BIOMD0000000143
type: SBMLModel
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
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

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

730663
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

metaid_0000043
type: Species
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

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

730651
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

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

metaid_0000028
type: Compartment
is version of: GO:0032009
constant: true
size: 1.0
spatial dimensions: 3.0
name: phagosome

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

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

metaid_0000027
type: Parameter
constant: true
value: 1.5

metaid_0000013
type: Parameter
constant: true
value: 50.0

metaid_0000041
type: Species
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

metaid_0000019
type: Parameter
constant: true
value: 0.045

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

metaid_0000018
type: Parameter
constant: true
value: 12.5

metaid_0000007
type: Parameter
constant: true
value: 10.0

metaid_0000035
type: Species
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
constant: false
is version of: PIRSF000293

metaid_0000022
type: Parameter
constant: true
value: 10.0

metaid_0000011
type: Parameter
constant: true
value: 0.1

metaid_0000073
type: SBMLUnitsDef
unit: 729904
name: micro mole

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

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

730362
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

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

730350
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

730338
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

metaid_0000044
type: Species
initial amount: NaN
initial concentration: 0.0
in compartment: metaid_0000029
is: CHEBI:18009
name: NADP
has only substance units: false
is: C00006
boundary condition: false
constant: false

730326
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

metaid_0000021
type: Parameter
constant: true
value: 30.0

metaid_0000010
type: Parameter
constant: true
value: 10.0

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

730591
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

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

730567
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

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

730157
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000038

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

730182
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

730145
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000037

730169
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

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

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

730121
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

metaid_0000050
type: Species
is version of: IPR000823
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000028
name: compound III

730109
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

metaid_0000032
type: Species
boundary condition: false
initial concentration: 300.0
constant: false
is version of: PIRSF000293
is version of: IPR000823
has only substance units: false
initial amount: NaN
name: Ferric peroxidase
in compartment: metaid_0000028

730096
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

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

metaid_0000026
type: Parameter
constant: true
value: 550.0

metaid_0000025
type: Parameter
constant: true
value: 288.0

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

730519
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000051

metaid_0000051
type: Species
in compartment: metaid_0000029
is: C00006
has only substance units: false
boundary condition: false
initial concentration: 0.0
name: NADP2
initial amount: NaN
is: CHEBI:18009
constant: false

730506
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000044

metaid_0000017
type: Parameter
constant: true
value: 25.0

metaid_0000006
type: Parameter
constant: true
value: 58.0

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

730072
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

730061
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

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

730048
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000035

730035
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

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

metaid_0000016
type: Parameter
constant: true
value: 60.0

metaid_0000005
type: Parameter
constant: true
value: 50.0

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

730009
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000035

729995
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

729983
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

metaid_0000033
type: Species
initial concentration: 0.0
in compartment: metaid_0000028
has only substance units: false
is version of: IPR000823
boundary condition: false
initial amount: NaN
is version of: PIRSF000293
name: compound I
constant: false

729969
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000009
type: Parameter
constant: true
value: 20.0

metaid_0000020
type: Parameter
constant: true
value: 30.0

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

730831
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

730819
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000037

730807
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

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

730795
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000039

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

730543
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

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

metaid_0000047
type: Species
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

metaid_0000015
type: Parameter
constant: true
value: 10.0

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

730699
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000049

730687
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000014
type: Parameter
constant: true
value: 500.0

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

730771
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

730759
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

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

730735
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

730723
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

metaid_0000024
type: Parameter
constant: true
value: 2.0

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

730482
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000049

730470
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

730458
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

730446
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

metaid_0000023
type: Parameter
constant: true
value: 10.0

metaid_0000061
type: Reaction
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
fast: false

730410
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

730422
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

730386
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000045

730398
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000046

metaid_0000004
type: Parameter
constant: true
value: 60.0

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

730627
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

730615
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

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

729943
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

729930
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

729917
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

metaid_0000008
type: Parameter
constant: true
value: 0.004

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

730278
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

730290
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

730302
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

730266
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

metaid_0000058
type: Reaction
kinetic law: 730254
product: 730242
product: 730230
reactant: 730218
reactant: 730206
fast: false
reversible: false
name: compound III-superoxide reaction

730242
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

730230
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

730218
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

730206
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

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

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

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