Plugin de routing para JOSM

Presentació del plugin de càlcul de rutes per a JOSM (Java OpenStreetMap)

WPMU to Wp3.1.3 Plugin compatibility spreadsheet

Assessment of Plugin compatibility through migration from WPMU 2.7.1 to WP3.1.3

The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets.

GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Unity assessment: desarrollo de un plugin de Unity evaluación basada en juegos y desarrollo de un juego de artes escénicas

En el ámbito educativo, gran parte de los docentes realizan la evaluación de alumnos mediante herramientas tradicionales: exámenes, cuestionario, trabajos, etc. Esta forma de evaluar presenta inconvenientes, por un lado, precisa que el profesor esté durante todo el proceso de evaluación y, por otro lado, exige tiempo y trabajo desmesurado. Por ello, en este proyecto nos dedicamos a crear una forma de evaluar diferente. Esta forma de evaluar consistirá, por un lado, en obtener información cuantitativa sobre cuánto ha aprendido el alumno a través de una puntuación. Este tipo de evaluación, se realizará mediante un videojuego. Por otro lado, consistirá en almacenar esta puntuación en algún sitio de acceso fácil y rápido para el profesor. Para este cometido hemos elegido una plataforma virtual, Moodle. Elegimos Moodle porque es una plataforma diseñada para ayudar a los profesores en su labor. Pueden gestionar sus asignaturas e interactuar con sus alumnos. El profesor crea un entorno centrado en el alumno que le ayuda a cimentar conocimientos según sus habilidades. Hemos elegido los videojuegos porque son una herramienta de enseñanza efectiva. Ofrecen una gran mejora en el rendimiento académico del alumno, así como potenciar la adquisición de conocimientos o incluso aumentar la motivación y el interés del jugador sobre el contenido del videojuego. Por tanto, en este proyecto también nos centraremos en crear un videojuego. Crearemos un videojuego orientado al teatro para fomentar el interés y la motivación de los jugadores en este campo. El videojuego estará basado en la obra de teatro llamada El Alcalde de Zalamea del autor Calderón de la Barca. Por último, para enviar la puntuación obtenida a Moodle desde el videojuego es necesario crear una comunicación entre estas dos tecnologías. Nuestro objetivo primordial en este proyecto es crear dos aplicaciones. Una en el videojuego que es la encargada de enviar la puntuación. Y otra en Moodle, encargada de almacenar la puntuación en la base de datos y mostrarla al profesor, de una forma intuitiva.

Improving Usability of Software Refactoring Tools

Post-deployment maintenance and evolution can account for up to 75% of the cost of developing a software system. Software refactoring can reduce the costs associated with evolution by improving system quality. Although refactoring can yield benefits, the process includes potentially complex, error-prone, tedious and time-consuming tasks. It is these tasks that automated refactoring tools seek to address. However, although the refactoring process is well-defined, current refactoring tools do not support the full process. To develop better automated refactoring support, we have completed a usability study of software refactoring tools. In the study, we analysed the task of software refactoring using the ISO 9241-11 usability standard and Fitts' List of task allocation. Expanding on this analysis, we reviewed 11 collections of usability guidelines and combined these into a single list of 38 guidelines. From this list, we developed 81 usability requirements for refactoring tools. Using these requirements, the software refactoring tools Eclipse 3.2, Condenser 1.05, RefactorIT 2.5.1, and Eclipse 3.2 with the Simian UI 2.2.12 plugin were studied. Based on the analysis, we have selected a subset of the requirements that can be incorporated into a prototype refactoring tool intended to address the full refactoring process.

Analysis and correction of voltage profile in low voltage distribution networks containing photovoltaic cells and electric vehicles

Voltage drop and rise at network peak and off–peak periods along with voltage unbalance are the major power quality problems in low voltage distribution networks. Usually, the utilities try to use adjusting the transformer tap changers as a solution for the voltage drop. They also try to distribute the loads equally as a solution for network voltage unbalance problem. On the other hand, the ever increasing energy demand, along with the necessity of cost reduction and higher reliability requirements, are driving the modern power systems towards Distributed Generation (DG) units. This can be in the form of small rooftop photovoltaic cells (PV), Plug–in Electric Vehicles (PEVs) or Micro Grids (MGs). Rooftop PVs, typically with power levels ranging from 1–5 kW installed by the householders are gaining popularity due to their financial benefits for the householders. Also PEVs will be soon emerged in residential distribution networks which behave as a huge residential load when they are being charged while in their later generation, they are also expected to support the network as small DG units which transfer the energy stored in their battery into grid. Furthermore, the MG which is a cluster of loads and several DG units such as diesel generators, PVs, fuel cells and batteries are recently introduced to distribution networks. The voltage unbalance in the network can be increased due to the uncertainties in the random connection point of the PVs and PEVs to the network, their nominal capacity and time of operation. Therefore, it is of high interest to investigate the voltage unbalance in these networks as the result of MGs, PVs and PEVs integration to low voltage networks. In addition, the network might experience non–standard voltage drop due to high penetration of PEVs, being charged at night periods, or non–standard voltage rise due to high penetration of PVs and PEVs generating electricity back into the grid in the network off–peak periods. In this thesis, a voltage unbalance sensitivity analysis and stochastic evaluation is carried out for PVs installed by the householders versus their installation point, their nominal capacity and penetration level as different uncertainties. A similar analysis is carried out for PEVs penetration in the network working in two different modes: Grid to vehicle and Vehicle to grid. Furthermore, the conventional methods are discussed for improving the voltage unbalance within these networks. This is later continued by proposing new and efficient improvement methods for voltage profile improvement at network peak and off–peak periods and voltage unbalance reduction. In addition, voltage unbalance reduction is investigated for MGs and new improvement methods are proposed and applied for the MG test bed, planned to be established at Queensland University of Technology (QUT). MATLAB and PSCAD/EMTDC simulation softwares are used for verification of the analyses and the proposals.

An extensible simulation framework for critical infrastructure security

We introduce the Network Security Simulator (NeSSi2), an open source discrete event-based network simulator. It incorporates a variety of features relevant to network security distinguishing it from general-purpose network simulators. Compared to the predecessor NeSSi, it was extended with a three-tier plugin architecture and a generic network model to shift its focus towards simulation framework for critical infrastructures. We demonstrate the gained adaptability by different use cases

A new method of detecting changes in corneal health in response to toxic insults

The size and arrangement of stromal collagen fibrils (CFs) influence the optical properties of the cornea and hence its function. The spatial arrangement of the collagen is still questionable in relation to the diameter of collagen fibril. In the present study, we introduce a new parameter, edge-fibrillar distance (EFD) to measure how two collagen fibrils are spaced with respect to their closest edges and their spatial distribution through normalized standard deviation of EFD (NSDEFD) accessed through the application of two commercially available multipurpose solutions (MPS): ReNu and Hippia. The corneal buttons were soaked separately in ReNu and Hippia MPS for five hours, fixed overnight in 2.5% glutaraldehyde containing cuprolinic blue and processed for transmission electron microscopy. The electron micrographs were processed using ImageJ user-coded plugin. Statistical analysis was performed to compare the image processed equivalent diameter (ED), inter-fibrillar distance (IFD), and EFD of the CFs of treated versus normal corneas. The ReNu-soaked cornea resulted in partly degenerated epithelium with loose hemidesmosomes and Bowman’s collagen. In contrast, the epithelium of the cornea soaked in Hippia was degenerated or lost but showed closely packed Bowman’s collagen. Soaking the corneas in both MPS caused a statistically significant decrease in the anterior collagen fibril, ED and a significant change in IFD, and EFD than those of the untreated corneas (p < 0.05, for all comparisons). The introduction of EFD measurement in the study directly provided a sense of gap between periphery of the collagen bundles, their spatial distribution; and in combination with ED, they showed how the corneal collagen bundles are spaced in relation to their diameters. The spatial distribution parameter NSDEFD indicated that ReNu treated cornea fibrils were uniformly distributed spatially, followed by normal and Hippia. The EFD measurement with relatively lower standard deviation and NSDEFD, a characteristic of uniform CFs distribution, can be an additional parameter used in evaluating collagen organization and accessing the effects of various treatments on corneal health and transparency.

Discovering Math APIs by Mining Unit Tests

In today's API-rich world, programmer productivity depends heavily on the programmer's ability to discover the required APIs. In this paper, we present a technique and tool, called MATHFINDER, to discover APIs for mathematical computations by mining unit tests of API methods. Given a math expression, MATHFINDER synthesizes pseudo-code to compute the expression by mapping its subexpressions to API method calls. For each subexpression, MATHFINDER searches for a method such that there is a mapping between method inputs and variables of the subexpression. The subexpression, when evaluated on the test inputs of the method under this mapping, should produce results that match the method output on a large number of tests. We implemented MATHFINDER as an Eclipse plugin for discovery of third-party Java APIs and performed a user study to evaluate its effectiveness. In the study, the use of MATHFINDER resulted in a 2x improvement in programmer productivity. In 96% of the subexpressions queried for in the study, MATHFINDER retrieved the desired API methods as the top-most result. The top-most pseudo-code snippet to implement the entire expression was correct in 93% of the cases. Since the number of methods and unit tests to mine could be large in practice, we also implement MATHFINDER in a MapReduce framework and evaluate its scalability and response time.

GitLine tresnaren zabaltzea: software produktu-lerroen kudeaketa

Gradu amaierako proiektu hau software produktu-lerroen testuinguruan kokatzen da, GitLine aplikazioan funtzionalitate batzuk gehituz. GitLine, Onekin ikerketa taldean [13] garatua, GitHub-en funtzionalitate gehigarriak eskaintzen dituen Firefox-eko plugin bat da. Plugin honek SPL produktu eraikitzaileari laguntza eskaintzen dio ezaugarri biltegiak eta produktu biltegiak sortu eta beraien arteko sinkronizazioa mantentzeko. Sinkronizazio hori hobetzeko, ikasleak hiru funtzionalitate berri inplementatu ditu. GitLine-en inplementatuta dagoen productFork funtzionalitateari, hau da, ezaugarri biltegi batetik aukeratutako ezaugarriekin produktu biltegia sortzeko funtzionalitateari, hobekuntza nabarmen bat gehitu dio ikasleak: baliozkoak diren produktu biltegiak bakarrik sortzen direla ziurtatzen du (balioztaketa). Hobekuntza honi esker, produktu biltegiak erabat sinkronizatuta daude ezaugarri biltegiarekin. Ezaugarri biltegi baten bizi-zikloa handitzeko, ikasleak ezaugarri biltegian ezaugarri berriak txertatzeko aukera inplementatu du (ezaugarria txertatu). Gainera, hasieran aipatutako ezaugarri biltegi eta produktu biltegien arteko sinkronizazio hori bermatzeko, ezaugarri berriak txertatzerakoan, ezaugarri berri horiek sortuta dauden produktu biltegietara hedatzeko aukera inplementatu du ere (ezaugarria hedatu).

WormSizer: high-throughput analysis of nematode size and shape.

The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.