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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.

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