730458
stoichiometry: 1.0
species: metaid_0000047
type: SpeciesReference

730157
stoichiometry: 2.0
species: metaid_0000038
type: SpeciesReference

metaid_0000071
kinetic law: 730783
product: 730771
reactant: 730759
fast: false
reversible: false
name: Superoxide diffusion phagosome/cytoplasm
type: Reaction

metaid_0000058
kinetic law: 730254
product: 730242
product: 730230
reactant: 730218
reactant: 730206
fast: false
reversible: false
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metaid_0000013
constant: true
value: 50.0
type: Parameter

730831
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species: metaid_0000042
type: SpeciesReference

729904
exponent: 1.0
scale: -6
multipler: 1.0
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type: SBMLUnit

metaid_0000044
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is: CHEBI:18009
name: NADP
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is: C00006
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metaid_0000027
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value: 1.5
type: Parameter

730651
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

730759
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type: SpeciesReference

metaid_0000004
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type: Parameter

730206
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730290
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730470
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730109
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metaid_0000050
is version of: IPR000823
constant: false
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initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000028
name: compound III
type: Species

metaid_0000065
kinetic law: 730579
product: 730567
fast: false
reversible: false
name: Oxygen diffusion
type: Reaction

metaid_0000059
kinetic law: 730314
reactant: 730278
product: 730290
reversible: false
name: NADPH autooxidation
product: 730302
type: Reaction
fast: false
is: R07172
is version of: http://identifiers.org/ec-code/1.6.3.1
reactant: 730266

730699
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species: metaid_0000049
type: SpeciesReference

730807
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

metaid_0000012
constant: true
value: 1.0E-6
type: Parameter

metaid_0000070
kinetic law: 730747
product: 730735
reactant: 730723
fast: false
reversible: false
name: Melatonin free radical diffusion phagosome/cytoplasm
type: Reaction

729969
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference

metaid_0000045
type: Species
boundary condition: false
is: C00704
initial concentration: 0.0
has only substance units: false
is: CHEBI:18421
in compartment: metaid_0000029
name: Superoxide
constant: false
initial amount: NaN

730278
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

metaid_0000026
constant: true
value: 550.0
type: Parameter

730121
stoichiometry: 1.0
species: metaid_0000050
type: SpeciesReference

metaid_0000005
constant: true
value: 50.0
type: Parameter

730422
stoichiometry: 1.0
species: metaid_0000043
type: SpeciesReference

metaid_0000031
is: C00027
in compartment: metaid_0000028
name: H2O2
constant: false
type: Species
boundary condition: false
is: CHEBI:16240
has only substance units: false
initial concentration: 0.0
initial amount: NaN

730326
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

metaid_0000051
type: Species
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is: C00006
has only substance units: false
boundary condition: false
initial concentration: 0.0
name: NADP2
initial amount: NaN
is: CHEBI:18009
constant: false

730627
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

metaid_0000064
kinetic law: 730555
product: 730543
fast: false
reversible: false
name: NADPH synthesis
type: Reaction

730182
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

730386
stoichiometry: 2.0
species: metaid_0000045
type: SpeciesReference

730302
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

metaid_0000056
kinetic law: 730133
product: 730121
reactant: 730109
reactant: 730096
fast: false
reversible: false
name: compound III formation
type: Reaction

metaid_0000011
constant: true
value: 0.1
type: Parameter

metaid_0000015
constant: true
value: 10.0
type: Parameter

730446
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

730169
stoichiometry: 1.0
species: metaid_0000039
type: SpeciesReference

730230
stoichiometry: 1.0
species: metaid_0000039
type: SpeciesReference

metaid_0000025
constant: true
value: 288.0
type: Parameter

metaid_0000046
boundary condition: false
initial concentration: 0.0
type: Species
in compartment: metaid_0000029
is: C00282
constant: false
name: Hydrogen
has only substance units: false
initial amount: NaN
is: CHEBI:18276

metaid_0000006
constant: true
value: 58.0
type: Parameter

metaid_0000067
kinetic law: 730639
product: 730627
reactant: 730615
fast: false
reversible: false
name: Oxygen diffusion- phagosome/cytoplasm
type: Reaction

730591
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

730218
stoichiometry: 1.0
species: metaid_0000050
type: SpeciesReference

W3 CDTF: Fri Jul 27 09:45:32 BST 2007

metaid_0000014
constant: true
value: 500.0
type: Parameter

metaid_0000057
reactant: 730157
kinetic law: 730194
fast: false
is: R00275
is version of: http://identifiers.org/ec-code/1.15.1.1
reversible: false
type: Reaction
product: 730182
reactant: 730145
product: 730169
name: H2O2 formation

BIOMD0000000143
reaction: metaid_0000068
species: metaid_0000037
species: metaid_0000045
parameter: metaid_0000027
parameter: metaid_0000013
species: metaid_0000041
parameter: metaid_0000019
is version of: GO:0016692
parameter: metaid_0000012
curated: true
parameter: metaid_0000018
parameter: metaid_0000007
species: metaid_0000035
parameter: metaid_0000022
parameter: metaid_0000011
species: metaid_0000031
units def: metaid_0000073
name: Olsen2003_neutrophil_oscillatory_metabolism
reaction: metaid_0000060
parameter: metaid_0000021
parameter: metaid_0000010
reaction: metaid_0000066
reaction: metaid_0000065
reaction: metaid_0000057
reaction: metaid_0000056
species: metaid_0000038
species: metaid_0000046
species: metaid_0000042
species: metaid_0000050
length unit: length
parameter: metaid_0000026
volume units: metaid_0000084
parameter: metaid_0000025
reaction: metaid_0000063
parameter: metaid_0000017
parameter: metaid_0000006
reaction: metaid_0000055
species: metaid_0000032
parameter: metaid_0000016
parameter: metaid_0000005
reaction: metaid_0000054
parameter: metaid_0000009
species: metaid_0000033
time units: metaid_0000134
parameter: metaid_0000020
compartment: metaid_0000029
notes: The model reproduces the time series of cytosolic and phagosomal species as depicted in Figure 2 of the paper. Model successfully reproduced using MathSBML and Jarnac To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
reaction: metaid_0000072
reaction: metaid_0000064
type: SBMLModel
species: metaid_0000039
species: metaid_0000049
species: metaid_0000047
substance units: metaid_0000073
parameter: metaid_0000015
species: metaid_0000043
reaction: metaid_0000069
species: metaid_0000051
parameter: metaid_0000014
is version of: GO:0030186
species: metaid_0000036
species: metaid_0000044
occurs in: http://identifiers.org/taxonomy/40674
reaction: metaid_0000071
species: metaid_0000040
reaction: metaid_0000070
parameter: metaid_0000024
reaction: metaid_0000062
parameter: metaid_0000023
species: metaid_0000034
reaction: metaid_0000061
parameter: metaid_0000004
reaction: metaid_0000067
area units: metaid_0000005
reaction: metaid_0000053
parameter: metaid_0000008
reaction: metaid_0000059
is: MODEL5564211615
compartment: metaid_0000028
is described by: http://identifiers.org/pubmed/12524266

730266
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

730687
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference

730771
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

metaid_0000010
constant: true
value: 10.0
type: Parameter

metaid_0000024
constant: true
value: 2.0
type: Parameter

metaid_0000047
boundary condition: false
initial concentration: 0.0
name: Melatonin free radical
constant: false
has only substance units: false
initial amount: NaN
in compartment: metaid_0000029
is version of: C01598
is version of: CHEBI:16796
type: Species

730615
stoichiometry: 1.0
species: metaid_0000039
type: SpeciesReference

metaid_0000066
kinetic law: 730603
reactant: 730591
fast: false
reversible: false
name: Oxygen diffusion
type: Reaction

metaid_0000007
constant: true
value: 10.0
type: Parameter

730567
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

metaid_0000061
is: R00275
product: 730410
kinetic law: 730434
reversible: false
product: 730422
reactant: 730386
is version of: http://identifiers.org/ec-code/1.15.1.1
reactant: 730398
name: H2O2 formation
type: Reaction
fast: false

730009
stoichiometry: 1.0
species: metaid_0000035
type: SpeciesReference

metaid_0000054
kinetic law: 730022
product: 730009
product: 729995
reactant: 729983
reactant: 729969
fast: false
reversible: false
name: Melatonin-compound I reaction
type: Reaction

730398
stoichiometry: 2.0
species: metaid_0000046
type: SpeciesReference

metaid_0000017
constant: true
value: 25.0
type: Parameter

metaid_0000040
boundary condition: false
in compartment: metaid_0000029
type: Species
is: CHEBI:16474
initial amount: NaN
is: C00005
constant: false
initial concentration: 0.0
name: NADPH
has only substance units: false

730242
stoichiometry: 1.0
species: metaid_0000033
type: SpeciesReference

metaid_0000037
constant: false
has only substance units: false
is: CHEBI:18421
in compartment: metaid_0000028
name: Superoxide
boundary condition: false
type: Species
initial concentration: 0.0
initial amount: NaN
is: C00704

metaid_0000020
constant: true
value: 30.0
type: Parameter

metaid_0000008
constant: true
value: 0.004
type: Parameter

metaid_0000034
has only substance units: false
initial concentration: 300.0
name: Melatonin
initial amount: NaN
in compartment: metaid_0000028
type: Species
is version of: C01598
boundary condition: false
is version of: CHEBI:16796
constant: false

metaid_0000069
kinetic law: 730711
product: 730699
reactant: 730687
fast: false
reversible: false
name: Melatonin diffusion phagosome/cytoplasm
type: Reaction

metaid_0000060
kinetic law: 730374
product: 730362
product: 730350
reactant: 730338
reactant: 730326
fast: false
reversible: false
name: NADP radical-Oxygen reaction
type: Reaction

metaid_0000016
constant: true
value: 60.0
type: Parameter

730035
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference

metaid_0000041
initial concentration: 0.0
initial amount: NaN
is: CHEBI:15379
boundary condition: false
is: C00007
in compartment: metaid_0000029
constant: false
has only substance units: false
name: Oxygen
type: Species

730362
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

730723
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

metaid_0000055
kinetic law: 730085
product: 730072
product: 730061
reactant: 730048
reactant: 730035
fast: false
reversible: false
name: Melatonin-compound II reaction
type: Reaction

729983
stoichiometry: 1.0
species: metaid_0000033
type: SpeciesReference

metaid_0000035
name: compound II
initial concentration: 0.0
in compartment: metaid_0000028
is version of: IPR000823
has only substance units: false
initial amount: NaN
boundary condition: false
type: Species
constant: false
is version of: PIRSF000293

metaid_0000009
constant: true
value: 20.0
type: Parameter

metaid_0000036
type: Species
boundary condition: false
is version of: CHEBI:16796
is version of: C01598
has only substance units: false
constant: false
initial amount: NaN
name: Melatonin free radical
in compartment: metaid_0000028
initial concentration: 0.0

metaid_0000021
constant: true
value: 30.0
type: Parameter

730048
stoichiometry: 1.0
species: metaid_0000035
type: SpeciesReference

metaid_0000068
kinetic law: 730675
product: 730663
reactant: 730651
fast: false
reversible: false
name: H2O2 diffusion phagosome/cytoplasm
type: Reaction

730096
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

metaid_0000029
is: GO:0005737
constant: true
size: 10.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

metaid_0000063
kinetic law: 730531
product: 730519
reactant: 730506
fast: false
reversible: false
name: NADP dimer formation
type: Reaction

730072
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

metaid_0000042
is: C00006
is: CHEBI:18009
boundary condition: false
has only substance units: false
type: Species
in compartment: metaid_0000029
name: NADP
initial amount: NaN
constant: false
initial concentration: 0.0

metaid_0000073
unit: 729904
name: micro mole
type: SBMLUnitsDef

729930
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

metaid_0000019
constant: true
value: 0.045
type: Parameter

metaid_0000039
is: CHEBI:15379
constant: false
in compartment: metaid_0000028
is: C00007
has only substance units: false
name: Oxygen
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boundary condition: false
initial amount: NaN
initial concentration: 0.0

730506
stoichiometry: 2.0
species: metaid_0000044
type: SpeciesReference

metaid_0000049
is version of: CHEBI:16796
is version of: C01598
constant: false
has only substance units: false
type: Species
initial concentration: 300.0
boundary condition: false
name: Melatonin
in compartment: metaid_0000029
initial amount: NaN

730145
stoichiometry: 2.0
species: metaid_0000037
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metaid_0000032
boundary condition: false
initial concentration: 300.0
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is version of: PIRSF000293
is version of: IPR000823
has only substance units: false
initial amount: NaN
name: Ferric peroxidase
in compartment: metaid_0000028

730795
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species: metaid_0000039
type: SpeciesReference

metaid_0000022
constant: true
value: 10.0
type: Parameter

730482
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species: metaid_0000049
type: SpeciesReference

metaid_0000062
kinetic law: 730494
product: 730482
product: 730470
reactant: 730458
reactant: 730446
fast: false
reversible: false
name: NADP free radical formation
type: Reaction

730543
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

730338
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species: metaid_0000044
type: SpeciesReference

metaid_0000028
is version of: GO:0032009
constant: true
size: 1.0
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name: phagosome
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730735
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species: metaid_0000047
type: SpeciesReference

730350
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

metaid_0000053
kinetic law: 729957
product: 729943
reactant: 729930
reactant: 729917
fast: false
reversible: false
name: Myeloperoxidase reaction
type: Reaction

730410
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

metaid_0000043
initial amount: NaN
initial concentration: 0.0
constant: false
boundary condition: false
is: CHEBI:16240
name: H2O2
in compartment: metaid_0000029
is: C00027
has only substance units: false
type: Species

metaid_0000072
kinetic law: 730843
product: 730831
product: 730819
reactant: 730807
reactant: 730795
fast: false
reversible: false
name: NADPH oxidase activity
type: Reaction

730061
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

metaid_0000018
constant: true
value: 12.5
type: Parameter

metaid_0000033
initial concentration: 0.0
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has only substance units: false
is version of: IPR000823
boundary condition: false
initial amount: NaN
is version of: PIRSF000293
type: Species
name: compound I
constant: false

729917
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

730519
stoichiometry: 1.0
species: metaid_0000051
type: SpeciesReference

metaid_0000038
has only substance units: false
type: Species
is: C00282
in compartment: metaid_0000028
initial amount: NaN
is: CHEBI:18276
boundary condition: false
name: Hydrogen
initial concentration: 0.0
constant: false

730663
stoichiometry: 1.0
species: metaid_0000043
type: SpeciesReference

729943
stoichiometry: 1.0
species: metaid_0000033
type: SpeciesReference

730819
stoichiometry: 2.0
species: metaid_0000037
type: SpeciesReference

729995
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

metaid_0000023
constant: true
value: 10.0
type: Parameter

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

W3 CDTF: Thu Jul 05 15:42:21 BST 2012