Bootstrap confidence levels for phylogenetic trees.

Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.

Análisis de datos de periódicos digitales

En este proyecto se ha desarrollado una aplicación Web cuya finalidad es ofrecer al usuario datos provenientes del análisis de texto de las noticias que se encuentran en periódicos online. La aplicación permite al usuario realizar búsquedas personalizadas sobre temáticas específicas y configurar algunos tipos de análisis sobre la información recuperada. Entre los análisis que son llevados a cabo destaca el análisis del sentimiento. Para ello se ofrece la posibilidad de que el usuario utilice sus propios diccionarios de pares palabra-valor, utilizados para realizar este tipo de análisis. Para la codificación de la herramienta, se ha utilizado el lenguaje de programación Python y la framework web Django. El almacenamiento de la información de la aplicación se ha realizado sobre una base de datos NoSQL de tipo MongoDB.

Diseño y desarrollo de un servicio big data en la nube para búsqueda, compartición de ficheros y data mining

En esta memoria se presenta el diseño y desarrollo de una aplicación en la nube destinada a la compartición de objetos y servicios. El desarrollo de esta aplicación surge dentro del proyecto de I+D+i, SITAC: Social Internet of Things – Apps by and for the Crowd ITEA 2 11020, que trata de crear una arquitectura integradora y un “ecosistema” que incluya plataformas, herramientas y metodologías para facilitar la conexión y cooperación de entidades de distinto tipo conectadas a la red bien sean sistemas, máquinas, dispositivos o personas con dispositivos móviles personales como tabletas o teléfonos móviles. El proyecto innovará mediante la utilización de un modelo inspirado en las redes sociales para facilitar y unificar las interacciones tanto entre personas como entre personas y dispositivos. En este contexto surge la necesidad de desarrollar una aplicación destinada a la compartición de recursos en la nube que pueden ser tanto lógicos como físicos, y que esté orientada al big data. Ésta será la aplicación presentada en este trabajo, el “Resource Sharing Center”, que ofrece un servicio web para el intercambio y compartición de contenido, y un motor de recomendaciones basado en las preferencias de los usuarios. Con este objetivo, se han usado tecnologías de despliegue en la nube, como Elastic Beanstalk (el PaaS de Amazon Web Services), S3 (el sistema de almacenamiento de Amazon Web Services), SimpleDB (base de datos NoSQL) y HTML5 con JavaScript y Twitter Bootstrap para el desarrollo del front-end, siendo Python y Node.js las tecnologías usadas en el back end, y habiendo contribuido a la mejora de herramientas de clustering sobre big data. Por último, y de cara a realizar el estudio sobre las pruebas de carga de la aplicación se ha usado la herramienta ApacheJMeter.

Smoothed bootstrap Malmquist index based on DEA model to compute productivity of tax offices

This paper analyses the productivity growth of the SUMA tax offices located in Spain evolved between 2004 and 2006 by using Malmquist Index based on Data Envelopment Analysis (DEA) models. It goes a step forward by smoothed bootstrap procedure which improves the quality of the results by generalising the samples, so that the conclusions obtained from them can be applied in order to increase productivity levels. Additionally, the productivity effect is divided into two different components, efficiency and technological change, with the objective of helping to clarify the role played by either the managers or the level of technology in the final performance figures.

The programming language python in earth system simulations

-scale vary from a planetary scale and million years for convection problems to 100km and 10 years for fault systems simulations. Various techniques are in use to deal with the time dependency (e.g. Crank-Nicholson), with the non-linearity (e.g. Newton-Raphson) and weakly coupled equations (e.g. non-linear Gauss-Seidel). Besides these high-level solution algorithms discretization methods (e.g. finite element method (FEM), boundary element method (BEM)) are used to deal with spatial derivatives. Typically, large-scale, three dimensional meshes are required to resolve geometrical complexity (e.g. in the case of fault systems) or features in the solution (e.g. in mantel convection simulations). The modelling environment escript allows the rapid implementation of new physics as required for the development of simulation codes in earth sciences. Its main object is to provide a programming language, where the user can define new models and rapidly develop high-level solution algorithms. The current implementation is linked with the finite element package finley as a PDE solver. However, the design is open and other discretization technologies such as finite differences and boundary element methods could be included. escript is implemented as an extension of the interactive programming environment python (see www.python.org). Key concepts introduced are Data objects, which are holding values on nodes or elements of the finite element mesh, and linearPDE objects, which are defining linear partial differential equations to be solved by the underlying discretization technology. In this paper we will show the basic concepts of escript and will show how escript is used to implement a simulation code for interacting fault systems. We will show some results of large-scale, parallel simulations on an SGI Altix system. Acknowledgements: Project work is supported by Australian Commonwealth Government through the Australian Computational Earth Systems Simulator Major National Research Facility, Queensland State Government Smart State Research Facility Fund, The University of Queensland and SGI.

Technical efficiency determinants within a dual banking system:a DEA-bootstrap approach

The purpose of this study is to provide a comparative analysis of the efficiency of Islamic and conventional banks in Gulf Cooperation Council (GCC) countries. In this study, we explain inefficiencies obtained by introducing firm-specific as well as macroeconomic variables. Our findings indicate that during the eight years of study, conventional banks largely outperform Islamic banks with an average technical efficiency score of 81% compared to 95.57%. However, it is clear that since 2008, efficiency of conventional banks was in a downward trend while the efficiency of their Islamic counterparts was in an upward trend since 2009. This indicates that Islamic banks have succeeded to maintain a level of efficiency during the subprime crisis period. Finally, for the whole sample, the analysis demonstrates the strong link of macroeconomic indicators with efficiency for GCC banks. Surprisingly, we have not found any significant relationship in the case of Islamic banks.

Bootstrap for Critical Branching Process with Non-Stationary Immigration

2000 Mathematics Subject Classification: Primary 60J80, Secondary 62F12, 60G99.

Rafael Travieso (left) and Kyle Tuntland (right) with a Burmese python at SRS-6, Shark River Slough

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514. This image is made available for non-commercial or educational use only.

Valentin Nechita (left) and Rafael Travieso (right) with a Burmese python at SRS-6, Shark River Slough

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514. This image is made available for non-commercial or educational use only.

Burmese python at SRS-6, Shark River Slough

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514. This image is made available for non-commercial or educational use only.