EuroPhenome: a repository for high-throughput mouse phenotyping data.

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

Evaluating fear of falling among community-dwelling older people: A qualitative pattern model based on the experience of falls

This research was conducted in the context of the project IRIS 8A Health and Society (2002-2008) and financially supported by the University of Lausanne. It was aomed at developping a model based on the elder people's experience and allowed us to develop a "Portrait evaluation" of fear of falling using their examples and words. It is a very simple evaluation, which can be used by professionals, but by the elder people themselves. The "Portrait evaluation" and the user's guide are on free access, but we would very much approciate to know whether other people or scientists have used it and collect their comments. (contact: Chantal.Piot-Ziegler@unil.ch)The purpose of this study is to create a model grounded in the elderly people's experience allowing the development of an original instrument to evaluate FOF.In a previous study, 58 semi-structured interviews were conducted with community-dwelling elderly people. The qualitative thematic analysis showed that fear of falling was defined through the functional, social and psychological long-term consequences of falls (Piot-Ziegler et al., 2007).In order to reveal patterns in the expression of fear of falling, an original qualitative thematic pattern analysis (QUAlitative Pattern Analysis - QUAPA) is developed and applied on these interviews.The results of this analysis show an internal coherence across the three dimensions (functional, social and psychological). Four different patterns are found, corresponding to four degrees of fear of falling. They are formalized in a fear of falling intensity model.This model leads to a portrait-evaluation for fallers and non-fallers. The evaluation must be confronted to large samples of elderly people, living in different environments. It presents an original alternative to the concept of self-efficacy to evaluate fear of falling in older people.The model of FOF presented in this article is grounded on elderly people's experience. It gives an experiential description of the three dimensions constitutive of FOF and of their evolution as fear increases, and defines an evaluation tool using situations and wordings based on the elderly people's discourse.

quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.

quantiNemo is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNemo is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc. quantiNemo is coded in C++ using an object-oriented approach and runs on any computer platform. Availability: Executables for several platforms, user's manual, and source code are freely available under the GNU General Public License at http://www2.unil.ch/popgen/softwares/quantinemo.

A programming environment having three levels of complexity for mobile robotics = Entorno de programación con tres niveles de complejidad para robótica móvil

This paper presents a programming environment for supporting learning in STEM, particularly mobile robotic learning. It was designed to maintain progressive learning for people with and without previous knowledge of programming and/or robotics. The environment was multi platform and built with open source tools. Perception, mobility, communication, navigation and collaborative behaviour functionalities can be programmed for different mobile robots. A learner is able to programme robots using different programming languages and editor interfaces: graphic programming interface (basic level), XML-based meta language (intermediate level) or ANSI C language (advanced level). The environment supports programme translation transparently into different languages for learners or explicitly on learners’ demand. Learners can access proposed challenges and learning interfaces by examples. The environment was designed to allow characteristics such as extensibility, adaptive interfaces, persistence and low software/hardware coupling. Functionality tests were performed to prove programming environment specifications. UV BOT mobile robots were used in these tests

Sovellus meteorologisen tiedon tuotantojärjestelmän seurantaan

Työssä käsitellään selainkäyttöliittymää käyttävien oliopohjaisten tietokantasovellusten toteuttamista. Erityisesti keskitytään olio- ja relaatiomallien yhteensovittamiseen ja oliopohjaisten selainkäyttöliittymien toteutukseen Java-servlettien ja JSP-sivujen avulla. Myös hajautetut sovellusarkkitehtuurit käydään läpi ja niiden toteuttamista arvioidaan servlet-sovellusten näkökulmasta. Työssä on toteutettu selainkäyttöliittymän avulla hallittava kaksitasoarkkitehtuuria käyttävä oliopohjainen sovellus Ilmatieteen laitoksen tuotantojärjestelmän seurantaan. Sovellus mahdollistaa mm. tuotantoajojen ja laajempien tuotantoketjujen suoritusaikojen tilastollisen seurannan. Työn tuloksena todettiin Java-servlettien ja JSP-sivujen olevan suorituskykyinen ja monipuolinen ratkaisu selainkäyttöliittymien toteuttamiseen. Olio- ja relaatiomallien väliset erot sekä käyttöliittymän eriyttäminen toimintalogiikasta osoittautuivat ongelmakohdiksi.

Verkkokäyttöliittymäohjelmiston toteuttaminen TradeXpress-tietojärjestelmään.

Työssä perehdytään verkkokäyttöliittymien suunnitteluun ja toteutukseen. Erityisen huomion kohteena ovat Java-ohjelmointikieli ja ohjelmistosuunnittelussa suurta huomiota herättäneet suunnittelumallit. Java on kehittynyt lyhyen elinikänsä aikana huomattavasti, ja viimeaikaiset vakioluokkakirjastot ovat mahdollistaneet monipuolisten ja siirrettävien ohjelmistojen toteuttamisen. Vaikka Java ei sovellukaan kaikkiin tarkoituksiin, on se luotettavuutensa, siirrettävyytensä ja luokkakirjastojensa ilmaisuvoiman ansiosta hyvin houkutteleva kieli käyttöliittymien tekemiseen. Suunnittelumallit ovat merkittävä osa ammattimaista oliosuunnittelua. Ne tarjoavat valmiita ratkaisuja yleisiin suunnitteluongelmiin ja säästävät siten aikaa suunnittelu- ja toteutusvaiheissa. Suunnittelumallit voidaan jakaa kolmeen ryhmään: luontimallit, rakennemallit ja toiminnalliset mallit. Käytännön osuudessa tarkastellaan Java-käyttöliittymän toteutusta olemassa olevaan Soneran TradeXpress-tietojärjestelmään. Tässä tehtävässä Java ja suunnittelumallit ovat olleet keskeisellä sijalla. Java-käyttöliittymä, JavaGUI, koostuu kahdesta osasta: asiakasappletista ja Jrls-palvelimesta. Näiden kahden väliseen tiedonsiirtoon käytetään pääasiassa Javan RMI-yhteyskäytäntöä. Jrls-palvelin toimii asiakkaana RLS-palvelimelle erityisen RLS-yhteyskäytännön avulla.

Simulation Supported Robot Programming using XML

The main objective of this master's thesis is to study robot programming using simulation software, and also how to embed the simulation software into company's own robot controlling software. The further goal is to study a new communication interface to the assembly line's components -more precisely how to connect the robot cell into this new communication system. Conveyor lines are already available where the conveyors use the new communication standard. The robot cell is not yet capable of communicating with to other devices using the new communication protocols. The main problem among robot manufacturers is that they all have their own communication systems and programming languages. There has not been any common programming language to program all the different robot manufacturers robots, until the RRS (Realistic Robot Simulation) standards were developed. The RRS - II makes it possible to create the robot programs in the simulation software and it gives a common user interface for different robot manufacturers robots. This thesis will present the RRS - II standard and the robot manufacturers situation for the RRS - II support. Thesis presents how the simulation software can be embedded into company's own robot controlling software and also how the robot cell can be connected to the CAMX (Computer Aided Manufacturing using XML) communication system.

Data Collection Agent Framework

Ohjelmistoteollisuudessa pitkiä ja vaikeita kehityssyklejä voidaan helpottaa käyttämällä hyväksi ohjelmistokehyksiä (frameworks). Ohjelmistokehykset edustavat kokoelmaa luokkia, jotka tarjoavat yleisiä ratkaisuja tietyn ongelmakentän tarpeisiin vapauttaen ohjelmistokehittäjät keskittymään sovelluskohtaisiin vaatimuksiin. Hyvin suunniteltujen ohjelmistokehyksien käyttö lisää suunnitteluratkaisujen sekä lähdekoodin uudelleenkäytettävyyttä enemmän kuin mikään muu suunnittelulähestymistapa. Tietyn kohdealueen tietämys voidaan tallentaa ohjelmistokehyksiin, joista puolestaan voidaan erikoistaa viimeisteltyjä ohjelmistotuotteita. Tässä diplomityössä kuvataan ohjelmistoagentteihin (software agents) perustuvaa ohjelmistokehyksen suunnittelua toteutusta. Pääpaino työssä on vaatimusmäärittelyä vastaavan suunnitelman sekä toteutuksen kuvaaminen ohjelmistokehykselle, josta voidaan erikoistaa erilaiseen tiedonkeruuseen kykeneviä ohjelmistoja Internet ympäristöön. Työn kokeellisessa osuudessa esitellään myös esimerkkisovellus, joka perustuu työssä kehitettyyn ohjelmistokehykseen.

A System-Level Simulation Model for a Protocol Processor

As the development of integrated circuit technology continues to follow Moore’s law the complexity of circuits increases exponentially. Traditional hardware description languages such as VHDL and Verilog are no longer powerful enough to cope with this level of complexity and do not provide facilities for hardware/software codesign. Languages such as SystemC are intended to solve these problems by combining the powerful expression of high level programming languages and hardware oriented facilities of hardware description languages. To fully replace older languages in the desing flow of digital systems SystemC should also be synthesizable. The devices required by modern high speed networks often share the same tight constraints for e.g. size, power consumption and price with embedded systems but have also very demanding real time and quality of service requirements that are difficult to satisfy with general purpose processors. Dedicated hardware blocks of an application specific instruction set processor are one way to combine fast processing speed, energy efficiency, flexibility and relatively low time-to-market. Common features can be identified in the network processing domain making it possible to develop specialized but configurable processor architectures. One such architecture is the TACO which is based on transport triggered architecture. The architecture offers a high degree of parallelism and modularity and greatly simplified instruction decoding. For this M.Sc.(Tech) thesis, a simulation environment for the TACO architecture was developed with SystemC 2.2 using an old version written with SystemC 1.0 as a starting point. The environment enables rapid design space exploration by providing facilities for hw/sw codesign and simulation and an extendable library of automatically configured reusable hardware blocks. Other topics that are covered are the differences between SystemC 1.0 and 2.2 from the viewpoint of hardware modeling, and compilation of a SystemC model into synthesizable VHDL with Celoxica Agility SystemC Compiler. A simulation model for a processor for TCP/IP packet validation was designed and tested as a test case for the environment.

Programming and analysing measurement experiments using the PicoCricket system

The aim of this project is to get used to another kind of programming. Since now, I used very complex programming languages to develop applications or even to program microcontrollers, but PicoCricket system is the evidence that we don’t need so complex development tools to get functional devices. PicoCricket system is the clear example of simple programming to make devices work the way we programmed it. There’s an easy but effective way to programs mall devices just saying what we want them to do. We cannot do complex algorithms and mathematical operations but we can program them in a short time. Nowadays, the easier and faster we produce, the more we earn. So the tendency is to develop fast, cheap and easy, and PicoCricket system can do it.

Scheduling dynamic dataflow graphs with model checking

With the shift towards many-core computer architectures, dataflow programming has been proposed as one potential solution for producing software that scales to a varying number of processor cores. Programming for parallel architectures is considered difficult as the current popular programming languages are inherently sequential and introducing parallelism is typically up to the programmer. Dataflow, however, is inherently parallel, describing an application as a directed graph, where nodes represent calculations and edges represent a data dependency in form of a queue. These queues are the only allowed communication between the nodes, making the dependencies between the nodes explicit and thereby also the parallelism. Once a node have the su cient inputs available, the node can, independently of any other node, perform calculations, consume inputs, and produce outputs. Data ow models have existed for several decades and have become popular for describing signal processing applications as the graph representation is a very natural representation within this eld. Digital lters are typically described with boxes and arrows also in textbooks. Data ow is also becoming more interesting in other domains, and in principle, any application working on an information stream ts the dataflow paradigm. Such applications are, among others, network protocols, cryptography, and multimedia applications. As an example, the MPEG group standardized a dataflow language called RVC-CAL to be use within reconfigurable video coding. Describing a video coder as a data ow network instead of with conventional programming languages, makes the coder more readable as it describes how the video dataflows through the different coding tools. While dataflow provides an intuitive representation for many applications, it also introduces some new problems that need to be solved in order for data ow to be more widely used. The explicit parallelism of a dataflow program is descriptive and enables an improved utilization of available processing units, however, the independent nodes also implies that some kind of scheduling is required. The need for efficient scheduling becomes even more evident when the number of nodes is larger than the number of processing units and several nodes are running concurrently on one processor core. There exist several data ow models of computation, with different trade-offs between expressiveness and analyzability. These vary from rather restricted but statically schedulable, with minimal scheduling overhead, to dynamic where each ring requires a ring rule to evaluated. The model used in this work, namely RVC-CAL, is a very expressive language, and in the general case it requires dynamic scheduling, however, the strong encapsulation of dataflow nodes enables analysis and the scheduling overhead can be reduced by using quasi-static, or piecewise static, scheduling techniques. The scheduling problem is concerned with nding the few scheduling decisions that must be run-time, while most decisions are pre-calculated. The result is then an, as small as possible, set of static schedules that are dynamically scheduled. To identify these dynamic decisions and to find the concrete schedules, this thesis shows how quasi-static scheduling can be represented as a model checking problem. This involves identifying the relevant information to generate a minimal but complete model to be used for model checking. The model must describe everything that may affect scheduling of the application while omitting everything else in order to avoid state space explosion. This kind of simplification is necessary to make the state space analysis feasible. For the model checker to nd the actual schedules, a set of scheduling strategies are de ned which are able to produce quasi-static schedulers for a wide range of applications. The results of this work show that actor composition with quasi-static scheduling can be used to transform data ow programs to t many different computer architecture with different type and number of cores. This in turn, enables dataflow to provide a more platform independent representation as one application can be fitted to a specific processor architecture without changing the actual program representation. Instead, the program representation is in the context of design space exploration optimized by the development tools to fit the target platform. This work focuses on representing the dataflow scheduling problem as a model checking problem and is implemented as part of a compiler infrastructure. The thesis also presents experimental results as evidence of the usefulness of the approach.

Cohesion Metrics for Improving Software Quality

Abstract Software product metrics aim at measuring the quality of software. Modu- larity is an essential factor in software quality. In this work, metrics related to modularity and especially cohesion of the modules, are considered. The existing metrics are evaluated, and several new alternatives are proposed. The idea of cohesion of modules is that a module or a class should consist of related parts. The closely related principle of coupling says that the relationships between modules should be minimized. First, internal cohesion metrics are considered. The relations that are internal to classes are shown to be useless for quality measurement. Second, we consider external relationships for cohesion. A detailed analysis using design patterns and refactorings confirms that external cohesion is a better quality indicator than internal. Third, motivated by the successes (and problems) of external cohesion metrics, another kind of metric is proposed that represents the quality of modularity of software. This metric can be applied to refactorings related to classes, resulting in a refactoring suggestion system. To describe the metrics formally, a notation for programs is developed. Because of the recursive nature of programming languages, the properties of programs are most compactly represented using grammars and formal lan- guages. Also the tools that were used for metrics calculation are described.

Représentation de trajectoires spatiotemporelles dans un système d’information géographique : le cas des activités d’observation de mammifères marins dans le Parc marin du Saguenay – Saint-Laurent

Parc marin du Saguenay - Saint-Laurent, Groupe de recherche et d'éducation sur les mammifères marins, GREMM, excursions aux baleines, bélugas, Tadoussac, règlementation, ArcCatalog, ArcMap.

An empirical study of the impact of two antipatterns on program comprehension

Les antipatrons sont de “mauvaises” solutions à des problèmes récurrents de conception logicielle. Leur apparition est soit due à de mauvais choix lors de la phase de conception soit à des altérations et des changements continus durant l’implantation des programmes. Dans la littérature, il est généralement admis que les antipatrons rendent la compréhension des programmes plus difficile. Cependant, peu d’études empiriques ont été menées pour vérifier l’impact des antipatrons sur la compréhension. Dans le cadre de ce travail de maîtrise, nous avons conçu et mené trois expériences, avec 24 sujets chacune, dans le but de recueillir des données sur la performance des sujets lors de tâches de compréhension et d’évaluer l’impact de l’existence de deux antipatrons, Blob et Spaghetti Code, et de leurs combinaisons sur la compréhension des programmes. Nous avons mesuré les performances des sujets en terme : (1) du TLX (NASA task load index) pour l’éffort ; (2) du temps consacré à l’exécution des tâches ; et, (3) de leurs pourcentages de réponses correctes. Les données recueillies montrent que la présence d’un antipatron ne diminue pas sensiblement la performance des sujets alors que la combinaison de deux antipatrons les entrave de façon significative. Nous concluons que les développeurs peuvent faire face à un seul antipatron, alors que la combinaison de plusieurs antipatrons devrait être évitée, éventuellement par le biais de détection et de réusinage.

Analyse de dépendance des programmes à objet en utilisant les modèles probabilistes des entrées

La tâche de maintenance ainsi que la compréhension des programmes orientés objet (OO) deviennent de plus en plus coûteuses. L’analyse des liens de dépendance peut être une solution pour faciliter ces tâches d’ingénierie. Cependant, analyser les liens de dépendance est une tâche à la fois importante et difficile. Nous proposons une approche pour l'étude des liens de dépendance internes pour des programmes OO, dans un cadre probabiliste, où les entrées du programme peuvent être modélisées comme un vecteur aléatoire, ou comme une chaîne de Markov. Dans ce cadre, les métriques de couplage deviennent des variables aléatoires dont les distributions de probabilité peuvent être étudiées en utilisant les techniques de simulation Monte-Carlo. Les distributions obtenues constituent un point d’entrée pour comprendre les liens de dépendance internes entre les éléments du programme, ainsi que leur comportement général. Ce travail est valable dans le cas où les valeurs prises par la métrique dépendent des entrées du programme et que ces entrées ne sont pas fixées à priori. Nous illustrons notre approche par deux études de cas.