Supporting Run-time Monitoring of UML-RT through Customizable Monitoring Configurations in PapyrusRT

Model Driven Engineering uses the principle that code can automatically be generated from software models which would potentially save time and cost of development. By this methodology, a systems structure and behaviour can be expressed in more abstract, high level terms without some of the accidental complexity that the use of a general purpose language can bring. Models are the actual implementation of the system unlike in traditional software development where models are often used for documentation purposes only. However once the code is generated from the model, testing and debugging activities tend to happen on the code level and the model is not updated. We believe that monitoring on the model level could potentially facilitate quality assurance activities as the errors are detected in the early phase of development. In this thesis, we create a Monitoring Configuration for an open source model driven engineering tool called PapyrusRT in Eclipse. We support the run-time monitoring of UML-RT elements with a tracing tool called LTTng. We annotate the model with monitoring information to be used by the code generator for adding tracepoint statements for the corresponding elements. We provide the option of a timing specification to discover latency errors on the model. We validate the results by creating and tracing real time models in PapyrusRT.

From data to applications in the Internet of Things

Con la crescita in complessità delle infrastrutture IT e la pervasività degli scenari di Internet of Things (IoT) emerge il bisogno di nuovi modelli computazionali basati su entità autonome capaci di portare a termine obiettivi di alto livello interagendo tra loro grazie al supporto di infrastrutture come il Fog Computing, per la vicinanza alle sorgenti dei dati, e del Cloud Computing per offrire servizi analitici complessi di back-end in grado di fornire risultati per milioni di utenti. Questi nuovi scenarii portano a ripensare il modo in cui il software viene progettato e sviluppato in una prospettiva agile. Le attività dei team di sviluppatori (Dev) dovrebbero essere strettamente legate alle attività dei team che supportano il Cloud (Ops) secondo nuove metodologie oggi note come DevOps. Tuttavia, data la mancanza di astrazioni adeguata a livello di linguaggio di programmazione, gli sviluppatori IoT sono spesso indotti a seguire approcci di sviluppo bottom-up che spesso risulta non adeguato ad affrontare la compessità delle applicazione del settore e l'eterogeneità dei compomenti software che le formano. Poichè le applicazioni monolitiche del passato appaiono difficilmente scalabili e gestibili in un ambiente Cloud con molteplici utenti, molti ritengono necessaria l'adozione di un nuovo stile architetturale, in cui un'applicazione dovrebbe essere vista come una composizione di micro-servizi, ciascuno dedicato a uno specifica funzionalità applicativa e ciascuno sotto la responsabilità di un piccolo team di sviluppatori, dall'analisi del problema al deployment e al management. Poichè al momento non si è ancora giunti a una definizione univoca e condivisa dei microservices e di altri concetti che emergono da IoT e dal Cloud, nè tantomento alla definzione di linguaggi sepcializzati per questo settore, la definzione di metamodelli custom associati alla produzione automatica del software di raccordo con le infrastrutture potrebbe aiutare un team di sviluppo ad elevare il livello di astrazione, incapsulando in una software factory aziendale i dettagli implementativi. Grazie a sistemi di produzione del sofware basati sul Model Driven Software Development (MDSD), l'approccio top-down attualmente carente può essere recuperato, permettendo di focalizzare l'attenzione sulla business logic delle applicazioni. Nella tesi viene mostrato un esempio di questo possibile approccio, partendo dall'idea che un'applicazione IoT sia in primo luogo un sistema software distribuito in cui l'interazione tra componenti attivi (modellati come attori) gioca un ruolo fondamentale.

Generation and Characterisation of a Canine EGFP-HMGA2 Prostate Cancer In Vitro Model

The architectural transcription factor HMGA2 is abundantly expressed during embryonic development. In several malignant neoplasias including prostate cancer, high re-expression of HMGA2 is correlated with malignancy and poor prognosis. The let-7 miRNA family is described to regulate HMGA2 negatively. The balance of let-7 and HMGA2 is discussed to play a major role in tumour aetiology. To further analyse the role of HMGA2 in prostate cancer a stable and highly reproducible in vitro model system is precondition. Herein we established a canine CT1258-EGFP-HMGA2 prostate cancer cell line stably overexpressing HMGA2 linked to EGFP and in addition the reference cell line CT1258-EGFP expressing solely EGFP to exclude EGFP-induced effects. Both recombinant cell lines were characterised by fluorescence microscopy, flow cytometry and immunocytochemistry. The proliferative effect of ectopically overexpressed HMGA2 was determined via BrdU assays. Comparative karyotyping of the derived and the initial CT1258 cell lines was performed to analyse chromosome consistency. The impact of the ectopic HMGA2 expression on its regulator let-7a was analysed by quantitative real-time PCR. Fluorescence microscopy and immunocytochemistry detected successful expression of the EGFP-HMGA2 fusion protein exclusively accumulating in the nucleus. Gene expression analyses confirmed HMGA2 overexpression in CT1258-EGFP-HMGA2 in comparison to CT1258-EGFP and native cells. Significantly higher let-7a expression levels were found in CT1258-EGFP-HMGA2 and CT1258-EGFP. The BrdU assays detected an increased proliferation of CT1258-HMGA2-EGFP cells compared to CT1258-EGFP and native CT1258. The cytogenetic analyses of CT1258-EGFP and CT1258-EGFP-HMGA2 resulted in a comparable hyperdiploid karyotype as described for native CT1258 cells. To further investigate the impact of recombinant overexpressed HMGA2 on CT1258 cells, other selected targets described to underlie HMGA2 regulation were screened in addition. The new fluorescent CT1258-EGFP-HMGA2 cell line is a stable tool enabling in vitro and in vivo analyses of the HMGA2-mediated effects on cells and the development and pathogenesis of prostate cancer.

Uma abordagem dirigida a modelo para a geração de casos de teste baseada na detecção de cenários implícitos

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2015.

A Metamodel for Collaboration Formalization

Part 11: Reference and Conceptual Models

Towards Distributed Model Transformations with LinTra

Performance and scalability of model transformations are becoming prominent topics in Model-Driven Engineering. In previous works we introduced LinTra, a platform for executing model transformations in parallel. LinTra is based on the Linda model of a coordination language and is intended to be used as a middleware where high-level model transformation languages are compiled. In this paper we present the initial results of our analyses on the scalability of out-place model-to-model transformation executions in LinTra when the models and the processing elements are distributed over a set of machines.

Towards flexible parsing of structured textual model representations

Existing parsers for textual model representation formats such as XMI and HUTN are unforgiving and fail upon even the smallest inconsistency between the structure and naming of metamodel elements and the contents of serialised models. In this paper, we demonstrate how a fuzzy parsing approach can transparently and automatically resolve a number of these inconsistencies, and how it can eventually turn XML into a human-readable and editable textual model representation format for particular classes of models.

Integration of a graph-based model indexer in commercial modelling tools

Softeam has over 20 years of experience providing UML-based modelling solutions, such as its Modelio modelling tool, and its Constellation enterprise model management and collaboration environment. Due to the increasing number and size of the models used by Softeam’s clients, Softeam joined the MONDO FP7 EU research project, which worked on solutions for these scalability challenges and produced the Hawk model indexer among other results. This paper presents the technical details and several case studies on the integration of Hawk into Softeam’s toolset. The first case study measured the performance of Hawk’s Modelio support using varying amounts of memory for the Neo4j backend. In another case study, Hawk was integrated into Constellation to provide scalable global querying of model repositories. Finally, the combination of Hawk and the Epsilon Generation Language was compared against Modelio for document generation: for the largest model, Hawk was two orders of magnitude faster.

Stress-testing centralised model stores

One of the current challenges in model-driven engineering is enabling effective collaborative modelling. Two common approaches are either storing the models in a central repository, or keeping them under a traditional file-based version control system and build a centralized index for model-wide queries. Either way, special attention must be paid to the nature of these repositories and indexes as networked services: they should remain responsive even with an increasing number of concurrent clients. This paper presents an empirical study on the impact of certain key decisions on the scalability of concurrent model queries, using an Eclipse Connected Data Objects model repository and a Hawk model index. The study evaluates the impact of the network protocol, the API design and the internal caching mechanisms and analyzes the reasons for their varying performance.

Story Driven Web Applications

Kern der vorliegenden Arbeit ist die Modellierung komplexer Webapplikationen mit dem Story-Driven-Modeling Ansatz.Ziel ist es hierbei,die komplette Applikation allein durch die Spezifikation von Modellen zu entwickeln. Das händische Erstellen von Quelltext ist nicht notwendig. Die vorliegende Arbeit zeigt sowohl den Forschungsweg, der die angestrebte Modellierung von Webapplikationen ermöglicht, als auch die resultierenden Ergebnisse auf. Zur Unterstützung des Entwicklungsprozesses wird weiterhin ein modellgetriebener Softwareentwicklungsprozess vorgestellt, der die Modellierung einer Webapplikation von der Aufnahme der Anforderungen, bis zur abschließenden Erzeugung des Quelltextes durch Codegenerierung aus den spezifizierten Modellen, abdeckt. Für den definierten Prozess wird ferner Werkzeugunterstützung innerhalb der Fujaba Toolsuite bereitgestellt. Im Rahmen der vorliegenden Arbeit wurde die bestehede Toolsuite hierzu um alle zur Prozessunterstützung notwendigen Werkzeuge erweitert. Darüber hinaus wurden im Rahmen der vorliegenden Arbeit die in Fujaba bestehenden Werkzeuge erweitert, um neben den klassischen Möglichkeiten zur Modellierung komplexer Java-Applikationen auch die Erzeugung von Webapplikationen zu ermöglichen. Neben der genauen Beschreibung des Entwicklungsprozesses werden im Rahmen dieser Arbeit die entstehenden Webapplikationen mit ihren spezifischen Eigenschaften genau beschrieben. Zur Erzeugung dieser Applikationen wird neben dem Entwicklungsprozess die Diagrammart der Workflowdiagramme eingeführt und beschrieben. Diese Diagramme dienen der Abbildung des intendierten Userworkflows der Applikation im Rahmen der Anforderungsanalyse und stellen im weiteren Entwicklungsverlauf ein dediziertes Entwicklungsartefakt dar. Basierend auf den Workflowdiagrammen werden sowohl die grafische Benutzerschnittstelle der Webapplikation beschrieben, als auch ein Laufzeitsystem initialisiert, welches basierend auf den im Workflowdiagramm abgebildeten Abläufen die Anwendung steuert. Dieses Laufzeitsystem wurde im Rahmen der vorliegenden Arbeit entwickelt und in der Prozessunterstützung verankert. Alle notwendigen Änderungen und Anpassungen und Erweiterungen an bereits bestehenden Teilen der Fujaba Toolsuite werden unter dem Aspekt der Erstellung clientseitiger Datenmodelle einer Webapplikation genau beschrieben und in Verbindung mit den zu erfüllenden Voraussetzungen erläutert. In diesem Zusammenhang wird ebenfalls beschrieben, wie Graphtransformationen zur Umsetzung von Businesslogik auf der Clientseite einer Webapplikation eingesetzt werden können und auf welche Weise Datenmodelländerungen zwischen unterschiedlichen Clients synchronisiert werden können. Insgesamt zeigt die vorliegende Arbeit einen Weg auf, den bestehenden Ansatz des StoryDriven-Modeling für die Erzeugung von Webapplikationen einzusetzen. Durch die im Rahmen dieser Arbeit beschriebene Herangehensweise werden hierbei gleichzeitig Webbrowser zu einer neuen Klasse von Graphersetzungs-Engines erweitert, indem Graphtransformationen innerhalb der Ajax-Engine des Browsers ausgeliefert und ausgeführt werden.

Preparation and characterization of multifunctional bio-based polymers exhibiting enhanced properties

Driven by environmental reasons and the expected depletion of crude oil, bio-based polymers are currently undergoing a renaissance in the attempt to replace fossil-based ones. The present work aims at contributing in the development of the steps that start from biomass and move to new polymeric multifunctional materials. The study focuses on two bio-based building blocks (itaconic and vanillic acids) characterized by exploitable functionalities, i.e. a lateral double bond and a substituted aromatic ring respectively, able to confer interesting properties to the final polymers. The lateral double bond of dimethyl itaconate was functionalized via thia-Michael addition reaction obtaining a thermo-stable building block that can undergo polycondensation under classical conditions of reaction. The addition of a long lateral chain allows the polymer to express antimicrobial activity against Staphylococcus aureus making it attractive for packaging and targeting antimicrobial applications. Moreover, the architecture of the homopolymer was modified by means of copolymerization with dimethyl 2,5-furandicarboxylate thus improving the rigidity and obtaining a thermo-processable material. Potential applications as thermoset or thermoplastic material have been discussed. As concerns vanillic acid, the presence of aromatic rings on the polymer backbone imparts high thermal stability, but brittle behaviour in the homopolymer. Therefore, the architecture of the polyester was successfully tuned by means of copolymerization with a flexible bio-based comonomer, i.e. ω-pentadecalactone, providing processable random copolymers. An in depth investigation of water transport mechanism has been undertaken on the synthesized polyesters. Since the copolymers present a succession of aromatic and aliphatic units, as a consequence of the chemical structure water vapor permeability interposes between polyethylene and poly(ethylene terephthalate) proving that the copolyesters are suitable for packaging applications. Moving towards a sustainable model of development, novel sustainable synthetic pathways for the eco-design of new bio-based polymeric structures with high value functionalities and different potential applications have been successfully developed.

Sensitization Prevalence, Antibody Cross-Reactivity and Immunogenic Peptide Profile of Api g 2, the Non-Specific Lipid Transfer Protein 1 of Celery

Background: Celery (Apium graveolens) represents a relevant allergen source that can elicit severe reactions in the adult population. To investigate the sensitization prevalence and cross-reactivity of Api g 2 from celery stalks in a Mediterranean population and in a mouse model. Methodology: 786 non-randomized subjects from Italy were screened for IgE reactivity to rApi g 2, rArt v 3 (mugwort pollen LTP) and nPru p 3 (peach LTP) using an allergen microarray. Clinical data of 32 selected patients with reactivity to LTP under investigation were evaluated. Specific IgE titers and cross-inhibitions were performed in ELISA and allergen microarray. Balb/c mice were immunized with purified LTPs; IgG titers were determined in ELISA and mediator release was examined using RBL-2H3 cells. Simulated endolysosomal digestion was performed using microsomes obtained from human DCs. Results: IgE testing showed a sensitization prevalence of 25.6% to Api g 2, 18.6% to Art v 3, and 28.6% to Pru p 3 and frequent co-sensitization and correlating IgE-reactivity was observed. 10/32 patients suffering from LTP-related allergy reported symptoms upon consumption of celery stalks which mainly presented as OAS. Considerable IgE cross-reactivity was observed between Api g 2, Art v 3, and Pru p 3 with varying inhibition degrees of individual patients' sera. Simulating LTP mono-sensitization in a mouse model showed development of more congruent antibody specificities between Api g 2 and Art v 3. Notably, biologically relevant murine IgE cross-reactivity was restricted to the latter and diverse from Pru p 3 epitopes. Endolysosomal processing of LTP showed generation of similar clusters, which presumably represent T-cell peptides. Conclusions: Api g 2 represents a relevant celery stalk allergen in the LTP-sensitized population. The molecule displays common B cell epitopes and endolysosomal peptides that encompass T cell epitopes with pollen and plant-food derived LTP.

Tonal Modulation and Subjective Time

This work investigated listeners` sense of the temporal expression of tonal modulation. One experiment described the effects on retrospective reproductions of sudden and gradual modulations to close and distant keys. The results showed that modulations elicit time underestimations as an inverse function of interkey distances, with a major impact for sudden modulations. A proposed vectorial model - ""Expected Development Fraction"" (EDF) - describes the development of expectations when an interkey distance is traversed during a certain time interval. This expected development is longer than the perceived duration, leading to underestimation of the time.

The genome of the blood fluke Schistosoma mansoni

Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.

Integration of Individualized Management Systems (MSs) as an Aggregating Factor of Sustainable Value for Organizations: An Overview Through a Review of the Literature

Nowadays, there exist various standards for individual management systems (MSs), at least, one for each stakeholder. New ones will be published. An integrated management system (IMS) aims to integrate some or all components of the business into one coherent and efficient MS. Maximizing integration is more and more a strategic priority in that it constitutes an opportunity to eliminate and/or reduce potential factors of destruction of value for the organizations and also to be more competitive and consequently promote its sustainable success. A preliminary investigation was conducted on a Portuguese industrial company which, over the years, has been adopting gradually, in whole or in part, individualized management system standards (MSSs). A research, through a questionnaire, was performed with the objective to develop, in a real business environment, an adequate and efficient IMS-QES (quality, environment, and safety) model and to potentiate for the future a generic IMS model to integrate other MSSs. The strategy and research methods have taken into consideration the case study. It was obtained a set of relevant conclusions resulting from the statistical analyses of the responses to the survey. Globally, the investigation results, by themselves, justified and prioritized the conception of a model of development of the IMS-QES and consequent definition and validation of a structure of an IMS-QES model, to be implemented at the small- and medium-sized enterprise (SME) where the investigation was conducted.