A Type System for a Stochastic CLS

The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the presence of positive and negative catalysers can modify these speeds. We claim that types are the right abstraction in order to represent the interaction between elements without specifying exactly the element positions. Our claim is supported through an example modelling the lactose operon

A Calculus of Looping Sequences with Local Rules

In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the compartment on which they are defined. Local rules are dynamic: they can be added, moved and erased. We enrich the new calculus with a parallel semantics where a reduction step is lead by any number of global and local rules that could be performed in parallel. A type system is developed to enforce the property that a compartment must contain only local rules with specific features. As a running example we model some interactions happening in a cell starting from its nucleus and moving towards its mitochondria.Comment: In Proceedings DCM 2011, arXiv:1207.682

QUALITATIVE AND QUANTITATIVE FORMAL MODELING OF BIOLOGICAL SYSTEMS

Nella tesi si sviluppa un formalismo basato su riscrittura di termini e lo si propone come strumento per la descrizione di sistemi biologici. Tale formalismo, chiamato calculus of looping sequences (cls) consente di descrivere proteine, dna e membrane come termini, e interazioni tra questi elementi come regole di riscrittura. Diverse varianti di cls sono studiate al fine di descrivere diversi aspetti dei sistemi biologici, inoltre vengono definite equivalenze sul comportamento dei sistemi (bisimulazioni) e una versione stocastica del formalismo che consente di sviluppare strumenti di simulazione

Type Directed Semantics for the Calculus of Looping Sequences

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. Here we enrich this calculus with a type discipline which preserves some biological properties deriving from the requirement of certain elements, and the repellency of others. In particular, the type system guarantees the soundness of the application of reduction rules with respect to the elements which are required (all requirements must be satisfied) and to the elements which are excluded (two elements which repel each other cannot occur in the same compartment). As an example, we model the possible interactions (and compatibility) of different blood types with different antigens. The type system does not allow transfusion with incompatible blood types

Measurable Stochastics for Brane Calculus

We give a stochastic extension of the Brane Calculus, along the lines of recent work by Cardelli and Mardare. In this presentation, the semantics of a Brane process is a measure of the stochastic distribution of possible derivations. To this end, we first introduce a labelled transition system for Brane Calculus, proving its adequacy w.r.t. the usual reduction semantics. Then, brane systems are presented as Markov processes over the measurable space generated by terms up-to syntactic congruence, and where the measures are indexed by the actions of this new LTS. Finally, we provide a SOS presentation of this stochastic semantics, which is compositional and syntax-driven.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

SOS Rules for Equivalences of Reaction Systems

Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by reactions. Entities can also be provided by an external context. RS semantics is defined in terms of an (unlabelled) rewrite system: given the current set of entities, a rewrite step consists of the application of all and only the enabled reactions. In this paper we define, for the first time, a labelled transition system for RSs in the structural operational semantics (SOS) style. This is achieved by distilling a signature whose operators directly correspond to the ingredients of RSs and by defining some simple SOS inference rules for any such operator to define the behaviour of the RS in a compositional way. The rich information recorded in the labels allows us to define an assertion language to tailor behavioural equivalences on some specific properties or entities. The SOS approach is suited to drive additional enhancements of RSs along features such as quantitative measurements of entities and communication between RSs. The SOS rules have been also exploited to design a prototype implementation in logic programming.Comment: Part of WFLP 2020 pre-proceeding

Measurable stochastics for Brane Calculus

AbstractThe main aim of this work is to give a stochastic extension of the Brane Calculus, along the lines of recent work by Cardelli and Mardare (2010) [12]. In this approach, the semantics of a process is a measure of the stochastic distribution of possible derivations. To this end, we first introduce a compositional, finitely branching labelled transition system for Brane Calculus; interestingly, the associated strong bisimulation is a congruence. Then, we give a stochastic semantics to Brane systems by defining them as Markov processes over the measurable space generated by terms up-to syntactic congruence, and where the measures are indexed by the actions of this new LTS. Finally, we provide an SOS presentation of this stochastic semantics, which is compositional and syntax-driven, and moreover the induced rate bisimilarity is a congruence

Investigating modularity in the analysis of process algebra models of biochemical systems

Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in a formalism which allows the problem to be tackled compositionally. In this paper we consider the extent to which the compositional structure which is inherent in process algebra models of biochemical systems can be exploited during model solution. In essence this means using the compositional structure to guide decomposed solution and analysis. Unfortunately the dynamic behaviour of biochemical systems exhibits strong interdependencies between the components of the model making decomposed solution a difficult task. Nevertheless we believe that if such decomposition based on process algebras could be established it would demonstrate substantial benefits for systems biology modelling. In this paper we present our preliminary investigations based on a case study of the pheromone pathway in yeast, modelling in the stochastic process algebra Bio-PEPA

Unwinding biological systems

Unwinding conditions have been fruitfully exploited in Information Flow Security to define persistent security properties. In this paper we investigate their meaning and possible uses in the analysis of biological systems. In particular, we elaborate on the notion of robustness and propose some instances of unwinding over the process algebra Bio-PEPA and over hybrid automata. We exploit such instances to analyse two case-studies: Neurospora crassa circadian system and Influenza kinetics models