Representation and simulation of biochemical processes using the π-calculus process algebra

Abstract

Despite the rapidly accumulating body of knowledge about protein networks, there is currently no convenient w a y of sharing and manipulation of such information. We suggest that a formal computer language for describing the biomolecular processes underlying protein networks is essential for rapid advancement in this eld. We propose to model biomolecular processes by using the-Calculus, a process algebra, originally developed for describing computer processes. Our model for biochemical processes is mathematically well-de ned, while remaining biologically faithful and transparent. It is amenable to computer simulation, analysis and formal veri cation. We h a v e developed a computer simulation system, the PiFCP, for execution and analysis of-calculus programs. The system allows us to trace, debug and monitor the behavior of biochemical networks under various manipulations. We present a-calculus model for the RTK-MAPK signal transduction pathway, formally represent detailed molecular and biochemical information, and study it by v arious PiFCP simulations.

Formal Cell Biology in Biocham

“…This cascade was also the first example treated by Regev, Silverman and Shapiro [22] in the pi-calculus process algebra which was an initial source of inspiration for our own work.…”

“…transition systems by either process calculi [22,45,46,47,48], rules [33,10,9], Petri nets [26,29], etc..., but also for formalizing the biological properties of the system known from biological experiments under various conditions, opens a whole avenue of research for designing automated reasoning tools inspired from circuit and program verification to help the modeler [15]. The temporal logics CTL (Computation Tree Logic), LTL (Linear Time Logic) and PLTL (Probabilistic LTL) with numerical constraints are used in the three semantics of reaction models, respectively, in the boolean semantics, the differential semantics and the stochastic semantics.…”

Modelling gene and protein regulatory networks with Answer Set Programming

“…Many of the approaches proposed to model regulatory networks such as Peleg et al (2002), Ciocchetta & Hillston (2008), Regev et al (2001) follow a simulation-perturbation strategy, i.e. to analyse the behaviour of a system, the biologist changes the input and observes the changes in the output.…”

Model Revision from Temporal Logic Properties in Computational Systems Biology

“…The pioneering use in [1] of the π-calculus process algebra for modeling cell signalling pathways, has been the source of inspiration of numerous works in the line of process calculi [2][3][4] and their stochastic extensions [5]. Recently, the question of formalizing the biological properties of the system has also been raised, and formal languages have been proposed for this task, most notably using temporal logics in either boolean [6,7], discrete [8][9][10] or continuous models [11,12].…”