BIOMD0000000301
type: SBMLModel
species: 267710
parameter: 267863
species: 267711
parameter: 267854
compartment: 267708
rule: 267793
parameter: 267866
parameter: 267857
parameter: 267869
name: Friedland2009_Ara_RTC3_counter
species: 267714
parameter: 267899
has version: GO:0006446
reaction: 267728
event: 267786
event: 267789
reaction: 267732
parameter: 267881
parameter: 267872
reaction: 267735
parameter: 267809
area units: area
substance units: metaid_0000010
event: 267777
event: 267783
parameter: 267884
reaction: 267750
reaction: 267741
parameter: 267860
reaction: 267753
reaction: 267744
species: 267726
time units: metaid_0000009
reaction: 267756
parameter: 267893
reaction: 267747
curated: true
parameter: 267824
rule: 267794
reaction: 267762
reaction: 267759
is described by: http://identifiers.org/pubmed/19478183
parameter: 267896
occurs in: http://identifiers.org/taxonomy/83333
is: MODEL1012220006
parameter: 267800
parameter: 267836
parameter: 267827
reaction: 267765
parameter: 267812
parameter: 267803
reaction: 267729
parameter: 267839
parameter: 267796
parameter: 267815
parameter: 267806
notes: This is the model of the RTC3 counter described in the article: Synthetic gene networks that count. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Science. 2009 May 29;324(5931):1199-202. PMID: 19478183 , DOI: 10.1126/science.1172005 Abstract: Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers. The 3 arabinose pulses are implemented using events, one for the start of pulses and one for the end. The variable pulse_flag changes arabinose consumption to fit behaviour during pulses and in between. To simulate two pulses only, set the pulse length of the third pulse to a negative value (though with an absolute value smaller than the pulse intervall length). Originally created by libAntimony v1.4 (using libSBML 3.4.1) This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
parameter: 267818
reaction: 267738
parameter: 267848
length unit: length
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species: 267720
parameter: 267890
event: 267792
has version: GO:0045975
parameter: 267830
species: 267709
parameter: 267842
parameter: 267833
species: 267717
reaction: 267727
volume units: metaid_0000008
parameter: 267845
parameter: 267821
parameter: 267875
parameter: 267797
parameter: 267851
species: 267723

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type: Species
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encodes: P00573
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is: SBO:0000250
in compartment: 267708
boundary condition: false
constant: false

267708
type: Compartment
is: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

267863
type: Parameter
constant: true
value: 3.0455

267711
type: Species
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initial amount: NaN
has only substance units: false
boundary condition: false
initial concentration: 0.176991329
in compartment: 267708
encodes: IPR000786
constant: false

267854
type: Parameter
constant: true
value: 3.0E-4

267866
type: Parameter
constant: true
value: 0.0701

267857
type: Parameter
constant: true
value: 3.8009

267869
type: Parameter
constant: true
value: 0.0

267714
type: Species
constant: false
in compartment: 267708
is part of: GO:0000428
is: SBO:0000252
boundary condition: false
initial amount: NaN
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has only substance units: false
initial concentration: 0.05230744612

267899
type: Parameter
constant: true
value: 22.0

267728
type: Reaction
reversible: false
fast: false
is: SBO:0000183
modifier: 433502
has version: GO:0051091
kinetic law: 433514
product: 433490
is version of: GO:0001121

267720
type: Species
constant: false
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boundary condition: false
is: C00259
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433490
type: SpeciesReference
stoichiometry: 1.0
species: 267709

267709
type: Species
boundary condition: false
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in compartment: 267708
has property: GO:0045975
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initial amount: NaN
initial concentration: 0.006796941377
constant: false

267786
type: Event
event assignment: 434059
trigger: 434047
use values from trigger time: true

267797
type: Parameter
constant: false
value: 0.0

434047
type: Trigger
persistant: true
initial value: true

267789
type: Event
event assignment: 434083
trigger: 434071
use values from trigger time: true

434071
type: Trigger
persistant: true
initial value: true

267732
type: Reaction
kinetic law: 433562
product: 433550
is version of: GO:0001121
is: SBO:0000183
fast: false
reversible: false

433550
type: SpeciesReference
stoichiometry: 1.0
species: 267710

267881
type: Parameter
constant: true
value: 0.01

267872
type: Parameter
constant: true
value: 0.0115

267735
type: Reaction
kinetic law: 433588
reactant: 433575
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false

433575
type: SpeciesReference
stoichiometry: 1.0
species: 267710

267809
type: Parameter
constant: true
value: 8.0E-4

267777
type: Event
event assignment: 433963
event assignment: 433951
trigger: 433939
use values from trigger time: true

433939
type: Trigger
persistant: true
initial value: true

267783
type: Event
event assignment: 434035
event assignment: 434023
trigger: 434011
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434011
type: Trigger
persistant: true
initial value: true

267884
type: Parameter
constant: true
value: 11.0

267750
type: Reaction
kinetic law: 433770
reactant: 433758
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false

433758
type: SpeciesReference
stoichiometry: 1.0
species: 267714

267741
type: Reaction
kinetic law: 433648
reactant: 433636
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false

433636
type: SpeciesReference
stoichiometry: 1.0
species: 267711

267860
type: Parameter
constant: true
value: 2.602

267753
type: Reaction
kinetic law: 433794
reactant: 433782
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false

433782
type: SpeciesReference
stoichiometry: 1.0
species: 267717

267717
type: Species
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boundary condition: false
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initial concentration: 6.338921181
is: SBO:0000252

267744
type: Reaction
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kinetic law: 433697
has version: GO:0045974
fast: false
reversible: false
modifier: 433672
modifier: 433684
product: 433660
is: SBO:0000184

433660
type: SpeciesReference
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species: 267714

267726
type: Species
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has only substance units: false
encodes: P07659
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267756
type: Reaction
kinetic law: 433830
modifier: 433818
product: 433806
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is: SBO:0000183
fast: false
reversible: false

433806
type: SpeciesReference
stoichiometry: 1.0
species: 267726

267893
type: Parameter
constant: true
value: 11.0

267747
type: Reaction
modifier: 433734
reversible: false
kinetic law: 433746
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product: 433709
fast: false
modifier: 433721
is: SBO:0000184
is version of: GO:0006412

433709
type: SpeciesReference
stoichiometry: 1.0
species: 267717

267824
type: Parameter
constant: true
value: 3.006

267762
type: Reaction
product: 433866
modifier: 433890
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has version: GO:0045974
kinetic law: 433902
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reversible: false
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433866
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species: 267723

267723
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constant: false
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initial concentration: 6.41674E-5

267759
type: Reaction
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reactant: 433842
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is: SBO:0000179
fast: false
reversible: false

433842
type: SpeciesReference
stoichiometry: 1.0
species: 267726

267896
type: Parameter
constant: false
value: NaN

267800
type: Parameter
constant: true
value: 0.1201

267836
type: Parameter
constant: true
value: 3.0E-4

267827
type: Parameter
constant: true
value: 0.8892

267765
type: Reaction
kinetic law: 433927
reactant: 433914
has version: GO:0030163
is: SBO:0000179
fast: false
reversible: false

433914
type: SpeciesReference
stoichiometry: 1.0
species: 267723

267812
type: Parameter
constant: true
value: 0.1177

267803
type: Parameter
constant: true
value: 0.8467

267729
type: Reaction
kinetic law: 433538
reactant: 433526
is version of: GO:0034661
is: SBO:0000179
fast: false
reversible: false

433526
type: SpeciesReference
stoichiometry: 1.0
species: 267709

267839
type: Parameter
constant: true
value: 0.0766

267796
type: Parameter
constant: true
value: 3.0E-4

267815
type: Parameter
constant: true
value: 0.0252

267806
type: Parameter
constant: true
value: 0.0571

267818
type: Parameter
constant: true
value: 0.0706

267738
type: Reaction
kinetic law: 433624
modifier: 433612
product: 433600
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false

433600
type: SpeciesReference
stoichiometry: 1.0
species: 267711

267848
type: Parameter
constant: true
value: 0.0056

267780
type: Event
event assignment: 433999
event assignment: 433987
trigger: 433975
use values from trigger time: true

433975
type: Trigger
persistant: true
initial value: true

267890
type: Parameter
constant: false
value: NaN

267792
type: Event
event assignment: 434107
trigger: 434095
use values from trigger time: true

434095
type: Trigger
persistant: true
initial value: true

267830
type: Parameter
constant: true
value: 7.9075

267842
type: Parameter
constant: true
value: 0.1007

267833
type: Parameter
constant: true
value: 0.07

267727
type: Reaction
kinetic law: 433478
reactant: 433466
is version of: GO:0019572
is: SBO:0000179
fast: false
reversible: false

433466
type: SpeciesReference
stoichiometry: 1.0
species: 267720

267845
type: Parameter
constant: true
value: 0.9923

267821
type: Parameter
constant: true
value: 0.0123

267875
type: Parameter
constant: true
value: 0.0069

267851
type: Parameter
constant: true
value: 0.003

267887
type: Parameter
constant: true
value: 0.01

267878
type: Parameter
constant: true
value: 20.0

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler

W3 CDTF: Wed Jan 19 02:14:29 GMT 2011

W3 CDTF: Fri Apr 08 13:29:50 BST 2011