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metaid_0000006
notes: Auxin target gene mRNA degradation rate. Computed from the mean half life of Aux/IAA mRNA in Narsai et al. The Plant Cell 2007.
is: SBO:0000356
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value: 0.007
name: d_r
type: Parameter

484199
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species: metaid_0000023
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metaid_0000023
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type: Species
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name: mRNA
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metaid_0000010
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484162
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species: metaid_0000019
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metaid_0000030
is: SBO:0000009
constant: true
value: 10.0
name: k_Am
type: Parameter

metaid_0000019
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name: Aux/IAA
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metaid_0000005
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value: 1.0
name: pi_I
type: Parameter

metaid_0000024
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constant: true
value: 10.0
name: f_c
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484101
stoichiometry: 1.0
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stoichiometry: 1.0
species: metaid_0000019
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484285
stoichiometry: 1.0
species: metaid_0000023
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metaid_0000025
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value: 10.0
name: w_A
type: Parameter

metaid_0000045
is: SBO:0000009
constant: false
value: 0.11
name: aux_basal
type: Parameter

484149
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

484077
stoichiometry: 1.0
species: metaid_0000021
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constant: false
boundary condition: false
name: auxin
initial amount: NaN
initial concentration: 1.11

483920
stoichiometry: 1.0
species: metaid_0000022
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BIOMD0000000352
volume units: volume
parameter: metaid_0000029
parameter: metaid_0000017
parameter: metaid_0000009
parameter: metaid_0000016
rule: metaid_0000066
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
reaction: metaid_0000049
area units: area
parameter: metaid_0000011
reaction: metaid_0000032
species: metaid_0000023
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parameter: metaid_0000010
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species: metaid_0000020
created:
  W3 CDTF: Fri Apr 01 11:17:29 BST 2011
modified:
  W3 CDTF: Tue Aug 23 15:18:22 BST 2011
rule: metaid_0000057
parameter: metaid_0000042
notes: This model is from the article: The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol. 2011 Jul 5;7:508. 21734647 , Abstract: The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex. Note: Figure 4 of the supplementary material of the reference article has been reproduced here. In this model, the fluctuations of auxin level is represented using sinux function. Time evolution of the variables AUX/IAA (I) and mRNA (R) are plotted, under the influence of fluctuations of auxin level. pi_A is varied between 0 and 2 by steps of…
parameter: metaid_0000028
creator:
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    orgname: CNRS
  n:
    given: Teva
    family: Vernoux
parameter: metaid_0000027
parameter: metaid_0000014
creator:
  ORG:
    orgname: INRIA
  n:
    given: Farcot
    family: Etienne
parameter: metaid_0000008
parameter: metaid_0000015
reaction: metaid_0000050
type: SBMLModel
reaction: metaid_0000048
reaction: metaid_0000047
reaction: metaid_0000031
species: metaid_0000036
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curated: true
reaction: metaid_0000034
parameter: metaid_0000026
species: metaid_0000021
parameter: metaid_0000025
rule: metaid_0000055
reaction: metaid_0000051
compartment: metaid_0000018
name: Vernoux2011_AuxinSignaling_AuxinFluctuating
parameter: metaid_0000007
time units: metaid_0000075
is version of: GO:0009734
is: MODEL1108110000
parameter: metaid_0000013
species: metaid_0000019
is described by: http://identifiers.org/pubmed/21734647
substance units: metaid_0000076
length unit: length
parameter: metaid_0000012
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parameter: metaid_0000006
species: metaid_0000022
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occurs in: http://identifiers.org/taxonomy/3701
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parameter: metaid_0000030
parameter: metaid_0000024
rule: metaid_0000056

484029
stoichiometry: 1.0
species: metaid_0000020
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metaid_0000026
is: SBO:0000481
constant: true
value: 10.0
name: w_I
type: Parameter

metaid_0000013
is: SBO:0000009
constant: true
value: 10.0
name: f_A
type: Parameter

metaid_0000016
is: SBO:0000282
constant: true
value: 10.0
name: K_II
type: Parameter

metaid_0000048
kinetic law: 484089
reactant: 484077
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: reac_degrDII
type: Reaction

metaid_0000033
kinetic law: 484017
modifier: 484004
reactant: 483992
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: reac_degrI
type: Reaction

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modifier: 484297
reversible: false
fast: false
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product: 484285
kinetic law: 484334
type: Reaction
is version of: GO:0009299
name: reac_prodR
modifier: 484322

metaid_0000014
is: SBO:0000009
constant: true
value: 10.0
name: gamma_I
type: Parameter

metaid_0000015
is: SBO:0000282
constant: true
value: 1.0
name: K_aux
type: Parameter

483943
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

metaid_0000029
is: SBO:0000153
constant: true
value: 1.0
name: pi_A
type: Parameter

metaid_0000009
is: SBO:0000356
constant: true
value: 0.003
name: d_IA
type: Parameter

metaid_0000047
kinetic law: 484065
reactant: 484053
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: reac_degrDIA
type: Reaction

metaid_0000034
kinetic law: 484041
reactant: 484029
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: reac_degrA
type: Reaction

484223
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

metaid_0000020
constant: false
is version of: Q94JM3
has only substance units: false
type: Species
name: ARF
boundary condition: false
is: SBO:0000252
in compartment: metaid_0000018
initial amount: NaN
initial concentration: 10.0

metaid_0000053
kinetic law: 484273
product: 484261
is version of: GO:0009058
is: SBO:0000393
fast: false
reversible: false
name: reac_prodA
type: Reaction

metaid_0000018
is version of: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: c_1
type: Compartment

484053
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

484261
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000011
is: SBO:0000341
constant: true
value: 1.0
name: k_IA
type: Parameter

metaid_0000008
is: SBO:0000356
constant: true
value: 0.003
name: d_II
type: Parameter

metaid_0000028
notes: Aux/IAA basal degradation rate (without auxin), based on half-lifes measured in Dreher et al. The Plant Cell 2006.
is: SBO:0000356
constant: true
value: 0.05
name: d_I
type: Parameter

metaid_0000031
reactant: 483908
fast: false
kinetic law: 483932
is: SBO:0000526
type: Reaction
is version of: GO:0006461
name: reac_DIA
reactant: 483896
product: 483920
reversible: true

metaid_0000042
is: SBO:0000338
constant: false
value: 10.0
name: kprime_IA
type: Parameter

metaid_0000052
kinetic law: 484248
modifier: 484236
product: 484223
is version of: GO:0009058
is: SBO:0000393
fast: false
reversible: false
name: reac_prodI
type: Reaction

483896
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000021
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type: Species
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name: Aux/IAA:Aux/IAA
boundary condition: false
initial amount: NaN
constant: false

metaid_0000017
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constant: true
value: 10.0
name: K_IA
type: Parameter

metaid_0000012
is: SBO:0000282
constant: true
value: 100.0
name: B_d
type: Parameter

metaid_0000027
is: SBO:0000481
constant: true
value: 10.0
name: w_D
type: Parameter

metaid_0000049
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reactant: 484101
product: 484113
type: Reaction
reversible: false
is: SBO:0000180
fast: false
kinetic law: 484137
name: reac_DIAxA
is version of: GO:0043241

metaid_0000022
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has part: P49677
name: Aux/IAA:ARF
constant: false
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initial amount: NaN
type: Species
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is: SBO:0000297

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type: Reaction
fast: false
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reactant: 483943
is: SBO:0000526
reversible: true
is version of: GO:0006461
product: 483968
name: reac_DII
reactant: 483956

metaid_0000007
notes: ARF degradation rate, based on the value for ARF1, cf. Salmon et al. The Plant Journal (2008)
is: SBO:0000356
constant: true
value: 0.003
name: d_A
type: Parameter

metaid_0000051
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reactant: 484199
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: reac_degrR
type: Reaction