Scalable reaction network modeling with automatic validation of consistency in Event-B

Constructing a large biological model is a difficult, error-prone process. Small errors in writing a part of the model cascade to the system level and their sources are difficult to trace back. In this paper we extend a recent approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to validate for model consistency step-by-step in an automated way. We demonstrate this approach on a model of the heat shock response in eukaryotes and its scalability on a model of the ErbB signaling pathway. All consistency properties of the model were proved automatically with computer support.</p

Twenty years of rewriting logic

AbstractRewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality. This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations; (ii) its semantic framework and logical framework uses; (iii) its language implementations and its formal tools; and (iv) its many applications to automated deduction, software and hardware specification and verification, security, real-time and cyber-physical systems, probabilistic systems, bioinformatics and chemical systems

Dynamic adaptation of service compositions with variability models

Web services run in complex contexts where arising events may compromise the quality of the whole system. Thus, it is desirable to count on autonomic mechanisms to guide the self-adaptation of service compositions according to changes in the computing infrastructure. One way to achieve this goal is by implementing variability constructs at the language level. However, this approach may become tedious, difficult to manage, and error-prone. In this paper, we propose a solution based on a semantically rich variability model to support the dynamic adaptation of service compositions. When a problematic event arises in the context, this model is leveraged for decision-making. The activation and deactivation of features in the variability model result in changes in a composition model that abstracts the underlying service composition. These changes are reflected into the service composition by adding or removing fragments of Business Process Execution Language (WS-BPEL) code, which can be deployed at runtime. In order to reach optimum adaptations, the variability model and its possible configurations are verified at design time using Constraint Programming. An evaluation demonstrates several benefits of our approach, both at design time and at runtime.This work has been developed with the support of MICINN under the project everyWare TIN2010-18011 and co-financed with ERDF.Alférez Salinas, GH.; Pelechano Ferragud, V.; Mazo, R.; Salinesi, C.; Díaz, D. (2014). Dynamic adaptation of service compositions with variability models. Journal of Systems and Software. 91:24-47. https://doi.org/10.1016/j.jss.2013.06.034S24479

Proceedings of The Multi-Agent Logics, Languages, and Organisations Federated Workshops (MALLOW 2010)

http://ceur-ws.org/Vol-627/allproceedings.pdfInternational audienceMALLOW-2010 is a third edition of a series initiated in 2007 in Durham, and pursued in 2009 in Turin. The objective, as initially stated, is to "provide a venue where: the cost of participation was minimum; participants were able to attend various workshops, so fostering collaboration and cross-fertilization; there was a friendly atmosphere and plenty of time for networking, by maximizing the time participants spent together"

Políticas de Copyright de Publicações Científicas em Repositórios Institucionais: O Caso do INESC TEC

A progressiva transformação das práticas científicas, impulsionada pelo desenvolvimento das novas Tecnologias de Informação e Comunicação (TIC), têm possibilitado aumentar o acesso à informação, caminhando gradualmente para uma abertura do ciclo de pesquisa. Isto permitirá resolver a longo prazo uma adversidade que se tem colocado aos investigadores, que passa pela existência de barreiras que limitam as condições de acesso, sejam estas geográficas ou financeiras. Apesar da produção científica ser dominada, maioritariamente, por grandes editoras comerciais, estando sujeita às regras por estas impostas, o Movimento do Acesso Aberto cuja primeira declaração pública, a Declaração de Budapeste (BOAI), é de 2002, vem propor alterações significativas que beneficiam os autores e os leitores. Este Movimento vem a ganhar importância em Portugal desde 2003, com a constituição do primeiro repositório institucional a nível nacional. Os repositórios institucionais surgiram como uma ferramenta de divulgação da produção científica de uma instituição, com o intuito de permitir abrir aos resultados da investigação, quer antes da publicação e do próprio processo de arbitragem (preprint), quer depois (postprint), e, consequentemente, aumentar a visibilidade do trabalho desenvolvido por um investigador e a respetiva instituição. O estudo apresentado, que passou por uma análise das políticas de copyright das publicações científicas mais relevantes do INESC TEC, permitiu não só perceber que as editoras adotam cada vez mais políticas que possibilitam o auto-arquivo das publicações em repositórios institucionais, como também que existe todo um trabalho de sensibilização a percorrer, não só para os investigadores, como para a instituição e toda a sociedade. A produção de um conjunto de recomendações, que passam pela implementação de uma política institucional que incentive o auto-arquivo das publicações desenvolvidas no âmbito institucional no repositório, serve como mote para uma maior valorização da produção científica do INESC TEC.The progressive transformation of scientific practices, driven by the development of new Information and Communication Technologies (ICT), which made it possible to increase access to information, gradually moving towards an opening of the research cycle. This opening makes it possible to resolve, in the long term, the adversity that has been placed on researchers, which involves the existence of barriers that limit access conditions, whether geographical or financial. Although large commercial publishers predominantly dominate scientific production and subject it to the rules imposed by them, the Open Access movement whose first public declaration, the Budapest Declaration (BOAI), was in 2002, proposes significant changes that benefit the authors and the readers. This Movement has gained importance in Portugal since 2003, with the constitution of the first institutional repository at the national level. Institutional repositories have emerged as a tool for disseminating the scientific production of an institution to open the results of the research, both before publication and the preprint process and postprint, increase the visibility of work done by an investigator and his or her institution. The present study, which underwent an analysis of the copyright policies of INESC TEC most relevant scientific publications, allowed not only to realize that publishers are increasingly adopting policies that make it possible to self-archive publications in institutional repositories, all the work of raising awareness, not only for researchers but also for the institution and the whole society. The production of a set of recommendations, which go through the implementation of an institutional policy that encourages the self-archiving of the publications developed in the institutional scope in the repository, serves as a motto for a greater appreciation of the scientific production of INESC TEC

An Unexpected Journey: Towards Runtime Verification of Multiagent Systems and Beyond

The Trace Expression formalism derives from works started in 2012 and is mainly used to specify and verify interaction protocols at runtime, but other applications have been devised. More specically, this thesis describes how to extend and apply such formalism in the engineering process of distributed articial intelligence systems (such as Multiagent systems). This thesis extends the state of the art through four dierent contributions: 1. Theoretical: the thesis extends the original formalism in order to represent also parametric and probabilistic specications (parametric trace expressions and probabilistic trace expressions respectively). 2. Algorithmic: the thesis proposes algorithms for verifying trace expressions at runtime in a decentralized way. The algorithms have been designed to be as general as possible, but their implementation and experimentation address scenarios where the modelled and observed events are communicative events (interactions) inside a multiagent system. 3. Application: the thesis analyzes the relations between runtime and static verication (e.g. model checking) proposing hybrid integrations in both directions. First of all, the thesis proposes a trace expression model checking approach where it shows how to statically verify LTL property on a trace expression specication. After that, the thesis presents a novel approach for supporting static verication through the addition of monitors at runtime (post-process). 4. Implementation: the thesis presents RIVERtools, a tool supporting the writing, the syntactic analysis and the decentralization of trace expressions