Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks

  • Authors:

  • Mostafa Herajy;Monika Heiner

  • Affiliations:

  • Department of Mathematics and Computer Science, Faculty of Science, Port Said University, 42521-Port Said, Egypt. mherajy@sci.psu.edu.eg;Computer Science Institute, Brandenburg University of Technology, D-03013 Cottbus, Germany. monika.heiner@informatik.tu-cottbus.de

  • Venue:
  • Fundamenta Informaticae - Dedicated to the Memory of Professor Manfred Kudlek
  • Year:
  • 2014

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Abstract

Computational steering is an interactive remote control of a long running application. The user can adopt it, e.g., to adjust simulation parameters on the fly. Simulation of large-scale biochemical networks is often computationally expensive, particularly stochastic and hybrid simulation. Such extremely time-consuming computations necessitate an interactive mechanism to permit users to try different paths and ask “what-if-questions” while the simulation is in progress. Furthermore, with the progress of computational modelling and the simulation of biochemical networks, there is a need to manage multi-scale models, which may contain species or reactions at different scales. In this context, Petri nets are of special importance, since they provide an intuitive visual representation of reaction networks. In this paper, we introduce a framework and its implementation for combining Petri nets and computational steering for the representation and interactive simulation of biochemical networks. The main merits of the developed framework are: intuitive representation of biochemical networks by means of Petri nets, distributed collaborative and interactive simulation, and tight coupling of simulation and visualisation.