metaid_0000017
is: SBO:0000009
constant: false
value: 0.286292104000314
name: phi
type: Parameter

metaid_0000022
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.00892944491541968
name: Vc
type: Parameter

022311
stoichiometry: 2.0
species: metaid_0000025
type: SpeciesReference

022275
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000013
is: SBO:0000009
constant: true
value: 3.74116898182615
name: Gamma
type: Parameter

metaid_0000027
has only substance units: false
is version of: CHEBI:16526
initial concentration: 24.5
name: CO2
in compartment: metaid_0000023
type: Species
initial amount: NaN
boundary condition: true
notes: [Pa]
constant: true

022371
stoichiometry: 2.0
species: metaid_0000026
type: SpeciesReference

022299
stoichiometry: 2.0
species: metaid_0000026
type: SpeciesReference

metaid_0000037
modifier: 022395
reversible: false
reactant: 022359
product: 022383
reactant: 022347
name: PGA production - v_o
kinetic law: 022407
type: Reaction
fast: false
reactant: 022371

022359
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000016
is: SBO:0000009
constant: true
value: 16.5788431231261
name: Ko
type: Parameter

022479
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

metaid_0000023
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast
type: Compartment

metaid_0000012
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307740792044142
name: gm
type: Parameter

022419
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000026
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_0000023
name: NADPH
type: Species

metaid_0000036
reactant: 022299
modifier: 022323
product: 022311
kinetic law: 022335
reactant: 022275
reactant: 022287
fast: false
name: PGA production - v_c
type: Reaction
reversible: false

022263
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

022431
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000020
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.00593820961819415
name: Vj
type: Parameter

BIOMD0000000386
reaction: metaid_0000039
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
species: metaid_0000024
name: Oxygenation
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
parameter: metaid_0000009
name: NADPH production
compartment: metaid_0000023
rule: metaid_0000032
type: SBMLModel
parameter: metaid_0000012
parameter: metaid_0000018
is: GO:0019253
modified:
  W3 CDTF: Fri Apr 20 20:52:27 BST 2012
rule: metaid_0000035
parameter: metaid_0000017
area units: 498119
species: metaid_0000028
is described by: http://identifiers.org/pubmed/22001849
name: Arnold2011_Sharkey2007_RuBisCO-CalvinCycle
species: metaid_0000025
substance units: metaid_0000007
reaction: metaid_0000038
parameter: metaid_0000022
name: PGA consumption
reaction: metaid_0000037
parameter: metaid_0000015
name: Carboxylation
function def: metaid_0000006
rule: metaid_0000033
occurs in: http://identifiers.org/taxonomy/33090
species: metaid_0000029
function def: metaid_0000004
parameter: metaid_0000016
curated: true
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
volume units: 498095
species: metaid_0000026
parameter: metaid_0000011
rule: metaid_0000030
parameter: metaid_0000021
is: MODEL1109270002
reaction: metaid_0000036
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 Sharkey et al. (2007, DOI:10.1111/j.1365-3040.2007.01710.x ). The parameter values are partly taken from Farquhar et al. (1980,DOI:10.1007/BF00386231 ) and Medlyn et al. (2002,DOI:10.1046/j.1365-3040.2002.00891.x ). 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_0000014
parameter: metaid_0000020
created:
  W3 CDTF: Wed Oct 19 15:51:41 BST 2011
units def: metaid_0000007
parameter: metaid_0000013
parameter: metaid_0000019
rule: metaid_0000034
function def: metaid_0000005
parameter: metaid_0000008
length unit: length
time units: 949038
species: metaid_0000027
function def: metaid_0000003
parameter: metaid_0000010
rule: metaid_0000031

metaid_0000019
is: SBO:0000009
constant: false
value: 0.00593820961819415
name: v_c
type: Parameter

metaid_0000015
is: SBO:0000009
constant: true
value: 27.2372124161502
name: Kc
type: Parameter

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

metaid_0000025
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_0000023
name: PGA
type: Species

metaid_0000010
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307674936008629
name: Rd
type: Parameter

metaid_0000029
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_0000023
name: NADP
type: Species

022347
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000039
kinetic law: 022491
product: 022479
reactant: 022467
fast: false
reversible: false
name: NADPH production
type: Reaction

022287
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

022383
stoichiometry: 1.5
species: metaid_0000025
type: SpeciesReference

metaid_0000018
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000196
constant: true
value: 0.0307585098788555
name: TPU
type: Parameter

metaid_0000021
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.110677228404984
name: Vp
type: Parameter

metaid_0000014
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307602623029146
name: Vcmax
type: Parameter

022467
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

metaid_0000008
is: SBO:0000009
constant: true
value: 3.2
name: Rp
type: Parameter

metaid_0000024
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_0000023
name: RuBP
type: Species

metaid_0000011
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307678189755062
name: J
type: Parameter

metaid_0000028
constant: true
has only substance units: false
name: O2
initial concentration: 21.0
type: Species
notes: [kPa]
initial amount: NaN
boundary condition: true
in compartment: metaid_0000023
is version of: CHEBI:15379

metaid_0000038
kinetic law: 022455
modifier: 022443
product: 022431
reactant: 022419
fast: false
reversible: false
name: PGA consumption
type: Reaction