Evaluación, instalación y configuración de herramientas de gestión de proyectos de desarrollo de software

Actualmente existen multitud de aplicaciones creadas para la gestión de proyectos software; cada una de ellas pretende dar solución y facilitar las tareas propias de los gestores y los desarrolladores pertenecientes a los equipos de desarrollo. Los equipos de desarrollo software suelen estar integrados por gran variedad de recursos, tanto humanos como materiales. Cada uno desempeña una función concreta en el proyecto, pudiendo no tener una dedicación plena al proyecto. Por eso, es necesario que dichos recursos sean compartidos entre la cartera proyectos existentes. Para resolver este planteamiento en las aplicaciones de gestión de proyectos, ha sido requisito fundamental que se puedan gestionar varios proyectos de forma simultánea (gestión multiproyecto), pudiendo repartir la dedicación de los recursos entre los proyectos existentes en la cartera. En la actualidad, existe un gran número de metodologías de gestión de proyectos, por lo que, en parte, el éxito del proyecto radica en la elección de la más adecuada. Entre todas las metodologías existentes, este estudio se ha centrado en las cada vez más utilizadas metodologías de gestión de proyectos ágiles; se describe en qué consisten, qué beneficios aportan frente a las metodologías clásicas y cuáles son las más utilizadas por sus ya contrastados beneficios y el valor que aportan a la gestión de proyectos. Por lo descrito anteriormente, otro requisito fundamental a la hora de valorar las aplicaciones de gestión de proyectos ha sido la capacidad de soportar y aplicar metodologías ágiles de gestión de proyectos. En este estudio también se ha tenido en cuenta el tipo de aplicación atendiendo a su instalación y acceso, y se ha realizado la diferenciación entre aplicaciones web- las cuales precisan ser instaladas en un servidor web y son accesibles desde cualquier dispositivo con navegador -, y aplicaciones de escritorio - las cuales precisan estar instaladas en un equipo de forma local y sólo pueden ser accedidas a ellas desde dicho equipo. En este estudio se han evaluado varias aplicaciones, intentando analizar el cumplimiento de las características comentadas anteriormente, dando como resultado tres aplicaciones seleccionadas siendo éstas las que pueden aportar más valor a la hora de gestionar una cartera de proyectos. ABSTRACT. At present, there are many applications aimed at managing software projects. Every application intends to solve and facilitate tasks to managers and developers belonging to the development teams. Software development teams are usually made up of many different human and material resources, each of them developing a specific task in the project and sometimes without a full dedication to the project. Therefore, these resources have to be shared within the existing project portfolio. To meet this need in project management applications, the main requirement is to be able to manage several projects simultaneously (multi-project management), thus allowing resources to be shared within the existing project portfolio. At present, there are a large number of project management methodologies and the success of the project lies in choosing the most appropriate one. Among all the existing methodologies, this study has focused on the increasingly used agile project management methodologies. The study describes the way they work, their added value in comparison traditional methodologies, and which ones are more often used due to their already verified benefits and value in managing projects. Taking into account the above-mention characteristics, another key requirement when assessing the project management applications has been their capacity to support and implement project management agile methodologies. This study has also taken into account the type of application according to its installation and access. A difference is established between web applications – which require to be installed in a web server and are accessible from any device with a web browser – and desktop applications, which must be installed in the equipment to be used and are only accessible from this equipment. The study has assessed several applications by analyzing the compliance with the above-mentioned characteristics and has chosen three applications that provide the management of the project portfolio with an added value.

Gestión de ideas innovadoras

El trabajo de fin de grado que se va a definir detalladamente en esta memoria, trata de poner de manifiesto muchos de los conocimientos que he adquirido a lo largo de la carrera, aplicándolos en un proyecto real. Se ha desarrollado una plataforma capaz de albergar ideas, escritas por personas de todo el mundo que buscan compartirlas con los demás, para que estas sean comentadas, valoradas y entre todos poder mejorarlas. Estas ideas pueden ser de cualquier ámbito, por tanto, se da la posibilidad de clasificarlas en las categorías que mejor encajen con la idea. La aplicación ofrece una API RESTful muy descriptiva, en la que se ha identificado y estructurado cada recurso, para que a través de los “verbos http” se puedan gestionar todos los elementos de una forma fácil y sencilla, independientemente del cliente que la utilice. La arquitectura está montada siguiendo el patrón de diseño modelo vista-controlador, utilizando las últimas tecnologías del mercado como Spring, Liferay, SmartGWT y MongoDB (entre muchas otras) con el objetivo de crear una aplicación segura, escalable y modulada, por lo que se ha tenido que integrar todos estos frameworks. Los datos de la aplicación se hacen persistentes en dos tipos de bases de datos, una relacional (MySQL) y otra no relacional (MongoDB), aprovechando al máximo las características que ofrecen cada una de ellas. El cliente propuesto es accesible mediante un navegador web, se basa en el portal de Liferay. Se han desarrollado varios “Portlets o Widgets”, que componen la estructura de contenido que ve el usuario final. A través de ellos se puede acceder al contenido de la aplicación, ideas, comentarios y demás contenidos sociales, de una forma agradable para el usuario, ya que estos “Portlets” se comunican entre sí y hacen peticiones asíncronas a la API RESTful sin necesidad de recargar toda la estructura de la página. Además, los usuarios pueden registrarse en el sistema para aportar más contenidos u obtener roles que les dan permisos para realizar acciones de administración. Se ha seguido una metodología “Scrum” para la realización del proyecto, con el objetivo de dividir el proyecto en tareas pequeñas y desarrollarlas de una forma ágil. Herramientas como “Jenkins” me han ayudado a una integración continua y asegurando mediante la ejecución de los test de prueba, que todos los componentes funcionan. La calidad ha sido un aspecto principal en el proyecto, se han seguido metodologías software y patrones de diseño para garantizar un diseño de calidad, reutilizable, óptimo y modulado. El uso de la herramienta “Sonar” ha ayudado a este cometido. Además, se ha implementado un sistema de pruebas muy completo de todos los componentes de la aplicación. En definitiva, se ha diseñado una aplicación innovadora de código abierto, que establece unas bases muy definidas para que si algún día se pone en producción, sirva a las personas para compartir pensamientos o ideas ayudando a mejorar el mundo en el que vivimos. ---ABSTRACT---The Final Degree Project, described in detail in this report, attempts to cover a lot of the knowledge I have acquired during my studies, applying it to a real project. The objective of the project has been to develop a platform capable of hosting ideas from people all over the world, where users can share their ideas, comment on and rate the ideas of others and together help improving them. Since these ideas can be of any kind, it is possible to classify them into suitable categories. The application offers a very descriptive API RESTful, where each resource has been identified and organized in a way that makes it possible to easily manage all the elements using the HTTP verbs, regardless of the client using it. The architecture has been built following the design pattern model-view-controller, using the latest market technologies such as Spring, Liferay, Smart GWT and MongoDB (among others) with the purpose of creating a safe, scalable and adjustable application. The data of the application are persistent in two different kinds of databases, one relational (MySQL) and the other non-relational (MongoDB), taking advantage of all the different features each one of them provides. The suggested client is accessible through a web browser and it is based in Liferay. Various “Portlets" or "Widgets” make up the final content of the page. Thanks to these Portlets, the user can access the application content (ideas, comments and categories) in a pleasant way as the Portlets communicate with each other making asynchronous requests to the API RESTful without the necessity to refresh the whole page. Furthermore, users can log on to the system to contribute with more contents or to obtain administrator privileges. The Project has been developed following a “Scrum” methodology, with the main objective being that of dividing the Project into smaller tasks making it possible to develop each task in a more agile and ultimately faster way. Tools like “Jenkins” have been used to guarantee a continuous integration and to ensure that all the components work correctly thanks to the execution of test runs. Quality has been one of the main aspects in this project, why design patterns and software methodologies have been used to guarantee a high quality, reusable, modular and optimized design. The “Sonar” technology has helped in the achievement of this goal. Furthermore, a comprehensive proofing system of all the application's components has been implemented. In conclusion, this Project has consisted in developing an innovative, free source application that establishes a clearly defined basis so that, if it someday will be put in production, it will allow people to share thoughts and ideas, and by doing so, help them to improve the World we live in.

3D simulation of complex shading affecting PV systems taking benefit from the power of graphics cards developed for the video game industry

Shading reduces the power output of a photovoltaic (PV) system. The design engineering of PV systems requires modeling and evaluating shading losses. Some PV systems are affected by complex shading scenes whose resulting PV energy losses are very difficult to evaluate with current modeling tools. Several specialized PV design and simulation software include the possibility to evaluate shading losses. They generally possess a Graphical User Interface (GUI) through which the user can draw a 3D shading scene, and then evaluate its corresponding PV energy losses. The complexity of the objects that these tools can handle is relatively limited. We have created a software solution, 3DPV, which allows evaluating the energy losses induced by complex 3D scenes on PV generators. The 3D objects can be imported from specialized 3D modeling software or from a 3D object library. The shadows cast by this 3D scene on the PV generator are then directly evaluated from the Graphics Processing Unit (GPU). Thanks to the recent development of GPUs for the video game industry, the shadows can be evaluated with a very high spatial resolution that reaches well beyond the PV cell level, in very short calculation times. A PV simulation model then translates the geometrical shading into PV energy output losses. 3DPV has been implemented using WebGL, which allows it to run directly from a Web browser, without requiring any local installation from the user. This also allows taken full benefits from the information already available from Internet, such as the 3D object libraries. This contribution describes, step by step, the method that allows 3DPV to evaluate the PV energy losses caused by complex shading. We then illustrate the results of this methodology to several application cases that are encountered in the world of PV systems design. Keywords: 3D, modeling, simulation, GPU, shading, losses, shadow mapping, solar, photovoltaic, PV, WebGL

Mejora de herramientas de Inteligencia de Negocio en su aplicación a la Gestión Educativa

Tras los distintos análisis diseñados por Jorge Beltrán Luna en el proyecto "Aplicación de Inteligencia de Negocio a la Gestión Educativa" [Beltrán2014] sobre el comportamiento de los alumnos de la Universidad Politécnica de Madrid en las asignaturas cursadas por estos durante el curso 2013-2014, se llegó a la conclusión que se debía desarrollar una aplicación web mediante la cual pudiesen configurarse estos análisis con distintos parámetros para adecuarlos a los requerimientos del usuario. Este proyecto ha cumplido con el objetivo anteriormente mencionado. Se ha desarrollado una aplicación web capaz de mostrar por medio de un navegador web, las gráficas y tablas generadas por el programa de minería de datos. Mediante esta aplicación el usuario puede realizar diversas funciones. Una de ellas es la de solicitar mediante el formulario recibido en la interfaz principal de la aplicación, la visualización de los resultados generados por el sistema de acuerdo con los parámetros seleccionados por el diseñador de los análisis. El usuario conseguirá observar los resultados que obtendría si ejecutase directamente los análisis desarrollados en el proyecto de Jorge Beltrán Luna [Beltrán2014] en la herramienta Rapidminer. Otra de las funciones que podría realizar el usuario sería la de realizar estos mismos análisis pero modificando sus parámetros de configuración para adecuar dichos análisis a los resultados que se quiere obtener. El resultado será el que se habría conseguido en la aplicación Rapidminer si se cambiasen los mismos parámetros que los modificados en la página web de este prototipo. Por último, se ha diseñado un botón con el cual el usuario podrá recuperar el último análisis realizado, con el fin de que no sea necesario esperar el tiempo que tarde en realizarse el análisis para visualizar los resultados. También se ha realizado una explicación detallada de la aplicación de la inteligencia de negocio en el ámbito educacional. ABSTRACT. After different analysis designed by Jorge Beltran Luna in the "Aplicación de Inteligencia de Negocio a la Gestión Educativa" [Beltrán2014] project on the behaviour of the students at the Universidad Politécnica de Madrid during the course 2013-14, the tutor of this project concluded that it should be interesting to develop a web application through which teachers could view and configure these analysis with different parameters. This project has fulfilled the aforementioned objective. A web application has been develop to show through a web browser, the graphs and charts generated by the data mining tool. Using this application, the user can perform various features. One of this features is to request, employing the formulary received in the main interface, to display an analysis according to the chosen parameters. The user will see the results that would be observed in case that the analysis had been directly executed using the project designed by Jorge Beltrán Luna [Beltrán2014] in the RapidMiner tool. Another feature that the user could perform would be to make these analysis modifying its settings Similar result would be obtained in the RapidMiner tool in the case that identical modifications were carried out in the configuration parameters. Finally, a button to allow with recall the last analysis has been implemented. It is not necessary to wait for the execution of this analysis to see newly the results. A detailed explanation on the usage of business intelligence in the educational field has also been performed.

University employees work schedule

The aim of this project is to create a website which is useful both employees and students of a university, so employees can add information, if they log in with username and password access, and students can view this information . Employees may modify and display information such as title, room, or their faculty (from a list defined by the administrator), and most importantly, their schedule, whether class, tutoring, free time, or any of tasks that the administrator define. There will be a manager, responsible for managing employees, the availables faculties and the types of tasks that employees can use on their schedule. Students may see the employees schedules and rooms on the homepage. They differentiate between differents tasks of employees, because these are in different colors. They can also filter information for faculty, employee or day. To achieve our goal, we decided to program in Java using Servlets, which we will use to generate response to requests coming from users from the website. We will also use JSP, allowing us to create different websites files. We use JSP files and not HTML, because we need that the pages are dynamic, since not only want to show specific information, we like that information can change depending on user requests. The JSP file allows us to generate HTML, but also using JAVA language, which is necessary for our purpose. As the information we store is not fixed. We want this information can be modified at any time by employees and admin, so we need a database, which can be accessed from anywhere. We decided SQLite databases because are integrated quite well in our application, and offer a quick response. To access the database from our program, we simply connect it to the database, and with very few lines of code, add, delete or modify entries in different tables that owns the database. To facilitate the initial creation of the database, and the first tables, we use a Mozilla Firefox browser plugin, called SQLite Manager, which allows us to do so from a more friendly interface. Finally, we need a server that supports and implements specifications Servlets and JSP. We decided on the TomCat server, which is a container Servlets, because is free, easy to use, and compatible with our program. We realized all the project with Eclipse environment, also free program that allows integrating database, server and program the JSP and Servlets. Once submitted all the tools we used, we must first organize the structure of the web, relating each Servlets with JSP files. Next, create the database and the different Servlets, and adjust the database accesses to make sure we do it right. From here simply is to build up the page step by step, showing in each place we need, and redirect to different pages. In this way, we can build a complex website, free, and without being an expert in the field. RESUMEN. El objetivo de este proyecto, es crear una página web que sirva tanto a empleados como a alumnos de una universidad, de tal manera que los empleados podrán añadir información, mediante el acceso con usuario y contraseña, y los alumnos podrán visualizar está información. Los empleados podrán modificar y mostrar información como su título, despacho, facultad a la que pertenecen (de entre una lista definida por el administrador), y lo más importante, sus horarios, ya sean de clase, tutorías, tiempo libre, o cualquiera de las tareas que el administrador defina. Habrá un administrador, encargado de gestionar los empleados existentes, las facultades disponibles y los tipos de tareas que podrán usar los empleados en su horario. Los alumnos, podrán visualizar los horarios y despacho de los empleados en la página principal. Diferenciarán entre las distintas tareas de los profesores, porque estas se encuentran en colores diferentes. Además, podrán filtrar la información, por facultad, empleado o día de la semana. Para conseguir nuestro objetivo, hemos decidido programar en Java, mediante el uso de Servlets, los cuales usaremos para generar respuesta antes las peticiones que llegan de los usuarios desde la página web. También usaremos archivos JSP, que nos permitirán crear las diferentes páginas webs. Usamos archivos JSP y no HTML, porque necesitamos que las diferentes páginas sean dinámicas, ya que no solo queremos mostrar una información concreta, si no que esta información puede variar en función de las peticiones de usuario. El archivo JSP nos permite generar HTML, pero a la vez usar lenguaje JAVA, algo necesario para nuestro cometido. Como la información que queremos almacenar no es fija, si no que en todo momento debe poder ser modificada por empleados y administrador, necesitamos una base de datos, a la que podamos acceder desde la web. Nos hemos decidido por bases SQLite, ya que se integran bastante bien en nuestra aplicación, y además ofrecen una rápida respuesta. Para acceder a la base de datos desde nuestro programa, simplemente debemos conectar el mismo a la base de datos, y con muy pocas líneas de código, añadir, eliminar o modificar entradas de las diferentes tablas que posee la base de datos. Para facilitar la creación inicial de la base de datos, y de las primeras tablas, usamos un complemento del navegador Mozilla Firefox, llamado SQLite Manager, que nos permite hacerlo desde una interfaz más amigable. Por último, necesitamos de un servidor que soporte e implemente las especificaciones de los Servlets y JSP. Nos decidimos por el servidor TomCat, que es un contenedor de Servlets gratuito, de fácil manejo, y compatible con nuestro programa. Todo el desarrollo del proyecto, lo realizamos desde el entorno Eclipse, programa también gratuito, que permite integrar la base de datos, el servidor y programar los JSP y Servlets. Una vez presentadas todas las herramientas que hemos utilizado, primero debemos organizar la estructura de la web, relacionando cada archivo JSP con los Servlets a los que debe acceder. A continuación creamos la base de datos y los diferentes Servlets, y ajustamos bien los accesos a la base de datos para comprobar que lo hacemos correctamente. A partir de aquí, simplemente es ir construyendo la página paso a paso, mostrando en cada lugar lo que necesitemos, y redirigiendo a las diferentes páginas. De esta manera, podremos construir una página web compleja, de manera gratuita, y sin ser un experto en la materia.

Contribución a las arquitecturas flexibles para la multiconferencia web adaptable a la demanda

Los sistemas de videoconferencia y colaboración en tiempo real para múltiples usuarios permiten a sus usuarios comunicarse por medio de vídeo, audio y datos. Históricamente estos han sido sistemas caros de obtener y de mantener. El paso de las décadas ha limado estos problemas acercado el mundo de comunicación en tiempo real a un grupo mucho más amplio, llegando a usarse en diversos ámbitos como la educación o la medicina. En este sentido, el último gran salto evolutivo al que hemos asistido ha sido la transición de este tipo de aplicaciones hacia la Web. Varias tecnologías han permitido este viaje hacia el navegador. Las Aplicaciones Ricas de Internet (RIAs), que permiten crear aplicaciones Web interactivas huyendo del clásico esquema de petición y respuesta y llevando funcionalidades propias de las aplicaciones nativas a la Web. Por otro lado, la computación en la nube o Cloud Computing, con su modelo de pago por uso de recursos virtualizados, ha llevado a la creación de servicios que se adaptan mejor a la demanda, han habilitado este viaje hacia el navegador. No obstante, como cada cambio, este salto presenta una serie de retos para los sistemas de videoconferencia establecidos. Esta tesis doctoral propone un conjunto de arquitecturas, mecanismos y algoritmos para adaptar los sistemas de multiconferencia al entorno Web, teniendo en cuenta que este es accedido desde dispositivos diferentes y mediante redes de acceso variadas. Para ello se comienza por el estudio de los requisitos que debe cumplir un sistema de videoconferencia en la Web. Como resultado se diseña, implementa y desarrolla un servicio de videoconferencia que permite la colaboración avanzada entre múltiples usuarios mediante vídeo, audio y compartición de escritorio. Posteriormente, se plantea un sistema de comunicación entre una aplicación nativa y Web, proponiendo técnicas de adaptación entre los dos entornos que permiten la conversación de manera transparente para los usuarios. Estos sistemas permiten facilitar la transición hacia tecnologías Web. Como siguiente paso, se identificaron los principales problemas que existen para la comunicación multiusuario en dispositivos de tamaño reducido (teléfonos inteligentes) utilizando redes de acceso heterogéneas. Se propone un mecanismo, combinación de transcodificación y algoritmos de adaptación de calidad para superar estas limitaciones y permitir a los usuarios de este tipo de dispositivos participar en igualdad de condiciones. La aparición de WebRTC como tecnología disruptiva en este entorno, permitiendo nuevas posibilidades de comunicación en navegadores, motiva la segunda iteración de esta tesis. Aquí se presenta un nuevo esquema de adaptación a la demanda para servidores de videoconferencia diseñado para las necesidades del entorno Web y para aprovechar las características de Cloud Computing. Finalmente, esta tesis repasa las conclusiones obtenidas como fruto del trabajo llevado a cabo, reflejando la evolución de la videoconferencia Web desde sus inicios hasta nuestros días. ABSTRACT Multiuser Videoconferencing and real-time collaboration systems allow users to communicate using video, audio and data streams. These systems have been historically expensive to obtain and maintain. Over the last few decades, technological breakthroughs have mitigated those costs and popularized real time video communication, allowing its use in environments such as education or health. The last big evolutionary leap forward has been the transition of these types of applications towards theWeb. Several technologies have allowed this journey to theWeb browser. Firstly, Rich Internet Applications (RIAs) enable the creation of dynamic Web pages that defy the classical request-response interaction and provide an experience similar to their native counterparts. On the other hand, Cloud Computing brings the leasing of virtualized hardware resources in a pay-peruse model and, with it, better scalability in resource-demanding services. However, as with every change, this evolution imposes a set of challenges on existing videoconferencing solutions. This dissertation proposes a set of architectures, mechanisms and algorithms that aim to adapt multi-conferencing systems to the Web platform, taking into account the variety of devices and access networks that come with it. To this end, this thesis starts with a study concerning the requirements that must be met by new Web videoconferencing systems. The result of this study is the design, development and implementation of a new videoconferencing services that provides advanced collaboration to its user by providing video and audio communication as well as desktop sharing. After this, a new communication system between Web and native applications is presented. This system proposes adaptation mechanisms to bridge the two worlds providing a seamless integration transparent to users who can now access the powerful native application via an easy Web interface. The next step is to identify the main challenges posed by multi-conferencing on small devices (smartphones) with heterogeneous access networks. This dissertation proposes a mechanism that combines transcoding and adaptive quality algorithms to overcome those limitations. A second iteration in this dissertation is motivated by WebRTC. WebRTC appears as a disrupting technology by enabling new real-time communication possibilities in browsers. A new mechanism for flexible videoconferencing server scalability is presented. This mechanism aims to address the strong scalability requirements in the Web environment by taking advantage of Cloud Computing. Finally, the dissertation discusses the results obtained throughout the study, capturing the evolution of Web videoconferencing systems.

The EMBL nucleotide sequence database

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

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.

The ARKdb: genome databases for farmed and other animals

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

CKAAPs DB: a conserved key amino acid positions database

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) Proteins, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly­peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

Creating local bibliographic databases: new tools for evidence-based health care*

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

A distributed systems approach to secure Internet mail

One of the obstacles to improved security of the Internet is ad hoc development of technologies with different design goals and different security goals. This paper proposes reconceptualizing the Internet as a secure distributed system, focusing specifically on the application layer. The notion is to redesign specific functionality, based on principles discovered in research on distributed systems in the decades since the initial development of the Internet. Because of the problems in retrofitting new technology across millions of clients and servers, any options with prospects of success must support backward compatibility. This paper outlines a possible new architecture for internet-based mail which would replace existing protocols by a more secure framework. To maintain backward compatibility, initial implementation could offer a web browser-based front end but the longer-term approach would be to implement the system using appropriate models of replication. (C) 2005 Elsevier Ltd. All rights reserved.

The science and technology of corpus, and corpus for science and technology

Corpus Linguistics is a young discipline. The earliest work was done in the 1960s, but corpora only began to be widely used by lexicographers and linguists in the late 1980s, by language teachers in the late 1990s, and by language students only very recently. This course in corpus linguistics was held at the Departamento de Linguistica Aplicada, E.T.S.I. de Minas, Universidad Politecnica de Madrid from June 15-19 1998. About 45 teachers registered for the course. 30% had PhDs in linguistics, 20% in literature, and the rest were doctorandi or qualified English teachers. The course was designed to introduce the use of corpora and other computational resources in teaching and research, with special reference to scientific and technological discourse in English. Each participant had a computer networked with the lecturer’s machine, whose display could be projected onto a large screen. Application programs were loaded onto the central server, and telnet and a web browser were available. COBUILD gave us permission to access the 323 million word Bank of English corpus, Mike Scott allowed us to use his Wordsmith Tools software, and Tim Johns gave us a copy of his MicroConcord program.

Towards a web-based progressive handwriting recognition environment for mathematical problem solving

The emergence of pen-based mobile devices such as PDAs and tablet PCs provides a new way to input mathematical expressions to computer by using handwriting which is much more natural and efficient for entering mathematics. This paper proposes a web-based handwriting mathematics system, called WebMath, for supporting mathematical problem solving. The proposed WebMath system is based on client-server architecture. It comprises four major components: a standard web server, handwriting mathematical expression editor, computation engine and web browser with Ajax-based communicator. The handwriting mathematical expression editor adopts a progressive recognition approach for dynamic recognition of handwritten mathematical expressions. The computation engine supports mathematical functions such as algebraic simplification and factorization, and integration and differentiation. The web browser provides a user-friendly interface for accessing the system using advanced Ajax-based communication. In this paper, we describe the different components of the WebMath system and its performance analysis.

ESpotter : adaptive named entity recognition for web browsing

Browsing constitutes an important part of the user information searching process on the Web. In this paper, we present a browser plug-in called ESpotter, which recognizes entities of various types on Web pages and highlights them according to their types to assist user browsing. ESpotter uses a range of standard named entity recognition techniques. In addition, a key new feature of ESpotter is that it addresses the problem of multiple domains on the Web by adapting lexicon and patterns to these domains.