BIOMD0000000012
type: SBMLModel
units def: metaid_0000029
is: MODEL6615351360
volume units: metaid_0000029
modified:
  W3 CDTF: Tue May 15 16:48:26 BST 2012
species: PX
rule: metaid_0240045
parameter: metaid_0000028
rule: metaid_1000237
is version of: GO:0040029
units def: metaid_0000030
rule: metaid_0240035
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
reaction: 905862
rule: metaid_0400235
reaction: 906042
notes: Repressilator: Elowitz MB, Leibler S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338. Repressilator: A synthetic oscillatory network of transcriptional regulators Citation Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature.403 : 335 - 338. http:// www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/full/ 403335a0_fs.html Description This file describes the deterministic version of the repressilator system. The authors of this model (see reference) use three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network that they called the repressilator. The model system was induced in Escherichia coli. In this system, LacI (variable X is the mRNA, variable PX is the protein) inhibits the tetracycline-resistance transposon tetR (Y, PY describe mRNA and protein). Protein tetR inhibits the gene Cl from phage Lambda (Z, PZ: mRNA, protein),and protein Cl inhibits lacI expression. With appropriate parameter values this system oscillates. The model is based upon the equations in Box 1 of the paper; however, these equations as printed are dimensionless, and the correct dimensions have been returned to the equations, and the parameters set to reproduce Figure 1C (left). The original Model was Generated by B.E. Shapiro using Cellerator Version 1.0 update 2.1127 using Mathematica 4.2 for Mac OS X (June 4, 2002), November 27, 2002 12:15:32, using (PowerMac,PowerPC, Mac OS X,MacOSX,Darwin) Nicolas Le Novere: Corrected version generated by SBMLeditor on Sun Aug 20 00:44:05 BST 2006. Removal of EmptySet species. Ran fine on COPASI 4.0 build 18 Bruce Shapiro: Revised with SBML editor 23 October 2006 20:39 PST. Define default units and correct reactions. The original cellerator reactions while being mathematically correct did not accurately reflect the intent of the authors.' The original notes were mostly removed because th…
species: 905781
parameter: metaid_0900235
parameter: metaid_0000024
reaction: 906002
units def: metaid_1000000
rule: metaid_0500035
reaction: 905982
substance units: metaid_1000000
parameter: metaid_0000032
species: PY
reaction: 905923
species: 905769
parameter: metaid_0500235
parameter: metaid_0000027
parameter: metaid_0000026
parameter: metaid_0800235
reaction: 905842
parameter: metaid_0000128
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nick
    family: Juty
rule: metaid_0230035
reaction: 905943
area units: area
curated: true
species: 905802
creator:
  ORG:
    orgname: Jet Propulsion Laboratory
  n:
    given: Bruce
    family: Shapiro
reaction: 905962
parameter: metaid_0000023
occurs in: http://identifiers.org/taxonomy/562
created:
  W3 CDTF: Tue Jan 20 14:03:56 GMT 2009
reaction: 905903
time units: metaid_0000030
parameter: metaid_0000022
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nicolas
    family: Le Novère
rule: metaid_0010335
parameter: metaid_0000133
parameter: metaid_0000132
is described by: http://identifiers.org/pubmed/10659856
name: Elowitz2000_Repressilator
reaction: 905823
compartment: 000002
parameter: metaid_0000025
length unit: length
reaction: 905882
rule: metaid_0100236
species: PZ
parameter: metaid_0000234
rule: metaid_0020435
reaction: 906022
parameter: metaid_0000233

metaid_0000029
type: SBMLUnitsDef
unit: 595464
name: cubic microns

595464
type: SBMLUnit
exponent: 1.0
scale: -15
multipler: 1.0
kind: LITRE

PX
type: Species
is: SBO:0000252
initial amount: 0.0
boundary condition: false
in compartment: 000002
initial concentration: NaN
constant: false
is: P03023
has only substance units: true
name: LacI protein
notes: lacI inhibitor

000002
type: Compartment
is: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

metaid_0000028
type: Parameter
is: SBO:0000332
constant: true
value: 2.0
name: mRNA half life

metaid_0000030
type: SBMLUnitsDef
unit: 595488
name: minute

595488
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

905862
type: Reaction
kinetic law: 595562
reactant: 595550
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: degradation of CI transcripts

595550
type: SpeciesReference
stoichiometry: 1.0
species: 905802

905802
type: Species
constant: false
initial concentration: NaN
name: cI mRNA
has only substance units: true
initial amount: 0.0
is: SBO:0000250
is version of: CHEBI:33699
is version of: C00046
in compartment: 000002
boundary condition: false
encodes: P03034

906042
type: Reaction
kinetic law: 595853
modifier: 595841
product: 595829
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: transcription of CI

PY
type: Species
is: P04483
constant: false
name: TetR protein
boundary condition: false
in compartment: 000002
initial concentration: NaN
has only substance units: true
notes: Tet repressor protein
is: SBO:0000252
initial amount: 0.0

595829
type: SpeciesReference
stoichiometry: 1.0
species: 905802

905781
type: Species
encodes: P04483
initial amount: 20.0
name: TetR mRNA
constant: false
is version of: CHEBI:33699
is version of: C00046
boundary condition: false
has only substance units: true
initial concentration: NaN
is: SBO:0000250
in compartment: 000002

metaid_0900235
type: Parameter
notes: Transcription rate from free promotor minus a0_tr
is: SBO:0000186
constant: false
value: NaN
name: a_tr

metaid_0000024
type: Parameter
notes: Protein copies per promoter and cell
is: SBO:0000186
constant: false
value: 216.404
name: alpha

906002
type: Reaction
kinetic law: 595781
modifier: 595769
product: 595757
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: transcription of LacI

PZ
type: Species
notes: lambda repressor
initial amount: 0.0
constant: false
name: cI protein
initial concentration: NaN
is: P03034
in compartment: 000002
is: SBO:0000252
boundary condition: false
has only substance units: true

595757
type: SpeciesReference
stoichiometry: 1.0
species: 905769

905769
type: Species
is version of: C00046
initial amount: 0.0
boundary condition: false
in compartment: 000002
has only substance units: true
name: LacI mRNA
encodes: P03023
is version of: CHEBI:33699
is: SBO:0000250
constant: false
initial concentration: NaN

metaid_1000000
type: SBMLUnitsDef
unit: 595476
name: item

595476
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM

905982
type: Reaction
kinetic law: 595745
reactant: 595733
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: degradation of CI

595733
type: SpeciesReference
stoichiometry: 1.0
species: PZ

metaid_0000032
type: Parameter
is: SBO:0000348
constant: false
value: NaN
name: average mRNA life time

905923
type: Reaction
kinetic law: 595673
modifier: 595660
product: 595647
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: translation of CI

595647
type: SpeciesReference
stoichiometry: 1.0
species: PZ

metaid_0500235
type: Parameter
notes: Transcrition from fully repressed promotor in transcripts per second and promotor
is: SBO:0000485
constant: true
value: 5.0E-4
name: tps_repr

metaid_0000027
type: Parameter
notes: Number of repressor molecules per cell giving half maximal repression, in monomers per cell
is: SBO:0000288
constant: true
value: 40.0
name: KM

metaid_0000026
type: Parameter
notes: Hill coefficient
is: SBO:0000190
constant: true
value: 2.0
name: n

metaid_0800235
type: Parameter
notes: Transcrition from free promotor in transcripts per second and promotor
is: SBO:0000186
constant: true
value: 0.5
name: tps_active

905842
type: Reaction
kinetic law: 595538
reactant: 595525
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: degradation of TetR transcripts

595525
type: SpeciesReference
stoichiometry: 1.0
species: 905781

metaid_0000128
type: Parameter
is: SBO:0000332
constant: true
value: 10.0
name: protein half life

905943
type: Reaction
kinetic law: 595697
reactant: 595685
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: degradation of LacI

595685
type: SpeciesReference
stoichiometry: 1.0
species: PX

905962
type: Reaction
kinetic law: 595721
reactant: 595709
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: degradation of TetR

595709
type: SpeciesReference
stoichiometry: 1.0
species: PY

metaid_0000023
type: Parameter
notes: Leakiness in protein copies per promoter and cell
is: SBO:0000485
constant: false
value: 0.2164
name: alpha0

905903
type: Reaction
kinetic law: 595635
modifier: 595623
product: 595611
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: translation of TetR

595611
type: SpeciesReference
stoichiometry: 1.0
species: PY

metaid_0000022
type: Parameter
notes: ratio of protein to mRNA decay rates
constant: false
value: 0.2
name: beta

metaid_0000133
type: Parameter
notes: Protein decay rate costant
is: SBO:0000356
constant: false
value: NaN
name: kd_prot

metaid_0000132
type: Parameter
notes: mRNA decay rate constant
is: SBO:0000356
constant: false
value: NaN
name: kd_mRNA

905823
type: Reaction
kinetic law: 595512
reactant: 595500
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: degradation of LacI transcripts

595500
type: SpeciesReference
stoichiometry: 1.0
species: 905769

metaid_0000025
type: Parameter
notes: Average number of proteins per transcript
constant: true
value: 20.0
name: translation efficiency

905882
type: Reaction
kinetic law: 595598
modifier: 595586
product: 595574
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: translation of LacI

595574
type: SpeciesReference
stoichiometry: 1.0
species: PX

metaid_0000234
type: Parameter
notes: Transcription rate from fully repressed promotor
is: SBO:0000485
constant: false
value: NaN
name: a0_tr

906022
type: Reaction
kinetic law: 595817
modifier: 595805
product: 595793
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: transcription of TetR

595793
type: SpeciesReference
stoichiometry: 1.0
species: 905781

metaid_0000233
type: Parameter
notes: Translation rate constant
is: SBO:0000016
constant: false
value: NaN
name: k_tl