THE BioSPI SYSTEM FOR SIMULATION OF BIOCHEMICAL PROCESSES

BioSPI is a computer application we have developed for simulating the behavior of biochemical systems specified in the pi calculus. It is based on the Logix system, which implements Flat Concurrent Prolog (FCP). The use of FCP allows both mobility and synchronized communication, two of the major features of the pi-calculus. To the best of our knowledge this is the only implementation of the full synchronous calculus, including mixed choice.

An appropriate surface PiFCP syntax, is used for the full polyadic pi-calculus syntax (insulated from general Logix procedures). Two compilers from PiFCP to FCP are available:

PI, which is based on the original non-deterministic semantics, allows semi-quantitative simulations.

SPI, uses a modification of the stochastic pi-calculus, and is suitable for exact quantitative simulations.

PI/SPI include several debugging tools for tracing step-wise execution of PiFCP programs, including tree traces and step-by-step execution mode. In stochastic simulations, the number of processes is monitored and recorded, as the internal clock progresses, to produce a fully ordered trace of all events.

More details on BioSPI are in our papers.

In order to obtain BioSPI, please follow this link.

A manual is available for Logix/FCP.

A manual for BioSPI will be available here soon. In the meantime, some useful appendices are available.

Links to other applications related to the pi-calculus are here.