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

Methodologies synthesis

This deliverable deals with the modelling and analysis of interdependencies between critical infrastructures, focussing attention on two interdependent infrastructures studied in the context of CRUTIAL: the electric power infrastructure and the information infrastructures supporting management, control and maintenance functionality. The main objectives are: 1) investigate the main challenges to be addressed for the analysis and modelling of interdependencies, 2) review the modelling methodologies and tools that can be used to address these challenges and support the evaluation of the impact of interdependencies on the dependability and resilience of the service delivered to the users, and 3) present the preliminary directions investigated so far by the CRUTIAL consortium for describing and modelling interdependencies

Availability modeling and evaluation on high performance cluster computing systems

Cluster computing has been attracting more and more attention from both the industrial and the academic world for its enormous computing power, cost effective, and scalability. Beowulf type cluster, for example, is a typical High Performance Computing (HPC) cluster system. Availability, as a key attribute of the system, needs to be considered at the system design stage and monitored at mission time. Moreover, system monitoring is a must to help identify the defects and ensure the system\u27s availability requirement. In this study, novel solutions which provide availability modeling, model evaluation, and data analysis as a single framework have been investigated. Three key components in the investigation are availability modeling, model evaluation, and data analysis. The general availability concepts and modeling techniques are briefly reviewed. The system\u27s availability model is divided into submodels based upon their functionalities. Furthermore, an object oriented Markov model specification to facilitate availability modeling and runtime configuration has been developed. Numerical solutions for Markov models are examined, especially on the uniformization method. Alternative implementations of the method are discussed; particularly on analyzing the cost of an alternative solution for small state space model, and different ways for solving large sparse Markov models. The dissertation also presents a monitoring and data analysis framework, which is responsible for failure analysis and availability reconfiguration. In addition, the event logs provided from the Lawrence Livermore National Laboratory have been studied and applied to validate the proposed techniques

Modelling and Simulation of Queuing Models through the concept of Petri Nets

In recent years Petri Nets has been in demand due to its visual depiction. Petri Nets are used as an effective method for portraying synchronization, a concurrency between different system activities. In queuing models Petri networks are used to represent distributed modeling of the system and thus evaluate their performance. By specifying suitable stochastic Petri Nets models, the authors concentrate on representing multi-class queuing systems of various queuing disciplines. The key idea is to define SPN models that simulate a given queue discipline 's behavior with some acceptable random choice. Authors have find system queuing with both a single server and multiple servers with load-dependent service rate. Petri networks in the queuing model have enhanced scalability by combining queuing and modeling power expressiveness of 'petri networks.' Examples of application of SPN models to performance evaluation of multiprocessor systems demonstrate the utility and effectiveness of this modeling method. In this paper, authors have made use of Stochastic Petri nets in queuing models to evaluate the performance of the system

WS-Pro: a Petri net based performance-driven service composition framework

As an emerging area gaining prevalence in the industry, Web Services was established to satisfy the needs for better flexibility and higher reliability in web applications. However, due to the lack of reliable frameworks and difficulties in constructing versatile service composition platform, web developers encountered major obstacles in large-scale deployment of web services. Meanwhile, performance has been one of the major concerns and a largely unexplored area in Web Services research. There is high demand for researchers to conceive and develop feasible solutions to design, monitor, and deploy web service systems that can adapt to failures, especially performance failures. Though many techniques have been proposed to solve this problem, none of them offers a comprehensive solution to overcome the difficulties that challenge practitioners. Central to the performance-engineering studies, performance analysis and performance adaptation are of paramount importance to the success of a software project. The industry learned through many hard lessons the significance of well-founded and well-executed performance engineering plans. An important fact is that it is too expensive to tackle performance evaluation, mostly through performance testing, after the software is developed. This is especially true in recent decades when software complexity has risen sharply. After the system is deployed, performance adaptation is essential to maintaining and improving software system reliability. Performance adaptation provides techniques to mitigate the consequence of performance failures and therefore is an important research issue. Performance adaptation is particularly meaningful for mission-critical software systems and software systems with inevitable frequent performance failures, such as Web Services. This dissertation focuses on Web Services framework and proposes a performance-driven service composition scheme, called WS-Pro, to support both performance analysis and performance adaptation. A formalism of transformation from WS-BPEL to Petri net is first defined to enable the analysis of system properties and facilitate quality prediction. A state-transition based proof is presented to show that the transformed Petri net model correctly simulates the behavior of the WS-BPEL process. The generated Petri net model was augmented using performance data supplied by both historical data and runtime data. Results of executing the Petri nets suggest that optimal composition plans can be achieved based on the proposed method. The performance of service composition procedure is an important research issue which has not been sufficiently treated by researchers. However, such an issue is critical for dynamic service composition, where re-planning must be done in a timely manner. In order to improve the performance of service composition procedure and enhance performance adaptation, this dissertation presents an algorithm to remove loops in the reachability graphs so that a large portion of the computation time of service composition can be moved to a pre-processing unit; hence the response time is shortened during runtime. We also extended the WS-Pro to the ubiquitous computing area to improve fault-tolerance

Automated Customer-Centric Performance Analysis of Generalised Stochastic Petri Nets Using Tagged Tokens

Since tokens in Generalised Stochastic Petri Net (GSPN) models are indistinguishable, it is not always possible to reason about customer-centric performance measures. To remedy this, we propose tagged tokens - a variant of the tagged customer technique used in the analysis of queueing networks. Under this scheme, one token in a structurally restricted net is tagged and its position tracked as it moves around the net. Performance queries can then be phrased in terms of the position of the tagged token. To date, the tagging of customers or tokens has been a time-consuming, manual and model-specific process. By contrast, we present here a completely automated methodology for the tagged token analysis of GSPNs. We first describe an intuitive graphical means of specifying the desired tagging configuration, along with the constraints on GSPN structure which must be observed for tagged tokens to be incorporated. We then present the mappings required for automatically converting a GSPN with a user-specified tagging structure into a Coloured GSPN (CGSPN), and thence into an unfolded GSPN which can be analysed for performance measures of interest by existing tools. We further show how our methodology integrates with Performance Trees, a formalism for the specification of performance queries. We have implemented our approach in the open source PIPE Petri net tool, and use this to illustrate the extra expressibility granted by tagged tokens through the analysis of a GSPN model of a hospitals Accident and Emergency department. © 2009 Elsevier B.V. All rights reserved