License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/DagSemProc.09091.6
URN: urn:nbn:de:0030-drops-19938
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2009/1993/
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Kuttler, Céline ; Lhoussaine, Cédric ; Nebut, Mirabelle

Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

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Abstract

Transcriptional attenuation at E.coli's tryptophan operon is a prime example of
RNA-mediated gene regulation. In this paper, we present
a discrete stochastic model for this phenomenon based on
chemical reactions. Our model is compact and intelligible,
due to n-ary reactions (which preclude object-centric
approaches) and to rule schemas that define finite
sets of chemical reactions. Stochastic simulations
with our model confirm results that were previously
obtained by master equations or differential equations.
In addition, our approach permits to reflect
mutation experiments by simple model modifications,
and to re-use model components for transcriptional attenuation
in other genes and organisms.

BibTeX - Entry

@InProceedings{kuttler_et_al:DagSemProc.09091.6,
  author =	{Kuttler, C\'{e}line and Lhoussaine, C\'{e}dric and Nebut, Mirabelle},
  title =	{{Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--22},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2009/1993},
  URN =		{urn:nbn:de:0030-drops-19938},
  doi =		{10.4230/DagSemProc.09091.6},
  annote =	{Keywords: Systems biology, rule-based modeling languages, stochastic simulation, kappa.}
}

Keywords: Systems biology, rule-based modeling languages, stochastic simulation, kappa.
Collection: 09091 - Formal Methods in Molecular Biology
Issue Date: 2009
Date of publication: 05.05.2009

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