Engineering model transformations with transML

The final publication is available at Springer via http://dx.doi.org/10.1007%2Fs10270-011-0211-2Model transformation is one of the pillars of model-driven engineering (MDE). The increasing complexity of systems and modelling languages has dramatically raised the complexity and size of model transformations as well. Even though many transformation languages and tools have been proposed in the last few years, most of them are directed to the implementation phase of transformation development. In this way, even though transformations should be built using sound engineering principles—just like any other kind of software—there is currently a lack of cohesive support for the other phases of the transformation development, like requirements, analysis, design and testing. In this paper, we propose a unified family of languages to cover the life cycle of transformation development enabling the engineering of transformations. Moreover, following an MDE approach, we provide tools to partially automate the progressive refinement of models between the different phases and the generation of code for several transformation implementation languages.This work has been sponsored by the Spanish Ministry of Science and Innovation with project METEORIC (TIN2008-02081), and by the R&D program of the Community of Madrid with projects “e-Madrid" (S2009/TIC-1650). Parts of this work were done during the research stays of Esther and Juan at the University of York, with financial support from the Spanish Ministry of Science and Innovation (grant refs. JC2009-00015, PR2009-0019 and PR2008-0185)

Petri net model decomposition - a model based approach supporting distributed execution

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Electrotécnica, Especialidade de Sistemas Digitais, pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaModel-based systems development has contributed to reducing the enormous difference between the continuous increase of systems complexity and the improvement of methods and methodologies available to support systems development. The choice of the modeling formalism is an important factor for success-fully increasing productivity. Petri nets proved to be a suitable candidate for being chosen as a system specification language due to their natural support of modeling processes with concurrency, synchronization and resource sharing, as well as the mechanisms of composition and decomposition. Also having a formal representation reinforces the choice, given that the use of verification tools is fundamental for complex systems development. This work proposes a method for partitioning Petri net models into concurrent sub-models, supporting their distributed implementation. The IOPT class (Input-Output Place Transition) is used as a reference class. It is extended by directed synchronous communication channels, enabling the com- munication between the generated sub-models. Three rules are proposed to perform the partition, and restrictions of the proposed partition method are identified. It is possible to directly compose models which result from the partitioning operation, through an operation of model addition. This allows the re-use of previously obtained models, as well as the easy modification of the intended system functionalities. The algorithms associated with the implementation of the partition operation are presented, as well as its rules and other procedures. The proposed methods are validated through several case studies emphasizing control components of automation systems

Guidelines for analysis and modelling of reactive software systems

Dissertação de mestrado em Engenharia InformáticaReactive software systems are distinguished by their ability to interact with the environment in which they operate. Their behaviour is affected by a finite set of events that change the system global state. Such systems can be divided into three components: Controller, Users and Physical Entities; this division allows to model the particular behaviour of each component separately. Coloured Petri Nets (CPNs) are a modeling language suitable for behavioural modelling, thus it can be used in the context of these systems. Among several advantages (and some shortcomings), they allow CPN models to be simulated and the formally verified. This dissertation presents a set of guidelines for analysis and modeling of reactive software systems. The guidelines suggest how different components of a system can be identified and characterised. The guidelines also recommend various alternatives for modelling the system components with the CPN modelling language. The guidelines are illustrated with a practical example, which is modelled by means of CPN Tools, a tool for designing CPN models. The application of the guidelines allows CPN models specifically targeted for reactive software systems to benefit from executability, modularity, parameterization, and configurability.Os sistemas de software reativos são caracterizados pela sua capacidade de interagir com o meio em que se inserem. O comportamento dum sistema deste tipo é influenciado por eventos que, quando ocorrem, alteram o estado global desse sistema. Tais sistemas podem ser divididos em três componentes: Controlador, Entidades Físicas e Utilizadores; o que permite modelar sepa- radamente o comportamento que caracteriza cada um desses componentes. As Redes de Petri Coloridas (RdP Coloridas) são uma linguagem de mo- delação adequada a sistemas com uma significativa componente comporta- mental, pelo que podem ser usadas no contexto dos sistemas de software reativos. Entre diversas vantagens (e algumas limitações) elas permitem que os modelos sejam simulados e formalmente verificados. Este trabalho apresenta um conjunto de diretrizes de analise e modelação de sistemas de software reativos. No processo de analise, sugere-se como podem ser identificados e caracterizados os diferentes componentes de um sistema. No processo de modelação, recomendam-se varias formas de modelar cada componente com RdP Coloridas. As diretrizes são ilustradas com um exemplo pratico, o qual é modelado com o auxílio da ferramenta de desenho de RdP Coloridas, CPN Tools. A aplicação das diretrizes no contexto referido permite obter modelos que beneficiam de executabilidade, modularidade, parameterização e configurabilidade

Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes

2015 Copyright is held by the owner/author(s). This article defines a novel spatial-temporal modelling and analysis methodology applied to a systems biology case study, namely phase variation patterning in bacterial colony growth. We employ coloured stochastic Petri nets to construct the model and run stochastic simulations to record the development of the circular colonies over time and space. The simulation output is visualised in 2D, and sector-like patterns are automatically detected and analysed. Space is modelled using 2.5 dimensions considering both a rectangular and circular geometry, and the effects of imposing different geometries on space are measured. We close by outlining an interpretation of the Petri net model in terms of finite difference approximations of partial differential equations (PDEs). One result is the derivation of the “best” nine-point diffusion model. Our multidimensional modelling and analysis approach is a precursor to potential future work on more complex multiscale modelling.EPSRC Research Grant EP I036168/1; German BMBF Research Grant 0315449H

The DS-Pnet modeling formalism for cyber-physical system development

This work presents the DS-Pnet modeling formalism (Dataflow, Signals and Petri nets), designed for the development of cyber-physical systems, combining the characteristics of Petri nets and dataflows to support the modeling of mixed systems containing both reactive parts and data processing operations. Inheriting the features of the parent IOPT Petri net class, including an external interface composed of input and output signals and events, the addition of dataflow operations brings enhanced modeling capabilities to specify mathematical data transformations and graphically express the dependencies between signals. Data-centric systems, that do not require reactive controllers, are designed using pure dataflow models. Component based model composition enables reusing existing components, create libraries of previously tested components and hierarchically decompose complex systems into smaller sub-systems. A precise execution semantics was defined, considering the relationship between dataflow and Petri net nodes, providing an abstraction to define the interface between reactive controllers and input and output signals, including analog sensors and actuators. The new formalism is supported by the IOPT-Flow Web based tool framework, offering tools to design and edit models, simulate model execution on the Web browser, plus model-checking and software/hardware automatic code generation tools to implement controllers running on embedded devices (C,VHDL and JavaScript). A new communication protocol was created to permit the automatic implementation of distributed cyber-physical systems composed of networks of remote components communicating over the Internet. The editor tool connects directly to remote embedded devices running DS-Pnet models and may import remote components into new models, contributing to simplify the creation of distributed cyber-physical applications, where the communication between distributed components is specified just by drawing arcs. Several application examples were designed to validate the proposed formalism and the associated framework, ranging from hardware solutions, industrial applications to distributed software applications

Verifizierbare Entwicklung eines satellitenbasierten Zugsicherungssystems mit Petrinetzen

Nowadays model-based techniques are widely used in system design and development, especially for safety-critical systems such as train control systems. Given a design model, executable codes could be generated automatically from the model following certain transformation rules. A high-quality model of a system provides a good understanding, a favourable structure, a reasonable scale and abstraction level as well as realistic behaviours with respect to the concurrent operation of independent subsystems. Motivated by this principle, a first Coloured Petri Net (CPN) model of a satellite-based train control system (SatZB) with the capability of continuous simulation is developed employing the BASYSNET method which adopts Petri nets as the means of description during the whole development process. After establishing the system model, the verification tasks are identified based on the hazard analysis of the train control system. To verify the identified tasks for quality assurance, verification by means of simulation, formal analysis and testing is carried out considering the four representing system properties: function, state, structure and behaviour. For structural analysis, the concept of open nets is proposed to check the reproducibility of empty markings of scenario nets, the existence of dead transitions in the scenario nets, and the terminating states of the scenario nets. The system behaviour, in which states are involved, is investigated by reachability analysis. Unlike the conventional method of reachability analysis by calculating the state space of the Petri net, techniques based on Petri net unfoldings are introduced in this thesis. As to the functional verification, two model-based test generation techniques, i.e., CPN-based and SPENAT (Safe Place Transition Nets with Attributes)-based techniques, are presented. In this thesis, the proposed methods are exemplified by the application to the on-board module of SatZB model. According to the verification results, no errors were found in the module. Therefore, the confidence in the quality of the on-board module has been significantly increased.Heutzutage werden in zahlreichen Anwendungen modellbasierte Techniken zur Systementwicklung, insbesondere für sicherheitskritische Systeme wie Eisenbahnleit- und -sicherungssysteme, verwendet. Aus einem Design Modell kann dabei ausführbarer Code automatisch nach bestimmten Transformationsregeln generiert werden. Ein hochwertiges Modell des Systems bietet für die Entwicklung ein gutes Verständnis, eine günstige Struktur, eine angemessene Größenordnung und Abstraktionsebene als auch realistische Verhaltensweisen in Bezug auf den gleichzeitigen Betrieb von unabhängigen Subsystemen. Motiviert von dieses Prinzip wird ein erstes Farbige Petri-Netz (CPN)-Modell eines satellitenbasierten Zugsicherungssystem (SatZB) unter Verwendung der BASYSNET Methode entwickelt, der Petri-Netze als Beschreibungsmittel während des gesamten Entwicklungsprozesses nutzt. Dieses Modell bietet die Möglichkeit zur kontinuierlichen Simulation des Systemverhaltens. Nach der Erstellung des Systemmodells werden die Verifikationsaufgaben auf der Grundlage der Gefährdungsanalyse des Zugsicherungssystems identifiziert. Die abgeleiteten Bedingungen werden zur Qualitätssicherung durch Simulation, formale Analysen und Tests unter Berücksichtigung der vier Systemeigenschaften (Funktion, Zustand, Struktur und Verhalten) verifiziert. Für die Strukturanalyse wird das Konzept der offenen Netzen vorgeschlagen, um die Reproduzierbarkeit der leeren Markierungen der Szenario-Netze, die Existenz der Toten Transitionen in den Szenario-Netze, und die Abschluss Zustände der Szenario-Netze zu prüfen. Das Systemverhalten wird dabei durch Zustände beschrieben und durch eine Erreichbarkeitsanalyse untersucht. Im Gegensatz zu der konventionellen Methode, welche die Erreichbarkeit durch die Berechnung des Zustandsraums des Petri-Netzes analysiert, werden in dieser Arbeit Techniken auf Basis von Petri-Netz-Entfaltung eingeführt. Für die funktionale Verifikation werden zwei modellbasierte Testgenerierungstechniken, eine CPN-basierte und eine SPENAT (Sicheres Petrinetz mit Attributen)-basierte, vorgestellt. In dieser Arbeit werden die vorgeschlagenen Methoden durch die Anwendung auf das On-Board-Modul des SatZB-Modells veranschaulicht. Dabei wurden nach dem Abschluss der Prüfungen keine Fehler im Modul gefunden, wodurch das Vertrauen in die Qualität des On-Board-Moduls deutlich erhöht wurde

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