Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

An algebra and conceptual model for semantic tagging of collaborative digital libraries

Cost-effective semantic description and annotation of shared knowledge resources has always been of great importance for digital libraries and large scale information systems in general. With the emergence of the Social Web and Web 2.0 technologies, a more effective semantic description and annotation, e.g., folksonomies, of digital library contents is envisioned to take place in collaborative and personalised environments. However, there is a lack of foundation and mathematical rigour for coping with contextualised management and retrieval of semantic annotations throughout their evolution as well as diversity in users and user communities. In this paper, we propose an ontological foundation for semantic annotations of digital libraries in terms of flexonomies. The proposed theoretical model relies on a high dimensional space with algebraic operators for contextualised access of semantic tags and annotations. The set of the proposed algebraic operators, however, is an adaptation of the set theoretic operators selection, projection, difference, intersection, union in database theory. To this extent, the proposed model is meant to lay the ontological foundation for a Digital Library 2.0 project in terms of geometric spaces rather than logic (description) based formalisms as a more efficient and scalable solution to the semantic annotation problem in large scale

Combining behavioural types with security analysis

Today's software systems are highly distributed and interconnected, and they increasingly rely on communication to achieve their goals; due to their societal importance, security and trustworthiness are crucial aspects for the correctness of these systems. Behavioural types, which extend data types by describing also the structured behaviour of programs, are a widely studied approach to the enforcement of correctness properties in communicating systems. This paper offers a unified overview of proposals based on behavioural types which are aimed at the analysis of security properties

Living Knowledge

Diversity, especially manifested in language and knowledge, is a function of local goals, needs, competences, beliefs, culture, opinions and personal experience. The Living Knowledge project considers diversity as an asset rather than a problem. With the project, foundational ideas emerged from the synergic contribution of different disciplines, methodologies (with which many partners were previously unfamiliar) and technologies flowed in concrete diversity-aware applications such as the Future Predictor and the Media Content Analyser providing users with better structured information while coping with Web scale complexities. The key notions of diversity, fact, opinion and bias have been defined in relation to three methodologies: Media Content Analysis (MCA) which operates from a social sciences perspective; Multimodal Genre Analysis (MGA) which operates from a semiotic perspective and Facet Analysis (FA) which operates from a knowledge representation and organization perspective. A conceptual architecture that pulls all of them together has become the core of the tools for automatic extraction and the way they interact. In particular, the conceptual architecture has been implemented with the Media Content Analyser application. The scientific and technological results obtained are described in the following

Engineering scalable modelling Languages

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Escuela Politécnica Superior, Departamento de Ingeniería Informática. Fecha de lectura: 08-11-2019Esta tesis tiene embargado el acceso al texto completo hasta el 08-05-2021Model-Driven Engineering (MDE) aims at reducing the cost of system development by raising the level of abstraction at which developers work. MDE-based solutions frequently involve the creation of Domain-Specific Modelling Languages (DSMLs). WhilethedefinitionofDSMLsandtheir(sometimesgraphical)supportingenvironments are recurring activities in MDE, they are mostly developed ad-hoc from scratch. The construction of these environments requires high expertise by developers, which currently need to spend large efforts for their construction. This thesis focusses on the development of scalable modelling environments for DSMLs based on patterns. For this purpose, we propose a catalogue of modularity patterns that can be used to extend a modelling language with services related to modularization and scalability. More specifically, these patterns allows defining model fragmentation strategies, scoping and visibility rules, model indexing services, and scoped constraints. Once the patterns have been applied to the meta-model of a modelling language, we synthesize a customized modelling environment enriched with the defined services, which become applicable to both existing monolithic legacy models and new models. A second contribution of this thesis is a set of concepts and technologies to facilitate the creation of graphical editors. For this purpose, we define heuristics which identify structures in the DSML abstract syntax, and automatically assign their diagram representation. Using this approach, developers can create a graphical representation by default from a meta-model, which later can be customised. These contributions have been implemented in two Eclipse plug-ins called EMFSplitter and EMF-Stencil. On one hand, EMF-Splitter implements the catalogue of modularity patterns and, on the other hand, EMF-Stencil supports the heuristics and the generation of a graphical modelling environment. Both tools were evaluated in different case studies to prove their versatility, efficiency, and capabilitieEl Desarrollo de Software Dirigido por Modelos (MDE, por sus siglas en inglés) tiene como objetivo reducir los costes en el desarrollo de aplicaciones, elevando el nivel de abstracciónconelqueactualmentetrabajanlosdesarrolladores. Lassolucionesbasadas en MDE frecuentemente involucran la creación de Lenguajes de Modelado de Dominio Específico (DSML, por sus siglas en inglés). Aunque la definición de los DSMLs y sus entornos gráficos de modelado son actividades recurrentes en MDE, actualmente en la mayoría de los casos se desarrollan ad-hoc desde cero. La construcción de estos entornos requiere una alta experiencia por parte de los desarrolladores, que deben realizar un gran esfuerzo para construirlos. Esta tesis se centra en el desarrollo de entornos de modelado escalables para DSML basados en patrones. Para ello, se propone un catálogo de patrones de modularidad que se pueden utilizar para extender un lenguaje de modelado con servicios relacionados con la modularización y la escalabilidad. Específicamente, los patrones permiten definir estrategias de fragmentación de modelos, reglas de alcance y visibilidad, servicios de indexación de modelos y restricciones de alcance. Una vez que los patrones se han aplicado al meta-modelo de un lenguaje de modelado, se puede generar automáticamente un entorno de modelado personalizado enriquecido con los servicios definidos, que se vuelven aplicables tanto a los modelos monolíticos existentes, como a los nuevos modelos. Una segunda contribución de esta tesis es la propuesta de conceptos y tecnologías para facilitar la creación de editores gráficos. Para ello, definimos heurísticas que identifican estructuras en la sintaxis abstracta de los DSMLs y asignan automáticamente su representación en el diagrama. Usando este enfoque, los desarrolladores pueden crear una representación gráfica por defecto a partir de un meta-modelo. Estas contribuciones se implementaron en dos plug-ins de Eclipse llamados EMFSplitter y EMF-Stencil. Por un lado, EMF-Splitter implementa el catálogo de patrones y, por otro lado, EMF-Stencil implementa las heurísticas y la generación de un entorno de modelado gráfico. Ambas herramientas se han evaluado con diferentes casos de estudio para demostrar su versatilidad, eficiencia y capacidade

An Object-Oriented Framework for Explicit-State Model Checking

This paper presents a conceptual architecture for an object-oriented framework to support the development of formal verification tools (i.e. model checkers). The objective of the architecture is to support the reuse of algorithms and to encourage a modular design of tools. The conceptual framework is accompanied by a C++ implementation which provides reusable algorithms for the simulation and verification of explicit-state models as well as a model representation for simple models based on guard-based process descriptions. The framework has been successfully used to develop a model checker for a subset of PROMELA