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

Formal executable descriptions of biological systems

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems

On the incorporation of interval-valued fuzzy sets into the Bousi-Prolog system: declarative semantics, implementation and applications

In this paper we analyse the benefits of incorporating interval-valued fuzzy sets into the Bousi-Prolog system. A syntax, declarative semantics and im- plementation for this extension is presented and formalised. We show, by using potential applications, that fuzzy logic programming frameworks enhanced with them can correctly work together with lexical resources and ontologies in order to improve their capabilities for knowledge representation and reasoning

Meta SOS - A Maude Based SOS Meta-Theory Framework

Meta SOS is a software framework designed to integrate the results from the meta-theory of structural operational semantics (SOS). These results include deriving semantic properties of language constructs just by syntactically analyzing their rule-based definition, as well as automatically deriving sound and ground-complete axiomatizations for languages, when considering a notion of behavioural equivalence. This paper describes the Meta SOS framework by blending aspects from the meta-theory of SOS, details on their implementation in Maude, and running examples.Comment: In Proceedings EXPRESS/SOS 2013, arXiv:1307.690

A Denotational Semantics for Communicating Unstructured Code

An important property of programming language semantics is that they should be compositional. However, unstructured low-level code contains goto-like commands making it hard to define a semantics that is compositional. In this paper, we follow the ideas of Saabas and Uustalu to structure low-level code. This gives us the possibility to define a compositional denotational semantics based on least fixed points to allow for the use of inductive verification methods. We capture the semantics of communication using finite traces similar to the denotations of CSP. In addition, we examine properties of this semantics and give an example that demonstrates reasoning about communication and jumps. With this semantics, we lay the foundations for a proof calculus that captures both, the semantics of unstructured low-level code and communication.Comment: In Proceedings FESCA 2015, arXiv:1503.0437

Encoding CSP into CCS

We study encodings from CSP into asynchronous CCS with name passing and matching, so in fact, the asynchronous pi-calculus. By doing so, we discuss two different ways to map the multi-way synchronisation mechanism of CSP into the two-way synchronisation mechanism of CCS. Both encodings satisfy the criteria of Gorla except for compositionality, as both use an additional top-level context. Following the work of Parrow and Sj\"odin, the first encoding uses a centralised coordinator and establishes a variant of weak bisimilarity between source terms and their translations. The second encoding is decentralised, and thus more efficient, but ensures only a form of coupled similarity between source terms and their translations.Comment: In Proceedings EXPRESS/SOS 2015, arXiv:1508.0634