Biological networks in metabolic P systems

The metabolic P algorithm is a procedure which determines, in a biochemically realistic way, the evolution of P systems representing biological phenomena. A new formulation of this algorithm is given and a graphical formalism is introduced which seems to be very natural in expressing biological networks by means of a two level representation: a basic biochemical level and a second one which regulates the dynamical interaction among the reactions of the first level. After some basic examples, the mitotic oscillator in amphibian embryos is considered as an important case study. Three formulations of this biological network are developed. The first two are directly derived by Goldbeter's differential equations representation. The last one, entirely deduced by translating the biological description of the phenomenon in our diagrams, exhibits an analogous pattern, but it is conceptually simpler and avoids many details on the kinetic aspects of the reactions.