Enhanced Operational Semantics in Systems Biology

We are faced with a great challenge: the cross-fertilization between the fields of formal methods for concurrency, in the computer science domain, and systems biology in the biological realm

A Fully Abstract Symbolic Semantics for Psi-Calculi

We present a symbolic transition system and bisimulation equivalence for psi-calculi, and show that it is fully abstract with respect to bisimulation congruence in the non-symbolic semantics. A psi-calculus is an extension of the pi-calculus with nominal data types for data structures and for logical assertions representing facts about data. These can be transmitted between processes and their names can be statically scoped using the standard pi-calculus mechanism to allow for scope migrations. Psi-calculi can be more general than other proposed extensions of the pi-calculus such as the applied pi-calculus, the spi-calculus, the fusion calculus, or the concurrent constraint pi-calculus. Symbolic semantics are necessary for an efficient implementation of the calculus in automated tools exploring state spaces, and the full abstraction property means the semantics of a process does not change from the original

Model checking probabilistic and stochastic extensions of the pi-calculus

We present an implementation of model checking for probabilistic and stochastic extensions of the pi-calculus, a process algebra which supports modelling of concurrency and mobility. Formal verification techniques for such extensions have clear applications in several domains, including mobile ad-hoc network protocols, probabilistic security protocols and biological pathways. Despite this, no implementation of automated verification exists. Building upon the pi-calculus model checker MMC, we first show an automated procedure for constructing the underlying semantic model of a probabilistic or stochastic pi-calculus process. This can then be verified using existing probabilistic model checkers such as PRISM. Secondly, we demonstrate how for processes of a specific structure a more efficient, compositional approach is applicable, which uses our extension of MMC on each parallel component of the system and then translates the results into a high-level modular description for the PRISM tool. The feasibility of our techniques is demonstrated through a number of case studies from the pi-calculus literature

Process Algebras

Process Algebras are mathematically rigorous languages with well defined semantics that permit describing and verifying properties of concurrent communicating systems. They can be seen as models of processes, regarded as agents that act and interact continuously with other similar agents and with their common environment. The agents may be real-world objects (even people), or they may be artifacts, embodied perhaps in computer hardware or software systems. Many different approaches (operational, denotational, algebraic) are taken for describing the meaning of processes. However, the operational approach is the reference one. By relying on the so called Structural Operational Semantics (SOS), labelled transition systems are built and composed by using the different operators of the many different process algebras. Behavioral equivalences are used to abstract from unwanted details and identify those systems that react similarly to external experiments

Proceedings of International Workshop "Global Computing: Programming Environments, Languages, Security and Analysis of Systems"

According to the IST/ FET proactive initiative on GLOBAL COMPUTING, the goal is to obtain techniques (models, frameworks, methods, algorithms) for constructing systems that are flexible, dependable, secure, robust and efficient. The dominant concerns are not those of representing and manipulating data efficiently but rather those of handling the co-ordination and interaction, security, reliability, robustness, failure modes, and control of risk of the entities in the system and the overall design, description and performance of the system itself. Completely different paradigms of computer science may have to be developed to tackle these issues effectively. The research should concentrate on systems having the following characteristics: • The systems are composed of autonomous computational entities where activity is not centrally controlled, either because global control is impossible or impractical, or because the entities are created or controlled by different owners. • The computational entities are mobile, due to the movement of the physical platforms or by movement of the entity from one platform to another. • The configuration varies over time. For instance, the system is open to the introduction of new computational entities and likewise their deletion. The behaviour of the entities may vary over time. • The systems operate with incomplete information about the environment. For instance, information becomes rapidly out of date and mobility requires information about the environment to be discovered. The ultimate goal of the research action is to provide a solid scientific foundation for the design of such systems, and to lay the groundwork for achieving effective principles for building and analysing such systems. This workshop covers the aspects related to languages and programming environments as well as analysis of systems and resources involving 9 projects (AGILE , DART, DEGAS , MIKADO, MRG, MYTHS, PEPITO, PROFUNDIS, SECURE) out of the 13 founded under the initiative. After an year from the start of the projects, the goal of the workshop is to fix the state of the art on the topics covered by the two clusters related to programming environments and analysis of systems as well as to devise strategies and new ideas to profitably continue the research effort towards the overall objective of the initiative. We acknowledge the Dipartimento di Informatica and Tlc of the University of Trento, the Comune di Rovereto, the project DEGAS for partially funding the event and the Events and Meetings Office of the University of Trento for the valuable collaboration

On Modelling and Analysis of Dynamic Reconfiguration of Dependable Real-Time Systems

This paper motivates the need for a formalism for the modelling and analysis of dynamic reconfiguration of dependable real-time systems. We present requirements that the formalism must meet, and use these to evaluate well established formalisms and two process algebras that we have been developing, namely, Webpi and CCSdp. A simple case study is developed to illustrate the modelling power of these two formalisms. The paper shows how Webpi and CCSdp represent a significant step forward in modelling adaptive and dependable real-time systems.Comment: Presented and published at DEPEND 201

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-

A Decidable Characterization of a Graphical Pi-calculus with Iterators

This paper presents the Pi-graphs, a visual paradigm for the modelling and verification of mobile systems. The language is a graphical variant of the Pi-calculus with iterators to express non-terminating behaviors. The operational semantics of Pi-graphs use ground notions of labelled transition and bisimulation, which means standard verification techniques can be applied. We show that bisimilarity is decidable for the proposed semantics, a result obtained thanks to an original notion of causal clock as well as the automatic garbage collection of unused names.Comment: In Proceedings INFINITY 2010, arXiv:1010.611

Formalising the pi-calculus using nominal logic

We formalise the pi-calculus using the nominal datatype package, based on ideas from the nominal logic by Pitts et al., and demonstrate an implementation in Isabelle/HOL. The purpose is to derive powerful induction rules for the semantics in order to conduct machine checkable proofs, closely following the intuitive arguments found in manual proofs. In this way we have covered many of the standard theorems of bisimulation equivalence and congruence, both late and early, and both strong and weak in a uniform manner. We thus provide one of the most extensive formalisations of a process calculus ever done inside a theorem prover. A significant gain in our formulation is that agents are identified up to alpha-equivalence, thereby greatly reducing the arguments about bound names. This is a normal strategy for manual proofs about the pi-calculus, but that kind of hand waving has previously been difficult to incorporate smoothly in an interactive theorem prover. We show how the nominal logic formalism and its support in Isabelle accomplishes this and thus significantly reduces the tedium of conducting completely formal proofs. This improves on previous work using weak higher order abstract syntax since we do not need extra assumptions to filter out exotic terms and can keep all arguments within a familiar first-order logic.Comment: 36 pages, 3 figure