BIOMD0000000387
type: SBMLModel
is: MODEL1109270003
rule: metaid_0000033
species: metaid_0000031
name: Oxygenation
rule: metaid_0000040
reaction: metaid_0000043
species: metaid_0000030
species: metaid_0000028
modified:
  W3 CDTF: Fri Apr 20 20:52:02 BST 2012
parameter: metaid_0000013
parameter: metaid_0000019
parameter: metaid_0000021
species: metaid_0000027
name: Arnold2011_Damour2007_RuBisCO-CalvinCycle
parameter: metaid_0000008
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 Damour and Urban (2007, [for PDF click here] ). The parameter values are partly taken from Farquhar et al. (1980,DOI:10.1007/BF00386231 ) and Urban et al. (2003,DOI:10.1093/treephys/23.5.289 ). 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 .
created:
  W3 CDTF: Wed Oct 19 15:52:11 BST 2011
units def: metaid_0000007
substance units: metaid_0000007
parameter: metaid_0000016
name: NADPH production
name: Carboxylation
volume units: 498095
time units: 949038
function def: metaid_0000006
is described by: http://identifiers.org/pubmed/22001849
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
parameter: metaid_0000010
parameter: metaid_0000014
function def: metaid_0000004
parameter: metaid_0000022
function def: metaid_0000003
parameter: metaid_0000009
rule: metaid_0000038
reaction: metaid_0000041
species: metaid_0000026
rule: metaid_0000039
rule: metaid_0000035
parameter: metaid_0000017
reaction: metaid_0000044
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
parameter: metaid_0000011
species: metaid_0000032
parameter: metaid_0000015
parameter: metaid_0000023
rule: metaid_0000034
species: metaid_0000029
function def: metaid_0000005
compartment: metaid_0000025
rule: metaid_0000037
rule: metaid_0000036
reaction: metaid_0000042
parameter: metaid_0000012
parameter: metaid_0000018
area units: 498119
parameter: metaid_0000020
length unit: length
parameter: metaid_0000024
occurs in: http://identifiers.org/taxonomy/33090
name: PGA consumption
encodes: GO:0019253
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
curated: true

metaid_0000031
type: Species
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_0000025
name: NADP

metaid_0000025
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast

metaid_0000043
type: Reaction
kinetic law: 035677
modifier: 035664
product: 035652
reactant: 035640
fast: false
reversible: false
name: PGA consumption

metaid_0000028
type: Species
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.21
initial amount: NaN
in compartment: metaid_0000025
name: NADPH

035652
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000026
type: Species
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_0000025
name: RuBP

035640
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000027
type: Species
is version of: CHEBI:17050
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.4
initial amount: NaN
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name: PGA

metaid_0000030
type: Species
name: O2
initial concentration: 21000.0
has only substance units: false
notes: [Pa]
boundary condition: true
constant: true
is version of: CHEBI:15379
in compartment: metaid_0000025
initial amount: NaN

metaid_0000013
type: Parameter
notes: equals 0.5 O2/tau Urban et al. (2003) (p. 291), Equation (8), Table 1
is: SBO:0000009
constant: false
value: 4.29040862748855
name: Gamma

metaid_0000019
type: Parameter
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constant: false
value: 0.025590660664217
name: phi

metaid_0000021
type: Parameter
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constant: false
value: 0.942054655190967
name: Vp

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

035483
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid_0000016
type: Parameter
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 26.7125313821435
name: Kc

metaid_0000010
type: Parameter
notes: Urban et al. (2003) Table 1
is: SBO:0000009
constant: true
value: 0.24
name: alpha

metaid_0000014
type: Parameter
is: SBO:0000009
constant: true
value: 1000.0
name: Q

metaid_0000022
type: Parameter
notes: Harley et al. (1992) Equation (9), Table 1; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000196
constant: true
value: 0.259027750094988
name: TPU

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

metaid_0000041
type: Reaction
name: PGA production - v_c
reactant: 035519
reactant: 035495
fast: false
reversible: false
reactant: 035507
modifier: 035543
kinetic law: 035556
product: 035531

035519
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species: metaid_0000028

035495
type: SpeciesReference
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035507
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metaid_0000029
type: Species
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name: CO2
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is version of: CHEBI:16526
boundary condition: true
notes: [Pa]

035531
type: SpeciesReference
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species: metaid_0000027

metaid_0000017
type: Parameter
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 187891.032274486
name: Ko

metaid_0000044
type: Reaction
kinetic law: 035714
product: 035701
reactant: 035689
fast: false
reversible: false
name: NADPH production

035701
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

035689
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

metaid_0000011
type: Parameter
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: false
value: 3.64863790509821
name: J

metaid_0000032
type: Species
boundary condition: true
is version of: CHEBI:28017
notes: [g/m²]
initial concentration: 0.5
constant: true
in compartment: metaid_0000025
initial amount: NaN
name: starch
has only substance units: false

metaid_0000015
type: Parameter
notes: Harley et al. (1992) Equation (9), Table 1; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 1.91141270310584
name: Vcmax

metaid_0000023
type: Parameter
is: SBO:0000009
constant: false
value: 0.999136712846952
name: Cst

metaid_0000042
type: Reaction
product: 035604
kinetic law: 035628
fast: false
modifier: 035616
reactant: 035592
name: PGA production - v_o
reactant: 035568
reactant: 035580
reversible: false

035604
type: SpeciesReference
stoichiometry: 1.5
species: metaid_0000027

035592
type: SpeciesReference
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species: metaid_0000028

035568
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

035580
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000012
type: Parameter
notes: Harley et al. (1992) Equation (9), Table 1
is: SBO:0000009
constant: true
value: 142.047003854271
name: Jmax

metaid_0000018
type: Parameter
is: SBO:0000009
constant: false
value: 0.675554869049198
name: Vj

metaid_0000020
type: Parameter
is: SBO:0000009
constant: false
value: 0.822489884906092
name: Vc

metaid_0000024
type: Parameter
notes: Urban et al. (2007) (p. 348)
is: SBO:0000009
constant: true
value: 0.0434
name: a