Today
Bookmark and Share    
Peer Reviewed
See detailModelling of Railways Signalling System Requirements by Controlled Natural Languages: A Case Study
Lenzini, Gabriele UL; Petrocchi, Marinella

in From Software Engineering to Formal Methods and Tools, and Back (2019)

The railway sector has been a source of inspiration for generations of researchers challenged to develop models and tools to analyze safety and reliability. Threats were coming mainly from within, due to ... [more ▼]

The railway sector has been a source of inspiration for generations of researchers challenged to develop models and tools to analyze safety and reliability. Threats were coming mainly from within, due to occasionally faults in hardware components. With the advent of smart trains, the railway industry is venturing into cybersecurity and the railway sector will become more and more compelled to protect assets from threats against information & communication technology. We discuss this revolution at large, while speculating that instruments developed for security requirements engineering can then come in support of in the railway sector. And we explore the use of one of them: the Controlled Natural Language for Data Sharing Agreement (CNL4DSA). We use it to formalize a few exemplifying signal management system requirements. Since CNL4DSA enables the automatic generation of enforceable access control policies, our exercise is preparatory to implementing the security-by design principle in railway signalling management engineering. [less ▲]

Detailed reference viewed: 30 (0 UL)
Full Text
Peer Reviewed
See detailThe Grand Chamber’s Take on Composite Procedures under the Single Supervisory Mechanism
Demkova, Simona UL

in Review of European Administrative Law (2019), 12(1), 209-220

The recent landmark judgment of Berlusconi (Fininvest)1 reaffirms the Union Courts’ initial stance regarding the division of jurisdiction for matters arising from composite procedures.2 Remarkably ... [more ▼]

The recent landmark judgment of Berlusconi (Fininvest)1 reaffirms the Union Courts’ initial stance regarding the division of jurisdiction for matters arising from composite procedures.2 Remarkably, however, in Berlusconi, the CJEU for the first time offers a conceptual discussion on the long discussed issue of jurisdiction in composite matters, and does so in the new context of the Single Supervisory Mechanism (SSM). In this respect, the Court first clarifies that where an EU institution enjoys discretion in the final decision-making under the arrangement of a composite procedure, the Union Courts shall have an exclusive jurisdiction over the procedure as a whole. Consequently, Member State courts are prevented from reviewing any steps leading to the adoption of a final decision, regardless of the legal effects thereof in the domestic legal order or the domestic procedural rules allowing for such a review. While seemingly logical, the binary approach to judicial vompetence opens more doors to uncertainty, than it closes. One key concern is regarding the appropriate conduct of review under exclusive jurisdiction; concretely whether and how the Union Courts are competent to review preliminary acts taken under national law. Generally, where interpretation of the respective national rules is clear, such a review would consist of a verification of compliance with the essential procedural guarantees by the Union institution or body, which took the final decision. This approach seems to apply also in cases where the Union institution has a limited discretion to review the national preliminary acts when taking the final decision. The following discussion identifies that despite the black-and-white understanding of discretion developed by the Court in Berlusconi, under more general jurisdiction, the Union Courts will always verify that decisions of the Union institutions are taken with all due care. [less ▲]

Detailed reference viewed: 32 (9 UL)
Full Text
See detailDu grand débat à la grande débacle
Kies, Raphaël UL

in forum (2019), 393

Detailed reference viewed: 20 (0 UL)
Full Text
See detailE-pétitions à la Chambre des Députés. Un succès déstabilisant
Kies, Raphaël UL

in Frieseisen, Claude; Moes, Regis; Polfer, Michel (Eds.) et al 100 ans de suffrage universel au Luxembourg (2019)

Depuis que la Chambre des Députés a introduit les pétitions électroniques en avril 2013, il ne se passe pas une semaine sans que les médias traditionnels et sociaux n’y fassent référence. Généralement ils ... [more ▼]

Depuis que la Chambre des Députés a introduit les pétitions électroniques en avril 2013, il ne se passe pas une semaine sans que les médias traditionnels et sociaux n’y fassent référence. Généralement ils le font pour informer le public du dépôt de nouvelles pétitions ou pour présenter et débattre des pétitions qui ont reçu un grand nombre de signatures. Un récent sondage réalisé en 2018 révèle par ailleurs qu’en moyenne 64 % des citoyens luxembourgeois disent avoir signé au moins une e-pétition sur le site de la Chambre des Députés1. Il est par conséquent assez logique que les e-pétitions soient perçues comme le principal instrument de démocratie participative du pays et qu’elles monopolisent régulièrement le débat public pendant des semaines en mettant à l’agenda des questions souvent controversées. Prenons l’exemple d’une e-pétition qui demandait que la langue luxembourgeoise devienne la principale langue du pays en obtenant un nombre très élevé de signatures. Bien que les e-pétitions soient rapidement devenues un instrument participatif incontournable, à la fois enrichissant et perturbateur du système politique luxembourgeois, elles n’ont été que très peu étudiées. L’objectif de cet article est d’offrir un tour d’horizon du fonctionnement et de la recherche autour des e-pétitions au Luxembourg. [less ▲]

Detailed reference viewed: 13 (0 UL)
Full Text
Peer Reviewed
See detailPDBe-KB: a community-driven resource for structural and functional annotations
Varadi, M.; Berrisford, J.; Deshpande, M. et al

in Nucleic Acids Res. (2019)

The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted ... [more ▼]

The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages—the PDBe-KB aggregated views of structure data—which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession. [less ▲]

Detailed reference viewed: 22 (0 UL)
Full Text
Peer Reviewed
See detailPrankWeb: a web server for ligand binding site prediction and visualization.
Jendele, Lukas; Krivak, Radoslav; Skoda, Petr et al

in Nucleic acids research (2019), 47(W1), 345-349

PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of ... [more ▼]

PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively. [less ▲]

Detailed reference viewed: 11 (0 UL)
Full Text
Peer Reviewed
See detailMachine Learning to Support the Presentation of Complex Pathway Graphs.
Nielsen, Sune, S UL; Ostaszewski, Marek UL; McGee, Fintan et al

in IEEE/ACM transactions on computational biology and bioinformatics (2019)

Visualization of biological mechanisms by means of pathway graphs is necessary to better understand the often complex underlying system. Manual layout of such pathways or maps of knowledge is a difficult ... [more ▼]

Visualization of biological mechanisms by means of pathway graphs is necessary to better understand the often complex underlying system. Manual layout of such pathways or maps of knowledge is a difficult and time consuming process. Node duplication is a technique that makes layouts with improved readability possible by reducing edge crossings and shortening edge lengths in drawn diagrams. In this article we propose an approach using Machine Learning (ML) to facilitate parts of this task by training a Support Vector Machine (SVM) with actions taken during manual biocuration. Our training input is a series of incremental snapshots of a diagram describing mechanisms of a disease, progressively curated by a human expert employing node duplication in the process. As a test of the trained SVM models, they are applied to a single large instance and 25 medium-sized instances of hand-curated biological pathways. Finally, in a user validation study, we compare the model predictions to the outcome of a node duplication questionnaire answered by users of biological pathways with varying experience. We successfully predicted nodes for duplication and emulated human choices, demonstrating that our approach can effectively learn human-like node duplication preferences to support curation of pathway diagrams in various contexts. [less ▲]

Detailed reference viewed: 24 (2 UL)
Full Text
Peer Reviewed
See detailrPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots.
Jelinek, Jan; Hoksza, David UL; Hajic, Jan et al

in Database : the journal of biological databases and curation (2019), 2019

Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important ... [more ▼]

Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acquire. Its experimental identification is extremely technically demanding, while computational prediction is not accurate enough, especially for large structures of long sequences. We address this difficult situation with rPredictorDB, a predictive database of RNA secondary structures that aims to form a middle ground between experimentally identified structures in PDB and predicted consensus secondary structures in Rfam. The database contains individual secondary structures predicted using a tool for template-based prediction of RNA secondary structure for the homologs of the RNA families with at least one homolog with experimentally solved structure. Experimentally identified structures are used as the structural templates and thus the prediction has higher reliability than de novo predictions in Rfam. The sequences are downloaded from public resources. So far rPredictorDB covers 7365 RNAs with their secondary structures. Plots of the secondary structures use the Traveler package for readable display of RNAs with long sequences and complex structures, such as ribosomal RNAs. The RNAs in the output of rPredictorDB are extensively annotated and can be viewed, browsed, searched and downloaded according to taxonomic, sequence and structure data. Additionally, structure of user-provided sequences can be predicted using the templates stored in rPredictorDB. [less ▲]

Detailed reference viewed: 20 (0 UL)
Full Text
Peer Reviewed
See detailDo graphical cues effectively inform users? A Socio-Technical Security Study in Accessing Wifi Networks
Ferreira, Ana; Huynen, Jean-Louis; Koenig, Vincent UL et al

in Proc. of the International Conference on Human Aspects of Information Security, Privacy, and Trust (2015, July 21)

We study whether the padlock and the signal strength bars, two visual cues shown in network managers, convey their intended messages. Since users often choose insecure networks when they should not ... [more ▼]

We study whether the padlock and the signal strength bars, two visual cues shown in network managers, convey their intended messages. Since users often choose insecure networks when they should not, finding the answer is not obvious; in our study we clarify whether the problem lies in uninformative and ambiguous cues or in the user who, despite understanding the cues, chooses otherwise. This paper describes experiments and comments the results that bring evidence to our study [less ▲]

Detailed reference viewed: 16 (0 UL)