Tools for efficient analysis of concurrent software systems

The ever increasing use of distributed computing as a method of providing added computing power and reliability has sparked interest in methods to model and analyze concurrent hardware/ software systems. Efficient automated analysis tools are needed to aid designers of such systems. The Distributed Systems Project at UCI has been developing a suite of tools (dubbed the P-NUT system) which supports efficient analysis of models of concurrent software. This paper presents the principles which guide the development of P-NUT tools and discusses the development of one of the tools: the Reachability Graph Builder (RGB). The P-NUT approach to tool development has resulted in the production of a highly efficient tool for constructing reachability graphs. The careful design of data structures and associated algorithms has significantly enlarged the class of models which can be analyzed

An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

Workflow-Net Based Cooperative Multi-Agent Systems

Workflow-nets are mathematical frameworks that are used to formally describe, model and implement workflows. First, we propose critical section workflow nets (abbreviated WFCSnet). This framework allows feedbacks in workflow systems while ensuring the soundness of the workflow. Feedback is generally not recommended in workflow systems as they threaten the soundness of the system. The proposed WFCSnet allows safe feedback and limits the maximum number of activities per workflow as required. A theorem for soundness of WFCSnet is presented. Serializability, Separability, Quasi-liveness and CS-Properties of WFCSnet are examined and some theorems and lemmas are proposed to mathematically formalize them. In this thesis, we define some formal constructs that we then build upon. We define the smallest formal sub-workflow that we call a unit. We propose some mathematical characteristics for the unit and show how it can be used. We study similarities between units and whether two units can be used interchangeably or not. We then use composites out of simple units to build more complex constructs and we study their properties. We define the concept of cooperation and propose a mathematical definition of the concept. We discuss the concept of task coverage and how it affects cooperation. We claim that task coverage is necessary for any task to be achieved and therefore, a necessity for cooperation. We use mathematical methods to determine the task coverage and the candidate cooperative partners based on their capabilities that can contribute to the desired task. Workflow-net based cooperative behaviour among agents is proposed. First, we propose a cooperative algebra, which takes the desired objective of cooperation as a plan and then transforms this plan into a workflow-net structure describing dependencies and concurrency among sub-workflow elements constituting the overall plan. Our proposed cooperative algebra converts the plan into a set of matrices that model the cooperative workflow among agents. We then propose a cooperative framework with operators that assign tasks to agents based on their capabilities to achieve the required task

A petri net toolkit for parallel program debugging

An effective debugger must support the language and operating system resource abstractions that are available to the programmer. Earlier debuggers worked at the machine architecture level: they dealt with machine instructions and registers. Current debuggers, designed for single process debugging, permit access to program variables and breakpoints and single-stepping at the level of high-level language statements. Eventhough the current debuggers, are already implemented to be a powerful tool, they still cannot do a job of parallel debugger. In this thesis, a computer simulation system has been established by Petri Nets execution providing a convenient and friendly interface as it allows the user to do parallel program debugging. The Parallel Debugger is simulated by providing a time parameter for each transition and thus simulating the net performance. Hitherto, this time parameter can either be constant or exponentially distributed

Socionic Multi-Agent Systems Based on Reflexive Petri Nets and Theories of Social Self-Organisation

This contribution summarises the core results of the transdisciplinary ASKO project, part of the German DFG's programme Sozionik, which combines sociologists' and computer scientists' skills in order to create improved theories and models of artificial societies. Our research group has (a) formulated a social theory, which is able to explain fundamental mechanisms of self-organisation in both natural and artificial societies, (b) modelled this in a mathematical way using a visual formalism, and (c) developed a novel multi-agent system architecture which is conceptually coherent, recursively structured (hence non-eclectic) and based on our social theory. The article presents an outline of both a sociological middle-range theory of social self-organisation in educational institutions, its formal, Petri net based model, including a simulation of one of its main mechanisms, and the multi-agent system architecture SONAR. It describes how the theory was created by a re-analysis of some grand social theories, by grounding it empirically, and finally how the theory was evaluated by modelling its concepts and statements.Multi-Agents Systems, Petri Nets, Self-Organisation, Social Theories

Modularization of biochemical networks based on classification of Petri net t-invariants

<p>Abstract</p> <p>Background</p> <p>Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.</p> <p>With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system.</p> <p>Methods</p> <p>Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied.</p> <p>Results</p> <p>We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in <it>Saccharomyces cerevisiae</it>) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability.</p> <p>Conclusion</p> <p>We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.</p

Simulation of Mass Vaccination Programs: Centralized versus Mobile Vaccination

Vaccines of different types and purposes are crucial for preventing the spread of deadly infectious diseases. However, deploying vaccines in highly populated areas proves to be a great challenge that must be evaluated and planned thoroughly before relying on any possible mass vaccination program. First, this paper highlights the significant differences between centralized and mobile mass vaccination programs. Then, it proposes workflows for these two programs. These workflows are used as a foundation for model building using Petri Nets. Finally, the models are implemented in the GPenSIM tool. This paper also presents a case study using the population in the municipality of Stavanger, showing the results of the simulations.publishedVersio

Representing Resources in Petri Net Models: Hardwiring or Soft-coding?

©2011 IEEE. Reprinted, with permission, from : Reggie Davidrajuh; Representing Resources in Petri Net Models : Hardwiring or Soft-coding?, 2011 IEEE International Conference on Service Operations, Logistics, and Informatics (SOLI), 2011; Beijing, China. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of the University of Stavanger's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to pubs‐[email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.This paper presents an interesting design problem in developing a new tool for discrete-event dynamic systems (DEDS). A new tool known as GPenSIM was developed for modeling and simulation of DEDS; GPenSIM is based on Petri Nets. The design issue this paper talks about is whether to represent resources in DEDS hardwired as a part of the Petri net structure (which is the widespread practice) or to soft code as common variables in the program code. This paper shows that soft coding resources give benefits such as simpler and skinny models