GridSPiM: A Framework for Simple Locality and Containment in the Stochastic π-Calculus

  • Authors:

  • Stephen Tyree;Rayus Kuplicki;Trevor Sarratt;Scott Fujan;John Hale

  • Affiliations:

  • Institute of Bioinformatics and Computational Biology, University of Tulsa, Tulsa, USA OK 74104;Institute of Bioinformatics and Computational Biology, University of Tulsa, Tulsa, USA OK 74104;Institute of Bioinformatics and Computational Biology, University of Tulsa, Tulsa, USA OK 74104;Institute of Bioinformatics and Computational Biology, University of Tulsa, Tulsa, USA OK 74104;Institute of Bioinformatics and Computational Biology, University of Tulsa, Tulsa, USA OK 74104

  • Venue:
  • BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
  • Year:
  • 2009

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Abstract

Process calculi hold great promise for modeling and analysis of cellular mechanics and behavior. While measured success has been achieved in their simulation of specific biochemical pathways and molecular mechanisms within the cell, several obstacles remain to their widespread adoption and use. Chiefly, these have to with the difficulty of modeling cell membranes and localized behavior, and limitations on the scalability of the execution model. This paper describes a multi-layered formalism --- GridSPiM --- that engages notions of concurrency, locality and encapsulation to provide a framework suitable for capturing the key aspects of cellular processes.