Preventive diagnosis of dairy cow lameness

This research aimed to develop a Fuzzy inference based on expert system to help preventing lameness in dairy cattle. Hoof length, nutritional parameters and floor material properties (roughness) were used to build the Fuzzy inference system. The expert system architecture was defined using Unified Modelling Language (UML). Data were collected in a commercial dairy herd using two different subgroups (H-1 and H-2), in order to validate the Fuzzy inference functions. The numbers of True Positive (TP), False Positive (FP), True Negative (TN), and False Negative (FN) responses were used to build the classifier system up, after an established gold standard comparison. A Lesion Incidence Possibility (LIP) developed function indicates the chances of a cow becoming lame. The obtained lameness percentage in H-1 and H-2 was 8.40% and 1.77%, respectively. The system estimated a Lesion Incidence Possibility (LIP) of 5.00% and 2.00% in H-1 and H-2, respectively. The system simulation presented 3.40% difference from real cattle lameness data for H-1, while for H-2, it was 0.23%; indicating the system efficiency in decision-making.

Controle e aquisição de dados experimentais com tecnologia bluetooth em dispositivos móveis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Costrutti ed Applicazioni di Programmazione Generica in Linguaggi Object-Oriented

Generic programming is likely to become a new challenge for a critical mass of developers. Therefore, it is crucial to refine the support for generic programming in mainstream Object-Oriented languages — both at the design and at the implementation level — as well as to suggest novel ways to exploit the additional degree of expressiveness made available by genericity. This study is meant to provide a contribution towards bringing Java genericity to a more mature stage with respect to mainstream programming practice, by increasing the effectiveness of its implementation, and by revealing its full expressive power in real world scenario. With respect to the current research setting, the main contribution of the thesis is twofold. First, we propose a revised implementation for Java generics that greatly increases the expressiveness of the Java platform by adding reification support for generic types. Secondly, we show how Java genericity can be leveraged in a real world case-study in the context of the multi-paradigm language integration. Several approaches have been proposed in order to overcome the lack of reification of generic types in the Java programming language. Existing approaches tackle the problem of reification of generic types by defining new translation techniques which would allow for a runtime representation of generics and wildcards. Unfortunately most approaches suffer from several problems: heterogeneous translations are known to be problematic when considering reification of generic methods and wildcards. On the other hand, more sophisticated techniques requiring changes in the Java runtime, supports reified generics through a true language extension (where clauses) so that backward compatibility is compromised. In this thesis we develop a sophisticated type-passing technique for addressing the problem of reification of generic types in the Java programming language; this approach — first pioneered by the so called EGO translator — is here turned into a full-blown solution which reifies generic types inside the Java Virtual Machine (JVM) itself, thus overcoming both performance penalties and compatibility issues of the original EGO translator. Java-Prolog integration Integrating Object-Oriented and declarative programming has been the subject of several researches and corresponding technologies. Such proposals come in two flavours, either attempting at joining the two paradigms, or simply providing an interface library for accessing Prolog declarative features from a mainstream Object-Oriented languages such as Java. Both solutions have however drawbacks: in the case of hybrid languages featuring both Object-Oriented and logic traits, such resulting language is typically too complex, thus making mainstream application development an harder task; in the case of library-based integration approaches there is no true language integration, and some “boilerplate code” has to be implemented to fix the paradigm mismatch. In this thesis we develop a framework called PatJ which promotes seamless exploitation of Prolog programming in Java. A sophisticated usage of generics/wildcards allows to define a precise mapping between Object-Oriented and declarative features. PatJ defines a hierarchy of classes where the bidirectional semantics of Prolog terms is modelled directly at the level of the Java generic type-system.

Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

Compensability index for compensation radiotherapy after treatment interruptions

Background The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. Methods We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. Results The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. Conclusions The compensability index calculation may serve as a decision support system based on existing and established recommendations.

UER technique: conceptualisation for agent oriented development

The problem of conceptualisation is the first step towards the identication of the functional requirements of a system. This article proposes two extensions of well-known object oriented techniques: UER (User-Environment-Responsibility) technique and enhanced CRC (Class-ResponsibilityCollaboration) cards. UER technique consists of (a) looking for the users of systems and describing the ways the system is used; (b) looking for the objects of the environment and describing the possible interactions; and (c) looking for the general requirements or goals of the system, the actions that it should carry out without explicit interaction. The enhanced CRC cards together with the internal use cases technique is used for dening collaborations between agents. These techniques can be easily integrated in UML (Unied Modelling Language) [2], dening the new notation symbols as stereotypes.

Estudio preliminar acerca del uso de protocolos y actos comunicativos FIPA en el sistema COMPUTAPLEX

Este trabajo corresponde con la implementación de componentes software dentro de la Plataforma COMPUTAPLEX, la cual tiene como objetivo facilitar a los investigadores la realización de tareas del proceso experimental de ingeniería de software. Uno de los aportes a esta plataforma tecnológica corresponde con el desarrolló de los componentes necesarios para la recuperación de datos experimentales disponibles en diversas fuentes de datos, para ello se hizo uso de un mecanismo capaz de unificar la extracción de información de MySQL, ficheros excel y ficheros SPSS. Con ello diferentes grupos de investigación asociados pueden compartir y tener acceso a repositorios experimentales que se mantienen tanto de manera local como externa. Por otra parte, se ha realizado un estudio de la tecnología de agentes en la que se describe sus definiciones, lenguajes de comunicación, especificación FIPA, JADE como implementación FIPA y parser XML. Además para este trabajo se ha definido e implementado una ontología de comunicación entre agentes, la misma que fue diseñada en la herramienta Protégé. En lo que se refiere al desarrollo de componentes se hizo uso de una amplía variedad de tecnologías que incluye lenguaje de programación Java, framework JADE para el desarrollo de agentes, librería JENA para manejo de ontologías, librería SAXParser para lectura de archivos XML y patrón de diseño Factory. Finalmente se describe la metodología de trabajo utilizada en el proyecto, la cual por medio de la realización de varios ciclos iterativos permitió obtener prototipos que poco a poco fueron cubriendo las necesidades del producto software.----ABSTRACT---- This work relates to the implementation of software components within the platform Computaplex, which aims to enable researchers to conduct experimental software engineering process tasks. One of the contributions to this platform technology corresponds to the development of components which are necessary for the recovery of experimental data available in different data sources, to archive this goal a mechanism able to unify the extraction of information from MySQL, Excel and SPSS files was made. Therefore, associated research groups can share and access experimental repositories that remain both locally and externally. Moreover, it has been conducted a study of agent technology in its definition is described, languages communication, FIPA, JADE and FIPA implementation and XML parser. In addition to this work, it has been defined and implemented an ontology for communication between agents, the same as was designed in the Protégé tool. In what refers to the development of components, a wide range of technologies have been made which includes Java programming language, framework JADE for agent development, JENA library for handling ontologies, SAXParser for reading XML files and Factory design pattern. Finally, describing the work methodology used in this project, which through the implementation of several iterative cycles allowed to obtain prototypes were gradually meeting the needs of the software product.

Herramienta Web para el modelado de consultas CEP (Complex Event Processing)

RESUMEN En los últimos años, debido al incremento en la demanda por parte de las empresas de tecnologías que posibiliten la monitorización y el análisis de un gran volumen de datos en tiempo real, la tecnología CEP (Complex Event Processing) ha surgido como una potencia en alza y su uso se ha incrementado notablemente en ciertos sectores como, por ejemplo, la gestión y automatización de procesos de negocios, finanzas, monitorización de redes y aplicaciones, así como redes de sensores inteligentes como el caso de estudio en el que nos centraremos. CEP se basa en un lenguaje de procesamiento de eventos (Event Processing Language,EPL) cuya utilización puede resultar bastante compleja para usuarios inexpertos. Esta complejidad supone un hándicap y, por lo tanto, un problema a la hora de que su uso se extienda. Este Proyecto Fin de Grado (PFG) pretende dar una solución a este problema, acercando al usuario la tecnología CEP mediante técnicas de abstracción y modelado. Para ello, este PFG ha definido un lenguaje de modelado específico dominio, sencillo e intuitivo para el usuario inexperto, al que se ha dado soporte mediante el desarrollo de una herramienta de modelado gráfico (CEP Modeler) en la que se pueden modelar consultas CEP de forma gráfica, sencilla y de manera más accesible para el usuario. ABSTRACT Over recent years, more and more companies demand technology for monitoring and analyzing a vast volume of data in real time. In this regard, the CEP technology (Complex Event Processing) has emerged as a novel approach to that end, and its use has increased dramatically in certain domains, such as, management and automation of business processes, finance, monitoring of networks and applications, as well as smart sensor networks as the case study in which we will focus. CEP is based on in the Event Processing Language (EPL). This language can be rather difficult to use for new users. This complexity can be a handicap, and therefore, a problem at the time of extending its use. This project aims to provide a solution to this problem, trying to approach the CEP technology to users through abstraction and modelling techniques. To that end, this project has defined an intuitive and simple domain-specific modelling language for new users through a web tool (CEP Modeler) for graphically modeling CEP queries, in an easier and more accessible way.

Método de desvio de obstáculos aplicado em veículo autônomo.

A operação de veículos autônomos necessita de meios para evitar colisões quando obstáculos não conhecidos previamente são interpostos em sua trajetória. Algoritmos para executar o desvio e sensores apropriados para a detecção destes obstáculos são essenciais para a operação destes veículos. Esta dissertação apresenta estudos sobre quatro algoritmos de desvio de obstáculos e tecnologia de três tipos de sensores aplicáveis à operação de veículos autônomos. Após os estudos teóricos, um dos algoritmos foi testado para a comprovação da aplicabilidade ao veículo de teste. A etapa experimental foi a realização de um programa, escrito em linguagem de programação Java, que aplicou o algoritmo Inseto 2 para o desvio de obstáculos em uma plataforma robótica (Robodeck) com o uso de sensores ultrassônicos embarcados na referida plataforma. Os experimentos foram conduzidos em ambiente fechado (indoor), bidimensional e horizontal (plano), fazendo o Robodeck executar uma trajetória. Para os testes, obstáculos foram colocados para simular situações variadas e avaliar a eficácia do algoritmo nestas configurações de caminho. O algoritmo executou o desvio dos obstáculos com sucesso e, quando havia solução para a trajetória, ela foi encontrada. Quando não havia solução, o algoritmo detectou esta situação e parou o veículo.

Partial completion of activity in business process specification

We examine the current workflow modelling capability from a new angle and demonstrate a weakness of current workflow specification languages in relation to execution of activities. This shortcoming is mainly due to serious limitations of the corresponding computational/execution model behind the business process modelling language constructs. The main purpose of this paper is the introduction of new specification/modelling constructs allowing for more precise representation of complex activity states during its execution. This new concept enables visibility of a new activity state–partial completion of activity, which in turn allows for a more flexible and precise enforcement/monitoring of automated business processes.

An efficient algorithm for partitioning parameterized polygons into rectangles

In this paper, we propose an algorithm for partitioning parameterized orthogonal polygons into rectangles. The algorithm is based on the plane-sweep technique and can be used for partitioning polygons which contain holes. The input to the algorithm consists of the contour of a parameterized polygon to be partitioned and the constraints for those parameters which reside in the contour. The algorithm uses horizontal cuts only and generates a minimum number of rectangles whose union is the original orthogonal polygon. The proposed algorithm can be used as the basis to build corner stitching data structure for parameterized VLSI layouts and has been implemented in Java programming language. Copyright © 2010 ACM, Inc.

A realtime Internet-based quality control application for hurricane surface wind observations

This thesis chronicles the design and implementation of a Internet/Intranet and database based application for the quality control of hurricane surface wind observations. A quality control session consists of selecting desired observation types to be viewed and determining a storm track based time window for viewing the data. All observations of the selected types are then plotted in a storm relative view for the chosen time window and geography is positioned for the storm-center time about which an objective analysis can be performed. Users then make decisions about data validity through visual nearest-neighbor comparison and inspection. The project employed an Object Oriented iterative development method from beginning to end and its implementation primarily features the Java programming language. ^

A realtime internet based quality control application for hurricane surface wind observations

This thesis chronicles the design and implementation of a Intemet/Intranet and database based application for the quality control of hurricane surface wind observations. A quality control session consists of selecting desired observation types to be viewed and determining a storm track based time window for viewing the data. All observations of the selected types are then plotted in a storm relative view for the chosen time window and geography is positioned for the storm-center time about which an objective analysis can be performed. Users then make decisions about data validity through visual nearestneighbor comparison and inspection. The project employed an Object Oriented iterative development method from beginning to end and its implementation primarily features the Java programming language.

Online MBPeT dashboard : enabling performance testing as a service in the cloud

In this thesis, tool support is addressed for the combined disciplines of Model-based testing and performance testing. Model-based testing (MBT) utilizes abstract behavioral models to automate test generation, thus decreasing time and cost of test creation. MBT is a functional testing technique, thereby focusing on output, behavior, and functionality. Performance testing, however, is non-functional and is concerned with responsiveness and stability under various load conditions. MBPeT (Model-Based Performance evaluation Tool) is one such tool which utilizes probabilistic models, representing dynamic real-world user behavior patterns, to generate synthetic workload against a System Under Test and in turn carry out performance analysis based on key performance indicators (KPI). Developed at Åbo Akademi University, the MBPeT tool is currently comprised of a downloadable command-line based tool as well as a graphical user interface. The goal of this thesis project is two-fold: 1) to extend the existing MBPeT tool by deploying it as a web-based application, thereby removing the requirement of local installation, and 2) to design a user interface for this web application which will add new user interaction paradigms to the existing feature set of the tool. All phases of the MBPeT process will be realized via this single web deployment location including probabilistic model creation, test configurations, test session execution against a SUT with real-time monitoring of user configurable metric, and final test report generation and display. This web application (MBPeT Dashboard) is implemented with the Java programming language on top of the Vaadin framework for rich internet application development. The Vaadin framework handles the complicated web communications processes and front-end technologies, freeing developers to implement the business logic as well as the user interface in pure Java. A number of experiments are run in a case study environment to validate the functionality of the newly developed Dashboard application as well as the scalability of the solution implemented in handling multiple concurrent users. The results support a successful solution with regards to the functional and performance criteria defined, while improvements and optimizations are suggested to increase both of these factors.