434071
persistant: true
initial value: true
type: Trigger

267881
constant: true
value: 0.01
type: Parameter

267783
event assignment: 434035
event assignment: 434023
trigger: 434011
use values from trigger time: true
type: Event

267726
initial amount: NaN
is: SBO:0000250
boundary condition: false
constant: false
type: Species
initial concentration: 0.00566438
is version of: CHEBI:33699
has only substance units: false
encodes: P07659
in compartment: 267708

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

267797
constant: false
value: 0.0
type: Parameter

267812
constant: true
value: 0.1177
type: Parameter

267839
constant: true
value: 0.0766
type: Parameter

267711
is: SBO:0000250
is version of: CHEBI:33699
initial amount: NaN
has only substance units: false
type: Species
boundary condition: false
initial concentration: 0.176991329
in compartment: 267708
encodes: IPR000786
constant: false

267875
constant: true
value: 0.0069
type: Parameter

267762
product: 433866
modifier: 433890
is version of: GO:0006412
has version: GO:0045974
kinetic law: 433902
modifier: 433878
reversible: false
fast: false
type: Reaction
is: SBO:0000184

267756
kinetic law: 433830
modifier: 433818
product: 433806
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
type: Reaction

433782
stoichiometry: 1.0
species: 267717
type: SpeciesReference

267720
constant: false
type: Species
is: CHEBI:17535
is: SBO:0000247
has only substance units: false
in compartment: 267708
boundary condition: false
is: C00259
initial amount: NaN
initial concentration: 0.0

433490
stoichiometry: 1.0
species: 267709
type: SpeciesReference

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

433550
stoichiometry: 1.0
species: 267710
type: SpeciesReference

267863
constant: true
value: 3.0455
type: Parameter

433939
persistant: true
initial value: true
type: Trigger

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

433806
stoichiometry: 1.0
species: 267726
type: SpeciesReference

267717
has only substance units: false
boundary condition: false
is homolog to: P42212
in compartment: 267708
is version of: IPR000786
constant: false
initial amount: NaN
initial concentration: 6.338921181
type: Species
is: SBO:0000252

267833
constant: true
value: 0.07
type: Parameter

267896
constant: false
value: NaN
type: Parameter

433600
stoichiometry: 1.0
species: 267711
type: SpeciesReference

267710
has only substance units: false
encodes: P00573
initial concentration: 0.3569405099
initial amount: NaN
is version of: CHEBI:33699
type: Species
is: SBO:0000250
in compartment: 267708
boundary condition: false
constant: false

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

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

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

433975
persistant: true
initial value: true
type: Trigger

267866
constant: true
value: 0.0701
type: Parameter

433660
stoichiometry: 1.0
species: 267714
type: SpeciesReference

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

267890
constant: false
value: NaN
type: Parameter

433842
stoichiometry: 1.0
species: 267726
type: SpeciesReference

267714
constant: false
type: Species
in compartment: 267708
is part of: GO:0000428
is: SBO:0000252
boundary condition: false
initial amount: NaN
is version of: P00573
has only substance units: false
initial concentration: 0.05230744612

267887
constant: true
value: 0.01
type: Parameter

267744
is version of: GO:0006412
kinetic law: 433697
has version: GO:0045974
fast: false
reversible: false
modifier: 433672
modifier: 433684
type: Reaction
product: 433660
is: SBO:0000184

267800
constant: true
value: 0.1201
type: Parameter

267827
constant: true
value: 0.8892
type: Parameter

433636
stoichiometry: 1.0
species: 267711
type: SpeciesReference

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

267878
constant: true
value: 20.0
type: Parameter

267848
constant: true
value: 0.0056
type: Parameter

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

267845
constant: true
value: 0.9923
type: Parameter

433709
stoichiometry: 1.0
species: 267717
type: SpeciesReference

267851
constant: true
value: 0.003
type: Parameter

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

433526
stoichiometry: 1.0
species: 267709
type: SpeciesReference

433575
stoichiometry: 1.0
species: 267710
type: SpeciesReference

267709
boundary condition: false
is version of: CHEBI:33697
is: SBO:0000250
in compartment: 267708
has property: GO:0045975
has only substance units: false
type: Species
initial amount: NaN
initial concentration: 0.006796941377
constant: false

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

433914
stoichiometry: 1.0
species: 267723
type: SpeciesReference

434011
persistant: true
initial value: true
type: Trigger

267899
constant: true
value: 22.0
type: Parameter

267806
constant: true
value: 0.0571
type: Parameter

267830
constant: true
value: 7.9075
type: Parameter

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

267860
constant: true
value: 2.602
type: Parameter

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

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

267747
modifier: 433734
reversible: false
kinetic law: 433746
has version: GO:0045974
product: 433709
fast: false
modifier: 433721
type: Reaction
is: SBO:0000184
is version of: GO:0006412

267872
constant: true
value: 0.0115
type: Parameter

267815
constant: true
value: 0.0252
type: Parameter

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

433758
stoichiometry: 1.0
species: 267714
type: SpeciesReference

BIOMD0000000301
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
type: SBMLModel
event: 267780
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

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

267857
constant: true
value: 3.8009
type: Parameter

267818
constant: true
value: 0.0706
type: Parameter

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

267821
constant: true
value: 0.0123
type: Parameter

267723
is: SBO:0000252
boundary condition: false
initial amount: NaN
has only substance units: false
in compartment: 267708
constant: false
type: Species
is part of: GO:0000428
is version of: P07659
initial concentration: 6.41674E-5

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

267842
constant: true
value: 0.1007
type: Parameter

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

433866
stoichiometry: 1.0
species: 267723
type: SpeciesReference

267893
constant: true
value: 11.0
type: Parameter

434047
persistant: true
initial value: true
type: Trigger

434095
persistant: true
initial value: true
type: Trigger

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

267759
kinetic law: 433854
reactant: 433842
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
type: Reaction

267803
constant: true
value: 0.8467
type: Parameter

267884
constant: true
value: 11.0
type: Parameter

433466
stoichiometry: 1.0
species: 267720
type: SpeciesReference

267869
constant: true
value: 0.0
type: Parameter

267824
constant: true
value: 3.006
type: Parameter

orgname: EMBL-EBI

given: Lukas
family: Endler

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

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