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

Formalization and Correctness of the PALS Architectural Pattern for Distributed Real-Time Systems

Many Distributed Real-Time Systems (DRTS), such as integrated modular avionics systems and distributed control systems in motor vehicles, are made up of a collection of components communicating asynchronously among themselves and with their environment that must change their state and respond to environment inputs within hard real-time bounds. Such systems are often safety-critical and need to be certi???ed; but their certi???cation is currently very hard due to their distributed nature. The Physically Asynchronous Logically Synchronous (PALS) architectural pattern can greatly reduce the design and veri???cation complexities of achieving virtual synchrony in a DTRS. This work presents a formal speci???cation of PALS as a formal model transformation that maps a synchronous design, together with a set of performance bounds of the underlying infrastructure, to a formal DRTS speci???cation that is semantically equivalent to the synchronous design. This semantic equivalence is proved, showing that the formal veri???cation of temporal logic properties of the DRTS can be reduced to their veri???cation on the much simpler synchronous design. An avionics system case study is used to illustrate the usefulness of PALS for formal verification purposes.unpublishednot peer reviewe

Events in Property Patterns

A pattern-based approach to the presentation, codification and reuse of property specifications for finite-state verification was proposed by Dwyer and his collegues. The patterns enable non-experts to read and write formal specifications for realistic systems and facilitate easy conversion of specifications between formalisms, such as LTL, CTL, QRE. In this paper, we extend the pattern system with events - changes of values of variables in the context of LTL.Comment: 14 pages, 3 figure

Trace checking of Metric Temporal Logic with Aggregating Modalities using MapReduce

Modern complex software systems produce a large amount of execution data, often stored in logs. These logs can be analyzed using trace checking techniques to check whether the system complies with its requirements specifications. Often these specifications express quantitative properties of the system, which include timing constraints as well as higher-level constraints on the occurrences of significant events, expressed using aggregate operators. In this paper we present an algorithm that exploits the MapReduce programming model to check specifications expressed in a metric temporal logic with aggregating modalities, over large execution traces. The algorithm exploits the structure of the formula to parallelize the evaluation, with a significant gain in time. We report on the assessment of the implementation - based on the Hadoop framework - of the proposed algorithm and comment on its scalability.Comment: 16 pages, 6 figures, Extended version of the SEFM 2014 pape

10031 Abstracts Collection -- Quantitative Models: Expressiveness and Analysis

From Jan 18 to Jan 22, 2010, the Dagstuhl Seminar 10031 ``Quantitative Models: Expressiveness and Analysis \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Workflow completion patterns

The most common correctness requirement for a (business) workflow is the completion requirement, imposing that, in some form, every case-instance of the workflow reaches its final state. In this paper, we define three workflow completion patterns, called the mandatory, optional and possible completion. These patterns are formalized in terms of the temporal logic CTL*, to remove ambiguities, allow for easy comparison, and have direct applicability. In contrast to the existing methods, we do not look at the control flow in isolation but include some data information as well. In this way the analysis remains tractable but gains precision. Together with our previous work on data-flow (anti-)patterns, this paper is a significant step towards a unifying framework for complete workflow verification, using the well-developed, stable, adaptable, and effective model-checking approach

Model Checking Classes of Metric LTL Properties of Object-Oriented Real-Time Maude Specifications

This paper presents a transformational approach for model checking two important classes of metric temporal logic (MTL) properties, namely, bounded response and minimum separation, for nonhierarchical object-oriented Real-Time Maude specifications. We prove the correctness of our model checking algorithms, which terminate under reasonable non-Zeno-ness assumptions when the reachable state space is finite. These new model checking features have been integrated into Real-Time Maude, and are used to analyze a network of medical devices and a 4-way traffic intersection system.Comment: In Proceedings RTRTS 2010, arXiv:1009.398