A Stochastic Pi Calculus for Concurrent Objects

International audienceWe present SpiCO, a new modeling and simulation language for system biology, based on the stochastic pi-calculus. SpiCO supports higher level modeling via multi-profile concurrent objects with static inheritance. We present a semantics for SpiCO in terms of continuous time Markov chains, and show how to compile SpiCO back into the biochemical stochastic pi-calculus while preserving semantics

The Attributed Pi Calculus with Priorities

International audienceWe present the attributed $\pi$-calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The $\pi$-calculus serves as a constraint language underlying the $\pi$-calculus. Interaction constraints subsume priorities, by which to express global aspects of populations. We present a nondeterministic and a stochastic semantics for the attributed $\pi$-calculus. We show how to encode the $\pi$-calculus with priorities and polyadic synchronization $\pi$@ and thus dynamic compartments, as well as the stochastic $\pi$-calculus with concurrent objects spico. We illustrate the usefulness of the attributed $\pi$-calculus for modeling biological systems at two particular examples: Euglena’s spatial movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda. Furthermore, population-based model is supported beside individual-based modeling. A stochastic simulation algorithm for the attributed $\pi$-calculus is derived from its stochastic semantics. We have implemented a simulator and present experimental results, that confirm the practical relevance of our approach

A Stochastic Pi Calculus for Concurrent Objects

International audienceWe present SpiCO, a new modeling and simulation language for system biology, based on the stochastic pi-calculus. SpiCO supports higher level modeling via multi-profile concurrent objects with static inheritance. We present a semantics for SpiCO in terms of continuous time Markov chains, and show how to compile SpiCO back into the biochemical stochastic pi-calculus while preserving semantics

Design Environments for Complex Systems

The paper describes an approach for modeling complex systems by hiding as much formal details as possible from the user, still allowing verification and simulation of the model. The interface is based on UML to make the environment available to the largest audience. To carry out analysis, verification and simulation we automatically extract process algebras specifications from UML models. The results of the analysis is then reflected back in the UML model by annotating diagrams. The formal model includes stochastic information to handle quantitative parameters. We present here the stochastic -calculus and we discuss the implementation of its probabilistic support that allows simulation of processes. We exploit the benefits of our approach in two applicative domains: global computing and systems biology

Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

Service discovery and negotiation with COWS

To provide formal foundations to current (web) services technologies, we put forward using COWS, a process calculus for specifying, combining and analysing services, as a uniform formalism for modelling all the relevant phases of the life cycle of service-oriented applications, such as publication, discovery, negotiation, deployment and execution. In this paper, we show that constraints and operations on them can be smoothly incorporated in COWS, and propose a disciplined way to model multisets of constraints and to manipulate them through appropriate interaction protocols. Therefore, we demonstrate that also QoS requirement specifications and SLA achievements, and the phases of dynamic service discovery and negotiation can be comfortably modelled in COWS. We illustrate our approach through a scenario for a service-based web hosting provider

A Process Algebraical Approach to Modelling Compartmentalized Biological Systems

This paper introduces Protein Calculus, a special modeling language designed for encoding and calculating the behaviors of compartmentilized biological systems. The formalism combines, in a unified framework, two successful computational paradigms - process algebras and membrane systems. The goal of Protein Calculus is to provide a formal tool for transforming collected information from in vivo experiments into coded definition of the different types of proteins, complexes of proteins, and membrane-organized systems of such entities. Using this encoded information as input, our calculus computes, in silico, the possible behaviors of a living system. This is the preliminary version of a paper that was published in Proceedings of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2: 642-646, 2007 (http://scitation.aip.org/dbt/dbt.jsp?KEY=APCPCS&Volume=963&Issue=2)