ConnectomeViewer - Multi-Modal Multi-Level Network Visualization and Analysis.

Introduction: The field of Connectomic research is growing rapidly, resulting from methodological advances in structural neuroimaging on many spatial scales. Especially progress in Diffusion MRI data acquisition and processing made available macroscopic structural connectivity maps in vivo through Connectome Mapping Pipelines (Hagmann et al, 2008) into so-called Connectomes (Hagmann 2005, Sporns et al, 2005). They exhibit both spatial and topological information that constrain functional imaging studies and are relevant in their interpretation. The need for a special-purpose software tool for both clinical researchers and neuroscientists to support investigations of such connectome data has grown. Methods: We developed the ConnectomeViewer, a powerful, extensible software tool for visualization and analysis in connectomic research. It uses the novel defined container-like Connectome File Format, specifying networks (GraphML), surfaces (Gifti), volumes (Nifti), track data (TrackVis) and metadata. Usage of Python as programming language allows it to by cross-platform and have access to a multitude of scientific libraries. Results: Using a flexible plugin architecture, it is possible to enhance functionality for specific purposes easily. Following features are already implemented: * Ready usage of libraries, e.g. for complex network analysis (NetworkX) and data plotting (Matplotlib). More brain connectivity measures will be implemented in a future release (Rubinov et al, 2009). * 3D View of networks with node positioning based on corresponding ROI surface patch. Other layouts possible. * Picking functionality to select nodes, select edges, get more node information (ConnectomeWiki), toggle surface representations * Interactive thresholding and modality selection of edge properties using filters * Arbitrary metadata can be stored for networks, thereby allowing e.g. group-based analysis or meta-analysis. * Python Shell for scripting. Application data is exposed and can be modified or used for further post-processing. * Visualization pipelines using filters and modules can be composed with Mayavi (Ramachandran et al, 2008). * Interface to TrackVis to visualize track data. Selected nodes are converted to ROIs for fiber filtering The Connectome Mapping Pipeline (Hagmann et al, 2008) processed 20 healthy subjects into an average Connectome dataset. The Figures show the ConnectomeViewer user interface using this dataset. Connections are shown that occur in all 20 subjects. The dataset is freely available from the homepage (connectomeviewer.org). Conclusions: The ConnectomeViewer is a cross-platform, open-source software tool that provides extensive visualization and analysis capabilities for connectomic research. It has a modular architecture, integrates relevant datatypes and is completely scriptable. Visit www.connectomics.org to get involved as user or developer.

ABCtoolbox: a versatile toolkit for approximate Bayesian computations.

BACKGROUND: The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS: Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION: ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

Local model predictive control experiences with differential driven wheeled mobile robots

This work extends a previously developed research concerning about the use of local model predictive control in differential driven mobile robots. Hence, experimental results are presented as a way to improve the methodology by considering aspects as trajectory accuracy and time performance. In this sense, the cost function and the prediction horizon are important aspects to be considered. The aim of the present work is to test the control method by measuring trajectory tracking accuracy and time performance. Moreover, strategies for the integration with perception system and path planning are briefly introduced. In this sense, monocular image data can be used to plan safety trajectories by using goal attraction potential fields

Mobile robot experimental modeling and control strategies using sensor fusion

This research work deals with the problem of modeling and design of low level speed controller for the mobile robot PRIM. The main objective is to develop an effective educational, and research tool. On one hand, the interests in using the open mobile platform PRIM consist in integrating several highly related subjects to the automatic control theory in an educational context, by embracing the subjects of communications, signal processing, sensor fusion and hardware design, amongst others. On the other hand, the idea is to implement useful navigation strategies such that the robot can be served as a mobile multimedia information point. It is in this context, when navigation strategies are oriented to goal achievement, that a local model predictive control is attained. Hence, such studies are presented as a very interesting control strategy in order to develop the future capabilities of the system. In this context the research developed includes the visual information as a meaningful source that allows detecting the obstacle position coordinates as well as planning the free obstacle trajectory that should be reached by the robot

Reconfigurable Architecture To Estimate The Motion Of An Underwater Vehicle

This work proposes a parallel architecture for a motion estimation algorithm. It is well known that image processing requires a huge amount of computation, mainly at low level processing where the algorithms are dealing with a great numbers of data-pixel. One of the solutions to estimate motions involves detection of the correspondences between two images. Due to its regular processing scheme, parallel implementation of correspondence problem can be an adequate approach to reduce the computation time. This work introduces parallel and real-time implementation of such low-level tasks to be carried out from the moment that the current image is acquired by the camera until the pairs of point-matchings are detected

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Disseny, creació i implementació de sistema e-comerce

Aquest projecte consisteix en la creació d'una botiga virtual per a l'empresa CREATIFHPROMOS, companyia del sector del reclam publicitari; per a dur a terme aquest projecte, es realitzarà un estudi de les plataformes actuals de comerç electrònic “Open Source” desenvolupades en PHP, per tal de, a partir dels requeriments de l'empresa, seleccionar la més adient per a la seva implantació,i, en cas de ser necessari, desenvolupar nous mòduls i funcionalitats per adaptar als requeriments recollits.

Estado del arte en soluciones de virtualización : Sistemas gestores de Cloud: OpenNebula

En el presente proyecto se ha abordado la tarea de acercar las tecnologías existentes de plataformas de gestión de infraestructuras ofrecidas en la nube (Cloud Management Platform, aka CMP) al mundo empresarial. En concreto, se ha desplegado una solución de explotación de infraestructuras privadas en la nube (IaaS) enfocada a la gestión de un datacenter virtualizado, utilizando para ello soluciones completamente basadas en software libre, en concreto, OpenNebula.

Estado del arte en soluciones de virtualización/sistemas gestores cloud : OpenStack

Los servicios cloud se utilizan cada vez más en todo tipo de entornos, y la tendencia no hará sino acentuarse en los próximos años. Amazon AWS es líder de servicios IaaS y todos pretenden imitarles con éxito. OpenStack es una de las soluciones OpenSource con más apoyo de la comunidad y de sponsors de renombre. El presente proyecto introduce la arquitectura OpenStack y desarrolla un proyecto real de explotación IaaS basado en ésta.

Prototipo de RINA sobre Ethernet

Este PFM se enmarca dentro del trabajo a realizar por el proyecto IRATI. IRATI es un proyecto STReP (Specific Targeted Research Project) financiado por la Unión Europea dentro del programa FP7 (Seventh Framework Programme for Research and Technological Development). El objetivo general de IRATI es conseguir una mayor compresión y exploración de RINA. El trabajo que se reportará en este PFM es (aproximadamente) la primera fase del diseño y desarrollo de un prototipo de RINA sobre Ethernet en el seno del Kernel (Linux), basándose y generando software libre.

Tarracomap: Development of an archaeological application on Google Maps navigation System

This paper describes the result of a research about diverse areas of the information technology world applied to cartography. Its final result is a complete and custom geographic information web system, designed and implemented to manage archaeological information of the city of Tarragona. The goal of the platform is to show on a web-focused application geographical and alphanumerical data and to provide concrete queries to explorate this. Various tools, between others, have been used: the PostgreSQL database management system in conjunction with its geographical extension PostGIS, the geographic server GeoServer, the GeoWebCache tile caching, the maps viewer and maps and satellite imagery from Google Maps, locations imagery from Google Street View, and other open source libraries. The technology has been chosen from an investigation of the requirements of the project, and has taken great part of its development. Except from the Google Maps tools which are not open source but are free, all design has been implemented with open source and free tools.

La necesidad de monitorización en enfermos cardiovasculares fuera de la esfera hospitalaria

En este artículo se presentan las razones por las cuales la monitorización en los enfermos cardiovasculares fuera de la esfera hospitalaria se considera imprescindible. Se verá igualmente cuales son los elementos a medir y controlar, no solo para valorar el estado del paciente, sino también como medio de autocontrol.

Incorporació de mecanismes de seguretat a la xarxa de l'empresa

Implantació de l'eina de software lliure PacketFence amb la qual gestionar els punts de xarxa corporatius d'una empresa de manera automàtica. Es pretén instal·lar i configurar un NAC (Network Access Control).

Improvement of a fully distributed decision making protocol for CRN

Este artículo presenta una propuesta de mejora del protocolo fully distributed decision making protocol for CRN con el fin de llevar a cabo la tarea de detección del espectro libre para las comunicaciones inalámbricas de una manera eficiente y segura.

Participació en un projecte de codi obert : Tomdroid

Memòria del treball de final de carrera sobre la participació en un projecte de codi obert: Tomdroid. Tomdroid és una versió del programa de notes Tomboy adaptat al sistema operatiu per a mòbils i tauletes Android.