Comparison of stochastic simulation tools

  • This report compares some stochastic simulation tools for biochemical reaction networks. The stochastic simulation tools are selected on the basis of some selection criteria. Simulations are performed for the different stochastic simulation tools on different benchmark models. This report gives an overview of how the comparison is carried out for the chosen tools. The tools are compared on a common evaluation protocol. The evaluation protocol comprises a set of benchmark models along with the parameters which are provided as input to the tools. The benchmark models are represented as Petri nets and fed in SBML (System Biology Markup Language) to the different tools. Experiments are performed on each tool and the results are recorded. The tools are finally compared based on the comparison criteria.

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Author: Sinha, Aman
Series (Serial Number):Computer science reports / Institut für Informatik (2014,01)
Document Type:Report
Year of Completion:2014
Release Date:2014/10/08
Tag:Benchmarks; Biochemical reaction networks; Evaluation protocol; SBML; Stochastic simulation
GND Keyword: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.