Oana Andrei

Structural operational semantics of p systems

The paper formally describes an operational semantics of P systems. We present an abstract syntax of P systems, then the notion of configurations, and we define the sets of inference rules corresponding to the three stages of an evolution step: maximal parallel rewriting, parallel communication, and parallel dissolving. Several results assuring the correctness of each set of inference rules are also presented. Finally, we define simulation and bisimulation relations between P systems.

PORGY: Strategy-Driven Interactive Transformation of Graphs

This paper investigates the use of graph rewriting systems as a modelling tool, and advocates the embedding of such systems in an interactive environment. One important application domain is the modelling of biochemical systems, where states are represented by port graphs and the dynamics is driven by rules and strategies. A graph rewriting tools capability to interactively explore the features of the rewriting system provides useful insights into possible behaviours of the model and its properties. We describe PORGY, a visual and interactive tool we have developed to model complex systems using port graphs and port graph rewrite rules guided by strategies, and to navigate in the derivation history. We demonstrate via examples some functionalities provided by PORGY.

A Higher-Order Graph Calculus for Autonomic Computing

In this paper, we present a high-level formalism based on port graph rewriting, strategic rewriting, and rewriting calculus. We argue that this formalism is suitable for modeling autonomic systems and briefly illustrate its expressivity for modeling properties of such systems.

Executable specifications of p systems

This paper presents a natural algebraic specification for the P systems. The specification is executable in Maude, a software system supporting rewriting and equational logic. We define the P system maximal parallel evolution as a specific rewriting strategy in Maude. By extending the Maude rewriting semantics with this strategy, we provide an operational semantics of the P systems. We present few examples of specifying and executing simple P systems, describing how target indications, dissolving and priorities are handled. Moreover, the Maude system allows the verification of various properties of the P systems expressed as linear temporal logic formulas by using a model checker.

Graph Rewriting and Strategies for Modeling Biochemical Networks

In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules, and generation of biochemical networks based on the representation of molecular complexes as a particular type of multi- graphs with ports called molecular graphs. The advantage of this approach is to obtain for free a rewriting calculus which allows defining at the same level transformation rules and strategies for modeling rule selection and application, in order to prototype network generation.

A Port Graph Calculus for Autonomic Computing and Invariant Verification

From our previous work on biochemical applications, the structure of port graph (or multigraph with ports) and a rewriting calculus have proved to be well-suited formalisms for modeling interactions between proteins. Then port graphs have been proposed as a formal model for distributed resources and grid infrastructures, where each resource is modeled by a node with ports. The lack of global information and the autonomous and distributed behavior of components are modeled by a multiset of port graphs and rewrite rules which are applied locally, concurrently, and non-deterministically. Some computations take place wherever it is possible and in parallel, while others may be controlled by strategies. In this paper, we first introduce port graphs as graphs with multiple edges and loops, with nodes having explicit connection points, called ports, and edges attaching to ports of nodes. We then define an abstract biochemical calculus that instantiates to a rewrite calculus on these graphs. Rules and strategies are themselves port graphs, i.e. first-class objects of the calculus. As a consequence, they can be rewritten as well, and rules can create new rules, providing a way of modeling adaptive systems. This approach also provides a formal framework to reason about computations and to verify useful properties. We show how structural properties of a modeled system can be expressed as strategies and checked for satisfiability at each step of the computation. This provides a way to ensure invariant properties of a system. This work is a contribution to the formal specification and verification of adaptive systems and to theoretical foundations of autonomic computing.

A Model and Analysis of the AKAP Scaffold

We study the biochemical processes involved in scaffold-mediated crosstalk between the cAMP and the Raf-1/MEK/ERK pathways. We model the system by a continuous time Markov chain with levels and analyse properties using Continuous Stochastic Logic and the symbolic probabilistic model checker PRISM. We consider two kinds of properties of the model, causal events and pulsating behaviour, and, in order to formulate these properties, we enrich the model with trend formulas. The system is currently under wet-lab investigation and our approach was developed in collaboration with the experimentalists.

Non-intrusive Formal Methods and Strategic Rewriting for a Chemical Application

The concept of formal islands allows adding to existing programming languages, formal features that can be compiled later on into the host language itself, therefore inducing no dependency on the formal language. We illustrate this approach with the TOM system that provides matching, normalization and strategic rewriting, and we give a formal island implementation for the simulation of a chemical reactor.

Probabilistic Formal Analysis of App Usage to Inform Redesign

Evaluation and redesign of user-intensive mobile applications is challenging because users are often heterogeneous, adopting different patterns of activity, at different times. We set out a process of integrating statistical, longitudinal analysis of actual logged behaviours, formal, probabilistic discrete state models of activity patterns, and hypotheses over those models expressed as probabilistic temporal logic properties to inform redesign. We employ formal methods not to the design of the mobile application, but to characterise the different probabilistic patterns of actual use over various time cuts within a population of users. We define the whole process from identifying questions that give us insight into application usage, to event logging, data abstraction from logs, model inference, temporal logic property formulation, visualisation of results, and interpretation in the context of redesign. We illustrate the process through a real-life case study, which results in a new and principled way for selecting content for an extension to the mobile application.

Probabilistic Model Checking of DTMC Models of User Activity Patterns

Software developers cannot always anticipate how users will actually use their software as it may vary from user to user, and even from use to use for an individual user. In order to address questions raised by system developers and evaluators about software usage, we define new probabilistic models that characterise user behaviour, based on activity patterns inferred from actual logged user traces. We encode these new models in a probabilistic model checker and use probabilistic temporal logics to gain insight into software usage. We motivate and illustrate our approach by application to the logged user traces of an iOS app.