828 research outputs found

    Petri nets for systems and synthetic biology

    Get PDF
    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

    On Zone-Based Analysis of Duration Probabilistic Automata

    Full text link
    We propose an extension of the zone-based algorithmics for analyzing timed automata to handle systems where timing uncertainty is considered as probabilistic rather than set-theoretic. We study duration probabilistic automata (DPA), expressing multiple parallel processes admitting memoryfull continuously-distributed durations. For this model we develop an extension of the zone-based forward reachability algorithm whose successor operator is a density transformer, thus providing a solution to verification and performance evaluation problems concerning acyclic DPA (or the bounded-horizon behavior of cyclic DPA).Comment: In Proceedings INFINITY 2010, arXiv:1010.611

    Parallel symbolic state-space exploration is difficult, but what is the alternative?

    Full text link
    State-space exploration is an essential step in many modeling and analysis problems. Its goal is to find the states reachable from the initial state of a discrete-state model described. The state space can used to answer important questions, e.g., "Is there a dead state?" and "Can N become negative?", or as a starting point for sophisticated investigations expressed in temporal logic. Unfortunately, the state space is often so large that ordinary explicit data structures and sequential algorithms cannot cope, prompting the exploration of (1) parallel approaches using multiple processors, from simple workstation networks to shared-memory supercomputers, to satisfy large memory and runtime requirements and (2) symbolic approaches using decision diagrams to encode the large structured sets and relations manipulated during state-space generation. Both approaches have merits and limitations. Parallel explicit state-space generation is challenging, but almost linear speedup can be achieved; however, the analysis is ultimately limited by the memory and processors available. Symbolic methods are a heuristic that can efficiently encode many, but not all, functions over a structured and exponentially large domain; here the pitfalls are subtler: their performance varies widely depending on the class of decision diagram chosen, the state variable order, and obscure algorithmic parameters. As symbolic approaches are often much more efficient than explicit ones for many practical models, we argue for the need to parallelize symbolic state-space generation algorithms, so that we can realize the advantage of both approaches. This is a challenging endeavor, as the most efficient symbolic algorithm, Saturation, is inherently sequential. We conclude by discussing challenges, efforts, and promising directions toward this goal

    Optimal trajectory generation for Petri nets

    Get PDF
    Recently, the increasing complexity of IT systems requires the early verification and validation of the system design in order to avoid the costly redesign. Furthermore, the efficiency of system operation can be improved by solving system optimization problems (like resource allocation and scheduling problems). Such combined optimization and validation, verification problems can be typically expressed as reachability problems with quantitative or qualitative measurements. The current paper proposes a solution to compute the optimal trajectories for Petri net-based reachability problems with cost parameters. This is an improved variant of the basic integrated verification and optimization method introduced in [11] combining the efficiency of Process Network Synthesis optimization algorithms with the modeling power of Petri nets

    TCTL model checking of Time Petri Nets

    Get PDF
    International audienceIn this paper, we consider \emph{subscript} TCTL for Time Petri Nets (TPN-TCTL) for which temporal operators are extended with a time interval, specifying a time constraint on the firing sequences. We prove that the model-checking of a TPN-TCTL formula on a bounded TPN is decidable and is a PSPACE-complete problem. We propose a zone based state space abstraction that preserves marking reachability and traces of the TPN. As for Timed Automata (TA), the abstraction may use an over-approximation operator on zones to enforce the termination. A coarser (and efficient) abstraction is then provided and proved exact w.r.t. marking reachability and traces (LTL properties). Finally, we consider a subset of TPN-TCTL properties for which it is possible to propose efficient on-the-fly model-checking algorithms. Our approach consists in computing and exploring the zone based state space abstractio

    Symbolic Model-Checking using ITS-tools

    Get PDF
    International audienceWe present the symbolic model-checking toolset ITS-tools. The model-checking back-end engine is based on hierarchical set decision diagrams (SDD) and supports reachability, CTL and LTL model-checking, using both classical and original algorithms. As front-end input language, we promote a Guarded Action Language (GAL), a simple yet expressive language for concurrency. Transformations from popular formalisms into GAL are provided enabling fully symbolic model-checking of third party (Uppaal, Spin, Divine...) specifications. The tool design allows to easily build your own transformation, leveraging tools from the meta-modeling community. The ITS-tools additionally come with a user friendly GUI embedded in Eclipse
    corecore