420947
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

905823
kinetic law: 420986
reactant: 420973
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: degradation of LacI transcripts
type: Reaction

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

906042
kinetic law: 421329
modifier: 421317
product: 421304
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: transcription of CI
type: Reaction

905943
kinetic law: 421172
reactant: 421160
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: degradation of LacI
type: Reaction

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

BIOMD0000000012
units def: metaid_0000029
is: MODEL6615351360
volume units: metaid_0000029
species: PX
rule: metaid_0240045
parameter: metaid_0000028
rule: metaid_1000237
is version of: GO:0040029
units def: metaid_0000030
rule: metaid_0240035
type: SBMLModel
creator:
  ORG:
    orgname: Jet Propulsion Laboratory
  n:
    given: Bruce
    family: Shapiro
reaction: 905862
rule: metaid_0400235
reaction: 906042
modified:
  W3 CDTF: Wed Jul 10 11:59:30 BST 2013
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
created:
  W3 CDTF: Tue Jan 20 14:03:56 GMT 2009
species: PY
reaction: 905923
species: 905769
notes: Elowitz2000 - Repressilator This model 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 the appropriate parameter values this system oscillates. This model is described in the article: A synthetic oscillatory network of transcriptional regulators. Elowitz MB, Leibler S. Nature. 2000 Jan; 403(6767):335-338 Abstract: Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an …
parameter: metaid_0500235
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nicolas
    family: Le Novère
parameter: metaid_0000027
parameter: metaid_0000026
parameter: metaid_0800235
reaction: 905842
parameter: metaid_0000128
rule: metaid_0230035
reaction: 905943
area units: area
curated: true
species: 905802
reaction: 905962
parameter: metaid_0000023
occurs in: http://identifiers.org/taxonomy/562
time units: metaid_0000030
parameter: metaid_0000022
reaction: 905903
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
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
length unit: length
reaction: 905882
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
rule: metaid_0100236
species: PZ
parameter: metaid_0000234
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nick
    family: Juty
rule: metaid_0020435
reaction: 906022
parameter: metaid_0000233

421232
stoichiometry: 1.0
species: 905769
type: SpeciesReference

421025
stoichiometry: 1.0
species: 905802
type: SpeciesReference

905923
kinetic law: 421148
modifier: 421136
product: 421124
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: translation of CI
type: Reaction

906022
kinetic law: 421292
modifier: 421280
product: 421268
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: transcription of TetR
type: Reaction

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

420960
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

905769
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: SBO:0000250
constant: false
is version of: CHEBI:33699
initial concentration: NaN
type: Species

421208
stoichiometry: 1.0
species: PZ
type: SpeciesReference

421051
stoichiometry: 1.0
species: PX
type: SpeciesReference

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

421304
stoichiometry: 1.0
species: 905802
type: SpeciesReference

906002
kinetic law: 421256
modifier: 421244
product: 421232
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: transcription of LacI
type: Reaction

420934
exponent: 1.0
scale: -15
multipler: 1.0
kind: LITRE
type: SBMLUnit

421184
stoichiometry: 1.0
species: PY
type: SpeciesReference

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

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

905903
kinetic law: 421112
modifier: 421100
product: 421088
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: translation of TetR
type: Reaction

metaid_1000000
unit: 420947
name: item
type: SBMLUnitsDef

metaid_0000029
unit: 420934
name: cubic microns
type: SBMLUnitsDef

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

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

421268
stoichiometry: 1.0
species: 905781
type: SpeciesReference

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

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

420999
stoichiometry: 1.0
species: 905781
type: SpeciesReference

421088
stoichiometry: 1.0
species: PY
type: SpeciesReference

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

420973
stoichiometry: 1.0
species: 905769
type: SpeciesReference

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

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

metaid_0000027
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
type: Parameter

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

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

905962
kinetic law: 421196
reactant: 421184
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: degradation of TetR
type: Reaction

421124
stoichiometry: 1.0
species: PZ
type: SpeciesReference

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

905982
kinetic law: 421220
reactant: 421208
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: degradation of CI
type: Reaction

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

905882
kinetic law: 421076
modifier: 421064
product: 421051
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: translation of LacI
type: Reaction

metaid_0000030
unit: 420960
name: minute
type: SBMLUnitsDef

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

PY
is: P04483
constant: false
name: TetR protein
type: Species
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

905842
kinetic law: 421012
reactant: 420999
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: degradation of TetR transcripts
type: Reaction

905862
kinetic law: 421038
reactant: 421025
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: degradation of CI transcripts
type: Reaction

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

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

421160
stoichiometry: 1.0
species: PX
type: SpeciesReference