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.
Regev
A
A
Department of Cell Research and Immunology, Life Sciences Faculty, Tel Aviv University, Tel Aviv 69978, Israel. aviv@wisdom.weizmann.ac.il
Silverman
W
W
Shapiro
E
E
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