237 research outputs found
Jmodeltest.org: selection of nucleotide substitution models on the cloud
No full textThis is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Jose Manuel Santorum, Diego Darriba, Guillermo L. Taboada, David Posada; jmodeltest.org: selection of nucleotide substitution models on the cloud, Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1310–1311, https://doi.org/10.1093/bioinformatics/btu032[Abstract] The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most popular. Still, to deal with large DNA alignments with hundreds or thousands of loci, users of jMT2 need to have access to High Performance Computing clusters, including installation and configuration capabilities, conditions not always met. Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users. Its main benefit is straightforward execution, avoiding any configuration/execution issues, and reducing significantly in most cases the time required to complete the analysis.
Availability and implementation:jmodeltest.org is accessible using modern browsers, such as Firefox, Chrome, Opera, Safari and IE from http://jmodeltest.org. User registration is not mandatory, but users wanting to have additional functionalities, like access to previous analyses, have the possibility of opening a user account.European Research Council; 2007-Stg 203161- PHYGENOMMinisterio de Ciencia e Innovación; TIN2010-1673
Bone-Eating Worms Spread: Insights into Shallow-Water Osedax (Annelida, Siboglinidae) from Antarctic, Subantarctic, and Mediterranean Waters
No full text0000-0002-7993-1523© 2015 Taboada et al. This is an open access article distributed under the terms of the Creative Commons Attribution License [4.0], which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
A New Record of Scaphytopius Magdalensis: Another Plant Disease Vector in Michigan (Homoptera: Cicadellidae)
No full textExcerpt: Several specimens of Scaphytopius magdalensis (Provancher) were collected by Burger (1966), and brought to the attention of the senior author for verification. This leafhopper, a vector of Blueberry Stunt, is widely distributed in the eastern United States, and southern Ontario and Quebec. This, the first record of a leafhopper virus vector for blueberries in Michigan, increases the list of leafhopper vectors of plant diseases in the state , given in Taboada and Hoffman (1965). to 14
Estructura de suelos manejados en siembra directa : efectos sobre la extracción y conversión de agua en el cultivo de soja (Glycine max L. Merril)
No full textEsta tesis tuvo por objetivo avanzar en el entendimiento de los factores que favorecen la compactación de suelos en siembra directa, analizar los mecanismos por los cuales las compactaciones afectan la productividad del agua en soja (Glycine max L. Merril), y analizar la efectividad de intervenciones mecánicas sobre su reversión. Para esto se 6 combinaron: muestreos de suelo a nivel regional, experimentos en invernáculo, un meta7 análisis de publicaciones y experimentos de campo. El muestreo regional mostró que la compactación entre 10-20 cm es un proceso ampliamente extendido, independientemente de la intensidad y aportes de carbono de las rotaciones. Los experimentos controlados mostraron que la compactación genera alteraciones en el crecimiento del sistema de raíces en su conjunto, no sólo en las raíces directamente afectadas. La compactación retrasó la profundización de raíces, y redujo la proliferación de raíces en estratos superficiales y profundos, más allá de 150 cm. Se observaron mecanismos compensatorios a nivel de absorción de agua por unidad de raíz, pero éstos se vieron limitados ante reducciones marcadas en la longitud de raíces. La compactación generó otros efectos que ameritan mayores estudios: redujo la cantidad y actividad de los nódulos directamente e indirectamente afectados. De acuerdo al meta-análisis, la descompactación mecánica permite aliviar las compactaciones y aumentar los rendimientos de soja de la región pampeana (~540 kg.ha-1 en promedio). La descompactación permitió incrementar la captación de agua en el perfil, y su extracción por el cultivo, aunque no la eficiencia de conversión a biomasa. Los efectos no parecen prolongarse más allá de 18-24 meses. Esta tesis permitió una mejor comprensión de los mecanismos por los cuales el deterioro estructural de los suelos en SD, y particularmente la compactación, afecta la utilización de agua y los rendimientos en soja, y en qué medida la descompactación puede aliviar estos efectos
Análisis y Diseño de una Herramienta de Informes de Productividad de Desarrollo Software
No full text[Resumen] A lo largo de este proyecto se analizan y diseñan las posibles soluciones al problema de no haber métricas multiproyecto en los gestores de proyectos, caso concreto del gestor Jira. Este problema es de gran importancia en las organizaciones en las que abundan los proyectos y en las que los empleados están asignados a varios equipos. La relevancia de tener información sobre los proyectos con una visión general es vital para poder obtener la mayor productividad en los mismos y es por ello que se propone este trabajo. Veremos el estado de las herramientas de gestión de proyectos y control de versiones que más popularidad tienen en los entornos de desarrollo software, profundizando en las opciones de Atlassian. Los métodos que tenemos para generar los informes de productividad los analizaremos y diseñaremos, además de hacer pruebas de concepto para ver los resultados posibles.[Abstract] Throughout this project, possible solutions to the problem of not having multi-project
metrics in the project managers, specific case of the Jira manager, are analyzed and designed.
This problem has great importance in organizations that have multiple projects and in which
employees are assigned to several teams. The relevance of having information about projects
with an overview is vital to be able to obtain the highest productivity in projects and that is
why this bachelor thesis is proposed.
We will see the status of the project management and version control tools that are most
popular in software development environments, deepening in Atlassian options. The methods
we have to generate the productivity reports will be analyzed and designed, as well as proof
of concept to see the possible results.Traballo fin de grao (UDC.FIC). Enxeñaría informática. Curso 2019/202
Nonblocking collectives for scalable Java communications
No full textThis is the peer reviewed version of the following article: Ramos, S., Taboada, G. L., Expósito, R. R., & Touriño, J. (2015). Nonblocking collectives for scalable Java communications. Concurrency and Computation: Practice and Experience, 27(5), 1169-1187, which has been published in final form at https://doi.org/10.1002/cpe.3279. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] This paper presents a Java implementation of the recently published MPI 3.0 nonblocking message passing collectives in order to analyze and assess the feasibility of taking advantage of these operations in shared memory systems using Java. Nonblocking collectives aim to exploit the overlapping between computation and communication for collective operations to increase scalability of message passing codes, as it has been carried out for nonblocking point‐to‐point primitives. This scalability has become crucial not only for clusters but also for shared memory systems because of the current trend of increasing the number of cores per chip, which is leading to the generalization of multi‐core and many‐core processors. Message passing libraries based on remote direct memory access, thread‐based progression, or implementing pure multi‐threading shared memory support could potentially benefit from the lack of imposed synchronization by nonblocking collectives. But, although the distributed memory scenario has been well studied, the shared memory one has not been tackled yet. Hence, nonblocking collectives support has been included in FastMPJ, a Message Passing in Java (MPJ) implementation, and evaluated on a representative shared memory system, obtaining significant improvements because of overlapping and lack of implicit synchronization, and with barely any overhead imposed over common blocking operations.Ministerio de Ciencia e Innovación; TIN2010-16735Xunta de Galicia; CN2012/211Xunta de Galicia; GRC2013/05
Common variants of NFE2L2 gene predisposes to acute respiratory distress syndrome in patients with severe sepsis
No full textThis work was funded by the Instituto de Salud Carlos III (CB06/06/1088, PI10/00393, PI14/00844, FI11/00074) and by the European Regional Development Funds “A way of making Europe.” MPY was supported by a post-doctoral fellowship from Fundación Ramón Areces, Madrid, Spain.Acosta-Herrera, M., Pino-Yanes, M., Blanco, J., Ballesteros, J.C., Ambrós, A., Corrales, A., Gandía, F., Subirá, C., Domínguez, D., Baluja, A., Añón, J.M., Adalia, R., Pérez-Méndez, L., Flores, C., Villar, J., Fernández, L.R., Espinosa, E., Campo, R.D., Fernández, R., Rodríguez, J.A., álvarez, J., González, E., Hernández, O., Solano, R., Pérez-Crespo, J., Arellano, P., Zavala, E., Martínez, J., Torres, A., Badia, J., Alba, F., Corpas, R., Muriel, A., Sagredo, V., Taboada, F., Albaiceta, G.M., Bobillo, F., Tamayo, L., Labattut, A.G., Carriedo, D., Collado, J., Diaz, F.J., Valledor, M., Antuña, M., de Frutos, M., López, M.J., Cortina, J.J., Saldaña, T., Caballero, A., álvarez, T., álvarez, B., Sandoval, J
Low‐latency Java communication devices on RDMA‐enabled networks
No full textThis is the peer reviewed version of the following article: Expósito, R. R., Taboada, G. L., Ramos, S., Touriño, J., & Doallo, R. (2015). Low‐latency Java communication devices on RDMA‐enabled networks. Concurrency and Computation: Practice and Experience, 27(17), 4852-4879., which has been published in final form at https://doi.org/10.1002/cpe.3473. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] Providing high‐performance inter‐node communication is a key capability for running high performance computing applications efficiently on parallel architectures. In fact, current systems deployments are aggregating a significant number of cores interconnected via advanced networking hardware with Remote Direct Memory Access (RDMA) mechanisms, that enable zero‐copy and kernel‐bypass features. The use of Java for parallel programming is becoming more promising thanks to some useful characteristics of this language, particularly its built‐in multithreading support, portability, easy‐to‐learn properties, and high productivity, along with the continuous increase in the performance of the Java virtual machine. However, current parallel Java applications generally suffer from inefficient communication middleware, mainly based on protocols with high communication overhead that do not take full advantage of RDMA‐enabled networks. This paper presents efficient low‐level Java communication devices that overcome these constraints by fully exploiting the underlying RDMA hardware, providing low‐latency and high‐bandwidth communications for parallel Java applications. The performance evaluation conducted on representative RDMA networks and parallel systems has shown significant point‐to‐point performance increases compared with previous Java communication middleware, allowing to obtain up to 40% improvement in application‐level performance on 4096 cores of a Cray XE6 supercomputer.Ministerio de Economía y Competitividad; TIN2013-42148-PXunta de Galicia; GRC2013/055Ministerio de Educación y Ciencia; AP2010-434
Exploratory Data Analysis and Data Envelopment Analysis of Urban Rail Transit
No full text[Abstract]
This paper deals with the efficiency and sustainability of urban rail transit (URT) using exploratory data analytics (EDA) and data envelopment analysis (DEA). The first stage of the proposed methodology is EDA with already available indicators (e.g., the number of stations and passengers), and suggested indicators (e.g., weekly frequencies, link occupancy rates, and CO2 footprint per journey) to directly characterize the efficiency and sustainability of this transport mode. The second stage is to assess the efficiency of URT with two original models, based on a thorough selection of input and output variables, which is one of the key contributions of EDA to this methodology. The first model compares URT against other urban transport modes, applicable to route personalization, and the second scores the efficiency of URT lines. The main outcome of this paper is the proposed methodology, which has been experimentally validated using open data from the Transport for London (TfL) URT network and additional sources.Ministerio de Economía, Industria y Competitividad; TIN2016-75845-PAgencia Estatal de Investigación; SNEO-20161147Xunta de Galicia; ED431G2019/01Xunta de Galicia; ED431C 2017/04Xunta de Galicia; ED431G2019/0
Efficient Java Communication Protocols on High-speed Cluster Interconnects
No full textThis paper presents communication strategies for achieving efficient parallel and distributed Java applications on clusters with high-speed interconnects. Communication performance is critical for the overall cluster performance. Previous efforts at obtaining efficient Java communications have a limited applicability on high-speed interconnects as they are focused on high level APIs like RMI, ignoring the particularities of these systems and their native high performance communication protocols. By relying on a custom Java socket implementation higher degrees of performance can be achieved exploiting high-speed interconnect facilities. Several protocol definitions are presented, looking for obtaining high performance Java communications. Moreover, the quality of the protocol implementations and their design decisions has been thoroughly evaluated on a Scalable Coherent Interface (SCI) and Gigabit Ethernet (GbE) testbed cluster. The results of this analysis have demonstrated that these Java protocols obtain similar results to native communications.
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