SpiCO

A stochastic pi calculus for concurrent objects. We present SpiCO, a new modeling and simulation language for systems biology. SpiCO is based on the stochastic $pi $ calculus. It supports higher level modeling via multi-profile concurrent objects with static inheritance. We present a semantics for SpiCO in terms of continuous time Markov chains, and show how to compile SpiCO back into the biochemical stochastic $pi $ calculus while preserving semantics.

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References in zbMATH (referenced in 10 articles )

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  1. Wright, Thomas; Stark, Ian: Modelling patterns of gene regulation in the bond-calculus (2020)
  2. John, Mathias; Schulz, Hans-Jörg; Schumann, Heidrun; Uhrmacher, Adelinde M.; Unger, Andrea: Constructing and visualizing chemical reaction networks from pi-calculus models (2013)
  3. John, Mathias; Lhoussaine, Cédric; Niehren, Joachim; Versari, Cristian: Biochemical reaction rules with constraints (2011)
  4. John, Mathias; Lhoussaine, Cédric; Niehren, Joachim; Uhrmacher, Adelinde M.: The attributed pi-calculus with priorities (2010)
  5. Kuttler, Céline; Lhoussaine, Cédric; Nebut, Mirabelle: Rule-based modeling of transcriptional attenuation at the tryptophan operon (2010)
  6. Phillips, Andrew: An abstract machine for the stochastic bioambient calculus (2009)
  7. Versari, Cristian; Busi, Nadia: Stochastic biological modelling in the presence of multiple compartments (2009)
  8. Pilegaard, Henrik; Nielson, Flemming; Nielson, Hanne Riis: Pathway analysis for BioAmbients (2008)
  9. Versari, Cristian; Busi, Nadia: Efficient stochastic simulation of biological systems with multiple variable volumes (2008)
  10. Kuttler, Céline; Lhoussaine, Cédric; Niehren, Joachim: A stochastic pi calculus for concurrent objects (2007)