Second Workshop on Practical Use of Coloured Petri Nets and Design/CPN.

This report contains the proceedings of the Second Workshop on Practical Use of Coloured Petri Nets and Design/CPN, October 13-15, 1999. The workshop was organised by the CPN group at the Department of Computer Science at the University of Aarhus, Denmark. The individual papers are available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop99

Analysis of Two-Layer Protocols: DCCP Simultaneous-Open and Hole Punching Procedures

The simultaneous-open procedure of the Datagram Congestion Control Protocol (DCCP), RFC 5596, was published in September 2009. Its design aims to overcome DCCP weaknesses when the Server is behind a middle box, such as Network Address Translators or firewalls. The original DCCP specification, RFC 4340, only allows the Client to initiate the call. The call request cannot reach the Server behind the middle box. A widely used solution to address this problem is called the hole punching technique. This technique requires the Server to initiate sending packets. Using Coloured Petri Nets (CPN) this paper models and analyses the DCCP procedure specified in RFC 5596. However, the difficulty is that detailed modelling of the address translation is also required. This causes state space explosion. We alleviate the state explosion using prioritized transitions and the sweep-line technique. Modelling and analysis approaches are discussed in the hope that it is helpful for others who wish to analyse similar protocols. Analysis results are also obtained for the simultaneous-open procedure specified in RFC 5596

A Polynomial Translation of pi-calculus FCPs to Safe Petri Nets

We develop a polynomial translation from finite control pi-calculus processes to safe low-level Petri nets. To our knowledge, this is the first such translation. It is natural in that there is a close correspondence between the control flows, enjoys a bisimulation result, and is suitable for practical model checking.Comment: To appear in special issue on best papers of CONCUR'12 of Logical Methods in Computer Scienc

Reconciling a component and process view

In many cases we need to represent on the same abstraction level not only system components but also processes within the system, and if for both representation different frameworks are used, the system model becomes hard to read and to understand. We suggest a solution how to cover this gap and to reconcile component and process views on system representation: a formal framework that gives the advantage of solving design problems for large-scale component systems.Comment: Preprint, 7th International Workshop on Modeling in Software Engineering (MiSE) at ICSE 201

Practical Use of High-level Petri Nets

This booklet contains the proceedings of the Workshop on Practical Use of High-level Petri Nets, June 27, 2000. The workshop is part of the 21st International Conference on Application and Theory of Petri Nets organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The workshop papers are available in electronic form via the web pages: http://www.daimi.au.dk/pn2000/proceeding

Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics.

BACKGROUND: The epidermal growth factor receptor (EGFR) signaling pathway plays a key role in regulation of cellular growth and development. While highly studied, it is still not fully understood how the signal is orchestrated. One of the reasons for the complexity of this pathway is the extensive network of inter-connected components involved in the signaling. In the aim of identifying critical mechanisms controlling signal transduction we have performed extensive analysis of an executable model of the EGFR pathway using the stochastic pi-calculus as a modeling language. RESULTS: Our analysis, done through simulation of various perturbations, suggests that the EGFR pathway contains regions of functional redundancy in the upstream parts; in the event of low EGF stimulus or partial system failure, this redundancy helps to maintain functional robustness. Downstream parts, like the parts controlling Ras and ERK, have fewer redundancies, and more than 50% inhibition of specific reactions in those parts greatly attenuates signal response. In addition, we suggest an abstract model that captures the main control mechanisms in the pathway. Simulation of this abstract model suggests that without redundancies in the upstream modules, signal transduction through the entire pathway could be attenuated. In terms of specific control mechanisms, we have identified positive feedback loops whose role is to prolong the active state of key components (e.g., MEK-PP, Ras-GTP), and negative feedback loops that help promote signal adaptation and stabilization. CONCLUSIONS: The insights gained from simulating this executable model facilitate the formulation of specific hypotheses regarding the control mechanisms of the EGFR signaling, and further substantiate the benefit to construct abstract executable models of large complex biological networks.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Petri net based development of globally-asynchronous locally-synchronous distributed embedded systems

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de ComputadoresA model-based development approach (MBDA) for Globally-Asynchronous Locally- Synchronous (GALS) Distributed Embedded Systems (DESs) is proposed. This approach relies on the GALS-DESs specification through (low- or high-level) Petri net classes, which ensure that the created models are GALS, locally deterministic, distributable, networkindependent, and platform-independent and support their simulation, verification, and implementation (using simulation, model-checking, and code generation tools). The use of network- and platform-independent models enable the use of heterogeneous communication networks to support the distributed components interaction and enable the use of heterogeneous platforms to support the components and the communication nodes implementation. To enable the proposed MBDA, Petri nets are extended with a set of the concepts, most notably time-domains and asynchronous-channels. Algorithms to support the verification of GALS-DES models and their decomposition into implementable sub-models are also proposed. A tool chain framework (IOPT-tools) was extended with this work proposals, supporting their validation and the GALS-DESs development.Fundação para a Ciência e a Tecnologia - grant ref. SFRH/BD/62171/200