Map4rdf - Faceted Browser for Geospatial Datasets

Recently we have seen a large increase in the amount of geospatial data that is being published using RDF and Linked Data principles. Eorts such as the W3C Geo XG, and most recently the GeoSPARQL initiative are providing the necessary vocabularies to pub- lish this kind of information on the Web of Data. In this context it is necessary to develop applications that consume and take advantage of these geospatial datasets. In this paper we present map4rdf, a faceted browsing tool for exploring and visualizing RDF datasets enhanced with geospatial information.

An Introductory Course on Constraint Logic Programming

The purpose of this document is to serve as the printed material for the seminar "An Introductory Course on Constraint Logic Programming". The intended audience of this seminar are industrial programmers with a degree in Computer Science but little previous experience with constraint programming. The seminar itself has been field tested, prior to the writing of this document, with a group of the application programmers of Esprit project P23182, "VOCAL", aimed at developing an application in scheduling of field maintenance tasks in the context of an electric utility company. The contents of this paper follow essentially the flow of the seminar slides. However, there are some differences. These differences stem from our perception from the experience of teaching the seminar, that the technical aspects are the ones which need more attention and clearer explanations in the written version. Thus, this document includes more examples than those in the slides, more exercises (and the solutions to them), as well as four additional programming projects, with which we hope the reader will obtain a clearer view of the process of development and tuning of programs using CLP. On the other hand, several parts of the seminar have been taken out: those related with the account of fields and applications in which C(L)P is useful, and the enumerations of C(L)P tools available. We feel that the slides are clear enough, and that for more information on available tools, the interested reader will find more up-to-date information by browsing the Web or asking the vendors directly. More details in this direction will actually boil down to summarizing a user manual, which is not the aim of this document.

Interfaz gráfica y fase de pruebas de software de vídeo forense (Sistema de codificación DV)

El presente proyecto fin de carrera, realizado por el ingeniero técnico en telecomunicaciones Pedro M. Matamala Lucas, es la fase final de desarrollo de un proyecto de mayor magnitud correspondiente al software de vídeo forense SAVID. El propósito del proyecto en su totalidad es la creación de una herramienta informática capacitada para realizar el análisis de ficheros de vídeo, codificados y comprimidos por el sistema DV –Digital Video-. El objetivo del análisis, es aportar información acerca de si la cinta magnética presenta indicios de haber sido manipulada con una edición posterior a su grabación original, además, de mostrar al usuario otros datos de interés como las especificaciones técnicas de la señal de vídeo y audio. Por lo tanto, se facilitará al usuario, analista de vídeo forense, información que le ayude a valorar la originalidad del contenido del soporte que es sujeto del análisis. El objetivo específico de esta fase final, es la creación de la interfaz de usuario del software, que informa tanto del código binario de los sectores significativos, como de su interpretación tras el análisis. También permitirá al usuario el reporte de los resultados, además de otras funcionalidades que le permitan la navegación por los sectores del código que han sido modificados como efecto colateral de la edición de la cinta magnética original. Otro objetivo importante del proyecto ha sido la investigación de metodologías y técnicas de desarrollo de software para su posterior implementación, buscando con esto, una mayor eficiencia en la gestión del tiempo y una mayor calidad de software con el fin de garantizar su evolución y sostenibilidad en el futuro. Se ha hecho hincapié en las metodologías ágiles que han ido ganando relevancia en el sector de las tecnologías de la información en las últimas décadas, sustituyendo a metodologías clásicas como el desarrollo en cascada. Su flexibilidad durante el ciclo de vida del software, permite obtener mejores resultados cuando las especificaciones no están del todo definidas, ajustándose de este modo a las condiciones del proyecto. Resumiendo las especificaciones técnicas del software, C++ es el lenguaje de programación orientado a objetos con el que se ha desarrollado, utilizándose la tecnología MFC -Microsoft Foundation Classes- para la implementación. Es un proyecto MFC de tipo cuadro de dialogo,creado, compilado y publicado, con la herramienta de desarrollo integrado Microsoft Visual Studio 2010. La arquitectura con la que se ha estructurado es la arquetípica de tres capas, compuesta por la interfaz de usuario, capa de negocio y capa de acceso a datos. Se ha visto necesario configurar el proyecto con compatibilidad con CLR –Common Languages Runtime- para poder implementar la funcionalidad de creación de reportes. Acompañando a la aplicación informática, se presenta la memoria del proyecto y sus anexos correspondientes a los documentos EDRF –Especificaciones Detalladas de Requisitos funcionales-, EIU –Especificaciones de Interfaz de Usuario , DT -Diseño Técnico- y Guía de Usuario. SUMMARY. This dissertation, carried out by the telecommunications engineer Pedro M. Matamala Lucas, is in its final stage and is part of a larger project for the software of forensic video called SAVID. The purpose of the entire project is the creation of a software tool capable of analyzing video files that are coded and compressed by the DV -Digital Video- System. The objective of the analysis is to provide information on whether the magnetic tape shows signs of having been tampered with after the editing of the original recording, and also to show the user other relevant data and technical specifications of the video signal and audio. Therefore the user, forensic video analyst, will have information to help assess the originality of the content of the media that is subject to analysis. The specific objective of this final phase is the creation of the user interface of the software that provides information about the binary code of the significant sectors and also its interpretation after analysis. It will also allow the user to report the results, and other features that will allow browsing through the sections of the code that have been modified as a secondary effect of the original magnetic tape being tampered. Another important objective of the project is the investigation of methodologies and software development techniques to be used in deployment, with the aim of greater efficiency in time management and enhanced software quality in order to ensure its development and maintenance in the future. Agile methodologies, which have become important in the field of information technology in recent decades, have been used during the execution of the project, replacing classical methodologies such as Waterfall Development. The flexibility, as the result of using by agile methodologies, during the software life cycle, produces better results when the specifications are not fully defined, thus conforming to the initial conditions of the project. Summarizing the software technical specifications, C + + the programming language – which is object oriented and has been developed using technology MFC- Microsoft Foundation Classes for implementation. It is a project type dialog box, created, compiled and released with the integrated development tool Microsoft Visual Studio 2010. The architecture is structured in three layers: the user interface, business layer and data access layer. It has been necessary to configure the project with the support CLR -Common Languages Runtime – in order to implement the reporting functionality. The software application is submitted with the project report and its annexes to the following documents: Functional Requirements Specifications - Detailed User Interface Specifications, Technical Design and User Guide.

Quality of Service (QoS) in MPLS networks

Telecommunications networks have been always expanding and thanks to it, new services have appeared. The old mechanisms for carrying packets have become obsolete due to the new service requirements, which have begun working in real time. Real time traffic requires strict service guarantees. When this traffic is sent through the network, enough resources must be given in order to avoid delays and information losses. When browsing through the Internet and requesting web pages, data must be sent from a server to the user. If during the transmission there is any packet drop, the packet is sent again. For the end user, it does not matter if the webpage loads in one or two seconds more. But if the user is maintaining a conversation with a VoIP program, such as Skype, one or two seconds of delay in the conversation may be catastrophic, and none of them can understand the other. In order to provide support for this new services, the networks have to evolve. For this purpose MPLS and QoS were developed. MPLS is a packet carrying mechanism used in high performance telecommunication networks which directs and carries data using pre-established paths. Now, packets are forwarded on the basis of labels, making this process faster than routing the packets with the IP addresses. MPLS also supports Traffic Engineering (TE). This refers to the process of selecting the best paths for data traffic in order to balance the traffic load between the different links. In a network with multiple paths, routing algorithms calculate the shortest one, and most of the times all traffic is directed through it, causing overload and packet drops, without distributing the packets in the other paths that the network offers and do not have any traffic. But this is not enough in order to provide the real time traffic the guarantees it needs. In fact, those mechanisms improve the network, but they do not make changes in how the traffic is treated. That is why Quality of Service (QoS) was developed. Quality of service is the ability to provide different priority to different applications, users, or data flows, or to guarantee a certain level of performance to a data flow. Traffic is distributed into different classes and each of them is treated differently, according to its Service Level Agreement (SLA). Traffic with the highest priority will have the preference over lower classes, but this does not mean it will monopolize all the resources. In order to achieve this goal, a set policies are defined to control and alter how the traffic flows. Possibilities are endless, and it depends in how the network must be structured. By using those mechanisms it is possible to provide the necessary guarantees to the real-time traffic, distributing it between categories inside the network and offering the best service for both real time data and non real time data. Las Redes de Telecomunicaciones siempre han estado en expansión y han propiciado la aparición de nuevos servicios. Los viejos mecanismos para transportar paquetes se han quedado obsoletos debido a las exigencias de los nuevos servicios, que han comenzado a operar en tiempo real. El tráfico en tiempo real requiere de unas estrictas garantías de servicio. Cuando este tráfico se envía a través de la red, necesita disponer de suficientes recursos para evitar retrasos y pérdidas de información. Cuando se navega por la red y se solicitan páginas web, los datos viajan desde un servidor hasta el usuario. Si durante la transmisión se pierde algún paquete, éste se vuelve a mandar de nuevo. Para el usuario final, no importa si la página tarda uno o dos segundos más en cargar. Ahora bien, si el usuario está manteniendo una conversación usando algún programa de VoIP (como por ejemplo Skype) uno o dos segundos de retardo en la conversación podrían ser catastróficos, y ninguno de los interlocutores sería capaz de entender al otro. Para poder dar soporte a estos nuevos servicios, las redes deben evolucionar. Para este propósito se han concebido MPLS y QoS MPLS es un mecanismo de transporte de paquetes que se usa en redes de telecomunicaciones de alto rendimiento que dirige y transporta los datos de acuerdo a caminos preestablecidos. Ahora los paquetes se encaminan en función de unas etiquetas, lo cual hace que sea mucho más rápido que encaminar los paquetes usando las direcciones IP. MPLS también soporta Ingeniería de Tráfico (TE). Consiste en seleccionar los mejores caminos para el tráfico de datos con el objetivo de balancear la carga entre los diferentes enlaces. En una red con múltiples caminos, los algoritmos de enrutamiento actuales calculan el camino más corto, y muchas veces el tráfico se dirige sólo por éste, saturando el canal, mientras que otras rutas se quedan completamente desocupadas. Ahora bien, esto no es suficiente para ofrecer al tráfico en tiempo real las garantías que necesita. De hecho, estos mecanismos mejoran la red, pero no realizan cambios a la hora de tratar el tráfico. Por esto es por lo que se ha desarrollado el concepto de Calidad de Servicio (QoS). La calidad de servicio es la capacidad para ofrecer diferentes prioridades a las diferentes aplicaciones, usuarios o flujos de datos, y para garantizar un cierto nivel de rendimiento en un flujo de datos. El tráfico se distribuye en diferentes clases y cada una de ellas se trata de forma diferente, de acuerdo a las especificaciones que se indiquen en su Contrato de Tráfico (SLA). EL tráfico con mayor prioridad tendrá preferencia sobre el resto, pero esto no significa que acapare la totalidad de los recursos. Para poder alcanzar estos objetivos se definen una serie de políticas para controlar y alterar el comportamiento del tráfico. Las posibilidades son inmensas dependiendo de cómo se quiera estructurar la red. Usando estos mecanismos se pueden proporcionar las garantías necesarias al tráfico en tiempo real, distribuyéndolo en categorías dentro de la red y ofreciendo el mejor servicio posible tanto a los datos en tiempo real como a los que no lo son.

A model for integrating learning object repository resources into web videoconference services

Reusing Learning Objects saves time and reduce development costs. Hence, achieving their interoperability in multiple contexts is essential when creating a Learning Object Repository. On the other hand, novel web videoconference services are available due to technological advancements. Several benefits can be gained by integrating Learning Objects into these services. For instance, they can allow sharing, co-viewing and synchronized co-browsing of these resources at the same time that provide real time communication. However, several efforts need to be undertaken to achieve the interoperability with these systems. In this paper, we propose a model to integrate the resources of the Learning Object Repositories into web videoconference services. The experience of applying this model in a real e-Learning scenario achieving interoperability with two different web videoconference services is also described.

An architecture for integrating learning object repository resources into web videoconference services

Reusing Learning Objects saves time and reduce development costs. Hence, achieving their interoperability in multiple contexts is essential when creating a Learning Object Repository. On the other hand, novel web videoconference services are available due to technological advancements. Several benefits can be gained by integrating Learning Objects into these services. For instance, they can allow sharing, co-viewing and synchronized co-browsing of these resources at the same time that provide real time communication. However, several efforts need to be undertaken to achieve the interoperability with these systems. In this paper, we propose a model to integrate the resources of the Learning Object Repositories into web videoconference services. The experience of applying this model in a real e-Learning scenario achieving interoperability with two different web videoconference services is also described.

Towards workflow ecosystems through standard representations

Workflows are increasingly used to manage and share scientific computations and methods. Workflow tools can be used to design, validate, execute and visualize scientific workflows and their execution results. Other tools manage workflow libraries or mine their contents. There has been a lot of recent work on workflow system integration as well as common workflow interlinguas, but the interoperability among workflow systems remains a challenge. Ideally, these tools would form a workflow ecosystem such that it should be possible to create a workflow with a tool, execute it with another, visualize it with another, and use yet another tool to mine a repository of such workflows or their executions. In this paper, we describe our approach to create a workflow ecosystem through the use of standard models for provenance (OPM and W3C PROV) and extensions (P-PLAN and OPMW) to represent workflows. The ecosystem integrates different workflow tools with diverse functions (workflow generation, execution, browsing, mining, and visualization) created by a variety of research groups. This is, to our knowledge, the first time that such a variety of workflow systems and functions are integrated.

Metodología para la estimación de indicadores armonizados a partir de los inventarios forestales nacionales europeos con especial énfasis en la biodiversidad forestal

Durante las últimas décadas el objetivo principal de la silvicultura y la gestión forestal en Europa ha pasado de ser la producción de madera a ser la gestión sostenible de los ecosistemas, por lo que se deben considerar todos los bienes y servicios que proporcionan los bosques. En consecuencia, es necesario contar con información forestal periódica de diversos indicadores forestales a nivel europeo para apoyar el desarrollo y la implementación de políticas medioambientales y que se realice una gestión adecuada. Para ello, se requiere un seguimiento intensivo sobre el estado de los bosques, por lo que los Inventarios Forestales Nacionales (IFN), (principal fuente de información forestal a gran escala), han aumentado el número de variables muestreadas para cumplir con los crecientes requerimientos de información. Sin embargo, las estimaciones proporcionadas por los diferentes países no son fácilmente comparables debido a las diferencias en las definiciones, los diseños de muestreo, las variables medidas y los protocolos de medición. Por esto, la armonización de los datos que proporcionan los diferentes países es fundamental para la contar con una información forestal sólida y fiable en la Unión europea (UE). La presente tesis tiene dos objetivos principales: (i) establecer el diseño de una metodología para evaluar la biodiversidad forestal en el marco del Inventario forestal nacional de España teniendo en cuenta las diferentes iniciativas nacionales e internacionales, con el objetivo de producir estimaciones comparables con las de otros países de la UE y (ii) armonizar los indicadores más relevantes para satisfacer los requerimientos nacionales e internacionales. Como consecuencia del estudio realizado para alcanzar el primer objetivo, la metodología diseñada para estimar la biodiversidad fue adoptada por el Tercer Inventario forestal nacional. Ésta se componía de indicadores agrupados en: cobertura del suelo, composición de árboles y especies de arbustos, riqueza de especies herbáceas y helechos, especies amenazadas, estructura, madera muerta, y líquenes epífitos. Tras el análisis del diseño metodológico y de los datos proporcionados, se observó la conveniencia de modificarla con el fin de optimizar los costes, viabilidad, calidad y cantidad de los datos registrados. En consecuencia, en el Cuarto Inventario Forestal Nacional se aplica una metodología modificada, puesto que se eliminó el muestreo de especies herbáceas y helechos, de líquenes epífitos y de especies amenazadas, se modificaron los protocolos de la toma de datos de estructura y madera muerta y se añadió el muestreo de especies invasoras, edad, ramoneo y grado de naturalidad de la masa. En lo que se refiere al segundo objetivo, se ha avanzado en la armonización de tres grupos de variables considerados como relevantes en el marco de los IFN: los indicadores de vegetación no arbórea (que juegan un papel relevante en los ecosistemas, es donde existe la mayor diversidad de plantas y hasta ahora no se conocían los datos muestreados en los IFN), la determinación de los árboles añosos (que tienen un importante papel como nicho ecológico y su identificación es especialmente relevante para la evaluación de la biodiversidad forestal) y el bosque disponible para el suministro de madera (indicador básico de los requerimientos internacionales de información forestal). Se llevó a cabo un estudio completo de la posible armonización de los indicadores de la vegetación no arbórea en los IFN. Para ello, se identificaron y analizaron las diferentes definiciones y diseños de muestreo empleados por los IFN, se establecieron definiciones de referencia y se propusieron y analizaron dos indicadores que pudiesen ser armonizados: MSC (mean species cover) que corresponde a la media de la fracción de cabida cubierta de cada especie por tipo de bosque y MTC (mean total cover). Se estableció una nueva metodología que permite identificar los árboles añosos con los datos proporcionados por los inventarios forestales nacionales con el objetivo de proporcionar una herramienta eficaz para facilitar la gestión forestal considerando la diversidad de los sistemas forestales. Se analizó el concepto de "bosque disponible para el suministro de madera" (FAWS) estudiando la consistencia de la información internacional disponible con el fin de armonizar su estimación y de proporcionar recomendaciones para satisfacer los requerimientos europeos. Como resultado, se elaboró una nueva definición de referencia de FAWS (que será adoptada por el proceso paneuropeo) y se analiza el impacto de la adopción de esta nueva definición en siete países europeos. El trabajo realizado en esta tesis, puede facilitar el suministrar y/o armonizar parcial o totalmente casi la mitad de los indicadores de información forestal solicitados por los requerimientos internacionales (47%). De éstos, prácticamente un 85% tienen relación con los datos inventariados empleando la metodología propuesta para la estimación de la biodiversidad forestal, y el resto, con el establecimiento de la definición de bosque disponible para el suministro de madera. No obstante, y pese a que esta tesis supone un avance importante, queda patente que las necesidades de información forestal son cambiantes y es imprescindible continuar el proceso de armonización de los IFN europeos. ABSTRACT Over the last few decades, the objectives on forestry and forest management in Europe have shifted from being primarily focused on wood production to sustainable ecosystem management, which should consider all the goods and services provided by the forest. Therefore, there is a continued need for forest indicators and assessments at EU level to support the development and implementation of a number of European environmental policies and to conduct a proper forest management. To address these questions, intensive monitoring on the status of forests is required. Therefore, the scope of National Forest Inventories (NFIs), (primary source of data for national and large-area assessments), has been broadened to include new variables to meet these increasing information requirements. However, estimates produced by different countries are not easily comparable because of differences in NFI definitions, plot configurations, measured variables, and measurement protocols. As consequence, harmonizing data produced at national level is essential for the production of sound EU forest information. The present thesis has two main aims: (i) to establish a methodology design to assess forest biodiversity in the frame of the Spanish National Forest Inventory taking into account the different national and international initiatives with the intention to produce comparable estimates with other EU countries and (ii) to harmonize relevant indicators for national and international requirements. In consequence of the work done related to the first objective, the established methodology to estimate forest biodiversity was adopted and launched under the Third National Forest Inventory. It was composed of indicators grouped into: cover, woody species composition, richness of herbaceous species and ferns, endangered species, stand structure, dead wood, and epiphytic lichens. This methodology was analyzed considering the provided data, time costs, feasibility, and requirements. Consequently, in the ongoing Fourth National Forest Inventory a modified methodology is applied: sampling of herbaceous species and ferns, epiphytic lichens and endangered species were removed, protocols regarding structure and deadwood were modified, and sampling of invasive species, age, browsing impact and naturalness were added. As regards the second objective, progress has been made in harmonizing three groups of variables considered relevant in the context of IFN: Indicators of non-tree vegetation (which play an important role in forest ecosystems, it is where the highest diversity of plants occur and so far the related sampled data in NFIs were not known), the identification of old-growth trees (which have an important role as ecological niche and its identification is especially relevant for the assessment of forest biodiversity) and the available forest for wood supply (basic indicator of international forestry information requirements). A complete analysis of ground vegetation harmonization possibilities within NFIs frame was carried on by identifying and analyzing the different definitions and sampling techniques used by NFIs, providing reference definitions related to ground vegetation and proposing and analyzing two ground vegetation harmonized indicators: “Mean species cover” (MSC) and “Mean total cover” (MTC) for shrubs by European forest categories. A new methodology based on NFI data was established with the aim to provide an efficient tool for policy makers to estimate the number of old-growth trees and thus to be able to perform the analysis of the effect of forest management on the diversity associated to forest systems. The concept of “forest available for wood supply” (FAWS) was discussed and clarified, analyzing the consistency of the available international information on FAWS in order to provide recommendations for data harmonization at European level regarding National Forest Inventories (NFIs). As a result, a new reference definition of FAWS was provided (which will be adopted in the pan-European process) and the consequences of the use of this new definition in seven European countries are analyzed. The studies carried on in this thesis, can facilitate the supply and/or harmonization partially or fully of almost half of the forest indicators (47%) needed for international requirements. Of these, nearly 85% are related to inventoried data using the proposed methodology for the estimation of forest biodiversity, and the rest, with the establishment of the definition of forest available for wood supply. However, despite this thesis imply an important development, forest information needs are changing and it is imperative to continue the process of harmonization of European NFIs.

Variant antigenic peptide promotes cytotoxic T lymphocyte adhesion to target cells without cytotoxicity

Timelapse video microscopy has been used to record the motility and dynamic interactions between an H-2Db-restricted murine cytotoxic T lymphocyte clone (F5) and Db-transfected L929 mouse fibroblasts (LDb) presenting normal or variant antigenic peptides from human influenza nucleoprotein. F5 cells will kill LDb target cells presenting specific antigen (peptide NP68: ASNENMDAM) after “browsing” their surfaces for between 8 min and many hours. Cell death is characterized by abrupt cellular rounding followed by zeiosis (vigorous “boiling” of the cytoplasm and blebbing of the plasma membrane) for 10–20 min, with subsequent cessation of all activity. Departure of cytotoxic T lymphocytes from unkilled target cells is rare, whereas serial killing is sometimes observed. In the absence of antigenic peptide, cytotoxic T lymphocytes browse target cells for much shorter periods, and readily leave to encounter other targets, while never causing target cell death. Two variant antigenic peptides, differing in nonamer position 7 or 8, also act as antigens, albeit with lower efficiency. A third variant peptide NP34 (ASNENMETM), which differs from NP68 in both positions and yet still binds Db, does not stimulate F5 cytotoxicity. Nevertheless, timelapse video analysis shows that NP34 leads to a significant modification of cell behavior, by up-regulating F5–LDb adhesive interactions. These data extend recent studies showing that partial agonists may elicit a subset of the T cell responses associated with full antigen stimulation, by demonstrating that TCR interaction with variant peptide antigens can trigger target cell adhesion and surface exploration without activating the signaling pathway that results in cytotoxicity.

RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers of regulatory elements such as promoters, binding sites and terminators. The complete repertoire of known and predicted DNA-binding transcriptional regulators can be considered to be included in this version. The database now distinguishes different allosteric conformations of regulatory proteins indicating the one active in binding and regulating the different promoters. A new set of operon predictions has been incorporated. The relational design has been modified accordingly. Furthermore, a major improvement is a graphic display enabling browsing of the database with a Java-based graphic user interface with three zoom-levels connected to properties of each chromo­somal element. The purpose of these modifications is to make RegulonDB a useful tool and control set for tran­scriptome experiments. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins

The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam and ProDom. Links to the InterPro graphical interface allow users to see at a glance whether proteins from the cluster share particular functional sites. CluSTr also provides cross-references to HSSP and PDB. The database is available for querying and browsing at http://www.ebi.ac.uk/clustr.

The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments

SBASE 8.0 is the eighth release of the SBASE library of protein domain sequences that contains 294 898 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to most major sequence databases and sequence pattern collections. The entries are clustered into over 2005 statistically validated domain groups (SBASE-A) and 595 non-validated groups (SBASE-B), provided with several WWW-based search and browsing facilities for online use. A domain-search facility was developed, based on non-parametric pattern recognition methods, including artificial neural networks. SBASE 8.0 is freely available by anonymous ‘ftp’ file transfer from ftp.icgeb.trieste.it. Automated searching of SBASE can be carried out with the WWW servers http://www.icgeb.trieste.it/sbase/ and http://sbase.abc.hu/sbase/.

The life sciences Global Image Database (GID)

Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solution to unlock the value of scientific images. The Global Image Database (GID) is a web-based (http://www.g wer.ch/qv/gid/gid.htm) structured central repository for scientific annotated images. The GID was designed to manage images from a wide spectrum of imaging domains ranging from microscopy to automated screening. The annotations in the GID define the source experiment of the images by describing who the authors of the experiment are, when the images were created, the biological origin of the experimental sample and how the sample was processed for visualization. A collection of experimental imaging protocols provides details of the sample preparation, and labeling, or visualization procedures. In addition, the entries in the GID reference these imaging protocols with the probe sequences or antibody names used in labeling experiments. The GID annotations are searchable by field or globally. The query results are first shown as image thumbnail previews, enabling quick browsing prior to original-sized annotated image retrieval. The development of the GID continues, aiming at facilitating the management and exchange of image data in the scientific community, and at creating new query tools for mining image data.

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data

The Plasmodium falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1–14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to Plasmodium parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.

The Comprehensive Microbial Resource

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.