Entorno gráfico de configuración para el soft-core OpenRISC

Aquest projecte consisteix en la realització d'un entorn gràfic que serveixi per generar SoCs basats en el processador soft-core OpenRISC. Aquest entorn permetrà afegir diferents components de manera dinàmica a un repositori d’IPs, mostrar i sel·leccionar qualsevol component disponible dins d’aquest repositori, amb la finalitat d’unir-los al bus del sistema i fer-los accessibles al processador OpenRISC. L’entorn també mostrarà en tot moment com va evolucionant el nostre SoC, guardarà cadascún dels projectes que es realitzen amb aquest entorn i finalment permetrà generar el SoC dissenyat.

Comparing Multilevel Clustering Methods on Weighted Graphs : The Case of Worldwide Air Passenger Traffic 2000-2004

Specific properties emerge from the structure of large networks, such as that of worldwide air traffic, including a highly hierarchical node structure and multi-level small world sub-groups that strongly influence future dynamics. We have developed clustering methods to understand the form of these structures, to identify structural properties, and to evaluate the effects of these properties. Graph clustering methods are often constructed from different components: a metric, a clustering index, and a modularity measure to assess the quality of a clustering method. To understand the impact of each of these components on the clustering method, we explore and compare different combinations. These different combinations are used to compare multilevel clustering methods to delineate the effects of geographical distance, hubs, network densities, and bridges on worldwide air passenger traffic. The ultimate goal of this methodological research is to demonstrate evidence of combined effects in the development of an air traffic network. In fact, the network can be divided into different levels of âeurooecohesionâeuro, which can be qualified and measured by comparative studies (Newman, 2002; Guimera et al., 2005; Sales-Pardo et al., 2007).

Acquired epileptic dysgraphia: a longitudinal study.

A male presenting with benign partial epilepsy with rolandic spikes from the age of 7 years was evaluated at age 11 years for worsening of his epilepsy associated with a specific regression of graphomotor skills. A longitudinal study over nearly 2 years showed an improvement in handwriting to an almost normal level under modified antiepileptic therapy. A detailed analysis with a computer-monitored graphics table showed at first a rapid improvement of skills followed by protracted slower progress. We argue that the initial rapid recovery of skills was directly linked to the improvement of his epilepsy. The slower late acquisition of motor programmes that had never been fully established was due to long-standing interference by his epilepsy. The specificity of the deficit within the graphomotor system and its possible neurobiological basis are also discussed. The analytical method and approach used in a single patient might provide an example for other patients in whom epilepsy can interfere in the acquisition, progress, and maintenance of new skills and can be responsible for selective deficits.

Structural Analysis of Networks

Network analysis naturally relies on graph theory and, more particularly, on the use of node and edge metrics to identify the salient properties in graphs. When building visual maps of networks, these metrics are turned into useful visual cues or are used interactively to filter out parts of a graph while querying it, for instance. Over the years, analysts from different application domains have designed metrics to serve specific needs. Network science is an inherently cross-disciplinary field, which leads to the publication of metrics with similar goals; different names and descriptions of their analytics often mask the similarity between two metrics that originated in different fields. Here, we study a set of graph metrics and compare their relative values and behaviors in an effort to survey their potential contributions to the spatial analysis of networks.

Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Avaluació de la tecnologia de les GPUs

En el projecte s’ha dut a terme un estudi sobre la tecnologia que aporten les targetes gràfiques (GPU) dins l’àmbit de programació d’aplicacions que tradicionalment eren executades en la CPU o altrament conegut com a GPGPU. S’ha fet una anàlisi profunda del marc tecnològic actual explicant part del maquinari de les targetes gràfiques i de què tracta el GPGPU. També s’han estudiat les diferents opcions que existeixen per poder realitzar els tests de rendiment que permetran avaluar el programari, quin programari està dissenyat per ser executat amb aquesta tecnologia i quin és el procediment a seguir per poder utilitzar-los. S’han efectuat diverses proves per avaluar el rendiment de programari dissenyat o compatible d’executar en la GPU, realitzant taules comparatives amb els temps de còmput. Un cop finalitzades les diferents proves del programari, es pot concloure que no tota aplicació processada en la GPU aporta un benefici. Per poder veure millores és necessari que l’aplicació reuneixi una sèrie de requisits com que disposi d’un elevat nombre d’operacions que es puguin realitzar en paral lel, que no existeixin condicionants per a l’execució de les operacions i que sigui un procés amb càlcul aritmètic intensiu.

LittleProc 2.0. : l'evolució als 16 bits, amb arquitectura superescalar i amb pipeline

Aquest projecte consisteix en evolucionar el LittleProc 1.0, un processador simple dissenyat per ser destinat al món de la docència per tres professors de la UAB. Aquestes evolucions consisteixen en aplicar diversos mètodes i arquitectures diferents per tal d’obtenir un millor rendiment del processador, arribant a executar programes amb la meitat de temps que tardava el LittleProc 1.0. Un cop implementades les diferents arquitectures per tal de millorar el rendiment, es realitzarà un estudi de quin tant per cent de millora ha sigut aquest rendiment.

MyHits: a new interactive resource for protein annotation and domain identification.

The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use the system anonymously, with full access to (i) standard bioinformatics programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large number of protein sequence databases, including standard (Swiss-Prot, TrEMBL) and locally developed databases (splice variants); (iii) databases of protein motifs (Prosite, Interpro); (iv) a precomputed list of matches ('hits') between the sequence and motif databases. All databases are updated on a weekly basis and the hit list is kept up to date incrementally. The MyHits server also includes a new collection of tools to generate graphical representations of pairwise and multiple sequence alignments including their annotated features. Free registration enables users to upload their own sequences and motifs to private databases. These are then made available through the same web interface and the same set of analytical tools. Registered users can manage their own sequences and annotations using only web tools and freeze their data in their private database for publication purposes.

The InterPro Database, 2003 brings increased coverage and new features.

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Dependencia de los algoritmos con el consumo de energía en sistemas HPC

El consumo energético es un aspecto cada vez más importante en el diseño de microprocesadores. Este trabajo experimenta con una técnica de control del consumo, el escalado dinámico de tensión y frecuencia (DVFS, siglas en inglés), para determinar cuan efectiva es la misma en la ejecución de programas con diferentes cargas de trabajo, intensivas en cómputo o memoria. Además, se ha extendido la experimentación a varios núcleos de ejecución, permitiendo comprobar en que medida las características de la ejecución en una arquitectura multicore afecta al desempeño de dicha técnica.

X-ray microtomography of Larger Foraminifera

X-ray microtomography has become a new tool in earth sciences to obtain non-destructive 3D-image data from geological objects in which variations in mineralogy, chemical composition and/or porosity create sufficient x-ray density contrasts.We present here first, preliminary results of an application to the external and internal morphology of Permian to Recent Larger Foraminifera. We use a SkyScan-1072 high-resolution desk-top micro-CT system. The system has a conical x-ray source with a spot size of about 5µm that runs at 20-100kV, 0-250µA, resulting in a maximal resolution of 5µm. X-ray transmission images are captured by a scintillator coupled via fibre optics to a 1024x1024 pixel 12-bit CCD. The object is placed between the x-ray source and the scintillator on a stub that rotates 360°around its vertical axis in steps as small as 0.24 degrees. Sample size is limited to 2 cm due to the absorption of geologic material for x-rays. The transmission images are back projected using a Feldkamp algorithm into a vertical stack of up to 1000 1Kx1K images that represent horizontal cuts of the object. This calculation takes 2 to several hours on a Double-Processor 2.4GHz PC. The stack of images (.bmp) can be visualized with any 3D-imaging software, used to produce cuts of Larger Foraminifera. Among other applications, the 3D-imaging software furnished by SkyScan can produce 3D-models by defining a threshold density value to distinguish "solid" from "void. Several models with variable threshold values and colors can be imbricated, rotated and cut together. The best results were obtained with microfossils devoid of chamber-filling cements (Permian, Eocene, Recent). However, even slight differences in cement mineralogy/composition can result in surprisingly good x-ray density contrasts.X-ray microtomography may develop into a powerful tool for larger microfossils with a complex internal structure, because it is non-destructive, requires no preparation of the specimens, and produces a true 3D-image data set. We will use these data sets in the future to produce cuts in any direction to compare them with arbitrary cuts of complex microfossils in thin sections. Many groups of benthic and planktonic foraminifera may become more easily determinable in thin section by this way.

Modificació d'un sistema de generació de grafisme per televisió amb la incorporació d'objectes generats amb OpenGL

Els objectius inicials d'aquest projecte eren la incorporació d'OpenGL a l'eina ja existent de generació de grafisme per televisió. Com que l'aplicador ja dissenyat es basava en un reduït tipus d'objectes sobre els quals es podien aplicar diferents paràmetres i agrupar-los de diferents maneres, calia trobar un nou tipus d'objecte que tingués alguna particularitat que el fes prou atractiu per a incorporar-lo a l'aplicació. El resultat va ser un objecte polièdric per a poder-hi mapar diferents textures i un text aplicant-hi una ombra en tres dimensions segons la posició del dibuix.

Estructura de datos avanzadas : clases disjuntas, montículos, árboles de búsqueda

En aquest treball s'amplia la implementació en Java de les estructures de dades iniciada per Esteve Mariné, utilitzant el seu disseny bàsic. Concretament, s'ha fet la programació de les estructures de a) classes disjuntes, utilitzant els algorismes de llistes encadenades i amb estructura d'arbre, b) monticles, amb els algorismes binari, binomial i de Fibonacci, i c) arbres de recerca basats en l'algorisme d'arbre binari vermell-negre, el qual complementa els dos ja existents amb algorismes d'encadenaments i AVL. Per a examinar l'evolució de les estructures, s'ha preparat un visualitzador gràfic interactiu amb l'usuari que permet fer les operacions bàsiques de l'estructura. Amb aquest entorn és possible desar les estructures, tornar a reproduir-les i desfer i tornar a repetir les operacions fetes sobre l'estructura. Finalment, aporta una metodologia, amb visualització mitjançant gràfics, de l'avaluació comparativa dels algorismes implementats, que permet modificar els paràmetres d'avaluació com ara nombre d'elements que s'han de tractar, algorismes que s'han de comparar i nombre de repeticions. Les dades obtingudes es poden exportar per a analitzar-les posteriorment.

Desenvolupament d'un Videojoc en 3D basat en OPENGL

L'objectiu d'aquest treball ha estat desenvolupar un videojoc en un entorn de tres dimensions utilitzant les llibreries gràfiques d'OpenGL. Aquesta aplicació s'ha desenvolupat en Java, cosa que dóna més independència perquè aquesta és precisament la filosofia d'aquest llenguatge de programació.

libmsvg : librería C minimalista para lectura y escritura de ficheros SVG

Este documento es la memoria de un proyecto de Fin de Máster en Software Libre cursado en la Universitat Oberta de Catalunya.El nombre del proyecto es "libmsvg" y se enmarca en la especialidad de desarrollo de aplicaciones de software libre."libmsvg" es una pequeña librería software, escrita en C, para leer y grabar ficheros en un subconjunto del formato SVG.SVG son las iniciales de Scalable Vector Graphics, un formato de gráficos vectoriales definido por el World Wide Web Consortium.En esta memoria se describe la concepción, diseño y desarrollo de la librería y los trabajos realizados para su publicación y puesta a disposición de la comunidad, como software libre.