BIOMD0000000385
type: SBMLModel
rule: metaid_0000039
name: Carboxylation
parameter: metaid_0000011
reaction: metaid_0000045
parameter: metaid_0000015
parameter: metaid_0000010
function def: metaid_0000004
modified:
  W3 CDTF: Fri Apr 20 20:52:45 BST 2012
species: metaid_0000031
parameter: metaid_0000014
rule: metaid_0000035
substance units: metaid_0000007
parameter: metaid_0000009
parameter: metaid_0000020
parameter: metaid_0000024
created:
  W3 CDTF: Wed Oct 19 15:51:13 BST 2011
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
length unit: length
time units: 949038
parameter: metaid_0000012
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
parameter: metaid_0000018
parameter: metaid_0000008
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
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
parameter: metaid_0000022
function def: metaid_0000005
compartment: metaid_0000028
species: metaid_0000030
parameter: metaid_0000026
area units: 498119
parameter: metaid_0000021
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
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
parameter: metaid_0000016
rule: metaid_0000041
rule: metaid_0000036
curated: true

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: 2.98814971559545
name: J

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

008108
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

metaid_0000031
type: Species
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

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

008096
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000034
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_0000028
name: NADP

metaid_0000015
type: Parameter
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

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

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

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

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

metaid_0000020
type: Parameter
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

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

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

007998
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000031

007974
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000029
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_0000028
name: RuBP

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

007986
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

metaid_0000033
type: Species
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
has only substance units: false

008011
type: SpeciesReference
stoichiometry: 1.5
species: metaid_0000030

metaid_0000030
type: Species
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

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

008059
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

008047
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000023
type: Parameter
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

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

metaid_0000013
type: Parameter
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

metaid_0000019
type: Parameter
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

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

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

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

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

007938
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000030

007914
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

007902
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

007926
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000031

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

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

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

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

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

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