Spike - Reproducible Simulation Experiments with Configuration File Branching

摘要

This paper presents Spike - a command line tool for continuous, stochastic & hybrid simulation of biochemical reaction networks represented as (coloured) Petri nets. It supports import from and export to various Petri net data formats, and also imports SBML models. Spike's abilities include the configuration of models by changing stoichiometrics (arc weights), initial conditions (markings) and kinetic parameters. It also unfolds coloured stochastic/continuous/hybrid Petri nets. To comply with the demand for reproducible simulation experiments, Spike builds on a script language in a human-readable format. Its core features permit the design of a set of simulation experiments by a single configuration file. These simulation experiments can be executed in parallel on a multi-core machine; distributed execution is in preparation.