BIOMD0000000322
type: SBMLModel
reaction: COPASI13
reaction: COPASI16
reaction: COPASI8
is: MODEL1012090000
created:
  W3 CDTF: Wed Dec 08 15:19:59 GMT 2010
parameter: COPASI3
area units: area
species: 187948
reaction: COPASI10
is described by: http://identifiers.org/pubmed/21283141
compartment: 187944
parameter: COPASI6
time units: 495249
species: 187946
is version of: GO:0010468
occurs in: http://identifiers.org/taxonomy/131567
reaction: COPASI14
parameter: COPASI4
parameter: COPASI7
notes: This a model from the article: Synthetic in vitro transcriptional oscillators. Kim J, Winfree E Mol. Syst. Biol. 2011 Feb 1;7:465. 21283141 , Abstract: The construction of synthetic biochemical circuits from simple components illuminates how complex beha viors can arise in chemistry and builds a foundation for future biological technologies. A simplified analog of genetic regulatory networks, in vitro transcriptional circuits, provides a modular platform for the systematic construction of arbitrary circuits and requires only two essential enzymes, bacteri ophage T7 RNA polymerase and Escherichia coli ribonuclease H, to produce and degrade RNA signals. In t his study, we design and experimentally demonstrate three transcriptional oscillators in vitro. First, a negative feedback oscillator comprising two switches, regulated by excitatory and inhibitory RNA si gnals, showed up to five complete cycles. To demonstrate modularity and to explore the design space fu rther, a positive-feedback loop was added that modulates and extends the oscillatory regime. Finally, a three-switch ring oscillator was constructed and analyzed. Mathematical modeling guided the design p rocess, identified experimental conditions likely to yield oscillations, and explained the system's ro bust response to interference by short degradation products. Synthetic transcriptional oscillators cou ld prove valuable for systematic exploration of biochemical circuit design principles and for controll ing nanoscale devices and orchestrating processes within artificial cells. Note: The paper describes 7 models (MODEL1012090000-6) and all these are submitted by the authors. This model (MODEL1012090000) corresponds to the Simple model for both mode I and II (Design I and II). The model reproduces timecourse figure plotted in the supplementary material (page 10 of Supplementary material) of the reference publication. To the extent possible under law, all copyright and related or neighbouring rights to this en…
curated: true
units def: 495225
reaction: COPASI11
reaction: COPASI9
substance units: 495275
length unit: length
units def: 495275
reaction: COPASI12
volume units: 495225
reaction: COPASI15
modified:
  W3 CDTF: Fri Jun 07 16:14:22 BST 2013
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
name: Kim2011_Oscillator_SimpleI
parameter: COPASI2
parameter: COPASI5
creator:
  ORG:
    orgname: Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
  n:
    given: Jongmin
    family: Kim
units def: 495249
function def: COPASI17
species: 187950
function def: COPASI18
name: Hill Cooperativity
species: 187949
name: Hill inhibition

COPASI13
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product: 495467
product: 495455
reactant: 495443
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reversible: false
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495467
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spatial dimensions: 3.0
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COPASI3
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constant: true
value: 2.5
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COPASI10
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COPASI4
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COPASI7
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COPASI11
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495371
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COPASI9
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495551
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COPASI2
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value: 0.57
name: alpha

COPASI5
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value: 6.5
name: n