Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

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

A Comparison of Petri Net Semantics under the Collective Token Philosophy

In recent years, several semantics for place/transition Petri nets have been proposed that adopt the collective token philosophy. We investigate distinctions and similarities between three such models, namely configuration structures, concurrent transition systems, and (strictly) symmetric (strict) monoidal categories. We use the notion of adjunction to express each connection. We also present a purely logical description of the collective token interpretation of net behaviours in terms of theories and theory morphisms in partial membership equational logic

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

A synchronous program algebra: a basis for reasoning about shared-memory and event-based concurrency

This research started with an algebra for reasoning about rely/guarantee concurrency for a shared memory model. The approach taken led to a more abstract algebra of atomic steps, in which atomic steps synchronise (rather than interleave) when composed in parallel. The algebra of rely/guarantee concurrency then becomes an instantiation of the more abstract algebra. Many of the core properties needed for rely/guarantee reasoning can be shown to hold in the abstract algebra where their proofs are simpler and hence allow a higher degree of automation. The algebra has been encoded in Isabelle/HOL to provide a basis for tool support for program verification. In rely/guarantee concurrency, programs are specified to guarantee certain behaviours until assumptions about the behaviour of their environment are violated. When assumptions are violated, program behaviour is unconstrained (aborting), and guarantees need no longer hold. To support these guarantees a second synchronous operator, weak conjunction, was introduced: both processes in a weak conjunction must agree to take each atomic step, unless one aborts in which case the whole aborts. In developing the laws for parallel and weak conjunction we found many properties were shared by the operators and that the proofs of many laws were essentially the same. This insight led to the idea of generalising synchronisation to an abstract operator with only the axioms that are shared by the parallel and weak conjunction operator, so that those two operators can be viewed as instantiations of the abstract synchronisation operator. The main differences between parallel and weak conjunction are how they combine individual atomic steps; that is left open in the axioms for the abstract operator.Comment: Extended version of a Formal Methods 2016 paper, "An algebra of synchronous atomic steps

A synchronous program algebra: a basis for reasoning about shared-memory and event-based concurrency

This research started with an algebra for reasoning about rely/guarantee concurrency for a shared memory model. The approach taken led to a more abstract algebra of atomic steps, in which atomic steps synchronise (rather than interleave) when composed in parallel. The algebra of rely/guarantee concurrency then becomes an instantiation of the more abstract algebra. Many of the core properties needed for rely/guarantee reasoning can be shown to hold in the abstract algebra where their proofs are simpler and hence allow a higher degree of automation. The algebra has been encoded in Isabelle/HOL to provide a basis for tool support for program verification. In rely/guarantee concurrency, programs are specified to guarantee certain behaviours until assumptions about the behaviour of their environment are violated. When assumptions are violated, program behaviour is unconstrained (aborting), and guarantees need no longer hold. To support these guarantees a second synchronous operator, weak conjunction, was introduced: both processes in a weak conjunction must agree to take each atomic step, unless one aborts in which case the whole aborts. In developing the laws for parallel and weak conjunction we found many properties were shared by the operators and that the proofs of many laws were essentially the same. This insight led to the idea of generalising synchronisation to an abstract operator with only the axioms that are shared by the parallel and weak conjunction operator, so that those two operators can be viewed as instantiations of the abstract synchronisation operator. The main differences between parallel and weak conjunction are how they combine individual atomic steps; that is left open in the axioms for the abstract operator.Comment: Extended version of a Formal Methods 2016 paper, "An algebra of synchronous atomic steps

Web Services: A Process Algebra Approach

It is now well-admitted that formal methods are helpful for many issues raised in the Web service area. In this paper we present a framework for the design and verification of WSs using process algebras and their tools. We define a two-way mapping between abstract specifications written using these calculi and executable Web services written in BPEL4WS. Several choices are available: design and correct errors in BPEL4WS, using process algebra verification tools, or design and correct in process algebra and automatically obtaining the corresponding BPEL4WS code. The approaches can be combined. Process algebra are not useful only for temporal logic verification: we remark the use of simulation/bisimulation both for verification and for the hierarchical refinement design method. It is worth noting that our approach allows the use of any process algebra depending on the needs of the user at different levels (expressiveness, existence of reasoning tools, user expertise)