Representation and simulation of biochemical processes using the pi-calculus process algebra.
Despite the rapidly accumulating body of knowledge about protein networks, there is currently no convenient way 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 field. We propose to model biomolecular processes by using the pi-Calculus, a process algebra, originally developed for describing computer processes. Our model for biochemical processes is mathematically well-defined, while remaining biologically faithful and transparent. It is amenable to computer simulation, analysis and formal verification. We have developed a computer simulation system, the PiFCP, for execution and analysis of pi-calculus programs. The system allows us to trace, debug and monitor the behavior of biochemical networks under various manipulations. We present a pi-calculus model for the RTK-MAPK signal transduction pathway, formally represent detailed molecular and biochemical information, and study it by various PiFCP simulations.
Department of Cell Research and Immunology, Life Sciences Faculty, Tel Aviv University, Tel Aviv 69978, Israel. aviv@wisdom.weizmann.ac.il
A
A
Regev
W
W
Silverman
E
E
Shapiro
D001671:Biochemistry / Q000706:statistics & numerical data*; D003198:Computer Simulation; D020928:Mitogen-Activated Protein Kinases / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008962:Models, Theoretical; D011381:Programming Languages; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000737:chemistry / Q000378:metabolism; D015398:Signal Transduction
D011506:Proteins; D020794:Receptor Protein-Tyrosine Kinases; D020928:Mitogen-Activated Protein Kinases