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800240
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BIOMD0000000315
parameter: 800316
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length unit: length
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notes: This is the model of the in vitro DNA oscillator called oligator with the optmized set of parameters described in the article: Programming an in vitro DNA oscillator using a molecular networking strategy. Montagne K, Plasson R, Sakai Y, Fujii T, Rondelez Y. Mol Syst Biol. 2011 Feb 1;7:466. PubmedID: 21283142 , Doi: 10.1038/msb.2010.120 Abstract: Living organisms perform and control complex behaviours by using webs of chemical reactions organized in precise networks. This powerful system concept, which is at the very core of biology, has recently become a new foundation for bioengineering. Remarkably, however, it is still extremely difficult to rationally create such network architectures in artificial, non-living and well-controlled settings. We introduce here a method for such a purpose, on the basis of standard DNA biochemistry. This approach is demonstrated by assembling de novo an efficient chemical oscillator: we encode the wiring of the corresponding network in the sequence of small DNA templates and obtain the predicted dynamics. Our results show that the rational cascading of standard elements opens the possibility to implement complex behaviours in vitro. Because of the simple and well-controlled environment, the corresponding chemical network is easily amenable to quantitative mathematical analysis. These synthetic systems may thus accelerate our understanding of the underlying principles of biological dynamic modules. The model reproduces the time courses in fig 2B. The parameter identifiers of the reaction constants are not the same as in the supplemental material, but are just called kXd and kXr for the forward and backwards constant of reaction X respectively. 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, Dhar…
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occurs in: http://identifiers.org/taxonomy/131567
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is: SBO:0000205
reversible: false
is version of: http://identifiers.org/ec-code/2.7.7.7
is version of: GO:0003887
type: Reaction

800332
is: SBO:0000338
constant: true
units: 637865
value: 0.610714285714
type: Parameter

800192
initial concentration: 0.0
name: alpha_T1
has version: CHEBI:16991
has only substance units: false
constant: false
in compartment: 800189
type: Species
is: SBO:0000250
boundary condition: false
has version: C00039
initial amount: NaN

637938
stoichiometry: 1.0
species: 800193
type: SpeciesReference

638329
stoichiometry: 1.0
species: 800205
type: SpeciesReference

800383
is: SBO:0000039
constant: true
units: 637816
value: 0.021546
type: Parameter

800208
boundary condition: false
is: SBO:0000250
has version: CHEBI:16991
type: Species
in compartment: 800189
name: T2_beta
has only substance units: false
initial amount: NaN
has version: C00039
constant: false
initial concentration: 0.0

800343
is: SBO:0000339
constant: true
units: 637816
value: 0.0294
type: Parameter

638144
stoichiometry: 1.0
species: 800197
type: SpeciesReference

800241
fast: false
is version of: GO:0003677
product: 638329
type: Reaction
kinetic law: 638341
reversible: true
reactant: 638303
is: SBO:0000180
product: 638316

637829
exponent: -1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

638267
stoichiometry: 1.0
species: 800201
type: SpeciesReference

800245
kinetic law: 638426
fast: false
is: SBO:0000205
reactant: 638402
is version of: GO:0003887
type: Reaction
is version of: http://identifiers.org/ec-code/2.7.7.7
product: 638414
reversible: false

800193
has version: CHEBI:16991
initial amount: NaN
constant: false
type: Species
is: SBO:0000250
name: alpha_T1_alpha
has only substance units: false
initial concentration: 0.0
boundary condition: false
has version: C00039
in compartment: 800189

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

W3 CDTF: Thu Feb 17 01:23:22 GMT 2011

W3 CDTF: Fri Apr 20 22:59:26 BST 2012