The planning coordinator: A design architecture for autonomous error recovery and on-line planning of intelligent tasks

Developing a robust, task level, error recovery and on-line planning architecture is an open research area. There is previously published work on both error recovery and on-line planning; however, none incorporates error recovery and on-line planning into one integrated platform. The integration of these two functionalities requires an architecture that possesses the following characteristics. The architecture must provide for the inclusion of new information without the destruction of existing information. The architecture must provide for the relating of pieces of information, old and new, to one another in a non-trivial rather than trivial manner (e.g., object one is related to object two under the following constraints, versus, yes, they are related; no, they are not related). Finally, the architecture must be not only a stand alone architecture, but also one that can be easily integrated as a supplement to some existing architecture. This thesis proposal addresses architectural development. Its intent is to integrate error recovery and on-line planning onto a single, integrated, multi-processor platform. This intelligent x-autonomous platform, called the Planning Coordinator, will be used initially to supplement existing x-autonomous systems and eventually replace them

In-silico-Systemanalyse von Biopathways

Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways. This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways. Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined. A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators. A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway. An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system. Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible. Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care

A modular, qualitative modelling of regulatory networks using Petri nets

International audienceAdvances in high-throughput technologies have enabled the de-lineation of large networks of interactions that control cellular processes. To understand behavioural properties of these complex networks, mathematical and computational tools are required. The multi-valued logical formalism, initially defined by R. Thomas and co-workers, proved well adapted to account for the qualitative knowledge available on regulatory interactions, and also to perform analyses of their dynamical properties. In this context, we present two representations of logical models in terms of Petri nets. In a first step, we briefly show how logical models of regulatory networks can be transposed into standard (place/transition) Petri nets, and discuss the capabilities of such representation. In the second part, we focus on logical regulatory modules and their composition, demonstrating that a high-level Petri net representation greatly facilitates the modelling of interconnected modules. Doing so, we introduce an explicit means to integrate signals from various interconnected modules, taking into account their spatial distribution. This provides a flexible modelling framework to handle regulatory networks that operate at both intra-and intercellular levels. As an illustration, we describe a simplified model of the segment-polarity module involved in the segmentation of the Drosophila embryo

Model-based engineering of animated interactive systems for the interactive television environment

Les interfaces graphiques étaient la plupart du temps statiques, et représentaient une succession d'états logiciels les uns après les autres. Cependant, les transitions animées entre ces états statiques font partie intégrante des interfaces utilisateurs modernes, et leurs processus de design et d'implémentations constituent un défi pour les designers et les développeurs. Cette thèse propose un processus de conception de systèmes interactifs centré sur les animations, ainsi qu'une architecture pour la définition et l'implémentation d'animations au sein des interfaces graphiques. L'architecture met en avant une approche à deux niveaux pour définir une vue haut niveau d'une animation (avec un intérêt particulier pour les objets animés, leurs propriétés à être animé et la composition d'animations) ainsi qu'une vue bas niveau traitant des aspects détaillés des animations tels que les timings et les optimisations. Concernant les spécifications formelles de ces deux niveaux, nous utilisons une approche qui facilite les réseaux de Petri orientés objets pour la conception, l'implémentation et la validation d'interfaces utilisateurs animées en fournissant une description complète et non-ambiguë de l'ensemble de l'interface utilisateur, y compris les animations. Enfin, nous décrivons la mise en pratique du processus présenté, illustré par un cas d'étude d'un prototype haute-fidélité d'une interface utilisateur, pour le domaine de la télévision interactive. Ce processus conduira à une spécification formelle et détaillée du système interactif, et incluera des animations utilisant des réseaux de Petri orientés objet (conçus avec l'outil PetShop CASE).Graphical User Interfaces used to be mostly static, representing one software state after the other. However, animated transitions between these static states are an integral part in modern user interfaces and processes for both their design and implementation remain a challenge for designers and developers. This thesis proposes a process for designing interactive systems focusing on animations, along with an architecture for the definition and implementation of animation in user interfaces. The architecture proposes a two levels approach for defining a high-level view of an animation (focusing on animated objects, their properties to be animated and on the composition of animations) and a low-level one dealing with detailed aspects of animations such as timing and optimization. For the formal specification of these two levels, we are using an approach facilitating object-oriented Petri nets to support the design, implementation and validation of animated user interfaces by providing a complete and unambiguous description of the entire user interface including animations. Finally, we describe the application of the presented process exemplified by a case study for a high-fidelity prototype of a user interface for the interactive Television domain. This process will lead to a detailed formal specification of the interactive system, including animations using object-oriented Petri nets (designed with the PetShop CASE tool)

Mathematical Formula Recognition and Automatic Detection and Translation of Algorithmic Components into Stochastic Petri Nets in Scientific Documents

A great percentage of documents in scientific and engineering disciplines include mathematical formulas and/or algorithms. Exploring the mathematical formulas in the technical documents, we focused on the mathematical operations associations, their syntactical correctness, and the association of these components into attributed graphs and Stochastic Petri Nets (SPN). We also introduce a formal language to generate mathematical formulas and evaluate their syntactical correctness. The main contribution of this work focuses on the automatic segmentation of mathematical documents for the parsing and analysis of detected algorithmic components. To achieve this, we present a synergy of methods, such as string parsing according to mathematical rules, Formal Language Modeling, optical analysis of technical documents in forms of images, structural analysis of text in images, and graph and Stochastic Petri Net mapping. Finally, for the recognition of the algorithms, we enriched our rule based model with machine learning techniques to acquire better results

Computer-aided HAZOP of batch processes

The modern batch chemical processing plants have a tendency of increasing technological complexity and flexibility which make it difficult to control the occurrence of accidents. Social and legal pressures have increased the demands for verifying the safety of chemical plants during their design and operation. Complete identification and accurate assessment of the hazard potential in the early design stages is therefore very important so that preventative or protective measures can be integrated into future design without adversely affecting processing and control complexity or capital and operational costs. Hazard and Operability Study (HAZOP) is a method of systematically identifying every conceivable process deviation, its abnormal causes and adverse hazardous consequences in the chemical plants. [Continues.

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

Methodology for automated Petri Net model generation to support Reliability Modelling

As the complexity of engineering systems and processes increases, determining their optimal performance also becomes increasingly complex. There are various reliability methods available to model performance but generating the models can become a significant task that is cumbersome, error-prone and tedious. Hence, over the years, work has been undertaken into automatically generating reliability models in order to detect the most critical components and design errors at an early stage, supporting alternative designs. Earlier work lacks full automation resulting in semi-automated methods since they require user intervention to import system information to the algorithm, focus on specific domains and cannot accurately model systems or processes with control loops and dynamic features. This thesis develops a novel method that can generate reliability models for complex systems and processes, based on Petri Net models. The process has been fully automated with software developed that extracts the information required for the model from a topology diagram that describes the system or process considered and generates the corresponding mathematical and graphical representations of the Petri Net model. Such topology diagrams are used in industrial sectors, ranging from aerospace and automotive engineering to finance, defence, government, entertainment and telecommunications. Complex real-life scenarios are studied to demonstrate the application of the proposed method, followed by the verification, validation and simulation of the developed Petri Net models. Thus, the proposed method is seen to be a powerful tool to automatically obtain the PN modelling formalism from a topology diagram, commonly used in industry, by: - Handling and efficiently modelling systems and processes with a large number of components and activities respectively, dependent events and control loops. - Providing generic domain applicability. - Providing software independence by generating models readily understandable by the user without requiring further manipulation by any industrial software. Finally, the method documented in this thesis enables engineers to conduct reliability and performance analysis in a timely manner that ensures the results feed into the design process

Performance evaluation and sequence control of an automatedmanufacturing system

In an automated sequential manufacturing system Programmable Logic Controllers (PLC) are widely used. As the control specification varies, the control software needs to be rewritten to accommodate the new specification. Since PLC has high flexibility, one can update the current system while it is running thereby making easier implementation. In order to design flexible, reusable and maintainable control software, a good modeling tool is required. Petri nets are such a tool. Which facilitates analysis of behavioral properties, performance evaluation, and systematic construction of discrete event simulators and controllers. In this thesis a system with one robot and five sequential work stations is used as an example of an automated system. To illustrate the Petri net method, performance and other properties of this system are evaluated. The PLC program is also developed for sequence control of the system