Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Towards a Maude tool for model checking temporal graph properties

We present our prototypical tool for the verification of graph transformation systems. The major novelty of our tool is that it provides a model checker for temporal graph properties based on counterpart semantics for quantified m-calculi. Our tool can be considered as an instantiation of our approach to counterpart semantics which allows for a neat handling of creation, deletion and merging in systems with dynamic structure. Our implementation is based on the object-based machinery of Maude, which provides the basics to deal with attributed graphs. Graph transformation systems are specified with term rewrite rules. The model checker evaluates logical formulae of second-order modal m-calculus in the automatically generated CounterpartModel (a sort of unfolded graph transition system) of the graph transformation system under study. The result of evaluating a formula is a set of assignments for each state, associating node variables to actual nodes

Symmetry Reduction Enables Model Checking of More Complex Emergent Behaviours of Swarm Navigation Algorithms

The emergent global behaviours of robotic swarms are important to achieve their navigation task goals. These emergent behaviours can be verified to assess their correctness, through techniques like model checking. Model checking exhaustively explores all possible behaviours, based on a discrete model of the system, such as a swarm in a grid. A common problem in model checking is the state-space explosion that arises when the states of the model are numerous. We propose a novel implementation of symmetry reduction, in the form of encoding navigation algorithms relatively with respect to a reference, based on the symmetrical properties of swarms in grids. We applied the relative encoding to a swarm navigation algorithm, Alpha, modelled for the NuSMV model checker. A comparison of the state-space and verification results with an absolute (or global) and a relative encoding of the Alpha algorithm highlights the advantages of our approach, allowing model checking larger grid sizes and number of robots, and consequently, verifying more complex emergent behaviours. For example, a property was verified for a grid with 3 robots and a maximum allowed size of 8x8 cells in a global encoding, whereas this size was increased to 16x16 using a relative encoding. Also, the time to verify a property for a swarm of 3 robots in a 6x6 grid was reduced from almost 10 hours to only 7 minutes. Our approach is transferable to other swarm navigation algorithms.Comment: Accepted for presentation in Towards Autonomous Robotic Systems (TAROS) 2015, Liverpool, U

Real-time and Probabilistic Temporal Logics: An Overview

Over the last two decades, there has been an extensive study on logical formalisms for specifying and verifying real-time systems. Temporal logics have been an important research subject within this direction. Although numerous logics have been introduced for the formal specification of real-time and complex systems, an up to date comprehensive analysis of these logics does not exist in the literature. In this paper we analyse real-time and probabilistic temporal logics which have been widely used in this field. We extrapolate the notions of decidability, axiomatizability, expressiveness, model checking, etc. for each logic analysed. We also provide a comparison of features of the temporal logics discussed

Towards the specification and verification of modal properties for structured systems

System specification formalisms should come with suitable property specification languages and effective verification tools. We sketch a framework for the verification of quantified temporal properties of systems with dynamically evolving structure. We consider visual specification formalisms like graph transformation systems (GTS) where program states are modelled as graphs, and the program behavior is specified by graph transformation rules. The state space of a GTS can be represented as a graph transition system (GTrS), i.e. a transition system with states and transitions labelled, respectively, with a graph, and with a partial morphism representing the evolution of state components. Unfortunately, GTrSs are prohibitively large or infinite even for simple systems, making verification intractable and hence calling for appropriate abstraction techniques

A Temporal Logic for Hyperproperties

Hyperproperties, as introduced by Clarkson and Schneider, characterize the correctness of a computer program as a condition on its set of computation paths. Standard temporal logics can only refer to a single path at a time, and therefore cannot express many hyperproperties of interest, including noninterference and other important properties in security and coding theory. In this paper, we investigate an extension of temporal logic with explicit path variables. We show that the quantification over paths naturally subsumes other extensions of temporal logic with operators for information flow and knowledge. The model checking problem for temporal logic with path quantification is decidable. For alternation depth 1, the complexity is PSPACE in the length of the formula and NLOGSPACE in the size of the system, as for linear-time temporal logic