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

A petri net formalization of a publish-subscribe process system.

Publish/subscribe systems are getting more and more integrated into the execution of business processes in process aware information systems. This integration enables the distribution of the process logic and increases the scalability and adaptability of the process enactment infrastructure. A consequence is however that the original specified process model doesn't accurately represent the actual running process anymore, as the publish/subscribe specific operations are not incorporated into the original model. In this paper we propose a formal model of a publish/subscribe system that can be integrated into a business process model, creating in this way an accurate representation of the actual runtime process. The resulting model can be used for model checking the executable process: inspect system properties, discover problems and validate changes.

Algorithmic Verification of Asynchronous Programs

Asynchronous programming is a ubiquitous systems programming idiom to manage concurrent interactions with the environment. In this style, instead of waiting for time-consuming operations to complete, the programmer makes a non-blocking call to the operation and posts a callback task to a task buffer that is executed later when the time-consuming operation completes. A co-operative scheduler mediates the interaction by picking and executing callback tasks from the task buffer to completion (and these callbacks can post further callbacks to be executed later). Writing correct asynchronous programs is hard because the use of callbacks, while efficient, obscures program control flow. We provide a formal model underlying asynchronous programs and study verification problems for this model. We show that the safety verification problem for finite-data asynchronous programs is expspace-complete. We show that liveness verification for finite-data asynchronous programs is decidable and polynomial-time equivalent to Petri Net reachability. Decidability is not obvious, since even if the data is finite-state, asynchronous programs constitute infinite-state transition systems: both the program stack and the task buffer of pending asynchronous calls can be potentially unbounded. Our main technical construction is a polynomial-time semantics-preserving reduction from asynchronous programs to Petri Nets and conversely. The reduction allows the use of algorithmic techniques on Petri Nets to the verification of asynchronous programs. We also study several extensions to the basic models of asynchronous programs that are inspired by additional capabilities provided by implementations of asynchronous libraries, and classify the decidability and undecidability of verification questions on these extensions.Comment: 46 pages, 9 figure

Reliability models for dataflow computer systems

The demands for concurrent operation within a computer system and the representation of parallelism in programming languages have yielded a new form of program representation known as data flow (DENN 74, DENN 75, TREL 82a). A new model based on data flow principles for parallel computations and parallel computer systems is presented. Necessary conditions for liveness and deadlock freeness in data flow graphs are derived. The data flow graph is used as a model to represent asynchronous concurrent computer architectures including data flow computers

Computer-aided analysis of concurrent systems

The introduction of concurrency into programs has added to the complexity of the software design process. This is most evident in the design of communications protocols where concurrency is inherent to the behavior of the system. The complexity exhibited by such software systems makes more evident the needs for computer-aided tools for automatically analyzing behavior.The Distributed Systems project at UCI has been developing a suite of tools, based on Petri nets, which support the design and evaluation of concurrent software systems. This paper focuses attention on one of the tools: the reachability graph analyzer (RGA). This tool provides mechanisms for proving general system properties (e.g., deadlock-freeness) as well as system-specific properties. The tool is sufficiently general to allow a user to apply complex user-defined analysis algorithms to reachability graphs. The alternating-bit protocol with a bounded channel is used to demonstrate the power of the tool and to point to future extensions

Dense-Timed Petri Nets: Checking Zenoness, Token liveness and Boundedness

We consider Dense-Timed Petri Nets (TPN), an extension of Petri nets in which each token is equipped with a real-valued clock and where the semantics is lazy (i.e., enabled transitions need not fire; time can pass and disable transitions). We consider the following verification problems for TPNs. (i) Zenoness: whether there exists a zeno-computation from a given marking, i.e., an infinite computation which takes only a finite amount of time. We show decidability of zenoness for TPNs, thus solving an open problem from [Escrig et al.]. Furthermore, the related question if there exist arbitrarily fast computations from a given marking is also decidable. On the other hand, universal zenoness, i.e., the question if all infinite computations from a given marking are zeno, is undecidable. (ii) Token liveness: whether a token is alive in a marking, i.e., whether there is a computation from the marking which eventually consumes the token. We show decidability of the problem by reducing it to the coverability problem, which is decidable for TPNs. (iii) Boundedness: whether the size of the reachable markings is bounded. We consider two versions of the problem; namely semantic boundedness where only live tokens are taken into consideration in the markings, and syntactic boundedness where also dead tokens are considered. We show undecidability of semantic boundedness, while we prove that syntactic boundedness is decidable through an extension of the Karp-Miller algorithm.Comment: 61 pages, 18 figure

A System for Deduction-based Formal Verification of Workflow-oriented Software Models

The work concerns formal verification of workflow-oriented software models using deductive approach. The formal correctness of a model's behaviour is considered. Manually building logical specifications, which are considered as a set of temporal logic formulas, seems to be the significant obstacle for an inexperienced user when applying the deductive approach. A system, and its architecture, for the deduction-based verification of workflow-oriented models is proposed. The process of inference is based on the semantic tableaux method which has some advantages when compared to traditional deduction strategies. The algorithm for an automatic generation of logical specifications is proposed. The generation procedure is based on the predefined workflow patterns for BPMN, which is a standard and dominant notation for the modeling of business processes. The main idea for the approach is to consider patterns, defined in terms of temporal logic,as a kind of (logical) primitives which enable the transformation of models to temporal logic formulas constituting a logical specification. Automation of the generation process is crucial for bridging the gap between intuitiveness of the deductive reasoning and the difficulty of its practical application in the case when logical specifications are built manually. This approach has gone some way towards supporting, hopefully enhancing our understanding of, the deduction-based formal verification of workflow-oriented models.Comment: International Journal of Applied Mathematics and Computer Scienc

Performance Bounds for Synchronized Queueing Networks

Las redes de Petri estocásticas constituyen un modelo unificado de las diferentes extensiones de redes de colas con sincronizaciones existentes en la literatura, válido para el diseño y análisis de prestaciones de sistemas informáticos distribuidos. En este trabajo se proponen técnicas de cálculo de cotas superiores e inferiores de las prestaciones de redes de Petri estocásticas en estado estacionario. Las cotas obtenidas son calculables en tiempo polinómico en el tamaño del modelo, por medio de la resolución de ciertos problemas de programación lineal definidos a partir de la matriz de incidencia de la red (en este sentido, las técnicas desarrolladas pueden considerarse estructurales). Las cotas calculadas dependen sólamente de los valores medios de las variables aleatorias que describen la temporización del sistema, y son independientes de los momentos de mayor orden. Esta independencia de la forma de las distribuciones de probabilidad asociadas puede considerarse como una útil generalización de otros resultados existentes para distribuciones particulares, puesto que los momentos de orden superior son, habitualmente, desconocidos en la realidad y difíciles de estimar. Finalmente, las técnicas desarrolladas se aplican al análisis de diferentes ejemplos tomados de la literatura sobre sistemas informáticos distribuidos y sistemas de fabricación. ******* Product form queueing networks have long been used for the performance evaluation of computer systems. Their success has been due to their capability of naturally expressing sharing of resources and queueing, that are typical situations of traditional computer systems, as well as to their efficient solution algorithms, of polynomial complexity on the size of the model. Unfortunately, the introduction of synchronization constraints usually destroys the product form solution, so that general concurrent and distributed systems are not easily studied with this class of models. Petri nets have been proved specially adequate to model parallel and distributed systems. Moreover, they have a well-founded theory of analysis that allows to investigate a great number of qualitative properties of the system. In the original definition, Petri nets did not include the notion of time, and tried to model only the logical behaviour of systems by describing the causal relations existing among events. This approach showed its power in the specification and analysis of concurrent systems in a way independent of the concept of time. Nevertheless the introduction of a timing specification is essential if we want to use this class of models for the performance evaluation of distributed systems. One of the main problems in the actual use of timed and stochastic Petri net models for the quantitative evaluation of large systems is the explosion of the computational complexity of the analysis algorithms. In general, exact performance results are obtained from the numerical solution of a continuous time Markov chain, whose dimension is given by the size of the state space of the model. Structural computation of exact performance measures has been possible for some subclasses of nets such as those with state machine topology. These nets, under certain assumptions on the stochastic interpretation are isomorphic to Gordon and Newell's networks, in queueing theory terminology. In the general case, efficient methods for the derivation of performance measures are still needed. Two complementary approaches to the derivation of exact measures for the analysis of distributed systems are the utilization of approximation techniques and the computation of bounds. Approximate values for the performance parameters are in general more efficiently derived than the exact ones. On the other hand, "exactness" only exists in theory! In other words, numerical algorithms must be applied in practice for the computation of exact values, therefore making errors is inevitable. Performance bounds are useful in the preliminary phases of the design of a system, in which many parameters are not known accurately. Several alternatives for those parameters should be quickly evaluated, and rejected those that are clearly bad. Exact (and even approximate) solutions would be computationally very expensive. Bounds become useful in these instances since they usually require much less computation effort. The computation of upper and lower bounds for the steady-state performance of timed and stochastic Petri nets is considered in this work. In particular, we study the throughput of transitions, defined as the average number of firings per time unit. For this measure we try to compute upper and lower bounds in polynomial time on the size of the net model, by means of proper linear programming problems defined from the incidence matrix of the net (in this sense, we develop structural techniques). These bounds depend only on the mean values and not on the higher moments of the probability distribution functions of the random variables that describe the timing of the system. The independence of the probability distributions can be viewed as a useful generalization of the performance results, since higher moments of the delays are usually unknown for real cases, and difficult to estimate and assess. From a different perspective, the obtained results can be applied to the analysis of queueing networks extended with some synchronization schemes. Monoclass queueing networks can be mapped on stochastic Petri nets. On the other hand, stochastic Petri nets can be interpreted as monoclass queueing networks augmented with synchronization primitives. Concerning the presentation of this manuscript, it should be mentioned that chapter 1 has been written with the object of giving the reader an outline of the stochastic Petri net model: its definition, terminology, basic properties, and related concepts, together with its deep relation with other classic stochastic network models. Chapter 2 is devoted to the presentation of the net subclasses considered in the rest of the work. The classification presented here is quite different from the one which is usual in the framework of Petri nets. The reason lies on the fact that our classification criterion, the computability of visit ratios for transitions, is introduced for the first time in the field of stochastic Petri nets in this work. The significance of that criterion is based on the important role that the visit ratios play in the computation of upper and lower bounds for the performance of the models. Nevertheless, classical important net subclasses are identified here in terms of the computability of their visit ratios from different parameters of the model. Chapter 3 is concerned with the computation of reachable upper and lower bounds for the most restrictive subclass of those presented in chapter 2: marked graphs. The explanation of this fact is easy to understand. The more simple is the model the more accessible will be the techniques an ideas for the development of good results. Chapter 4 provides a generalization for live and bounded free choice nets of the results presented in the previous chapter. Quality of obtained bounds is similar to that for strongly connected marked graphs: throughput lower bounds are reachable for bounded nets while upper bounds are reachable for 1-bounded nets. Chapter 5 considers the extension to other net subclasses, like mono-T-semiflow nets, FRT-nets, totally open deterministic systems of sequential processes, and persistent nets. The results are of diverse colours. For mono-T-semiflow nets and, therefore, for general FRT-nets, it is not possible (so far) to obtain reachable throughput bounds. On the other hand, for bounded ordinary persistent nets, tight throughput upper bounds are derived. Moreover, in the case of totally open deterministic systems of sequential processes the exact steady-state performance measures can be computed in polynomial time on the net size. In chapter 6 bounds for other interesting performance measures are derived from throughput bounds and from classical queueing theory laws. After that, we explore the introduction of more information from the probability distribution functions of service times in order to improve the bounds. In particular, for Coxian service delay of transitions it is possible to improve the throughput upper bounds of previous chapters which held for more general forms of distribution functions. This improvement shows to be specially fruitful for live and bounded free choice nets. Chapter 7 is devoted to case studies. Several examples taken from literature in the fields of distributed computing systems and manufacturing systems are modelled by means of stochastic Petri nets and evaluated using the techniques developed in previous chapters. Finally, some concluding remarks and considerations on possible extensions of the work are presented