GSOS for non-deterministic processes with quantitative aspects

Recently, some general frameworks have been proposed as unifying theories for processes combining non-determinism with quantitative aspects (such as probabilistic or stochastically timed executions), aiming to provide general results and tools. This paper provides two contributions in this respect. First, we present a general GSOS specification format (and a corresponding notion of bisimulation) for non-deterministic processes with quantitative aspects. These specifications define labelled transition systems according to the ULTraS model, an extension of the usual LTSs where the transition relation associates any source state and transition label with state reachability weight functions (like, e.g., probability distributions). This format, hence called Weight Function SOS (WFSOS), covers many known systems and their bisimulations (e.g. PEPA, TIPP, PCSP) and GSOS formats (e.g. GSOS, Weighted GSOS, Segala-GSOS, among others). The second contribution is a characterization of these systems as coalgebras of a class of functors, parametric on the weight structure. This result allows us to prove soundness of the WFSOS specification format, and that bisimilarities induced by these specifications are always congruences.Comment: In Proceedings QAPL 2014, arXiv:1406.156

Modeling biological systems with delays in Bio-PEPA

Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed, or to provide abstraction of some behavior of the system resulting more compact models. In this paper we enrich the stochastic process algebra Bio-PEPA, with the possibility of assigning delays to actions, yielding a new non-Markovian process algebra: Bio-PEPAd. This is a conservative extension meaning that the original syntax of Bio-PEPA is retained and the delay specification which can now be associated with actions may be added to existing Bio-PEPA models. The semantics of the firing of the actions with delays is the delay-as-duration approach, earlier presented in papers on the stochastic simulation of biological systems with delays. These semantics of the algebra are given in the Starting-Terminating style, meaning that the state and the completion of an action are observed as two separate events, as required by delays. Furthermore we outline how to perform stochastic simulation of Bio-PEPAd systems and how to automatically translate a Bio-PEPAd system into a set of Delay Differential Equations, the deterministic framework for modeling of biological systems with delays. We end the paper with two example models of biological systems with delays to illustrate the approach.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

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 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-

Analysis of a Multimedia Stream using Stochastic Process Algebra

It is now well recognised that the next generation of distributed systems will be distributed multimedia systems. Central to multimedia systems is quality of service, which defines the non-functional requirements on the system. In this paper we investigate how stochastic process algebra can be used in order to determine the quality of service properties of distributed multimedia systems. We use a simple multimedia stream as our basic example. We describe it in the Stochastic Process Algebra PEPA and then we analyse whether the stream satisfies a set of quality of service parameters: throughput, end-to-end latency, jitter and error rates

Stochastic abstraction of programs: towards performance-driven development

Distributed computer systems are becoming increasingly prevalent, thanks to modern technology, and this leads to significant challenges for the software developers of these systems. In particular, in order to provide a certain service level agreement with users, the performance characteristics of the system are critical. However, developers today typically consider performance only in the later stages of development, when it may be too late to make major changes to the design. In this thesis, we propose a performance driven approach to development — based around tool support that allows developers to use performance modelling techniques, while still working at the level of program code. There are two central themes to the thesis. The first is to automatically relate performance models to program code. We define the Simple Imperative Remote Invocation Language (SIRIL), and provide a probabilistic semantics that interprets a program as a Markov chain. To make such an interpretation both computable and efficient, we develop an abstract interpretation of the semantics, from which we can derive a Performance Evaluation Process Algebra (PEPA) model of the system. This is based around abstracting the domain of variables to truncated multivariate normal measures. The second theme of the thesis is to analyse large performance models by means of compositional abstraction. We use two abstraction techniques based on aggregation of states — abstract Markov chains, and stochastic bounds — and apply both of them compositionally to PEPA models. This allows us to model check properties in the three-valued Continuous Stochastic Logic (CSL), on abstracted models. We have implemented an extension to the Eclipse plug-in for PEPA, which provides a graphical interface for specifying which states in the model to aggregate, and for performing the model checking

Process algebra for performance evaluation

This paper surveys the theoretical developments in the field of stochastic process algebras, process algebras where action occurrences may be subject to a delay that is determined by a random variable. A huge class of resource-sharing systems – like large-scale computers, client–server architectures, networks – can accurately be described using such stochastic specification formalisms. The main emphasis of this paper is the treatment of operational semantics, notions of equivalence, and (sound and complete) axiomatisations of these equivalences for different types of Markovian process algebras, where delays are governed by exponential distributions. Starting from a simple actionless algebra for describing time-homogeneous continuous-time Markov chains, we consider the integration of actions and random delays both as a single entity (like in known Markovian process algebras like TIPP, PEPA and EMPA) and as separate entities (like in the timed process algebras timed CSP and TCCS). In total we consider four related calculi and investigate their relationship to existing Markovian process algebras. We also briefly indicate how one can profit from the separation of time and actions when incorporating more general, non-Markovian distributions