Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

Workshop on Modelling of Objects, Components, and Agents, Aarhus, Denmark, August 27-28, 2001

This booklet contains the proceedings of the workshop Modelling of Objects, Components, and Agents (MOCA'01), August 27-28, 2001. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark and the "Theoretical Foundations of Computer Science" Group at the University of Hamburg, Germany. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop01

Z and high level Petri nets

High level Petri nets have tokens with values, traditionally called colors, and transitions that produce tokens in a functional way, using the consumed tokens as arguments of the function application. Large nets should be designed in a topdown approach and therefore we introduce a hierarchical net model which combines a data flow diagram technique with a high level Petri net model. We use Z to specify this net model, which is in fact the metamodel for specific systems. Specific models we specify partly by diagrams and partly in Z. We give some advantages and disadvantages of using Z in this way. Finally we show how to specify systems by means of an example

Context-aware workflow management in eHealth applications

Workflows are a technology to structure work in functional, non-overlapping steps. They define not only the order of execution of the steps, and describe whether steps are executed in parallel, they also specify who or what tool has to fulfill which step. Workflows offer the possibility to automate work, to increase the understandability of processes, and they ease the control of process execution. The tools to manage workflows, so called workflow management systems (WfMSs), are traditionally rigid as they separate workflow definition done at build time from workflow execution done at run time. This makes them ill-suited for managing flexible and unstructured workflows. In this thesis, we focus on the support of flexible processes in eHealth, which are affected by more foreseen than unforeseen events. To bridge the gap between rigid WfMSs and flexible workflows, we developed a concept for dynamic and context-aware workflow management called Flexwoman. Although our focus lies on flexible eHealth processes, Flexwoman is a generic approach that can be applied to several different application domains. Flexwoman supports the usage of context information to adapt processes automatically at run time to foreseen events. Processes can also be manually adapted to handle unforeseen events. To achieve this flexibility, context information from different sensors is unified and thus can be analyzed in the same way. The analysis and adaptation of workflows is executed with a rule engine. A rule engine can store, reason about and apply knowledge automatically and efficiently. Rules and application logic are separated, thus, rules can be changed during run time without affecting application logic or process description. Workflows are internally described by Hierarchical Colored Petri nets (HCPNs) and executed by a HCPN execution engine. HCPNs allow for a deterministic execution of workflows and can represent workflows on different levels of detail. In summary, in Flexwoman, significant context changes (events) trigger automated adaptations that replace parts of the workflow by sub workflows, which can in turn be adapted. The adaptations and the rules for context-aware adaptation are saved in the organizational memory for later reuse. Flexwoman’s event based behavior facilitates proactive adaptations instead of only allowing for adaptations while entering or leaving a task. Replacements are not bound to special places defined at build time but each part of the workflow, which has not been executed yet, can be replaced at run time. We implemented and evaluated the concept. The evaluations show i) that all required functionality is available, ii) that the system scales with a growing number of rules, and iii) that the system correctly handles failure situations

Coloured Petri nets for multi-level, multiscale, and multi-dimensional modelling of biological systems

Owing to the availability of data of one biological phenomenon at different levels/scales, modelling of biological systems is moving from single level/scale to multiple levels/scales, which introduces a number of challenges. Coloured Petri nets (ColPNs) have been successfully applied to multilevel, multiscale and multidimensional modelling of some biological systems, addressing many of these challenges. In this article, we first review the basics of ColPNs and some popular extensions, and then their applications for multilevel, multiscale and multidimensional modelling of biological systems. This understanding of how to use ColPNs for modelling biological systems will assist readers in selecting appropriate ColPN classes for specific modelling circumstances

Toward Accessible Multilevel Modeling in Systems Biology: A Rule-based Language Concept

Promoted by advanced experimental techniques for obtaining high-quality data and the steadily accumulating knowledge about the complexity of life, modeling biological systems at multiple interrelated levels of organization attracts more and more attention recently. Current approaches for modeling multilevel systems typically lack an accessible formal modeling language or have major limitations with respect to expressiveness. The aim of this thesis is to provide a comprehensive discussion on associated problems and needs and to propose a concrete solution addressing them

Sixth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools Aarhus, Denmark, October 24-26, 2005

This booklet contains the proceedings of the Sixth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 24-26, 2005. 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

A Conceptual Framework for Adapation

This paper presents a white-box conceptual framework for adaptation that promotes a neat separation of the adaptation logic from the application logic through a clear identification of control data and their role in the adaptation logic. The framework provides an original perspective from which we survey archetypal approaches to (self-)adaptation ranging from programming languages and paradigms, to computational models, to engineering solutions