A new occurrence counting analysis for bioambients

  • Authors:

  • Roberta Gori;Francesca Levi

  • Affiliations:

  • Department of Computer Science, University of Pisa, Italy;DISI, University of Genova, Italy

  • Venue:
  • APLAS'05 Proceedings of the Third Asian conference on Programming Languages and Systems
  • Year:
  • 2005

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Abstract

This paper concerns the application of formal methods to biological systems, modelled specifically in BioAmbients [30]. BioAmbients [30] is a variant of the Mobile Ambients (MA) [7] calculus, designed precisely for more faithfully capturing basic biological concepts. We propose a new static analysis for BioAmbients which computes approximate information about the run-time behaviour of a system. The analysis is derived following the abstract interpretation approach and introduces two main novelties with respect to the analyses in literature [25,24,26,27]: (i) it records information about the number of occurrences of objects; (ii) it maintains more detailed information about the possible contents of ambients, at any time. In this way, the analysis gives substantially more precise results and captures both the quantitative and causal aspect which are really important for reasoning on the temporal and spatial structure of biological systems. The interest of the analysis is demonstrated by considering a few simple examples which point out the limitations of the existing analyses for BioAmbients.