Ninth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 20-22, 2008

This booklet contains the proceedings of the Ninth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 20-22, 2008. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop0

Third Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, August 29-31, 2001

This booklet contains the proceedings of the Third Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, August 29-31, 2001. The workshop is organised by the CPN group at Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop01

Translation Of AADL To PNML To Ensure The Utilization Of Petri Nets

Architecture Analysis and Design Language (AADL), which is used to design and analyze software and hardware architectures of embedded and real-time systems, has proven to be a very efficient way of expressing the non-functional properties of safety-critical systems and architectural modeling. Petri nets are the graphical and mathematical modeling tools used to describe and study information processing systems characterized as concurrent and distributed. As AADL lacks the formal semantics needed to show the functional properties of such systems, the objective of this research was to extend AADL to enable other Petri nets to be incorporated into Petri Net Markup Language (PNML), an interchange language for Petri nets. PNML makes it possible to incorporate different types of analysis using different types of Petri net. To this end, the interchange format Extensible Markup Language (XML) was selected and AADL converted to AADL-XML (the XML format of AADL) and Petri nets to PNML, the XML-format of Petri nets, via XSLT script. PNML was chosen as the transfer format for Petri nets due to its universality, which enables designers to easily map PNML to many different types of Petri nets. Manual conversion of AADL to PNML is error-prone and tedious and thus requires automation, so XSLT script was utilized for the conversion of the two languages in their XML format. Mapping rules were defined for the conversion from AADL to PNML and the translation to XSLT automated. Finally, a PNML plug-in was designed and incorporated into the Open Source AADL Tool Environment (OSATE)

Eighth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 22-24, 2007

This booklet contains the proceedings of the Eighth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 22-24, 2007. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop0

Faster simulation of (Coloured) Petri nets using parallel computing

International audienceFast simulation, i.e., automatic computation of sequential runs, is widely used to analyse Petri nets. In particular, it enables for quantitative statistical analysis by observing large sets of runs. Moreover, fast simulation may be used to actually run a Petri net model as a (prototype) implementation of a system, in which case such a net would embed fragments of the code of the system. In both these contexts, being able to perform faster simulation is highly desirable. In this paper, we propose a way to accelerate fast simulation by exploiting parallel computing, targeting both the multi-core cpus available nowadays in every laptop or workstation, and larger parallel computers including those with distributed memory (clusters). We design an algorithm to do so and assess in particular its correctness and completeness through its formal modelling as a Petri net whose state space is analysed. We also present a benchmark of a prototype implementation that clearly shows how our algorithm effectively accelerates fast simulation, in particular in the case of large concurrent coloured Petri nets, which is precisely the kind of nets that are usually slow to simulate

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

Tenth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools Aarhus, Denmark, October 19-21, 2009

This booklet contains the proceedings of the Tenth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 19-21, 2009. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.cs.au.dk/CPnets/events/workshop0

A systems biology approach to multi-scale modelling and analysis of planar cell polarity in drosophila melanogaster wing

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Systems biology aims to describe and understand biology at a global scale where biological systems function as a result of complex mechanisms that happen at several scales. Modelling and simulation are computational tools that are invaluable for description, understanding and prediction these mechanisms in a quantitative and integrative way. Thus multi-scale methods that couple the design, simulation and analysis of models spanning several spatial and temporal scales is becoming a new emerging focus of systems biology. This thesis uses an exemplar – Planar cell polarity (PCP) signalling – to illustrate a generic approach to model biological systems at different spatial scales, using the new concept of Hierarchically Coloured Petri Nets (HCPN). PCP signalling refers to the coordinated polarisation of cells within the plane of various epithelial tissues to generate sub-cellular asymmetry along an axis orthogonal to their apical-basal axes. This polarisation is required for many developmental events in both vertebrates and non-vertebrates. Defects in PCP in vertebrates are responsible for developmental abnormalities in multiple tissues including the neural tube, the kidney and the inner ear. In Drosophila wing, PCP is seen in the parallel orientation of hairs that protrude from each of the approximately 30,000 epithelial cells to robustly point toward the wing tip. This work applies HCPN to model a tissue comprising multiple cells hexagonally packed in a honeycomb formation in order to describe the phenomenon of Planar Cell Polarity (PCP) in Drosophila wing. HCPN facilitate the construction of mathematically tractable, compact and parameterised large-scale models. Different levels of abstraction that can be used in order to simplify such a complex system are first illustrated. The PCP system is first represented at an abstract level without modelling details of the cell. Each cell is then sub-divided into seven virtual compartments with adjacent cells being coupled via the formation of intercellular complexes. A more detailed model is later developed, describing the intra- and inter-cellular signalling mechanisms involved in PCP signalling. The initial model is for a wild-type organism, and then a family of related models, permitting different hypotheses to be explored regarding the mechanisms underlying PCP, are constructed. Among them, the largest model consists of 800 cells which when unfolded yields 164,000 places (each of which is described by an ordinary differential equation). This thesis illustrates the power and validity of the approach by showing how the models can be easily adapted to describe well-documented genetic mutations in the Drosophila wing using the proposed approach including clustering and model checking over time series of primary and secondary data, which can be employed to analyse and check such multi-scale models similar to the case of PCP. The HCPN models support the interpretation of biological observations reported in literature and are able to make sensible predictions. As HCPN model multi-scale systems in a compact, parameterised and scalable way, this modelling approach can be applied to other large-scale or multi-scale systems.This study was funded by Brunel University

Seventh Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 24-26, 2006

This booklet contains the proceedings of the Seventh Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 24-26, 2006. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop0