Abstract
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 stoichiometries (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.
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Acknowledgement
Spike uses software libraries (data format conversions, simulation algorithms) which have been previously developed by former staff members and numerous student projects at Brandenburg Technical University (BTU), chair Data Structures and Software Dependability.
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Chodak, J., Heiner, M. (2019). Spike – Reproducible Simulation Experiments with Configuration File Branching. In: Bortolussi, L., Sanguinetti, G. (eds) Computational Methods in Systems Biology. CMSB 2019. Lecture Notes in Computer Science(), vol 11773. Springer, Cham. https://doi.org/10.1007/978-3-030-31304-3_19
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DOI: https://doi.org/10.1007/978-3-030-31304-3_19
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