MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

On the acquisition of high-resolution maps with open source software and commercials off-the-shelf quad-rotors

Mosaics are high-resolution images obtained aerially and employed in several scientific research areas, such for example, in the field of environmental monitoring and precision agriculture. Although many high resolution maps are obtained by commercial demand, they can also be acquired with commercial aerial vehicles which provide more experimental autonomy and availability. For what regard to mosaicing-based aerial mission planners, there are not so many - if any - free of charge software. Therefore, in this paper is presented a framework designed with open source tools and libraries as an alternative to commercial tools to carry out mosaicing tasks.

UBURYO: open source software for managing microcredits in education

One of the major problems in developing countries is minority access to higher education. Traditional scholarships usually focus on paying tuition fees for bringing brilliant students to developed countries (from where they seldom return). But local grants seldom target the more needy students. We propose a system of student loans to pay tuition fees in exchange for technical work. This appears to be a satisfactory and sustainable solution. We also provide UBURYO (a Kirundi word meaning opportunity). UBURYO is the free open source software, that we have developed, to manage this loan system in a simple, trustworthy, fair and efficient way.

A systematic mapping study on the open source software development process.

Abstract?Background: There is no globally accepted open source software development process to define how open source software is developed in practice. A process description is important for coordinating all the software development activities involving both people and technology. Aim: The research question that this study sets out to answer is: What activities do open source software process models contain? The activity groups on which it focuses are Concept Exploration, Software Requirements, Design, Maintenance and Evaluation. Method: We conduct a systematic mapping study (SMS). A SMS is a form of systematic literature review that aims to identify and classify available research papers concerning a particular issue. Results: We located a total of 29 primary studies, which we categorized by the open source software project that they examine and by activity types (Concept Exploration, Software Requirements, Design, Maintenance and Evaluation). The activities present in most of the open source software development processes were Execute Tests and Conduct Reviews, which belong to the Evaluation activities group. Maintenance is the only group that has primary studies addressing all the activities that it contains. Conclusions: The primary studies located by the SMS are the starting point for analyzing the open source software development process and proposing a process model for this community. The papers in our paper pool that describe a specific open source software project provide more regarding our research question than the papers that talk about open source software development without referring to a specific open source software project.

A framework for building distributed social network websites

Las redes son la esencia de comunidades y sociedades humanas; constituyen el entramado en el que nos relacionamos y determinan cómo lo hacemos, cómo se disemina la información o incluso cómo las cosas se llevan a cabo. Pero el protagonismo de las redes va más allá del que adquiere en las redes sociales. Se encuentran en el seno de múltiples estructuras que conocemos, desde las interaciones entre las proteínas dentro de una célula hasta la interconexión de los routers de internet. Las redes sociales están presentes en internet desde sus principios, en el correo electrónico por tomar un ejemplo. Dentro de cada cliente de correo se manejan listas contactos que agregadas constituyen una red social. Sin embargo, ha sido con la aparición de los sitios web de redes sociales cuando este tipo de aplicaciones web han llegado a la conciencia general. Las redes sociales se han situado entre los sitios más populares y con más tráfico de la web. Páginas como Facebook o Twitter manejan cifras asombrosas en cuanto a número de usuarios activos, de tráfico o de tiempo invertido en el sitio. Pero las funcionalidades de red social no están restringidas a las redes sociales orientadas a contactos, aquellas enfocadas a construir tu lista de contactos e interactuar con ellos. Existen otros ejemplos de sitios que aprovechan las redes sociales para aumentar la actividad de los usuarios y su involucración alrededor de algún tipo de contenido. Estos ejemplos van desde una de las redes sociales más antiguas, Flickr, orientada al intercambio de fotografías, hasta Github, la red social de código libre más popular hoy en día. No es una casualidad que la popularidad de estos sitios web venga de la mano de sus funcionalidades de red social. El escenario es más rico aún, ya que los sitios de redes sociales interaccionan entre ellos, compartiendo y exportando listas de contactos, servicios de autenticación y proporcionando un valioso canal para publicitar la actividad de los usuarios en otros sitios web. Esta funcionalidad es reciente y aún les queda un paso hasta que las redes sociales superen su condición de bunkers y lleguen a un estado de verdadera interoperabilidad entre ellas, tal como funcionan hoy en día el correo electrónico o la mensajería instantánea. Este trabajo muestra una tecnología que permite construir sitios web con características de red social distribuída. En primer lugar, se presenta una tecnología para la construcción de un componente intermedio que permite proporcionar cualquier característica de gestión de contenidos al popular marco de desarrollo web modelo-vista-controlador (MVC) Ruby on Rails. Esta técnica constituye una herramienta para desarrolladores que les permita abstraerse de las complejidades de la gestión de contenidos y enfocarse en las particularidades de los propios contenidos. Esta técnica se usará también para proporcionar las características de red social. Se describe una nueva métrica de reusabilidad de código para demostrar la validez del componente intermedio en marcos MVC. En segundo lugar, se analizan las características de los sitios web de redes sociales más populares, con el objetivo de encontrar los patrones comunes que aparecen en ellos. Este análisis servirá como base para definir los requisitos que debe cumplir un marco para construir redes sociales. A continuación se propone una arquitectura de referencia que proporcione este tipo de características. Dicha arquitectura ha sido implementada en un componente, Social Stream, y probada en varias redes sociales, tanto orientadas a contactos como a contenido, en el contexto de una asociación vecinal tanto como en proyectos de investigación financiados por la UE. Ha sido la base de varios proyectos fin de carrera. Además, ha sido publicado como código libre, obteniendo una comunidad creciente y está siendo usado más allá del ámbito de este trabajo. Dicha arquitectura ha permitido la definición de un nuevo modelo de control de acceso social que supera varias limitaciones presentes en los modelos de control de acceso para redes sociales. Más aún, se han analizado casos de estudio de sitios de red social distribuídos, reuniendo un conjunto de caraterísticas que debe cumplir un marco para construir redes sociales distribuídas. Por último, se ha extendido la arquitectura del marco para dar cabida a las características de redes sociales distribuídas. Su implementación ha sido validada en proyectos de investigación financiados por la UE. Abstract Networks are the substance of human communities and societies; they constitute the structural framework on which we relate to each other and determine the way we do it, the way information is diseminated or even the way people get things done. But network prominence goes beyond the importance it acquires in social networks. Networks are found within numerous known structures, from protein interactions inside a cell to router connections on the internet. Social networks are present on the internet since its beginnings, in emails for example. Inside every email client, there are contact lists that added together constitute a social network. However, it has been with the emergence of social network sites (SNS) when these kinds of web applications have reached general awareness. SNS are now among the most popular sites in the web and with the higher traffic. Sites such as Facebook and Twitter hold astonishing figures of active users, traffic and time invested into the sites. Nevertheless, SNS functionalities are not restricted to contact-oriented social networks, those that are focused on building your own list of contacts and interacting with them. There are other examples of sites that leverage social networking to foster user activity and engagement around other types of content. Examples go from early SNS such as Flickr, the photography related networking site, to Github, the most popular social network repository nowadays. It is not an accident that the popularity of these websites comes hand-in-hand with their social network capabilities The scenario is even richer, due to the fact that SNS interact with each other, sharing and exporting contact lists and authentication as well as providing a valuable channel to publize user activity in other sites. These interactions are very recent and they are still finding their way to the point where SNS overcome their condition of data silos to a stage of full interoperability between sites, in the same way email and instant messaging networks work today. This work introduces a technology that allows to rapidly build any kind of distributed social network website. It first introduces a new technique to create middleware that can provide any kind of content management feature to a popular model-view-controller (MVC) web development framework, Ruby on Rails. It provides developers with tools that allow them to abstract from the complexities related with content management and focus on the development of specific content. This same technique is also used to provide the framework with social network features. Additionally, it describes a new metric of code reuse to assert the validity of the kind of middleware that is emerging in MVC frameworks. Secondly, the characteristics of top popular SNS are analysed in order to find the common patterns shown in them. This analysis is the ground for defining the requirements of a framework for building social network websites. Next, a reference architecture for supporting the features found in the analysis is proposed. This architecture has been implemented in a software component, called Social Stream, and tested in several social networks, both contact- and content-oriented, in local neighbourhood associations and EU-founded research projects. It has also been the ground for several Master’s theses. It has been released as a free and open source software that has obtained a growing community and that is now being used beyond the scope of this work. The social architecture has enabled the definition of a new social-based access control model that overcomes some of the limitations currenly present in access control models for social networks. Furthermore, paradigms and case studies in distributed SNS have been analysed, gathering a set of features for distributed social networking. Finally the architecture of the framework has been extended to support distributed SNS capabilities. Its implementation has also been validated in EU-founded research projects.

Web-based education in Spanish Universities. A Comparison of Open Source E-Learning Platforms

Web-based education or „e-learning‟ has become a critical component in higher education for the last decade, replacing other distance learning methods, such as traditional computer training or correspondence learning. The number of university students who take on-line courses is continuously increasing all over the world. In Spain, nearly a 90% of the universities have an institutional e-learning platform and over 60% of the traditional on-site courses use this technology as a supplement to the traditional face-to-face classes. This new form of learning allows the disappearance of geographical barriers and enables students to schedule their own learning process, among some other advantages. On-line education is developed through specific software called „e-learning platform‟ or „virtual learning environment‟ (VLE). A considerable number of web-based tools to deliver distance courses are currently available. Open source software packages such as Moodle, Sakai, dotLRN or Dokeos are the most commonly used in the virtual campuses of Spanish universities. This paper analyzes the possibilities that virtual learning environments provide university teachers and learners and offers a technical comparison among some of the most popular e-learning learning platforms.

Modeling and Simulation of Upper Brachial Plexus Injury

This article presents the first musculoskeletal model and simulation of upper plexus brachial injury. From this model is possible to analyse forces and movement ranges in order to develop a robotic exoskeleton to improve rehabilitation. The software that currently exists for musculoskeletal modeling is varied and most have advanced features for proper analysis and study of motion simulations. Whilst more powerful computer packages are usually expensive, there are other free and open source packages available which offer different tools to perform animations and simulations and which obtain forces and moments of inertia. Among them, Musculoskeletal Modeling Software was selected to construct a model of the upper limb, which has 7 degrees of freedom and 10 muscles. These muscles are important for two of the movements simulated in this article that are part of the post-surgery rehabilitation protocol. We performed different movement animations which are made using the inertial measurement unit to capture real data from movements made by a human being. We also performed the simulation of forces produced in elbow flexion-extension and arm abduction-adduction of a healthy subject and one with upper brachial plexus injury in a postoperative state to compare the force that is capable of being produced in both cases.

Diferencias entre las Actividades de Mantenimiento en los Procesos de Desarrollo Tradicional y Open Source

Antecedentes. La creciente importancia del Open Source Software (OSS) ha llevado a los investigadores a estudiar cómo los procesos OSS difieren de los procesos de la ingeniería del software tradicional. Objetivo. Determinar las diferencias y similitudes entre las actividades del proceso de mantenimiento seguido por la comunidad OSS y el establecido por el estándar IEEE 1074:2006. Método. Para conocer las actividades que conforman el proceso de desarrollo OSS realizamos un Systematic Mapping Study. Posteriormente, realizamos un emparejamiento entre las actividades del estándar IEEE 1074:2006 con las actividades del proceso OSS. Resultados. Encontramos un total de 22 estudios primarios. De estos estudios, el 73% contaba con actividades relacionadas con el proceso de mantenimiento. Conclusiones. El proceso de mantenimiento tradicional del software no encaja con lo que ocurre en la comunidad OSS. En su lugar, puede ser mejor caracterizar la dinámica general de la evolución OSS como reinvención. Esta reinvención emerge continuamente de la adaptación, aprendizaje, y mejora de las funcionalidadess y calidad del OSS. Los proyectos OSS evolucionan a través de mejoras menores donde participan tanto usuarios como desarrolladores.

Evaluating social choice techniques into intelligent environments by agent based social simulation

The primary hypothesis stated by this paper is that the use of social choice theory in Ambient Intelligence systems can improve significantly users satisfaction when accessing shared resources. A research methodology based on agent based social simulations is employed to support this hypothesis and to evaluate these benefits. The result is a six-fold contribution summarized as follows. Firstly, several considerable differences between this application case and the most prominent social choice application, political elections, have been found and described. Secondly, given these differences, a number of metrics to evaluate different voting systems in this scope have been proposed and formalized. Thirdly, given the presented application and the metrics proposed, the performance of a number of well known electoral systems is compared. Fourthly, as a result of the performance study, a novel voting algorithm capable of obtaining the best balance between the metrics reviewed is introduced. Fifthly, to improve the social welfare in the experiments, the voting methods are combined with cluster analysis techniques. Finally, the article is complemented by a free and open-source tool, VoteSim, which ensures not only the reproducibility of the experimental results presented, but also allows the interested reader to adapt the case study presented to different environments.

Context modelling for natural Human Computer Interaction applications in e-health

The conception of IoT (Internet of Things) is accepted as the future tendency of Internet among academia and industry. It will enable people and things to be connected at anytime and anyplace, with anything and anyone. IoT has been proposed to be applied into many areas such as Healthcare, Transportation，Logistics, and Smart environment etc. However, this thesis emphasizes on the home healthcare area as it is the potential healthcare model to solve many problems such as the limited medical resources, the increasing demands for healthcare from elderly and chronic patients which the traditional model is not capable of. A remarkable change in IoT in semantic oriented vision is that vast sensors or devices are involved which could generate enormous data. Methods to manage the data including acquiring, interpreting, processing and storing data need to be implemented. Apart from this, other abilities that IoT is not capable of are concluded, namely, interoperation, context awareness and security & privacy. Context awareness is an emerging technology to manage and take advantage of context to enable any type of system to provide personalized services. The aim of this thesis is to explore ways to facilitate context awareness in IoT. In order to realize this objective, a preliminary research is carried out in this thesis. The most basic premise to realize context awareness is to collect, model, understand, reason and make use of context. A complete literature review for the existing context modelling and context reasoning techniques is conducted. The conclusion is that the ontology-based context modelling and ontology-based context reasoning are the most promising and efficient techniques to manage context. In order to fuse ontology into IoT, a specific ontology-based context awareness framework is proposed for IoT applications. In general, the framework is composed of eight components which are hardware, UI (User Interface), Context modelling, Context fusion, Context reasoning, Context repository, Security unit and Context dissemination. Moreover, on the basis of TOVE (Toronto Virtual Enterprise), a formal ontology developing methodology is proposed and illustrated which consists of four stages: Specification & Conceptualization, Competency Formulation, Implementation and Validation & Documentation. In addition, a home healthcare scenario is elaborated by listing its well-defined functionalities. Aiming at representing this specific scenario, the proposed ontology developing methodology is applied and the ontology-based model is developed in a free and open-source ontology editor called Protégé. Finally, the accuracy and completeness of the proposed ontology are validated to show that this proposed ontology is able to accurately represent the scenario of interest.

Dashboard configurable para la gestión y administración de una instancia de OpenStack

En este documento está descrito detalladamente el trabajo realizado para completar todos objetivos marcados para este Trabajo de Fin de Grado, que tiene como meta final el desarrollo de un dashboard configurable de gestión y administración para instancias de OpenStack. OpenStack es una plataforma libre y de código abierto utilizada como solución de Infraestructura como Servicio (Infrastructure as a Service, IaaS) en clouds tanto públicos, que ofrecen sus servicios cobrando el tiempo de uso o los recursos utilizados, como privados para su utilización exclusiva en el entorno de una empresa. El proyecto OpenStack se inició como una colaboración entre la NASA y RackSpace, y a día de hoy es mantenido por las empresas más potentes del sector tecnológico a través de la Fundación OpenStack. La plataforma OpenStack permite el acceso a sus servicios a través de una Interfaz de Linea de Comandos (Command Line Interface, CLI), una API RESTful y una interfaz web en forma de dashboard. Esta última es ofrecida a través del servicio Horizon. Este servicio provee de una interfaz gráfica para acceder, gestionar y automatizar servicios basados en cloud. El dashboard de Horizon presente algunos problemas como que: solo admite opciones de configuración mediante código Python, lo que hace que el usuario no tenga ninguna capacidad de configuración y que el administrador esté obligado a interactuar directamente con el código. no tiene soporte para múltiples regiones que permitan que un usuario pueda distribuir sus recursos por distintos centros de datos en diversas localizaciones como más le convenga. El presente Trabajo de Fin de Grado, que es la fase inicial del proyecto FI-Dash, pretende solucionar estos problemas mediante el desarrollo de un catálogo de widget de la plataformaWireCloud que permitirán al usuario tener todas las funcionalidades ofrecidas por Horizon a la vez que le ofrecen capacidades de configuración y añaden funcionalidades no presentes en Horizon como el soporte de múltiples regiones. Como paso previo al desarrollo del catálogo de widgets se ha llevado a cabo un estudio de las tecnologías y servicios ofrecidos por OpenStack, así como de las herramientas que pudieran ser necesarias para la realización del trabajo. El proceso de desarrollo ha sido dividido en distintas fases de acuerdo con los distintos componentes que forman parte del dashboard cada uno con una funcion de gestion sobre un tipo de recurso distinto. Las otras fases del desarrollo han sido la integración completa del dashboard en la plataforma WireCloud y el diseño de una interfaz gráfica usable y atractiva.---ABSTRACT---Throughout this document it is described the work performed in order to achieve all of the objectives set for this Final Project, which has as its main goal the development of a configurable dashboard for managing and administrating OpenStack instances. OpenStack is a free and open source platform used as Infrastructure as a Service (IaaS) for both public clouds, which offer their services through payments on time or resources used, and private clouds for use only in the company’s environment. The OpenStack project started as a collaboration between NASA and Rackspace, and nowadays is maintained by the most powerful companies in the technology sector through the OpenStack Foundation. The OpenStack project provides access to its services through a Command Line Interface (CLI), a RESTful API and a web interface as dashboard. The latter is offered through a service called Horizon. This service provides a graphical interface to access, manage and automate cloud-based services. Horizon’s dashboard presents some problems such as: Only supports configuration options using Python code, which grants the user no configuration capabilities and forces the administrator to interact directly. No support for multiple regions that allow a user to allocate his resources by different data centers in different locations at his convenience. This Final Project, which is the initial stage of the FI-Dash project, aims to solve these problems by developing a catalog of widgets for the WireCloud platform that will allow the user to have all the features offered by Horizon while offering configuration capabilities and additional features not present in Horizon such as support for multiple regions. As a prelude to the development of the widget catalog, a study of technologies and services offered by OpenStack as well as tools that may be necessary to carry out the work has been conducted. The development process has been split in phases matching the different components that are part of the dashboard, having each one of them a function of management of one kind of resource. The other development phases have been the achieving of full integration with WireCloud and the design of a graphical interface that is both usable and atractive.

A Model-based Repository for Open Source Service and Component Integration.

Open source is a software development paradigm that has seen a huge rise in recent years. It reduces IT costs and time to market, while increasing security and reliability. However, the difficulty in integrating developments from different communities and stakeholders prevents this model from reaching its full potential. This is mainly due to the challenge of determining and locating the correct dependencies for a given software artifact. To solve this problem we propose the development of an extensible software component repository based upon models. This repository should be capable of solving the dependencies between several components and work with already existing repositories to access the needed artifacts transparently. This repository will also be easily expandable, enabling the creation of modules that support new kinds of dependencies or other existing repository technologies. The proposed solution will work with OSGi components and use OSGi itself.

Intensive Metrics for the Study of the Evolution of Open Source Projects: Case Studies from Apache Software Foundation Projects

Based on the empirical evidence that the ratio of email messages in public mailing lists to versioning system commits has remained relatively constant along the history of the Apache Software Foundation (ASF), this paper has as goal to study what can be inferred from such a metric for projects of the ASF. We have found that the metric seems to be an intensive metric as it is independent of the size of the project, its activity, or the number of developers, and remains relatively independent of the technology or functional area of the project. Our analysis provides evidence that the metric is related to the technical effervescence and popularity of project, and as such can be a good candidate to measure its healthy evolution. Other, similar metrics -like the ratio of developer messages to commits and the ratio of issue tracker messages to commits- are studied for several projects as well, in order to see if they have similar characteristics.

Studying the laws of software evolution in a long-lived FLOSS project

ome free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case

Development of a wake model for wind farms based on an open source CFD solver. Strategies on parabolization and turbulence modeling

Wake effect represents one of the most important aspects to be analyzed at the engineering phase of every wind farm since it supposes an important power deficit and an increase of turbulence levels with the consequent decrease of the lifetime. It depends on the wind farm design, wind turbine type and the atmospheric conditions prevailing at the site. Traditionally industry has used analytical models, quick and robust, which allow carry out at the preliminary stages wind farm engineering in a flexible way. However, new models based on Computational Fluid Dynamics (CFD) are needed. These models must increase the accuracy of the output variables avoiding at the same time an increase in the computational time. Among them, the elliptic models based on the actuator disk technique have reached an extended use during the last years. These models present three important problems in case of being used by default for the solution of large wind farms: the estimation of the reference wind speed upstream of each rotor disk, turbulence modeling and computational time. In order to minimize the consequence of these problems, this PhD Thesis proposes solutions implemented under the open source CFD solver OpenFOAM and adapted for each type of site: a correction on the reference wind speed for the general elliptic models, the semi-parabollic model for large offshore wind farms and the hybrid model for wind farms in complex terrain. All the models are validated in terms of power ratios by means of experimental data derived from real operating wind farms.