metaid_0000023
notes: LPI = 15 (mature leaves LPI 10-20, p. 667); additionally legend of Figure 1; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.00624227154326423
name: Rd
type: Parameter

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

metaid_0000033
initial amount: NaN
initial concentration: 21.0
in compartment: metaid_0000028
notes: [kPa]
name: O2
is version of: CHEBI:15379
constant: true
boundary condition: true
type: Species
has only substance units: false

008011
stoichiometry: 1.5
species: metaid_0000030
type: SpeciesReference

metaid_0000018
is: SBO:0000009
constant: false
value: 0.116856926991465
name: phi
type: Parameter

metaid_0000024
is: SBO:0000009
constant: false
value: 0.611525371598211
name: v_c
type: Parameter

metaid_0000042
reversible: false
fast: false
product: 007938
reactant: 007914
kinetic law: 007962
type: Reaction
name: PGA production - v_c
reactant: 007902
modifier: 007950
reactant: 007926

metaid_0000014
is: SBO:0000196
constant: true
value: 1000.0
name: PPFD
type: Parameter

007890
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000028
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast
type: Compartment

008108
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

metaid_0000022
is: SBO:0000009
constant: true
value: 118.69
name: k
type: Parameter

metaid_0000032
boundary condition: true
initial amount: NaN
has only substance units: false
type: Species
is version of: CHEBI:16526
notes: [Pa]
initial concentration: 35.0
constant: true
in compartment: metaid_0000028
name: CO2

007998
stoichiometry: 2.0
species: metaid_0000031
type: SpeciesReference

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

007914
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

metaid_0000019
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000196
constant: true
value: 0.227712577291006
name: TPU
type: Parameter

metaid_0000025
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.666248728058741
name: Vc
type: Parameter

metaid_0000043
reactant: 007998
reactant: 007974
type: Reaction
modifier: 008023
reversible: false
fast: false
name: PGA production - v_o
reactant: 007986
product: 008011
kinetic law: 008035

metaid_0000015
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 1.4749455852483
name: Vcmax
type: Parameter

007974
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

007938
stoichiometry: 2.0
species: metaid_0000030
type: SpeciesReference

metaid_0000029
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_0000028
name: RuBP
type: Species

metaid_0000021
notes: "relative humidity >50%" (p. 675)
is: SBO:0000009
constant: true
value: 0.6
name: h
type: Parameter

metaid_0000031
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_0000028
name: NADPH
type: Species

008059
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

metaid_0000026
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.611525371598211
name: Vj
type: Parameter

007902
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

metaid_0000044
kinetic law: 008084
modifier: 008071
product: 008059
reactant: 008047
fast: false
reversible: false
name: PGA consumption
type: Reaction

metaid_0000016
is: SBO:0000009
constant: true
value: 27.8535785188479
name: Kc
type: Parameter

metaid_0000012
is: SBO:0000009
constant: true
value: 112.989573402043
name: Jmax
type: Parameter

metaid_0000011
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: false
value: 2.98814971559545
name: J
type: Parameter

007986
stoichiometry: 1.0
species: metaid_0000033
type: SpeciesReference

007926
stoichiometry: 2.0
species: metaid_0000031
type: SpeciesReference

BIOMD0000000385
rule: metaid_0000039
name: Carboxylation
modified:
  W3 CDTF: Fri Apr 20 20:52:45 BST 2012
parameter: metaid_0000011
reaction: metaid_0000045
parameter: metaid_0000015
parameter: metaid_0000010
function def: metaid_0000004
species: metaid_0000031
parameter: metaid_0000014
rule: metaid_0000035
substance units: metaid_0000007
parameter: metaid_0000009
parameter: metaid_0000020
parameter: metaid_0000024
volume units: 498095
reaction: metaid_0000043
rule: metaid_0000037
function def: metaid_0000006
species: metaid_0000032
reaction: metaid_0000044
units def: metaid_0000007
name: Oxygenation
parameter: metaid_0000023
species: metaid_0000029
parameter: metaid_0000027
parameter: metaid_0000013
species: metaid_0000033
parameter: metaid_0000019
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
length unit: length
time units: 949038
parameter: metaid_0000012
type: SBMLModel
parameter: metaid_0000018
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
parameter: metaid_0000008
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
rule: metaid_0000040
reaction: metaid_0000042
is: MODEL1109270001
rule: metaid_0000038
name: NADPH production
name: PGA consumption
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 Schultz (2003, DOI:10.1071/FP02146 ). 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 .
name: Arnold2011_Schultz2003_RuBisCO-CalvinCycle
species: metaid_0000034
is: GO:0019253
parameter: metaid_0000022
function def: metaid_0000005
compartment: metaid_0000028
species: metaid_0000030
parameter: metaid_0000026
area units: 498119
parameter: metaid_0000021
parameter: metaid_0000025
parameter: metaid_0000017
occurs in: http://identifiers.org/taxonomy/33090
function def: metaid_0000003
is described by: http://identifiers.org/pubmed/22001849
created:
  W3 CDTF: Wed Oct 19 15:51:13 BST 2011
parameter: metaid_0000016
rule: metaid_0000041
rule: metaid_0000036
curated: true

metaid_0000034
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_0000028
name: NADP
type: Species

metaid_0000020
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.468615384615385
name: g0
type: Parameter

008047
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

metaid_0000030
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_0000028
name: PGA
type: Species

metaid_0000027
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.768408279573721
name: Vp
type: Parameter

metaid_0000045
kinetic law: 008120
product: 008108
reactant: 008096
fast: false
reversible: false
name: NADPH production
type: Reaction

metaid_0000017
is: SBO:0000009
constant: true
value: 41.9469718861558
name: Ko
type: Parameter

metaid_0000010
notes: Table 1, sunleaves (20-30°C)
is: SBO:0000009
constant: true
value: 0.19
name: alpha
type: Parameter

metaid_0000013
notes: LPI = 15 (mature leaves LPI 10-20, p. 667); additionally legend of Figure 1
is: SBO:0000009
constant: true
value: 3.81695
name: Gamma
type: Parameter

008096
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference