metaid_0000026
boundary condition: true
in compartment: metaid_0000022
is version of: CHEBI:16526
constant: true
notes: 0.7* 350 [µbar] (p. 1172)
name: CO2
type: Species
initial concentration: 245.0
initial amount: NaN
has only substance units: false

metaid_0000016
constant: false
value: 0.531787796640465
name: Vomax
type: Parameter

995648
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000012
notes: assumed J = 0.9 Jmax (p. 1172); converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: false
value: 4.8582995951417
name: J
type: Parameter

995454
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000023
is version of: CHEBI:16710
constant: true
boundary condition: true
has only substance units: false
initial concentration: 2.0
initial amount: NaN
in compartment: metaid_0000022
name: RuBP
type: Species

metaid_0000037
kinetic law: 995624
modifier: 995612
product: 995600
reactant: 995588
fast: false
reversible: false
name: PGA consumption
type: Reaction

metaid_0000027
in compartment: metaid_0000022
initial concentration: 210.0
constant: true
has only substance units: false
boundary condition: true
notes: [mbar]
type: Species
initial amount: NaN
is version of: CHEBI:15379
name: O2

metaid_0000017
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 406.066146391504
name: Kc
type: Parameter

995600
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

metaid_0000013
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 42.8926627111176
name: Gamma
type: Parameter

995490
stoichiometry: 2.0
species: metaid_0000025
type: SpeciesReference

995478
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

metaid_0000022
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast
type: Compartment

metaid_0000036
kinetic law: 995576
product: 995564
reactant: 995551
reactant: 995538
reactant: 995526
fast: false
reversible: false
name: PGA production - v_o
type: Reaction

995538
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

metaid_0000024
is version of: CHEBI:17050
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.4
initial amount: NaN
in compartment: metaid_0000022
name: PGA
type: Species

metaid_0000014
notes: (p. 1170)
is: SBO:0000009
constant: true
value: 0.9
name: teta
type: Parameter

995551
stoichiometry: 2.0
species: metaid_0000025
type: SpeciesReference

metaid_0000028
is version of: CHEBI:25523
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.29
initial amount: NaN
in compartment: metaid_0000022
name: NADP
type: Species

metaid_0000011
is: SBO:0000009
constant: true
value: 1000.0
name: Q
type: Parameter

metaid_0000008
constant: true
value: 3.2
name: Rp
type: Parameter

995502
stoichiometry: 2.0
species: metaid_0000024
type: SpeciesReference

metaid_0000018
notes: Bernacchi et al. (2001) Equation (8), Table 1
constant: true
value: 276.900084789612
name: Ko
type: Parameter

metaid_0000021
is: SBO:0000009
constant: false
value: 0.646926785453086
name: Vc
type: Parameter

metaid_0000035
kinetic law: 995514
product: 995502
reactant: 995490
reactant: 995478
reactant: 995466
fast: false
reversible: false
name: PGA production - v_c
type: Reaction

metaid_0000025
is version of: CHEBI:16474
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.21
initial amount: NaN
in compartment: metaid_0000022
name: NADPH
type: Species

995526
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

metaid_0000015
notes: average of corresponding values of Table 2; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 2.53232284114507
name: Vcmax
type: Parameter

995588
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000010
notes: (p. 1170)
is: SBO:0000009
constant: true
value: 0.3
name: alpha
type: Parameter

995466
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

metaid_0000020
is: SBO:0000009
constant: false
value: 0.263964911408408
name: phi
type: Parameter

BIOMD0000000384
species: metaid_0000028
parameter: metaid_0000020
name: Carboxylation
rule: metaid_0000031
parameter: metaid_0000008
parameter: metaid_0000010
parameter: metaid_0000009
volume units: 498095
time units: 949038
parameter: metaid_0000017
type: SBMLModel
rule: metaid_0000034
function def: metaid_0000004
rule: metaid_0000029
curated: true
parameter: metaid_0000012
reaction: metaid_0000037
species: metaid_0000026
reaction: metaid_0000038
name: Oxygenation
encodes: GO:0019253
name: PGA consumption
substance units: metaid_0000007
length unit: length
parameter: metaid_0000016
function def: metaid_0000003
name: Arnold2011_Medlyn2002_RuBisCO-CalvinCycle
is: MODEL1109270000
is described by: http://identifiers.org/pubmed/22001849
rule: metaid_0000032
species: metaid_0000024
reaction: metaid_0000036
function def: metaid_0000006
parameter: metaid_0000019
species: metaid_0000023
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
notes: This model is from the article: A quantitative comparison of Calvin–Benson cycle models Anne Arnold, Zoran Nikoloski Trends in Plant Science 2011 Oct 14. 22001849 , Abstract: The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering. Note: Model of the Calvin cycle with focus on the RuBisCO reaction by Medlyn et al. (2002, DOI:10.1046/j.1365-3040.2002.00891.x ). The parameter values are widely taken from Farquhar et al. (1980,DOI:10.1007/BF00386231 ). The initial metabolite values are chosen from the data set of Zhu et al. (2007,DOI:10.1104/pp.107.103713) . A detailed description of all modifications is given in the model described by Arnold and Nikoloski (2011,PMID:22001849 .
parameter: metaid_0000015
species: metaid_0000027
units def: metaid_0000007
created:
  W3 CDTF: Wed Oct 19 15:50:44 BST 2011
area units: 498119
occurs in: http://identifiers.org/taxonomy/33090
rule: metaid_0000030
reaction: metaid_0000035
modified:
  W3 CDTF: Fri Apr 20 20:53:00 BST 2012
parameter: metaid_0000021
parameter: metaid_0000011
function def: metaid_0000005
name: NADPH production
rule: metaid_0000033
compartment: metaid_0000022
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
parameter: metaid_0000018
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
parameter: metaid_0000013
species: metaid_0000025
parameter: metaid_0000014

metaid_0000038
kinetic law: 995660
product: 995648
reactant: 995636
fast: false
reversible: false
name: NADPH production
type: Reaction

metaid_0000009
is: SBO:0000009
constant: true
value: 0.5
name: Nt
type: Parameter

995564
stoichiometry: 1.5
species: metaid_0000024
type: SpeciesReference

metaid_0000019
is: SBO:0000009
constant: false
value: 0.899589030506691
name: Vj
type: Parameter

995636
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference