Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models

BACKGROUND: Hybrid simulation of (computational) biochemical reaction networks, which combines stochastic and deterministic dynamics, is an important direction to tackle future challenges due to complex and multi-scale models. Inherently hybrid computational models of biochemical networks entail two time scales: fast and slow. Therefore, it is intricate to efficiently and accurately analyse them using only either deterministic or stochastic simulation. However, there are only a few software tools that support such an approach. These tools are often limited with respect to the number as well as the functionalities of the provided hybrid simulation algorithms. RESULTS: We present Snoopy’s hybrid simulator, an efficient hybrid simulation software which builds on Snoopy, a tool to construct and simulate Petri nets. Snoopy’s hybrid simulator provides a wide range of state-of-the-art hybrid simulation algorithms. Using this tool, a computational model of biochemical networks can be constructed using a (coloured) hybrid Petri net’s graphical notations, or imported from other compatible formats (e.g. SBML), and afterwards executed via dynamic or static hybrid simulation. CONCLUSION: Snoopy’s hybrid simulator is a platform-independent tool providing an accurate and efficient simulation of hybrid (biological) models. It can be downloaded free of charge as part of Snoopy from http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Snoopy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12918-017-0449-6) contains supplementary material, which is available to authorized users.