BIOMD0000000067
type: SBMLModel
species: metaid_0000030
occurs in: http://identifiers.org/taxonomy/83333
name: Fung2005_Metabolic_Oscillator
reaction: metaid_0000044
species: metaid_0000025
reaction: metaid_0000036
volume units: metaid_0000323
parameter: metaid_0000017
species: metaid_0000028
parameter: metaid_0000018
compartment: metaid_0000024
parameter: metaid_0000004
reaction: metaid_0000042
parameter: metaid_0000005
reaction: metaid_0000043
parameter: metaid_0000020
parameter: metaid_0000021
parameter: metaid_0000012
reaction: metaid_0000035
substance units: metaid_0000022
curated: true
parameter: metaid_0000008
species: metaid_0000031
length unit: length
created:
  W3 CDTF: Mon Aug 28 09:43:27 BST 2006
species: metaid_0000026
parameter: metaid_0000016
reaction: metaid_0000040
reaction: metaid_0000041
species: metaid_0000029
reaction: metaid_0000039
area units: area
is: MODEL6624231052
reaction: metaid_0000034
parameter: metaid_0000015
parameter: metaid_0000009
parameter: metaid_0000011
parameter: metaid_0000003
creator:
  ORG:
    orgname: California Institute of Technology
  n:
    given: Harish
    family: Dharuri
parameter: metaid_0000023
species: metaid_0000032
species: metaid_0000027
reaction: metaid_0000037
reaction: metaid_0000038
is described by: http://identifiers.org/pubmed/15875027
reaction: metaid_0000033
parameter: metaid_0000019
time units: metaid_0000023
reaction: metaid_0000045
notes: A Synthetic Gene-Metabolic Oscillator Reference: Fung et al; Nature (2005) 435:118-122 Name of kinetic law Reaction Glycolytic flux, V_gly: nil -> AcCoA; Flux to TCA cycle/ETOH, V_TCA: AcCoA -> TCA/EtOH; HOAc ex/import,reversible, V_out: HOAc -> HOAc_E V_Pta: AcCoA + Pi -> AcP + CoA reversible, V_Ack: AcP + ADP -> OAc + ATP V_Acs: OAC + ATP -> AcCoA +PPi Acetic acid-base equillibrium, reversible, V_Ace: OAC + H -> HOAc Expression of LacI, R_LacI: nil -> LacI Expression of Acs, R_Acs: nil -> Acs Expression of Pta, R_Pta: nil -> Pta LacI degradation, R_dLacI: LacI -> nil Acs degradation, R_dAcs: Acs -> nil Pta degradation, R_dPta: Pta -> nil For this model the differential equation for V_Ace was changed from: C*(AcP*H-K_eq*OAC) with C = 100 in the supplemental material to C*(OAc*H-K_eq*HOAc) with C = 100, as in Bulter et. al; PNAS(2004),101,2299-2304 , and a value for K_eq of 5*10^-4 after communication with the authors. translated to SBML by: Lukas Endler(luen at tbi.univie.ac.at), Christoph Flamm (xtof at tbi.univie.ac.at) Biomodels Curation The model reproduces 3a of the paper for glycolytic flux Vgly = 0.5. The authors have agreed that the values on Y-axis are marked wrong and hence there is a discrepancy between model simulation results and the figure. Also, note that the values of concentration and time are in dimensionless units. The model was successfully tested on MathSBML and Jarnac.
parameter: metaid_0000006
parameter: metaid_0000007
modified:
  W3 CDTF: Wed May 16 11:20:40 BST 2012
parameter: metaid_0000022
parameter: metaid_0000013
parameter: metaid_0000014
is version of: GO:0045990
parameter: metaid_0000010

metaid_0000030
type: Species
is: P27550
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000024
name: Acetyl-CoA synthase

metaid_0000024
type: Compartment
is: GO:0005622
constant: true
size: 1.0
spatial dimensions: 3.0
name: Intracellular

metaid_0000044
type: Reaction
kinetic law: 812104
reactant: 812091
is version of: GO:0030163
fast: false
reversible: false
name: Acs degradation

812091
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000025
type: Species
initial concentration: 0.0
is: C00024
is: CHEBI:15351
constant: false
has only substance units: false
in compartment: metaid_0000024
name: Acetyl-CoA
initial amount: NaN
boundary condition: false

metaid_0000036
type: Reaction
reactant: 811790
reversible: false
kinetic law: 811826
name: Phosphate acetyl transferase flux
is: http://identifiers.org/ec-code/2.3.1.8
fast: false
is: R00230
product: 811802
modifier: 811814

811790
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

811802
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000026
type: Species
constant: false
is: CHEBI:15350
boundary condition: false
initial concentration: 0.0
has only substance units: false
initial amount: NaN
is: C00227
in compartment: metaid_0000024
name: Acetyl phosphate

metaid_0000031
type: Species
is: P0A9M8
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000024
name: Phosphate acetyl transferase

metaid_0000017
type: Parameter
constant: true
value: 2.0

metaid_0000028
type: Species
has only substance units: false
initial concentration: 0.0
name: protonated acetate
is version of: C00033
boundary condition: false
in compartment: metaid_0000024
is version of: CHEBI:30089
constant: false
initial amount: NaN

metaid_0000018
type: Parameter
constant: true
value: 2.0

metaid_0000004
type: Parameter
constant: true
value: 10.0

metaid_0000042
type: Reaction
kinetic law: 812055
modifier: 812043
product: 812031
has part: GO:0006412
has part: GO:0006351
fast: false
reversible: false
name: Phosphate acetyl transferase synthase

metaid_0000029
type: Species
is part of: GO:0017053
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000024
name: lac repressor

812031
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

metaid_0000005
type: Parameter
constant: true
value: 80.0

metaid_0000043
type: Reaction
kinetic law: 812079
reactant: 812067
is version of: GO:0030163
fast: false
reversible: false
name: LacI degradation

812067
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000020
type: Parameter
constant: true
value: 10.0

metaid_0000021
type: Parameter
constant: true
value: 0.001

metaid_0000012
type: Parameter
constant: true
value: 1.0E-7

metaid_0000035
type: Reaction
kinetic law: 811778
product: 811766
reactant: 811754
is version of: GO:0015123
fast: false
reversible: true
name: Intercellular transport of Acetate

811766
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

metaid_0000032
type: Species
is version of: C00033
initial amount: NaN
constant: false
boundary condition: true
has only substance units: false
in compartment: metaid_0000024
is version of: CHEBI:30089
name: acetate export
initial concentration: 0.0

811754
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

metaid_0000008
type: Parameter
constant: true
value: 0.1

metaid_0000016
type: Parameter
constant: true
value: 0.1

metaid_0000040
type: Reaction
kinetic law: 811983
modifier: 811971
product: 811959
has part: GO:0006412
has part: GO:0006351
fast: false
reversible: false
name: LacI synthesis

811959
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000041
type: Reaction
kinetic law: 812019
modifier: 812007
product: 811995
has part: GO:0006412
has part: GO:0006351
fast: false
reversible: false
name: Acetyl-CoA synthase synthesis

811995
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000039
type: Reaction
kinetic law: 811947
product: 811935
reactant: 811923
fast: false
reversible: true
name: Acid-base equilibrium

811935
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

811923
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000027
type: Species
initial concentration: 0.0
has only substance units: false
name: Acetate
is: C00033
is: CHEBI:30089
constant: false
boundary condition: false
in compartment: metaid_0000024
initial amount: NaN

metaid_0000034
type: Reaction
kinetic law: 811742
reactant: 811730
has version: GO:0006099
fast: false
reversible: false
name: Flux to TCA cycle

811730
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

metaid_0000015
type: Parameter
constant: true
value: 0.0

metaid_0000009
type: Parameter
constant: true
value: 1.0

metaid_0000011
type: Parameter
constant: true
value: 100.0

metaid_0000003
type: Parameter
constant: true
value: 0.5

metaid_0000023
type: Parameter
constant: true
value: 0.06

metaid_0000037
type: Reaction
kinetic law: 811863
product: 811851
reactant: 811839
is version of: GO:0008776
is version of: http://identifiers.org/ec-code/2.7.2.1
fast: false
reversible: true
name: Acetate kinase

811851
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

811839
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000038
type: Reaction
reactant: 811875
is version of: http://identifiers.org/ec-code/6.2.1.1
kinetic law: 811911
modifier: 811899
is version of: GO:0019427
is: R00235
name: Acetyl-CoA synthase flux
reversible: false
fast: false
product: 811887

811875
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

811887
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

metaid_0000033
type: Reaction
kinetic law: 811718
product: 811706
has version: GO:0006096
fast: false
reversible: false
name: Glycolytic flux

811706
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

metaid_0000019
type: Parameter
constant: true
value: 10.0

metaid_0000045
type: Reaction
kinetic law: 812128
reactant: 812116
is version of: GO:0030163
fast: false
reversible: false
name: Pta degradation

812116
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

metaid_0000006
type: Parameter
constant: true
value: 0.06

metaid_0000007
type: Parameter
constant: true
value: 0.8

metaid_0000022
type: Parameter
constant: true
value: 2.0

metaid_0000013
type: Parameter
constant: true
value: 5.0E-4

metaid_0000014
type: Parameter
constant: true
value: 0.01

metaid_0000010
type: Parameter
constant: true
value: 1.0