BIOMD0000000436
type: SBMLModel
parameter: 340909
parameter: 340727
event: 343136
parameter: 341030
event: 343208
parameter: 341440
reaction: 342014
time units: 340375
parameter: 340667
parameter: 341150
parameter: 341283
is version of: GO:0006690
parameter: 341054
event: 343064
parameter: 340982
parameter: 341464
rule: 341598
is version of: PW:0000565
parameter: 341513
parameter: 340835
parameter: 341234
units def: 340459
reaction: 341635
length unit: 844677
parameter: 341042
parameter: 341320
parameter: 340873
name: Gupta2009 - Eicosanoid Metabolism
reaction: 342449
area units: 844749
species: 340594
reaction: 342232
units def: 340483
parameter: 341066
parameter: 340994
units def: 340507
reaction: 342053
parameter: 341344
reaction: 341684
rule: 341586
compartment: 340581
parameter: 341477
reaction: 342269
parameter: 341018
species: metaid 5
parameter: 341561
parameter: 341332
reaction: 341732
parameter: 340691
parameter: 340885
parameter: 341102
parameter: 341368
parameter: 341006
parameter: 341416
reaction: 342145
reaction: 342654
reaction: 342365
parameter: 340679
reaction: 341841
parameter: 341356
parameter: 340922
parameter: 341489
parameter: 340823
parameter: 341573
parameter: 341404
parameter: 340763
reaction: 342317
reaction: 342184
species: metaid 3
notes: Gupta2009 - Eicosanoid Metabolism Integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. This model is described in the article: An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S. Biophys. J. 2009 Jun; 96(11):4542-51. Abstract: There is increasing evidence for a major and critical involvement of lipids in signal transduction and cellular trafficking, and this has motivated large-scale studies on lipid pathways. The Lipid Metabolites and Pathways Strategy consortium is actively investigating lipid metabolism in mammalian cells and has made available time-course data on various lipids in response to treatment with KDO(2)-lipid A (a lipopolysaccharide analog) of macrophage RAW 264.7 cells. The lipids known as eicosanoids play an important role in inflammation. We have reconstructed an integrated network of eicosanoid metabolism and signaling based on the KEGG pathway database and the literature and have developed a kinetic model. A matrix-based approach was used to estimate the rate constants from experimental data and these were further refined using generalized constrained nonlinear optimization. The resulting model fits the experimental data well for all species, and simulated enzyme activities were similar to their literature values. The quantitative model for eicosanoid metabolism that we have developed can be used to design experimental studies utilizing genetic and pharmacological perturbations to probe fluxes in lipid pathways. This model is hosted on BioModels Database and identified by: BIOMD0000000436 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . 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 …
parameter: 341114
species: metaid 1
parameter: 341247
parameter: 340811
volume units: 103022
occurs in: http://identifiers.org/taxonomy/40674
rule: 341622
event: 342702
species: metaid 7

340909
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.116

340411
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 2.778E-4
kind: SECOND

340727
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 1.0E-15

343136
type: Event
event assignment: 343196
event assignment: 343184
event assignment: 343172
event assignment: 343160
trigger: 343148
use values from trigger time: true

341404
type: Parameter
constant: false
units: 340507
value: -158.43

340531
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 2.778E-4
kind: SECOND

340519
type: SBMLUnit
exponent: 1.0
scale: -12
multipler: 1.0
kind: MOLE

341392
type: Parameter
constant: false
units: 340483
value: 315.3137

340495
type: SBMLUnit
exponent: 1.0
scale: -12
multipler: 1.0
kind: MOLE

341198
type: Parameter
constant: false
units: 340399
value: 1.0

341186
type: Parameter
constant: false
units: dimensionless
value: 1.0

343148
type: Trigger
persistant: true
initial value: true

341030
type: Parameter
constant: true
units: 340375
value: 12.0

340387
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND

343208
type: Event
event assignment: 343268
event assignment: 343256
event assignment: 343244
event assignment: 343232
trigger: 343220
use values from trigger time: true

343220
type: Trigger
persistant: true
initial value: true

341440
type: Parameter
constant: true
units: 340507
value: 24.31

342014
type: Reaction
kinetic law: 342040
reactant: 342027
fast: false
reversible: false

342027
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

metaid 1
type: Species
in compartment: 340581
name: Arachidonic acid
initial amount: 25.0
substance units: 340483
initial concentration: NaN
has only substance units: true
boundary condition: false
constant: false
is: C00219
is: LMFA01030001

340581
type: Compartment
is version of: GO:0005623
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

340667
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 1.0E-15

341150
type: Parameter
constant: true
units: dimensionless
value: 1.3335

341283
type: Parameter
constant: true
units: 340399
value: 0.0846

341054
type: Parameter
constant: true
units: dimensionless
value: 0.0

343064
type: Event
event assignment: 343124
event assignment: 343112
event assignment: 343100
event assignment: 343088
trigger: 343076
use values from trigger time: true

343076
type: Trigger
persistant: true
initial value: true

340982
type: Parameter
constant: true
units: 340375
value: 1.0

341464
type: Parameter
constant: true
units: 340507
value: 5.48

341513
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units: 340483
value: 179.96

340835
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units: 340399
value: 1.0E-15

341234
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units: 340399
value: 0.0439

340471
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scale: -6
multipler: 1.0
kind: GRAM

341635
type: Reaction
kinetic law: 341672
product: 341660
reactant: 341647
fast: false
reversible: false

341660
type: SpeciesReference
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species: metaid 1

341647
type: SpeciesReference
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species: 340594

340594
type: Species
constant: true
substance units: 340483
boundary condition: true
initial concentration: NaN
in compartment: 340581
is version of: CHEBI:35366
has only substance units: true
initial amount: 1.0
notes: Fatty acyls

341042
type: Parameter
constant: false
units: 340375
value: 0.0

341320
type: Parameter
constant: true
units: dimensionless
value: 1.0282

340873
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.029

342449
type: Reaction
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product: 342473
reactant: 342461
fast: false
reversible: false

342473
type: SpeciesReference
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species: metaid 8

metaid 8
type: Species
boundary condition: false
in compartment: 340581
initial concentration: NaN
initial amount: 0.0
is: LMFA03010021
is: C14717
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substance units: 340483
has only substance units: true

342461
type: SpeciesReference
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species: metaid 7

metaid 7
type: Species
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initial amount: 0.0
is: LMFA03010019
constant: false
has only substance units: true
substance units: 340483
boundary condition: false
in compartment: 340581
initial concentration: NaN

342232
type: Reaction
kinetic law: 342257
reactant: 342244
fast: false
reversible: false

342244
type: SpeciesReference
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species: metaid 6

metaid 6
type: Species
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has only substance units: true
boundary condition: false
is: LMFA03010002
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substance units: 340483
initial concentration: NaN
is: C00639

341066
type: Parameter
constant: false
units: dimensionless
value: 0.0

340994
type: Parameter
constant: true
units: 340375
value: 2.0

342053
type: Reaction
kinetic law: 342079
reactant: 342066
fast: false
reversible: false

342066
type: SpeciesReference
stoichiometry: 1.0
species: metaid 2

metaid 2
type: Species
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constant: false
boundary condition: false
has only substance units: true
substance units: 340483
initial concentration: NaN
initial amount: 0.0
in compartment: 340581

341344
type: Parameter
constant: true
units: dimensionless
value: 0.543

341684
type: Reaction
kinetic law: 341720
product: 341708
reactant: 341696
fast: false
reversible: false

341708
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

341696
type: SpeciesReference
stoichiometry: 1.0
species: 340630

340630
type: Species
substance units: dimensionless
boundary condition: false
constant: false
initial amount: 0.0
notes: Arachidonic acid-containing glycerophospholipids
has only substance units: false
in compartment: 340581
initial concentration: NaN
is version of: CHEBI:49172

341477
type: Parameter
constant: true
units: 340507
value: 27.08

342269
type: Reaction
kinetic law: 342305
product: 342293
reactant: 342281
fast: false
reversible: false

342293
type: SpeciesReference
stoichiometry: 1.0
species: metaid 4

metaid 4
type: Species
is: LMFA03010004
is: C00696
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: 340581

342281
type: SpeciesReference
stoichiometry: 1.0
species: 340606

340606
type: Species
is version of: CHEBI:15554
constant: false
boundary condition: false
has only substance units: true
substance units: 340483
initial concentration: NaN
initial amount: 0.0
in compartment: 340581

341018
type: Parameter
constant: true
units: 340375
value: 8.0

metaid 5
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is: LMFA03010051
constant: false
boundary condition: false
has only substance units: true
substance units: 340483
initial concentration: NaN
initial amount: 0.0
in compartment: 340581

341561
type: Parameter
constant: true
units: 340483
value: 41.93

341332
type: Parameter
constant: true
units: dimensionless
value: 1.2987

341732
type: Reaction
kinetic law: 341768
product: 341756
reactant: 341744
fast: false
reversible: false

341756
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

341744
type: SpeciesReference
stoichiometry: 1.0
species: 340642

340642
type: Species
substance units: 340483
in compartment: 340581
is version of: CHEBI:49183
initial concentration: NaN
notes: Glycerophosphocholines
has only substance units: true
initial amount: 1.0
constant: false
boundary condition: false

340691
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 1.0E-15

340885
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.014

341102
type: Parameter
constant: true
units: 340399
value: 2.0

341368
type: Parameter
constant: true
units: dimensionless
value: 0.5927

341006
type: Parameter
constant: true
units: 340375
value: 4.0

341416
type: Parameter
constant: true
units: 340507
value: -158.43

342145
type: Reaction
kinetic law: 342171
reactant: 342158
fast: false
reversible: false

342158
type: SpeciesReference
stoichiometry: 1.0
species: metaid 3

metaid 3
type: Species
is: LMFA03010003
constant: false
boundary condition: false
has only substance units: true
substance units: 340483
initial concentration: NaN
initial amount: 0.0
in compartment: 340581

342654
type: Reaction
kinetic law: 342690
product: 342678
reactant: 342666
fast: false
reversible: false

342678
type: SpeciesReference
stoichiometry: 1.0
species: 340606

342666
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

342365
type: Reaction
kinetic law: 342401
product: 342389
reactant: 342377
fast: false
reversible: false

342389
type: SpeciesReference
stoichiometry: 1.0
species: metaid 5

342377
type: SpeciesReference
stoichiometry: 1.0
species: metaid 4

340679
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 1.0E-15

341841
type: Reaction
kinetic law: 341889
modifier: 341877
product: 341865
reactant: 341853
fast: false
reversible: false

340618
type: Species
is version of: CHEBI:16412
constant: false
boundary condition: false
has only substance units: false
substance units: dimensionless
initial concentration: NaN
initial amount: 0.5
in compartment: 340581

341865
type: SpeciesReference
stoichiometry: 1.0
species: 340606

341853
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

341356
type: Parameter
constant: true
units: dimensionless
value: 0.7549

340922
type: Parameter
is: SBO:0000002
constant: true
units: 340459
value: 1.0

341489
type: Parameter
constant: true
units: 340507
value: -4.874

340823
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.061

341573
type: Parameter
constant: true
units: 340483
value: 425.43

340763
type: Parameter
is: SBO:0000009
constant: true
units: 340543
value: 0.024

340568
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND

340555
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: GRAM

342317
type: Reaction
kinetic law: 342353
product: 342341
reactant: 342329
fast: false
reversible: false

342341
type: SpeciesReference
stoichiometry: 1.0
species: metaid 7

342329
type: SpeciesReference
stoichiometry: 1.0
species: metaid 4

342184
type: Reaction
kinetic law: 342220
product: 342208
reactant: 342196
fast: false
reversible: false

342208
type: SpeciesReference
stoichiometry: 1.0
species: metaid 6

342196
type: SpeciesReference
stoichiometry: 1.0
species: 340606

341114
type: Parameter
constant: true
units: 340399
value: -0.6667

341247
type: Parameter
constant: true
units: 340399
value: -0.0913

340811
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 1.0E-15

342702
type: Event
event assignment: 342786
event assignment: 342774
event assignment: 342762
event assignment: 342750
event assignment: 342738
event assignment: 342726
trigger: 342714
use values from trigger time: true

341078
type: Parameter
constant: false
units: 340399
value: 0.0

341090
type: Parameter
constant: false
units: dimensionless
value: 0.0

342714
type: Trigger
persistant: true
initial value: true

341428
type: Parameter
constant: true
units: 340507
value: 112.28

ORG:
  orgname: University of California, San Diego
n:
  given: Daren L.
  family: Stephens

340787
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.098

342896
type: Event
event assignment: 342956
event assignment: 342944
event assignment: 342932
event assignment: 342920
trigger: 342908
use values from trigger time: true

342908
type: Trigger
persistant: true
initial value: true

340934
type: Parameter
is: SBO:0000002
constant: false
units: 340423
value: 1.0

340447
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: GRAM

340435
type: SBMLUnit
exponent: 1.0
scale: -12
multipler: 1.0
kind: MOLE

340703
type: Parameter
is: SBO:0000009
constant: true
units: 340543
value: 1.0E-15

ORG:
  orgname: University of California, San Diego
n:
  given: Shankar
  family: Subramaniam

340775
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.111

340958
type: Parameter
constant: true
units: 340375
value: 0.0

341162
type: Parameter
constant: true
units: dimensionless
value: 0.0

341295
type: Parameter
constant: true
units: dimensionless
value: 1.0

341210
type: Parameter
constant: true
units: 340399
value: 0.3014

340799
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.204

340946
type: Parameter
constant: true
units: 340483
value: 1.0

341525
type: Parameter
constant: true
units: 340483
value: 267.93

ORG:
  orgname: San Diego Supercomputer Center and Department of Bioengineering, UCSD
n:
  given: Byrnes
  family: Robert

342092
type: Reaction
kinetic law: 342131
product: 342118
reactant: 342105
fast: false
reversible: false

342118
type: SpeciesReference
stoichiometry: 1.0
species: metaid 3

342105
type: SpeciesReference
stoichiometry: 1.0
species: 340606

341174
type: Parameter
constant: false
units: dimensionless
value: 1.0

341549
type: Parameter
constant: true
units: 340483
value: 214.77

W3 CDTF: Fri Jan 22 22:59:01 GMT 2010

340970
type: Parameter
constant: true
units: 340375
value: 0.5

342534
type: Reaction
kinetic law: 342582
modifier: 342570
product: 342558
reactant: 342546
fast: false
reversible: false

342558
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

342546
type: SpeciesReference
stoichiometry: 1.0
species: 340594

341962
type: Reaction
kinetic law: 342001
product: 341988
reactant: 341975
fast: false
reversible: false

341988
type: SpeciesReference
stoichiometry: 1.0
species: metaid 2

341975
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

341222
type: Parameter
constant: true
units: 340399
value: -0.1572

341126
type: Parameter
constant: true
units: 340399
value: 0.0

341780
type: Reaction
kinetic law: 341829
modifier: 341817
product: 341805
reactant: 341793
fast: false
reversible: false

341805
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

341793
type: SpeciesReference
stoichiometry: 1.0
species: 340642

341259
type: Parameter
constant: true
units: 340399
value: 0.0976

342798
type: Event
event assignment: 342884
event assignment: 342872
event assignment: 342859
event assignment: 342847
event assignment: 342834
event assignment: 342822
trigger: 342810
use values from trigger time: true

342810
type: Trigger
persistant: true
initial value: true

341537
type: Parameter
constant: true
units: 340483
value: 396.41

340860
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.054

341307
type: Parameter
constant: true
units: dimensionless
value: 1.2292

342968
type: Event
event assignment: 343052
event assignment: 343040
event assignment: 343028
event assignment: 343016
event assignment: 343004
event assignment: 342992
trigger: 342980
use values from trigger time: true

342980
type: Trigger
persistant: true
initial value: true

342594
type: Reaction
kinetic law: 342642
modifier: 342630
product: 342618
reactant: 342606
fast: false
reversible: false

342618
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

342606
type: SpeciesReference
stoichiometry: 1.0
species: 340642

340897
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.034

341901
type: Reaction
kinetic law: 341950
modifier: 341938
product: 341926
reactant: 341914
fast: false
reversible: false

341926
type: SpeciesReference
stoichiometry: 1.0
species: 340606

341914
type: SpeciesReference
stoichiometry: 1.0
species: metaid 1

341380
type: Parameter
constant: false
units: dimensionless
value: 1.0

340715
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.33

340848
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 3.116

340751
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.187

342498
type: Reaction
kinetic law: 342522
reactant: 342510
fast: false
reversible: false

342510
type: SpeciesReference
stoichiometry: 1.0
species: metaid 8

340655
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 355.637

341138
type: Parameter
constant: true
units: dimensionless
value: 0.0

341271
type: Parameter
constant: true
units: 340399
value: 0.0711

340739
type: Parameter
is: SBO:0000009
constant: true
units: 340399
value: 0.007

341452
type: Parameter
constant: true
units: 340507
value: -39.93

342413
type: Reaction
kinetic law: 342437
reactant: 342425
fast: false
reversible: false

342425
type: SpeciesReference
stoichiometry: 1.0
species: metaid 5

W3 CDTF: Tue Dec 11 19:15:40 GMT 2012

341501
type: Parameter
constant: true
units: 340483
value: 315.3137

ORG:
  orgname: University of California, San Diego
n:
  given: Mano Ram
  family: Maurya

ORG:
  orgname: University of California, San Diego
n:
  given: Shakti
  family: Gupta

ORG:
  orgname: University of California, San Diego
n:
  given: Edward A.
  family: Dennis