metaid 7
is: C05957
type: Species
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

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

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

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

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

340630
substance units: dimensionless
type: Species
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

343076
persistant: true
initial value: true
type: Trigger

340618
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
type: Species

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

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

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

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

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

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

341647
stoichiometry: 1.0
species: 340594
type: SpeciesReference

342810
persistant: true
initial value: true
type: Trigger

341988
stoichiometry: 1.0
species: metaid 2
type: SpeciesReference

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

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

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

341708
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

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

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

342461
stoichiometry: 1.0
species: metaid 7
type: SpeciesReference

342968
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
type: Event

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

340606
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
type: Species

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

342678
stoichiometry: 1.0
species: 340606
type: SpeciesReference

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

342449
kinetic law: 342486
product: 342473
reactant: 342461
fast: false
reversible: false
type: Reaction

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

341234
constant: true
units: 340399
value: 0.0439
type: Parameter

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

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

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

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

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

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

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

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

342244
stoichiometry: 1.0
species: metaid 6
type: SpeciesReference

metaid 3
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
type: Species

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

342158
stoichiometry: 1.0
species: metaid 3
type: SpeciesReference

341805
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

341975
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

342329
stoichiometry: 1.0
species: metaid 4
type: SpeciesReference

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

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

342473
stoichiometry: 1.0
species: metaid 8
type: SpeciesReference

342118
stoichiometry: 1.0
species: metaid 3
type: SpeciesReference

342510
stoichiometry: 1.0
species: metaid 8
type: SpeciesReference

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

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

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

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

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

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

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

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

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

342980
persistant: true
initial value: true
type: Trigger

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

metaid 5
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
type: Species

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

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

342425
stoichiometry: 1.0
species: metaid 5
type: SpeciesReference

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

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

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

342798
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
type: Event

metaid 6
constant: false
has only substance units: true
boundary condition: false
is: LMFA03010002
initial amount: 0.0
in compartment: 340581
substance units: 340483
type: Species
initial concentration: NaN
is: C00639

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

340471
exponent: 1.0
scale: -6
multipler: 1.0
kind: GRAM
type: SBMLUnit

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

341660
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

BIOMD0000000436
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
type: SBMLModel
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
reaction: 341841
parameter: 341356
parameter: 340679
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

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

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

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

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

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

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

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

340594
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
type: Species

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

341865
stoichiometry: 1.0
species: 340606
type: SpeciesReference

342105
stoichiometry: 1.0
species: 340606
type: SpeciesReference

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

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

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

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

340835
is: SBO:0000009
constant: true
units: 340399
value: 1.0E-15
type: Parameter

342908
persistant: true
initial value: true
type: Trigger

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

342618
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

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

341914
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

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

343220
persistant: true
initial value: true
type: Trigger

342281
stoichiometry: 1.0
species: 340606
type: SpeciesReference

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

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

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

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

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

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

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

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

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

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

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

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

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

342389
stoichiometry: 1.0
species: metaid 5
type: SpeciesReference

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

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

341853
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

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

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

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

metaid 2
is: LMFA03060085
constant: false
boundary condition: false
has only substance units: true
substance units: 340483
initial concentration: NaN
initial amount: 0.0
in compartment: 340581
type: Species

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

342196
stoichiometry: 1.0
species: 340606
type: SpeciesReference

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

341926
stoichiometry: 1.0
species: 340606
type: SpeciesReference

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

342293
stoichiometry: 1.0
species: metaid 4
type: SpeciesReference

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

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

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

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

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

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

342714
persistant: true
initial value: true
type: Trigger

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

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

342377
stoichiometry: 1.0
species: metaid 4
type: SpeciesReference

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

341696
stoichiometry: 1.0
species: 340630
type: SpeciesReference

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

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

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

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

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

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

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

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

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

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

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

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

341756
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

342341
stoichiometry: 1.0
species: metaid 7
type: SpeciesReference

342546
stoichiometry: 1.0
species: 340594
type: SpeciesReference

342066
stoichiometry: 1.0
species: metaid 2
type: SpeciesReference

342606
stoichiometry: 1.0
species: 340642
type: SpeciesReference

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

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

342702
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
type: Event

342027
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

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

341513
constant: true
units: 340483
value: 179.96
type: Parameter

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

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

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

342208
stoichiometry: 1.0
species: metaid 6
type: SpeciesReference

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

342666
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

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

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

342558
stoichiometry: 1.0
species: metaid 1
type: SpeciesReference

341744
stoichiometry: 1.0
species: 340642
type: SpeciesReference

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

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

341793
stoichiometry: 1.0
species: 340642
type: SpeciesReference

343148
persistant: true
initial value: true
type: Trigger

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

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

given: Shakti
family: Gupta

orgname: University of California, San Diego

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

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

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