Stochastic simulation efficiency

  • The work described in this report can be broadly divided into two sections. The first section considers two export features. We describe how the export for stochastic Petri nets to SBML level 1 has been added to the Petri net modelling and simulation tool Snoopy. This task was accomplished by making appropriate changes to the existing export code to generate SBML level 2. Also we demonstrate in detail, how the direct export for coloured Petri nets to both levels (i.e. 1 and 2) of SBML was realised. The next section summarises the performed comparison of different stochastic simulation tools for biochemical reaction networks. We first compare BioNetGen and SSC with each other by performing simulations on non-coloured Petri nets. Then, we compare the remaining four tools, i.e. Cain, Marcie, Snoopy and Stochkit with each other by performing simulation on coloured Petri nets. This work builds on results by Aman Sinha [19].

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Author: Swapnil, Chiru
Series (Serial Number):Computer science reports / Institut für Informatik (2014,02)
Document Type:Report
Year of Completion:2014
Release Date:2014/10/08
Tag:Biochemical reaction networks; Export; MathML; Petri Nets; SBML; Stochastic simulation
GND Keyword:Export; Petri-Netz; Stochastisches Modell
Institutes:Fakultät 1 MINT - Mathematik, Informatik, Physik, Elektro- und Informationstechnik / Institut für Informatik
Institution name at the time of publication:Fakultät für Mathematik, Naturwissenschaften und Informatik (eBTU) / Institut für Informatik
Licence (German):Keine Lizenz vergeben. Es gilt das deutsche Urheberrecht.