A Stochastic Pi-calculus Model for the Intrinsic Apoptopic Pathway

Abstract

An abstract model for the intrinsic apoptopic pathway is presented. It is encoded in the stochastic pi-calculus formalism and has been tested using the SPiM simulator. The model is consistent with the current knowledge about this phenomenon. The use of this formalism allows the construction of abstract models that can be tested through virtual experiments, thus providing the ability to save resources from real experiment-based tests. Furthermore, the formalism has a proved equivalent graphical representation for describing biomolecular processes, allowing those unfamiliar with the computer science formalisms to be able to use it.The advances in the biological science and the search of the explanations for the behavior of biological processes such as Ageing and Programmed Cell Death (PCD), make us wonder about the possibilities of finding descriptions for these processes that allow us to understand them, in order to be able to reproduce, and even control them. The need of understanding biological processes has encouraged the search for new ways to describe them, since the most common techniques (differential equations) are not suitable enough for this purpose. As result, plenty of new techniques have been developed in many areas of science, some of which are contributions from the computer science theories of processes and concurrency, the process algebras.The main features of this calculus are the ability to describe: i) interactions and comunication between processes through the concept of name-passing; ii) structure dynamic changes in processes through mobility; and iii) stochastic behaviour by the use of a stochastic semantics. Among the advantages of this formal language for describing biological processes is the ability to test the model without actually building it physically, thus saving resources from its construction until the model has been theoretically proved to be satisfactory.