Spatial Analysis of BioAmbients

Programming language technology can contribute to the development and understanding of Systems Biology by providing formal calculi for specifying and analysing the dynamic behaviour of biological systems. Our focus is on BioAmbients, a variation of the ambient calculi developed for modelling mobility in computer systems. We present a static analysis for capturing the spatial structure of biological systems and we illustrate it on a few examples.

[1]  Corrado Priami,et al.  Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..

[2]  Corrado Priami,et al.  An enhanced CFA for security policies , 2003 .

[3]  Luca Cardelli,et al.  Mobile Ambients , 1998, FoSSaCS.

[4]  Cosimo Laneve,et al.  Core Formal Molecular Biology , 2003, ESOP.

[5]  Luca Cardelli,et al.  BioAmbients: an abstraction for biological compartments , 2004, Theor. Comput. Sci..

[6]  Robin Milner,et al.  Communicating and mobile systems - the Pi-calculus , 1999 .

[7]  Flemming Nielson,et al.  Security for Mobility , 2002, FOSAD.

[8]  Benjamin C. Pierce,et al.  Theoretical Aspects of Computer Software , 2001, Lecture Notes in Computer Science.

[9]  Aviv Regev,et al.  Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra , 2000, Pacific Symposium on Biocomputing.

[10]  Flemming Nielson,et al.  A Succinct Solver for ALFP , 2002, Nord. J. Comput..

[11]  Onami,et al.  Bio-calculus: Its Concept and Molecular Interaction. , 1999, Genome informatics. Workshop on Genome Informatics.

[12]  Luca Cardelli,et al.  Brane Calculi , 2004, CMSB.

[13]  Davide Sangiorgi,et al.  Controlling interference in ambients , 2000, POPL '00.

[14]  Michele Bugliesi,et al.  Boxed Ambients , 2001, TACS.

[15]  Robin Milner,et al.  Theories for the Global Ubiquitous Computer , 2004, FoSSaCS.