VGrid: una infraestructura grid virtual con fines educacionales

La computación Grid es una tecnología enfocada a compartir recursos heterogéneos a gran escala. Sin embargo, su alto coste de implantación, así como la elevada experiencia necesaria para su mantenimiento, la hacen inviable en el contexto educacional. Multitud de universidades disponen de esta tecnología o acceso a un Grid externo, orientado fundamentalmente a la investigación y/o computación intensiva. Por lo tanto no está disponible para satisfacer objetivos educacionales, limitando el conocimiento de esta tecnología a los estudiantes únicamente como concepto teórico y a lo sumo a la prueba de algunos comandos de ejecución y monitorización de trabajos simples. Como posible solución didáctica se propone la virtualización como medio para crear un pequeño Grid funcional que puede ser utilizado en un computador individual, evitando los requisitos económicos y de gestión necesarios en un Grid real. El objetivo fundamental de esta plataforma es mostrar la tecnología Grid a los estudiantes, desde un punto de vista práctico y permitirles interaccionar con un Grid de apariencia real, dotándoles de los conocimientos y experiencia básica requerida para trabajar en entornos laborales basados en la tecnología Grid.SUMMARY -- Grids are highly distributed and heterogeneous systems based on the resource sharing world-wide. As a result, their implantation costs are high as well as the experience needed to their maintenance. Those facts makes them unfeasible in educational contexts. Many Universities have their own Grid or access to an external one to make research and intensive computation. However, they are not usually available for educational objectives. Consequently, student knowledge of this technology is limited to theoretical concepts or, in the best scenario, to some executions and monitoring commands to see its functionality. This article proposes the use of virtualization as a possible solution to create a functional Grid, which can be used on a single computer, avoiding the economic and management requirements of a real Grid. The main objective of this framework is to introduce students to Grid technology from a practical point of view, letting them interact with a real-appearance Grid, giving them the education and basic experience required to work in real Grid environments.Peer Reviewe

RosneT: a block tensor algebra library for out-of-core quantum computing simulation

With recent Quantum Devices showing increasing capabilities to perform controlled operations, further development on Quantum Algorithms may benefit from Quantum Simulations on classical hardware. Among important applications one finds verification and debugging of Quantum Algorithms, and elucidating the frontier for real Quantum Advantage of new devices [1]. Tensor Networks are regarded as an efficient numerical representation of a Quantum Circuit, but exponential growth forces tensors to be distributed among computing nodes. A number of methods and libraries have appeared recently to implement Quantum Simulators with Tensor Networks [2], [3] intended for HPC clusters. In this work we develop a Python library called RosneT using a task-based programming model able to extend all tensor operations into distributed systems, and prepared for existing and upcoming Exascale supercomputers. It is compatible with the Python ecosystem, and offers a simple programming interface for developers

QoS Provisioning by Meta-Scheduling in Advance within SLA-Based Grid Environments

The establishment of agreements between users and the entities which manage the Grid resources is still a challenging task. On the one hand, an entity in charge of dealing with the communication with the users is needed, with the aim of signing resource usage contracts and also implementing some renegotiation techniques, among others. On the other hand, some mechanisms should be implemented which decide if the QoS requested could be achieved and, in such case, ensuring that the QoS agreement is provided. One way of increasing the probability of achieving the agreed QoS is by performing meta-scheduling of jobs in advance, that is, jobs are scheduled some time before they are actually executed. In this way, it becomes more likely that the appropriate resources are available to run the jobs when needed. So, this paper presents a framework built on top of Globus and the GridWay meta-scheduler to provide QoS by means of performing meta-scheduling in advance. Thanks to this, QoS requirements of jobs are met (i.e. jobs are finished within a deadline). Apart from that, the mechanisms needed to manage the communication between the users and the system are presented and implemented through SLA contracts based on the WS-Agreement specification

La prensa sevillana en las redes sociales : Twitter y Facebook

El mundo contemporáneo está cambiando, y su reflejo ha comenzado, de forma tardía, a seguirle el paso. La comunicación ha visto cómo sus modelos saltaban por los aires, desde los puramente idealistas hasta los duramente materialistas. Las soluciones para salir de su particular crisis han venido de la mano de los problemas. Una nueva comunicación no es sólo el salvavidas, sino la oportunidad de hacer al periodismo más grande. La prensa, el medio tradicional por antonomasia; y los medios locales, los eternos hermanos pobres del panorama mediático, no son considerados una buena combinación en el panorama actual (R. Gómez, D. Alandete, 2012). Diarios locales cierran por todo el país, pero Sevilla cuenta con cuatro periódicos de pago que luchan por mantenerse en pie con sus particulares líneas editoriales, estilos o recursos. A lo largo de las siguientes páginas, planteamos una forma de acercarnos al modo en que estos cuatro medios afrontan la llegada, para quedarse, de una nueva forma de comunicar, de informar y de relacionarse con el público. ABC de Sevilla, El Correo de Andalucía, Diario de Sevilla y Estadio Deportivo han optado por seguir estrategias diferentes en las dos grandes redes sociales… o incluso por no tener un plan concreto respecto a ellas. Los datos, el análisis y las comparativas nos permitirán conocer un poco más sobre la manera en que, queriéndolo o no, la prensa local sevillana se ha acercado a la otrora considerada enemiga: la comunicación en internet

Task-based programming in COMPSs to converge from HPC to big data

Task-based programming has proven to be a suitable model for high-performance computing (HPC) applications. Different implementations have been good demonstrators of this fact and have promoted the acceptance of task-based programming in the OpenMP standard. Furthermore, in recent years, Apache Spark has gained wide popularity in business and research environments as a programming model for addressing emerging big data problems. COMP Superscalar (COMPSs) is a task-based environment that tackles distributed computing (including Clouds) and is a good alternative for a task-based programming model for big data applications. This article describes why we consider that task-based programming models are a good approach for big data applications. The article includes a comparison of Spark and COMPSs in terms of architecture, programming model, and performance. It focuses on the differences that both frameworks have in structural terms, on their programmability interface, and in terms of their efficiency by means of three widely known benchmarking kernels: Wordcount, Kmeans, and Terasort. These kernels enable the evaluation of the more important functionalities of both programming models and analyze different work flows and conditions. The main results achieved from this comparison are (1) COMPSs is able to extract the inherent parallelism from the user code with minimal coding effort as opposed to Spark, which requires the existing algorithms to be adapted and rewritten by explicitly using their predefined functions, (2) it is an improvement in terms of performance when compared with Spark, and (3) COMPSs has shown to scale better than Spark in most cases. Finally, we discuss the advantages and disadvantages of both frameworks, highlighting the differences that make them unique, thereby helping to choose the right framework for each particular objective.This work is supported by the Spanish Government (SEV2015-0493), by the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P), by Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272). Javier Conejero’s postdoctoral contract is cofinanced by the Ministry of Economy and Competitiveness under the Juan de la Cierva Formación postdoctoral fellowship number FJCI-2015-24651. This work is also supported by the Intel-BSC Exascale Lab. The Human Brain Project receives funding from the EU’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no 604102.Peer ReviewedPostprint (author's final draft

Mutation analysis of HPS1, the gene mutated in Hermansky-Pudlak syndrome, in patients with isolated platelet dense-granule deficiency

Background and objectives: isolated platelet dense granule (PDG) deficiency is a heterogeneous disorder frequently found among patients with mild to moderate bleeding diatheses. However, the molecular basis of this disorder is unknown. Genes involved in other rare bleeding disorders with associated reduction in the numbers of platelet dense-granules may play a role in isolated PDG deficiency. Among such genes, HPS1 is known to play a key role in the genesis of PDG and as many as 18 different HPS1 mutations have been identified in patients with Hermansky-Pudlak syndrome. Recently, we have identified subjects with one HPS1 heterozygous mutation displaying significant reductions in PDG without the clinical phenotype of Hermansky-Pudlak syndrome. This suggested that HPS1 mutations could be involved in isolated PDG deficiency. Design and methods: we sequenced all coding exons, and flanking intron regions of HPS1 in 16 patients with mild to severe PDG deficiency, most of whom had mild bleeding episodes. Nine patients reported a familial history of bleeding diathesis with PDG deficiency. We also evaluated the prevalence of HPS1 variations in 215 controls. Transmission electron microscopy was used to evaluate the number and morphology of PDG from patients and selected controls. Results: no patient with PDG deficiency carried severe mutations of the HPS1 gene. We identified 6 previously described and 5 new polymorphisms in the HPS1 gene. Platelet electron microscopy in controls carrying these polymorphisms revealed that they did not significantly modify the number or morphology of PDG. Interpretation and conclusions: mutations affecting the HPS1 gene play a minor role in isolated PDG deficiency. These results support a molecular heterogeneity responsible for the number and morphology of PDG

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration

This article is available from: http://www.biomedcentral.com/1471-2105/9/5[Background] Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation.[Results] We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval.[Conclusion] The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http:// bioinf.comav.upv.es/est2uni. This site also provides detailed instructions for installation and configuration of the software package. The code is under active development to incorporate new analyses, methods, and algorithms as they are released by the bioinformatics community.Partially funded by "Conselleria de Agricultura, Pesca y Alimentacion de la Comunidad Valenciana" and Spanish "Ministerio de Ciencia y Tecnologia" (research grants GEN2001-4885-C05 and GEN2003-20237-C06).Peer reviewe

Rational design of a genetic finite state machine: Combining biology, engineering, and mathematics for bio-computer research

[EN] The recent success of biological engineering is due to a tremendous amount of research effort and the increasing number of market opportunities. Indeed, this has been partially possible due to the contribution of advanced mathematical tools and the application of engineering principles in genetic-circuit development. In this work, we use a rationally designed genetic circuit to show how models can support research and motivate students to apply mathematics in their future careers. A genetic four-state machine is analyzed using three frameworks: Deterministic and stochastic modeling through di erential and master equations, and a spatial approach via a cellular automaton. Each theoretical framework sheds light on the problem in a complementary way. It helps in understanding basic concepts of modeling and engineering, such as noise, robustness, and reaction¿di usion systems. 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Ambiguity in Hamlet’s economic terms 1.3.88-136 and its rendering into German: August Wilhelm Schlegel’s translation

Como es sabido, a pesar de su complejidad textual, las obras de William Shakespeare han generado un número considerable de traducciones a las principales lenguas del mundo. En este sentido, el presente estudio tiene un doble propósito: en primer lugar, trata de identificar y analizar las ambigüedades de algunos términos usados por Shakespeare en Hamlet 1.3.88-136 y, a continuación, realiza un cotejo de la traducción alemana de August Wilhelm Schlegel con el texto original, a fin de comprobar en qué medida se recrean los diversos sentidos y los múltiples significados de estos términos en la versión alemana.As is well known, in spite of their textual complexity, the works of William Shakespeare have given rise to a considerable number of translations into the major languages of the world. The aim of this article is twofold: firstly, to identify and analyze the ambiguities of some terms used by Shakespeare in Hamlet 1.3.88-136. Then, to contrast the German translation by August Wilhelm Schlegel with the original text, in order to point out to what extent the various senses and the multiple meanings of these terms have been preserved in this German version

Executing linear algebra kernels in heterogeneous distributed infrastructures with PyCOMPSs

Python is a popular programming language due to the simplicity of its syntax, while still achieving a good performance even being an interpreted language. The adoption from multiple scientific communities has evolved in the emergence of a large number of libraries and modules, which has helped to put Python on the top of the list of the programming languages [1]. Task-based programming has been proposed in the recent years as an alternative parallel programming model. PyCOMPSs follows such approach for Python, and this paper presents its extensions to combine task-based parallelism and thread-level parallelism. Also, we present how PyCOMPSs has been adapted to support heterogeneous architectures, including Xeon Phi and GPUs. Results obtained with linear algebra benchmarks demonstrate that significant performance can be obtained with a few lines of Python.This work has been supported by the Spanish Government (SEV2015-0493), by the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P), by Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272). Javier Conejero postdoctoral contract is co-financed by the Ministry of Economy and Competitiveness under Juan de la Cierva Formación postdoctoral fellowship number FJCI-2015-24651. Cristian Ramon-Cortes predoctoral contract is financed by the Ministry of Economy and Competitiveness under the contract BES-2016-076791. This work is supported by the Intel-BSC Exascale Lab. This work has been supported by the European Commission through the Horizon 2020 Research and Innovation program under contract 687584 (TANGO project).Peer ReviewedPostprint (published version