Diseño e implementación de persistencia en bases de datos basadas en Google App Engine

El mundo de la web admite actualmente los productos desarrollados tanto por desarrolladores profesionales como por usuarios finales con un conocimiento más limitado. A pesar de la diferencia que se puede suponer de calidad entre los productos de ambos, las dos soluciones pueden ser reconocidas y empleadas en una aplicación. En la Web 2.0, este comportamiento se observa en el desarrollo de componentes web. Lo que se persigue en el trabajo es desarrollar un modelo de persistencia que, apoyado por un lado servidor y por uno cliente, recoja las métricas de calidad de los componentes cuando los usuarios interaccionan con ellos. A partir de estas métricas, es posible mejorar la calidad de estos componentes. La forma en la que se van a recoger las métricas es a través de PicBit, la aplicación desarrollada para que los usuarios puedan interconectar diferentes componentes entre ellos sin restricciones, de forma que tras interactuar con ellos puedan expresar su grado de satisfacción, que se recoge para la evaluación de la calidad. Se definen también unas métricas intrínsecas al componente, no determinadas por el usuario y que sirven como referencia de la evaluación. Cuando se tienen tanto las métricas intrínsecas como procedentes del usuario, se realiza una correlación entre ellas que permite analizar las posibles desviaciones entre ellas y determinar la calidad propia del componente. Las conclusiones que se pueden obtener del trabajo es que cuando los usuarios pueden realizar pruebas de usabilidad de forma libre, sin restricciones, es mayor la posibilidad de obtener resultados favorables porque estos resultados muestran cómo usará un usuario final la aplicación. Este método de trabajo se ve favorecido por el número de herramientas que se pueden utilizar hoy para monitorizar el flujo de usuario en el servicio.---ABSTRACT---Nowadays, the web world deals with products developed both by professional developers and by end-users with some limited knowledge. Although the difference between both can be important in quality terms, both are accepted and included in web applications. In web 2.0, this behavior can be recognized in the web components development. The goal pursued in the work presented is to create a persistent model that, supported by an end and a back side, will pick the quality measures of the components when the users interact with them. These measures are the starting point for improving the components. The way in which the measures are going to be picked is through PicBit, the application we have developed in order to allow the users playing with the components without restrictions or rules, so after the interaction they can give their satisfaction mark with the application. This will be the value used to evaluate the quality. Some own measures are also defined, which does not depend on the user and which will be used as a reference point of the evaluation. When the measures from users and own ones are got, their correlation is analyzed to study the differences between them and to establish the quality of the component. The conclusion that can be gained from the project is the importance of giving freedom for users when doing usability tests because it increases the chance to get positive results, in the way the users execute the operations they want with the application. This method is fortunate for having such a number of tools to monitor the user flow when using the service.

Generación automática de ficheros de configuración para encaminadores

Este Proyecto Fin de Grado (PFG) tiene como objetivo diseñar e implementar un sistema que genere un fichero de texto que contenga la configuración básica de un encaminador. De esta manera se desea mejorar la eficiencia del personal del departamento donde se va a implantar dicho sistema, liberando a los miembros del mismo de un trabajo repetitivo que se hace varias veces al día. Hasta ahora, esta configuración la realiza cada instalador. Para ello, una vez que se ha cargado y probado la configuración en distintos equipos de manera satisfactoria, se generan un conjunto de plantillas que sirven de modelo para las siguientes configuraciones. Aunque el instalador toma estas plantillas como punto de partida, tiene que modificar manualmente todas las variables que dependen de cada configuración particular. Por tanto, aunque no ha de ejecutar todos los comandos paso a paso, sí debe hacer una revisión total de cada plantilla para generar la configuración adecuada y después cargarla en el encaminador. Para cada configuración se consultan un total de entre tres y siete plantillas. Si a esto se añade que en el departamento se configuran encaminadores de la marca Cisco y Teldat, que de cada marca se utilizan distintos modelos y que la empresa ofrece cuatro tipos de servicio, cada uno con sus particularidades, la tarea de configurar un equipo es costosa. El sistema estará constituido por un servidor web que alojará una base de datos y un programa que permite realizar operaciones de consulta sobre la misma, un sitio web sencillo que hará las funciones de interfaz de usuario y una aplicación que permite generar el fichero de texto que contiene la configuración del encaminador en base a una serie de condicionantes. La base de datos desarrollada es una representación de la utilizada en el entorno real que tiene como objetivo realizar simulaciones del funcionamiento que tendrá el sistema. Por su parte, la funcionalidad del sitio web debe ser la de ofrecer al usuario una interfaz sencilla de utilizar y de interpretar, a través de la cual se puedan realizar consultas a la base de datos así como presentar los resultados de dichas consultas de forma ordenada. La aplicación se encargará de validar los datos a partir de los que se va a generar la configuración, determinar qué plantillas se deben consultar en función a aspectos como el servicio a configurar o la marca del encaminador y finalmente generar el fichero de texto resultado. De este modo, el instalador simplemente tendrá que volcar la información de dicho fichero sobre el encaminador. El sistema se ha diseñado de manera que sea lo más flexible a cambios, puesto que la idea de los miembros del departamento es ampliar la funcionalidad de esta herramienta. ABSTRACT. This Final Degree Project is focused on the design and implementation of a system which is able to generate a text file that contains the basic configuration of a router. With this system we want to improve the efficiency of the department members where this system is going to be introduced, releasing them from repetitive work which is done several times per day. Up to now, each installer has to configure the router manually. After checking the configuration of several devices successfully, they create a set of templates which work as models. Although the installers use those templates, they have to modify the variables that depend on the specific features of each kind of configuration. Thus, even though they don´t have to execute the commands step by step, they have to do a review of each used template in order to generate the right configuration. For each configuration, three to seven templates have to be checked. In addition, if the configured routers are both Cisco and Teldat, there are several models per brand and the company offers four types of services to be installed, so the configuration becomes a hard task to do. The system is comprised of a web server in which both the database and the program responsible for doing queries are hosted, a simple web site that will be the graphic user interface, and an application focused on generating the text file which contains the router configuration based on a set of conditions. The developed database is the representation of the real one and its aim is to simulate the way the system will work. The function of the web site is to offer an easy interface whereby you can submit a query or you can see the obtained results as a data table. Furthermore, the application has to validate the data in which the text file with the router configuration is based on. Then, it has to decide which templates it is going to use according to different aspects, such as the brand of the router or the type of service we want to configure. Finally, the application generates a text file with the necessary commands. As a result of this, the user of the system only has to copy the contents of this file to the router. The system has been designed to be flexible to changes because the members of the department want to increase the utility of this tool in the future.

Proyecto y lugar en la arquitectura doméstica de Jørn Utzon

En medio de un bosque danés, de altos arboles que se mueven al fuerte viento nórdico bajo el débil sol de las latitudes altas, y cargado de unos cuantos tableros de madera que consiguió de una exposición ya terminada, realizó Utzon su maqueta a escala real de su primera casa familiar en Hellebæk (1950-52) a la edad de treinta y dos años. De la misma manera que el pintor William Turner necesitó atarse a lo alto de un mástil de un barco, para vivir en directo una de las muchas tormentas que tantas y tantas veces había pintado en sus cuadros, el joven Utzon consideró indispensable introducirse dentro de la maqueta de su propia casa antes de construirla, para valorar in situ las potencialidades de aquel proyecto en relación al lugar. La obra de Jørn Utzon (1918-2008) es una arquitectura expectante y atenta del lugar donde se ubica. Jørn Utzon es un arquitecto de origen nórdico, que descubre su verdadera idiosincrasia en la cultura mediterránea, cultura en la que reside durante casi la mitad de toda su vida. Esta tesis se ha centrado en analizar exhaustivamente la relación de su arquitectura doméstica con el lugar donde se halla. Aspecto tan citado en la bibliografía existente de su obra, aunque nunca desarrollado de manera exhaustiva. El objetivo del análisis ha sido intentar encontrar invariantes o patrones que pudieran subyacer en su obra residencial en relación a ese tema. Para dicho análisis, se ha tomado una muestra suficientemente amplia de veinte viviendas o conjuntos residenciales (entre ellas sus cuatro viviendas familiares proyectadas), repartidas por cinco países (Suecia, Dinamarca, Reino Unido, España y Nueva Gales del Sur), que constituyen la tercera parte de su obra doméstica y la mitad de su obra construida residencial, así como las citas explícitas del autor sobre este tema en su obra escrita, y los planos o croquis de su obra gráfica. Como metodología de trabajo se ha recurrido a la consulta de las fuentes primarias: viajando y conociendo in-situ las casas seleccionadas en Dinamarca, Suecia, España y Australia; viviendo un mes en una de las casas (Can Lis) gracias a una beca del Gobierno danés y la Utzon Foundation; y realizando entrevistas a las personas que más cerca estuvieron del arquitecto en su entorno familiar y profesional. Asimismo, también se ha publicado parte de su contenido en medios internacionales: 4th International Utzon Symposium (7/3/2013-9/3/2014) y la página web oficial de Can Lis dependiente de la Utzon Foundation (www.canlis.dk). Las doce invariantes encontradas en relación al proyecto y lugar en los proyectos seleccionados, han sido agrupadas en torno a tres grandes elementos sobre los que Utzon constantemente reflexiona en sus escritos propios: horizonte, sol y material autóctono. Elementos que tienen su origen en la influencia que la navegación tuvo en su vida, y en su carácter espiritual y austero en lo material. La historia de Utzon es la de un nórdico, de vocación navegante, que encuentra su lugar en la cultura mediterránea, rodeado entre piedras de Marés, mientras divisa en silencio el horizonte marino en el umbral entre luz y sombra. ABSTRACT In the middle of a Danish forest, with high trees which move with the Nordic wind under the weak sun of high latitudes, and with the help of some wooden canvases acquired from an already completed exhibition, Jørn Utzon built a real-scale model of his first family house in Hellebæk (1950-52) at the age of thirty-two. In the same way that William Turner needed to be tied up on the top of a boat flagpole in order to have a first-hand experience of one of the many storms that he had depicted in his paintings so many times before, the young Utzon thought it was crucial to go into the model of his own house before building it, to evaluate in situ the potential of that project in relation to the place. Utzon’s work is architecture interested in and attentive of the place where it is situated. Jørn Utzon (1918-2008) is an architect of Nordic origin who discovered his own idiosyncrasy in the Mediterranean culture, in which he resided for half of his live. This thesis has focused on an exhaustive analysis of the relation between his domestic architecture and the place where it is located. This issue has been often cited in the existing bibliography, although it has never been exhaustively developed. The analysis objective has been to attempt to find invariants and patterns that could exist in his domestic work in relation to this subject. For this analysis, a sufficiently large sample has been selected: twenty houses or housing complexes (among others his own four family houses), distributed in five countries (Sweden, Denmark, United Kingdom, Spain and New South Wales), which constitute the third part of his domestic work, and half of his residential constructed projects, as well as Utzon’s written texts about this theme, and the drawings and sketches of his graphic work. The methodology used was based on consultation of primary sources: travelling and examining in situ the selected houses in Denmark, Sweden, Spain and Australia; living for a month in one of the houses (Can Lis) thanks to a research grant from the Danish Government and the Utzon Foundation; and interviewing people from his closest family and professional circles. Furthermore, part of the thesis has been published in international media: 4th International Utzon Symposium (7/3/2013-9/3/2014) and on the official web site of Can Lis, an Utzon Foundation subsidiary(www.canlis.dk). The twelve invariants discovered in relation to the project and the location of the selected projects, have been grouped according to three elements which Utzon continuously reflects upon in his own writings: the horizon, the sun and autochthonous material. Elements which originate from the influence that navigation had in his life, and from his spiritual and austere character. The story of Utzon is that of a Nordic person, with the vocation of a navigator, who found his place in the Mediterranean culture, surrounded with Marés stones, while silently making out the sea horizon on the threshold between light and shadow.

Computerized polymorphic marker identification: Experimental validation and a predicted human polymorphism catalog

A computational system for the prediction of polymorphic loci directly and efficiently from human genomic sequence was developed and verified. A suite of programs, collectively called pompous (polymorphic marker prediction of ubiquitous simple sequences) detects tandem repeats ranging from dinucleotides up to 250 mers, scores them according to predicted level of polymorphism, and designs appropriate flanking primers for PCR amplification. This approach was validated on an approximately 750-kilobase region of human chromosome 3p21.3, involved in lung and breast carcinoma homozygous deletions. Target DNA from 36 paired B lymphoblastoid and lung cancer lines was amplified and allelotyped for 33 loci predicted by pompous to be variable in repeat size. We found that among those 36 predominately Caucasian individuals 22 of the 33 (67%) predicted loci were polymorphic with an average heterozygosity of 0.42. Allele loss in this region was found in 27/36 (75%) of the tumor lines using these markers. pompous provides the genetic researcher with an additional tool for the rapid and efficient identification of polymorphic markers, and through a World Wide Web site, investigators can use pompous to identify polymorphic markers for their research. A catalog of 13,261 potential polymorphic markers and associated primer sets has been created from the analysis of 141,779,504 base pairs of human genomic sequence in GenBank. This data is available on our Web site (pompous.swmed.edu) and will be updated periodically as GenBank is expanded and algorithm accuracy is improved.

Prediction of operons in microbial genomes

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P ≥ 0.98) to belong to the same operon. The sensitivity of our method is 30–50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans­membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2/.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Protein Information Resource: a community resource for expert annotation of protein data

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.

YPD™, PombePD™ and WormPD™: model organism volumes of the BioKnowledge™ Library, an integrated resource for protein information

The BioKnowledge Library is a relational database and web site (http://www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharo­myces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD™). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease.

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure–structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure–structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.

rrndb: the Ribosomal RNA Operon Copy Number Database

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu.

Mendel, a database of nomenclature for sequenced plant genes

The Mendel database contains names for plant-wide families of sequenced plant genes. The names have either been approved by the Commission on Plant Gene Nomenclature (CPGN), an organization of the International Society for Plant Molecular Biology (ISPMB), or are identified as provisional or temporary names. Mendel also identifies the corresponding genes in individual species of plants. Mendel can be searched through the mirror sites at Cornell (http://genome.cornell.edu/cgi-bin/WebAce/webace?db=mendel) and Stanford (http://genome-www.stanford.edu/Mendel/). In addition, parts of Mendel can be downloaded from the CPGN Web site (http://mbclserver.rutgers.edu/CPGN/).

The Molecular Biology Database Collection: an updated compilation of biological database resources

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www.nar.oupjournals.org.

The Research Funding Service: a model for expanded library services

Traditionally, libraries have provided a modest amount of information about grants and funding opportunities to researchers in need of research funding. Ten years ago, the University of Washington (UW) Health Sciences Libraries and Information Center joined in a cooperative effort with the School of Medicine to develop a complete, library-based grant and funding service for health sciences researchers called the Research Funding Service. The library provided space, access to the library collection, equipment, and electronic resources, and the School of Medicine funded staff and operations. The range of services now includes individual consultation appointments, an extensive Web site, classes on funding database searching and writing grant applications, a discussion series that frequently hosts guest speakers, a monthly newsletter with funding opportunities of interest to the six health sciences schools, extensive files on funding sources, and referral services.

Experiences with free and open courses using on-line multimedia resources

This paper analyzes the learning experiences and opinions obtained from a group of undergraduate students in their interaction with several on-line multimedia resources included in a free on-line course about Computer Networks. These new educational resources employed are based on the Web2.0 approach such as blogs, videos and virtual labs which have been added in a web-site for distance self-learning.