Design and Development of Software Tools for Bio-PEPA

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Supporting user-oriented analysis for multi-view domain-specific visual languages

This is the post-print version of the final paper published in Information and Software Technology. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2008 Elsevier B.V.The integration of usable and flexible analysis support in modelling environments is a key success factor in Model-Driven Development. In this paradigm, models are the core asset from which code is automatically generated, and thus ensuring model correctness is a fundamental quality control activity. For this purpose, a common approach is to transform the system models into formal semantic domains for verification. However, if the analysis results are not shown in a proper way to the end-user (e.g. in terms of the original language) they may become useless. In this paper we present a novel DSVL called BaVeL that facilitates the flexible annotation of verification results obtained in semantic domains to different formats, including the context of the original language. BaVeL is used in combination with a consistency framework, providing support for all steps in a verification process: acquisition of additional input data, transformation of the system models into semantic domains, verification, and flexible annotation of analysis results. The approach has been validated analytically by the cognitive dimensions framework, and empirically by its implementation and application to several DSVLs. Here we present a case study of a notation in the area of Digital Libraries, where the analysis is performed by transformations into Petri nets and a process algebra.Spanish Ministry of Education and Science and MODUWEB

Software Agent Architecture for Managing Inter-Organizational Collaborations

The growing importance of cooperation among organizations, as a result of globalization, current market opportunities and technological advances, encourages organizations to dynamically establish inter-organizational collaborations. These collaborations are carried out by executing collaborative business processes among the organizations. In this work we propose an agent-based software architecture for managing inter-organizational collaborations. Two types of agents are provided: the Collaboration Administrator Agent and the Process Administrator Agent. The former allows organizations setting up collaborations. The latter allows organizations executing collaborative business processes. A Colored Petri Net model specifying the role, which an organization fulfills in a collaborative process, is used to carry out the behavior of the Process Administrator Agent that represents the organization. Planning and execution of the actions of the Process Administrator Agents are driven by a Colored Petri Net machine embedded to them. Thus, Process Administrator Agents do not require to have defined at design-time the protocols they can support. In addition, we propose a model-driven development method for generating Colored Petri Net models from a collaborative process model defined as interaction protocol. Finally, an implementation of the agent-based software architecture and methods based on model-driven development are presented.La creciente importancia de la cooperación entre las organizaciones, como consecuencia de la globalización, las oportunidades actuales de mercado y los avances tecnológicos, alienta a las organizaciones a establecer en forma dinámica colaboraciones inter-organizacionales. Estas colaboraciones se llevan a cabo mediante la ejecución de procesos de negocio colaborativos entre las organizaciones. En este trabajo de investigación se propone una arquitectura basada en agentes de software para la gestión de colaboraciones inter-organizacionales. La arquitectura provee dos tipos de agentes: el Agente Administrador de Colaboraciones y el Agente Administrador de Proceso. El primer agente permite a las organizaciones a establecer colaboraciones. El segundo agente habilita a las organizaciones ejecutar procesos de negocio colaborativos. El rol que una organización desempeña en un proceso colaborativo es especificado mediante un modelo de redes de Petri coloreadas. Este modelo es usado para dirigir el comportamiento del Agente Administrador de Proceso, el cual representa a una organización. La ejecución de los planes y las acciones del Agente Administrador de Proceso son dirigidas mediante una máquina de redes de Petri coloreadas embebida en el agente. Entonces, los Agentes Administrador de Proceso no requieren tener definido en tiempo de diseño los protocolos que dan soporte a su comportamiento. Adicionalmente, se propone un método basado en el desarrollo dirigido por modelos para la generación en forma automática de modelos de redes de Petri coloreadas a partir de un modelo de procesos de negocio colaborativo definido como protocolo de interacción. Finalmente, la implementación de la arquitectura y los métodos basados en el desarrollo dirigido por modelos son presentados.Fil: Tello Leal, Edgar. Universidad Autónoma de Tamaulipas; MéxicoFil: Chiotti, Omar Juan Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo y Diseño (i); ArgentinaFil: Villarreal, Pablo David. Universidad Tecnologica Nacional. Facultad Regional Santa Fe. Centro de Investigacion y Desarrollo de Ingenieria En Sistemas de Informacion; Argentin

AADLib, A Library of Reusable AADL Models

The SAE Architecture Analysis and Design Language is now a well-established language for the description of critical embedded systems, but also cyber-physical ones. A wide range of analysis tools is already available, either as part of the OSATE tool chain, or separate ones. A key missing elements of AADL is a set of reusable building blocks to help learning AADL concepts, but also experiment already existing tool chains on validated real-life examples. In this paper, we present AADLib, a library of reusable model elements. AADLib is build on two pillars: 1/ a set of ready-to- use examples so that practitioners can learn more about the AADL language itself, but also experiment with existing tools. Each example comes with a full description of available analysis and expected results. This helps reducing the learning curve of the language. 2/ a set of reusable model elements that cover typical building blocks of critical systems: processors, networks, devices with a high level of fidelity so that the cost to start a new project is reduced. AADLib is distributed under a Free/Open Source License to further disseminate the AADL language. As such, AADLib provides a convenient way to discover AADL concepts and tool chains, and learn about its features

Model-based dependability analysis : state-of-the-art, challenges and future outlook

Abstract: Over the past two decades, the study of model-based dependability analysis has gathered significant research interest. Different approaches have been developed to automate and address various limitations of classical dependability techniques to contend with the increasing complexity and challenges of modern safety-critical system. Two leading paradigms have emerged, one which constructs predictive system failure models from component failure models compositionally using the topology of the system. The other utilizes design models - typically state automata - to explore system behaviour through fault injection. This paper reviews a number of prominent techniques under these two paradigms, and provides an insight into their working mechanism, applicability, strengths and challenges, as well as recent developments within these fields. We also discuss the emerging trends on integrated approaches and advanced analysis capabilities. Lastly, we outline the future outlook for model-based dependability analysis

A Modular Integrated Development Environment for Coloured Petri Net Models

Distributed software systems are becoming increasingly popular and used. Most of modern distributed systems provide the application of concurrency, also in- cluding resource sharing, communication and synchronization between different modules. These distributed systems comes with the challenges concerning data synchronization, scalability and performance, among others. By modelling these systems helps with solving these challenges, and there exists multiple tools for this. CPN Tools is one of these tools. CPN Tools is used for editing, simulating and analyzing Coloured Petri nets models. A need has been identified to devel- oped new software for develop new and up to date tools for editing, simulating and analyzing Coloured Petri nets to further development and fit the increasing need for distributed systems. Answering this need, a new simulating tool has been proposed. This thesis proposes an editor focusing on the modelling and visualization with the potentially integrate this simulator. This editor consists of an application running on Electron and using GoJS for modelling. This has resulted in a modelling tool for creating CPN models, with the possibility of increased abstraction of the models of the modern distributed systems.Masteroppgave i Programvareutvikling samarbeid med HVLPROG399MAMN-PRO

Profiling the publish/subscribe paradigm for automated analysis using colored Petri nets

UML sequence diagrams are used to graphically describe the message interactions between the objects participating in a certain scenario. Combined fragments extend the basic functionality of UML sequence diagrams with control structures, such as sequences, alternatives, iterations, or parallels. In this paper, we present a UML profile to annotate sequence diagrams with combined fragments to model timed Web services with distributed resources under the publish/subscribe paradigm. This profile is exploited to automatically obtain a representation of the system based on Colored Petri nets using a novel model-to-model (M2M) transformation. This M2M transformation has been specified using QVT and has been integrated in a new add-on extending a state-of-the-art UML modeling tool. Generated Petri nets can be immediately used in well-known Petri net software, such as CPN Tools, to analyze the system behavior. Hence, our model-to-model transformation tool allows for simulating the system and finding design errors in early stages of system development, which enables us to fix them at these early phases and thus potentially saving development costs

Model-driven design, simulation and implementation of service compositions in COSMO

The success of software development projects to a large extent depends on the quality of the models that are produced in the development process, which in turn depends on the conceptual and practical support that is available for modelling, design and analysis. This paper focuses on model-driven support for service-oriented software development. In particular, it addresses how services and compositions of services can be designed, simulated and implemented. The support presented is part of a larger framework, called COSMO (COnceptual Service MOdelling). Whereas in previous work we reported on the conceptual support provided by COSMO, in this paper we proceed with a discussion of the practical support that has been developed. We show how reference models (model types) and guidelines (design steps) can be iteratively applied to design service compositions at a platform independent level and discuss what tool support is available for the design and analysis during this phase. Next, we present some techniques to transform a platform independent service composition model to an implementation in terms of BPEL and WSDL. We use the mediation scenario of the SWS challenge (concerning the establishment of a purchase order between two companies) to illustrate our application of the COSMO framework