use values from trigger time: true
name: AddGA4

omegaGA4
type: Parameter
constant: false
units: substance
value: 0.0
name: omegaGA4

CDMT00168
type: Trigger
persistant: true
initial value: true

re35
type: Reaction
kinetic law: CDMT00138
modifier: 351398
modifier: CDMT00070
product: CDMT00069
reactant: CDMT00068
fast: false
reversible: false
name: gid translation

deltaGID
type: LocalParameter
units: substance
value: 19.2990314378105
name: deltaGA3ox

CDMT00069
type: SpeciesReference
stoichiometry: 1.0
species: s2

CDMT00068
type: SpeciesReference
stoichiometry: 1.0
species: s33

re13
type: Reaction
modifier: 351202
reactant: CDMT00028
kinetic law: CDMT00124
fast: false
product: CDMT00030
reactant: CDMT00029
name: GA15-GA20ox association
reversible: false
modifier: 351190

CDMT00028
type: SpeciesReference
stoichiometry: 1.0
species: s24

ka15
type: LocalParameter
units: substance
value: 2073.22402517968
name: ka15

CDMT00030
type: SpeciesReference
stoichiometry: 1.0
species: s31

CDMT00029
type: SpeciesReference
stoichiometry: 1.0
species: s27

re2
type: Reaction
name: GA4-GID association
reversible: false
reactant: CDMT00002
modifier: 351051
reactant: CDMT00003
modifier: 351063
product: CDMT00004
fast: false
kinetic law: CDMT00115

CDMT00002
type: SpeciesReference
stoichiometry: 1.0
species: s1

CDMT00003
type: SpeciesReference
stoichiometry: 1.0
species: s2

CDMT00004
type: SpeciesReference
stoichiometry: 1.0
species: s65

la
type: LocalParameter
units: substance
value: 1.35
name: la

re26
type: Reaction
kinetic law: CDMT00133
modifier: 351338
product: CDMT00056
reactant: CDMT00055
fast: false
reversible: false
name: GA4.GID lid closing

http://identifiers.org/biomodels.db/BIOMD0000000422#q
type: LocalParameter
units: substance
value: 0.025118864315096
name: q

CDMT00056
type: SpeciesReference
stoichiometry: 1.0
species: s62

CDMT00055
type: SpeciesReference
stoichiometry: 1.0
species: s65

length
type: SBMLUnitsDef
unit: CDMT00074
name: length

CDMT00074
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: METRE

re17
type: Reaction
kinetic law: CDMT00128
modifier: 351265
product: CDMT00042
product: CDMT00041
reactant: CDMT00040
fast: false
reversible: false
name: GA24.GA20ox dissociation

kd24
type: LocalParameter
units: substance
value: 0.01588492846351
name: kd24

CDMT00042
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00041
type: SpeciesReference
stoichiometry: 1.0
species: s25

CDMT00040
type: SpeciesReference
stoichiometry: 1.0
species: s30

CDMT00094
type: Reaction
kinetic law: CDMT00145
modifier: 351482
product: CDMT00096
reactant: CDMT00095
fast: false
reversible: false
name: ga20ox decay

CDMT00096
type: SpeciesReference
stoichiometry: 1.0
species: s11

CDMT00095
type: SpeciesReference
stoichiometry: 1.0
species: s39

re39
type: Reaction
reversible: false
modifier: 351542
reactant: CDMT00108
name: GA4.GID-DELLA2 association
modifier: 351554
reactant: CDMT00107
fast: false
product: CDMT00109
kinetic law: CDMT00150

CDMT00108
type: SpeciesReference
stoichiometry: 1.0
species: s16

CDMT00107
type: SpeciesReference
stoichiometry: 1.0
species: s62

CDMT00109
type: SpeciesReference
stoichiometry: 1.0
species: s36

s36
type: Species
in compartment: default
name: GA4-GID-DELLA2
has part: Q9LQT8
has part: CHEBI:32902
initial amount: 0.01
has part: Q9MAA7
boundary condition: false
constant: false
initial concentration: NaN
has only substance units: true

ua2
type: LocalParameter
units: substance
value: 316.2278
name: ua2

CDMT00089
type: Reaction
kinetic law: CDMT00143
modifier: 351458
product: CDMT00091
reactant: CDMT00090
fast: false
reversible: false
name: della decay

CDMT00091
type: SpeciesReference
stoichiometry: 1.0
species: s34

CDMT00090
type: SpeciesReference
stoichiometry: 1.0
species: s40

re5
type: Reaction
kinetic law: CDMT00118
modifier: 351111
product: CDMT00013
product: CDMT00012
reactant: CDMT00011
fast: false
reversible: false
name: GA4.GID.DELLA1 dissociation

ud1
type: LocalParameter
units: substance
value: 0.133045441797809
name: ud1

CDMT00013
type: SpeciesReference
stoichiometry: 1.0
species: s16

CDMT00012
type: SpeciesReference
stoichiometry: 1.0
species: s62

CDMT00011
type: SpeciesReference
stoichiometry: 1.0
species: s45

re38
type: Reaction
kinetic law: CDMT00149
modifier: 351530
product: CDMT00106
reactant: CDMT00105
fast: false
reversible: false
name: GA3ox decay

gammaGA3ox
type: LocalParameter
units: substance
value: 3.514
name: gammaGA3ox

CDMT00106
type: SpeciesReference
stoichiometry: 1.0
species: s5

CDMT00105
type: SpeciesReference
stoichiometry: 1.0
species: s28

CDMT00097
type: Reaction
kinetic law: CDMT00146
modifier: 351494
product: CDMT00099
reactant: CDMT00098
fast: false
reversible: false
name: ga3ox decay

CDMT00099
type: SpeciesReference
stoichiometry: 1.0
species: s35

CDMT00098
type: SpeciesReference
stoichiometry: 1.0
species: s41

re9
type: Reaction
reactant: CDMT00019
modifier: 351151
modifier: 351138
reactant: CDMT00020
product: CDMT00021
kinetic law: CDMT00121
fast: false
name: GA12-GA20ox association
reversible: false

CDMT00019
type: SpeciesReference
stoichiometry: 1.0
species: s23

CDMT00020
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00021
type: SpeciesReference
stoichiometry: 1.0
species: s32

ka12
type: LocalParameter
units: substance
value: 2904.11853677638
name: ka12

re40
type: Reaction
kinetic law: CDMT00151
modifier: 351566
product: CDMT00112
product: CDMT00111
reactant: CDMT00110
fast: false
reversible: false
name: GA4.GID.DELLA2 dissociation

ud2
type: LocalParameter
units: substance
value: 2.8184
name: ud2

CDMT00112
type: SpeciesReference
stoichiometry: 1.0
species: s16

CDMT00111
type: SpeciesReference
stoichiometry: 1.0
species: s62

CDMT00110
type: SpeciesReference
stoichiometry: 1.0
species: s36

re8
type: Reaction
kinetic law: CDMT00120
product: CDMT00017
reactant: CDMT00001
fast: false
reversible: false
name: GA12 supply

CDMT00017
type: SpeciesReference
stoichiometry: 1.0
species: s23

CDMT00001
type: SpeciesReference
stoichiometry: 1.0
species: s3

s3
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: GA12_source

re44
type: Reaction
kinetic law: CDMT00161
modifier: 351602
product: CDMT00160
reactant: CDMT00159
fast: false
reversible: false
name: degradation of GA24

CDMT00160
type: SpeciesReference
stoichiometry: 1.0
species: s69

CDMT00159
type: SpeciesReference
stoichiometry: 1.0
species: s25

RemoveGA4
type: Event
event assignment: CDMT00174
trigger: CDMT00169
use values from trigger time: true
name: RemoveGA4

CDMT00169
type: Trigger
persistant: true
initial value: true

time
type: SBMLUnitsDef
unit: CDMT00075
name: time

CDMT00075
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND

s70
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: sa8_degraded

CDMT00100
type: Reaction
kinetic law: CDMT00147
modifier: 351506
product: CDMT00102
reactant: CDMT00101
fast: false
reversible: false
name: GA20ox decay

gammaGA20ox
type: LocalParameter
units: substance
value: 3.514
name: gammaGA20ox

CDMT00102
type: SpeciesReference
stoichiometry: 1.0
species: s6

s6
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: GA20ox_source

CDMT00101
type: SpeciesReference
stoichiometry: 1.0
species: s27

omegaGA12
type: Parameter
constant: false
units: substance
value: 0.006602803853512
name: omegaGA12

re21
type: Reaction
reactant: CDMT00046
modifier: 351302
fast: false
name: GA9-GA3ox association
kinetic law: CDMT00130
product: CDMT00048
reactant: CDMT00047
modifier: 351290
reversible: false

CDMT00046
type: SpeciesReference
stoichiometry: 1.0
species: s26

ka9
type: LocalParameter
units: substance
value: 2073.22402517968
name: ka9

CDMT00048
type: SpeciesReference
stoichiometry: 1.0
species: s29

CDMT00047
type: SpeciesReference
stoichiometry: 1.0
species: s28

area
type: SBMLUnitsDef
unit: CDMT00073
name: area

CDMT00073
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: METRE

re11
type: Reaction
kinetic law: CDMT00123
modifier: 351177
product: CDMT00027
product: CDMT00026
reactant: CDMT00025
fast: false
reversible: false
name: GA15 production

km12
type: LocalParameter
units: substance
value: 198.80427707769
name: km12

CDMT00027
type: SpeciesReference
stoichiometry: 1.0
species: s24

CDMT00026
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00025
type: SpeciesReference
stoichiometry: 1.0
species: s32

re33
type: Reaction
kinetic law: CDMT00136
modifier: 351374
modifier: CDMT00064
product: CDMT00063
reactant: CDMT00062
fast: false
reversible: false
name: ga20ox translation

deltaGA20ox
type: LocalParameter
units: substance
value: 0.192990314378105
name: deltaGA20ox

CDMT00063
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00062
type: SpeciesReference
stoichiometry: 1.0
species: s6

re15
type: Reaction
kinetic law: CDMT00126
modifier: 351228
product: CDMT00036
product: CDMT00035
reactant: CDMT00034
fast: false
reversible: false
name: GA24 production

km15
type: LocalParameter
units: substance
value: 763.777072066507
name: km15

CDMT00036
type: SpeciesReference
stoichiometry: 1.0
species: s25

CDMT00035
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00034
type: SpeciesReference
stoichiometry: 1.0
species: s31

muGA3ox
type: Parameter
constant: true
units: substance
value: 0.102600014140148
name: muGA3ox

re28
type: Reaction
kinetic law: CDMT00140
modifier: 351422
modifier: CDMT00082
product: CDMT00081
reactant: CDMT00080
fast: false
reversible: false
name: gid transcription (activated by DELLA)

thetaGID
type: LocalParameter
units: substance
value: 5.5995E-4
name: thetaGID

CDMT00081
type: SpeciesReference
stoichiometry: 1.0
species: s42

CDMT00080
type: SpeciesReference
stoichiometry: 1.0
species: s15

http://identifiers.org/biomodels.db/BIOMD0000000422#R
type: Parameter
constant: true
units: substance
value: 1.0
name: R

appliedGA4
type: Parameter
constant: true
units: substance
value: 2.0
name: appliedGA4

re14
type: Reaction
kinetic law: CDMT00125
modifier: 351215
product: CDMT00033
product: CDMT00032
reactant: CDMT00031
fast: false
reversible: false
name: GA15.GA20ox dissociation

kd15
type: LocalParameter
units: substance
value: 0.008827838388125
name: kd15

CDMT00033
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00032
type: SpeciesReference
stoichiometry: 1.0
species: s24

CDMT00031
type: SpeciesReference
stoichiometry: 1.0
species: s31

re3
type: Reaction
kinetic law: CDMT00116
modifier: 351075
product: CDMT00007
product: CDMT00006
reactant: CDMT00005
fast: false
reversible: false
name: GA4.GID dissociation

ld
type: LocalParameter
units: substance
value: 2.84315148627376
name: ld

CDMT00007
type: SpeciesReference
stoichiometry: 1.0
species: s2

CDMT00006
type: SpeciesReference
stoichiometry: 1.0
species: s1

CDMT00005
type: SpeciesReference
stoichiometry: 1.0
species: s65

re18
type: Reaction
kinetic law: CDMT00129
modifier: 351278
product: CDMT00045
product: CDMT00044
reactant: CDMT00043
fast: false
reversible: false
name: GA9 production

km24
type: LocalParameter
units: substance
value: 2.58846077319221
name: km24

CDMT00045
type: SpeciesReference
stoichiometry: 1.0
species: s26

CDMT00044
type: SpeciesReference
stoichiometry: 1.0
species: s27

CDMT00043
type: SpeciesReference
stoichiometry: 1.0
species: s30

re6
type: Reaction
kinetic law: CDMT00119
modifier: 351123
product: CDMT00016
product: CDMT00015
reactant: CDMT00014
fast: false
reversible: false
name: DELLA ubiquitination

um
type: LocalParameter
units: substance
value: 6.92208879449283
name: um

CDMT00016
type: SpeciesReference
stoichiometry: 1.0
species: s22

CDMT00015
type: SpeciesReference
stoichiometry: 1.0
species: s62

CDMT00014
type: SpeciesReference
stoichiometry: 1.0
species: s45

s66
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: GA4_source

muGA
type: Parameter
constant: true
units: substance
value: 0.290804218727464
name: muGA

W3 CDTF: Fri Jul 20 18:39:15 BST 2012

tGA4on
type: Parameter
constant: true
units: substance
value: 500.0
name: tGA4on

W3 CDTF: Fri Aug 03 14:19:38 BST 2012

re41
type: Reaction
kinetic law: CDMT00152
product: CDMT00114
reactant: CDMT00113
fast: false
reversible: false
name: GA4 supply

A1
type: LocalParameter
units: substance
value: 0.0307
name: A1

CDMT00114
type: SpeciesReference
stoichiometry: 1.0
species: s1

CDMT00113
type: SpeciesReference
stoichiometry: 1.0
species: s66

re45
type: Reaction
kinetic law: CDMT00164
modifier: 351614
product: CDMT00163
reactant: CDMT00162
fast: false
reversible: false
name: degradation of GA9

CDMT00163
type: SpeciesReference
stoichiometry: 1.0
species: s70

CDMT00162
type: SpeciesReference
stoichiometry: 1.0
species: s26

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

ORG:
  orgname: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
n:
  given: Markus R.
  family: Owen