Quick Direct-method Controlled (QDC): a simulator of metabolic experiments

Authors

  • Davide Cangelosi Institute Gianna Gaslini, Genova
  • Salvatore Fabbiano University of Salamanca
  • Claudio Felicioli Noname Research, Pisa
  • Luca Freschi Universite' Laval, Quebec City.
  • Roberto Marangoni University of Pisa

DOI:

https://doi.org/10.14806/ej.19.1.505

Keywords:

gillespie's algorithm, control actions, metabolic networks

Abstract

Quick Direct-method Controlled (QDC) is a stochastic simulator based on the direct method version of Gillespie’s Stochastic Simulation Algorithm (SSA). It has been specifically designed to simulate experiments performed on metabolic networks, when external operators can act on the system, modifying its spontaneous behaviour. Users of QDC can simulate different experimental controls: i.e., add or remove chemical species at a given time; change the rate of a reaction at a given moment; and describe reactions with complex stoichiometry that take place once the stoichiometric condition is verified (here called immediate reactions). Moreover, even though QDC is not designed to manage compartments, it can simulate up-take and excretion reactions. QDC represents a useful tool for the specific field of interest thanks to its computational performances and simple input language.

Supplementary files

Author Biographies

  • Davide Cangelosi, Institute Gianna Gaslini, Genova
    Computational biology unity, post-doc.
  • Salvatore Fabbiano, University of Salamanca
    Department of Biology, Ph.D. student
  • Claudio Felicioli, Noname Research, Pisa
    Founder and researcher at Noname Res.
  • Luca Freschi, Universite' Laval, Quebec City.
    Department of Biology, Ph.D. student.
  • Roberto Marangoni, University of Pisa

    Computer Science Dept.

    Researcher

    Professor of Bioinformatics

EMBnet.journal 19.1

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Additional Files

Published

2013-07-24

Issue

Vol. 19 No. 1

Section

Technical Notes

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