An XML Messaging Service for Mobile Devices

In recent years, XML has been accepted as the format of messages for several applications. Prominent examples include SOAP for Web services, XMPP for instant messaging, and RSS and Atom for content syndication. This XML usage is understandable, as the format itself is a well-accepted standard for structured data, and it has excellent support for many popular programming languages, so inventing an application-specific format no longer seems worth the effort. Simultaneously with this XML's rise to prominence there has been an upsurge in the number and capabilities of various mobile devices. These devices are connected through various wireless technologies to larger networks, and a goal of current research is to integrate them seamlessly into these networks. These two developments seem to be at odds with each other. XML as a fully text-based format takes up more processing power and network bandwidth than binary formats would, whereas the battery-powered nature of mobile devices dictates that energy, both in processing and transmitting, be utilized efficiently. This thesis presents the work we have performed to reconcile these two worlds. We present a message transfer service that we have developed to address what we have identified as the three key issues: XML processing at the application level, a more efficient XML serialization format, and the protocol used to transfer messages. Our presentation includes both a high-level architectural view of the whole message transfer service, as well as detailed descriptions of the three new components. These components consist of an API, and an associated data model, for XML processing designed for messaging applications, a binary serialization format for the data model of the API, and a message transfer protocol providing two-way messaging capability with support for client mobility. We also present relevant performance measurements for the service and its components. As a result of this work, we do not consider XML to be inherently incompatible with mobile devices. As the fixed networking world moves toward XML for interoperable data representation, so should the wireless world also do to provide a better-integrated networking infrastructure. However, the problems that XML adoption has touch all of the higher layers of application programming, so instead of concentrating simply on the serialization format we conclude that improvements need to be made in an integrated fashion in all of these layers.

Metadata Federation of PICES Member Countries

(Document pdf contains 193 pages) Executive Summary (pdf, < 0.1 Mb) 1. Introduction (pdf, 0.2 Mb) 1.1 Data sharing, international boundaries and large marine ecosystems 2. Objectives (pdf, 0.3 Mb) 3. Background (pdf, < 0.1 Mb) 3.1 North Pacific Ecosystem Metadatabase 3.2 First federation effort: NPEM and the Korea Oceanographic Data Center 3.2 Continuing effort: Adding Japan’s Marine Information Research Center 4. Metadata Standards (pdf, < 0.1 Mb) 4.1 Directory Interchange Format 4.2 Ecological Metadata Language 4.3 Dublin Core 4.3.1. Elements of DC 4.4 Federal Geographic Data Committee 4.5 The ISO 19115 Metadata Standard 4.6 Metadata stylesheets 4.7 Crosswalks 4.8 Tools for creating metadata 5. Communication Protocols (pdf, < 0.1 Mb) 5.1 Z39.50 5.1.1. What does Z39.50 do? 5.1.2. Isite 6. Clearinghouses (pdf, < 0.1 Mb) 7. Methodology (pdf, 0.2 Mb) 7.1 FGDC metadata 7.1.1. Main sections 7.1.2. Supporting sections 7.1.3. Metadata validation 7.2 Getting a copy of Isite 7.3 NSDI Clearinghouse 8. Server Configuration and Technical Issues (pdf, 0.4 Mb) 8.1 Hardware recommendations 8.2 Operating system – Red Hat Linux Fedora 8.3 Web services – Apache HTTP Server version 2.2.3 8.4 Create and validate FGDC-compliant Metadata in XML format 8.5 Obtaining, installing and configuring Isite for UNIX/Linux 8.5.1. Download the appropriate Isite software 8.5.2. Untar the file 8.5.3. Name your database 8.5.4. The zserver.ini file 8.5.5. The sapi.ini file 8.5.6. Indexing metadata 8.5.7. Start the Clearinghouse Server process 8.5.8. Testing the zserver installation 8.6 Registering with NSDI Clearinghouse 8.7 Security issues 9. Search Tutorial and Examples (pdf, 1 Mb) 9.1 Legacy NSDI Clearinghouse search interface 9.2 New GeoNetwork search interface 10. Challenges (pdf, < 0.1 Mb) 11. Emerging Standards (pdf, < 0.1 Mb) 12. Future Activity (pdf, < 0.1 Mb) 13. Acknowledgments (pdf, < 0.1 Mb) 14. References (pdf, < 0.1 Mb) 15. Acronyms (pdf, < 0.1 Mb) 16. Appendices 16.1. KODC-NPEM meeting agendas and minutes (pdf, < 0.1 Mb) 16.1.1. Seattle meeting agenda, August 22–23, 2005 16.1.2. Seattle meeting minutes, August 22–23, 2005 16.1.3. Busan meeting agenda, October 10–11, 2005 16.1.4. Busan meeting minutes, October 10–11, 2005 16.2. MIRC-NPEM meeting agendas and minutes (pdf, < 0.1 Mb) 16.2.1. Seattle Meeting agenda, August 14-15, 2006 16.2.2. Seattle meeting minutes, August 14–15, 2006 16.2.3. Tokyo meeting agenda, October 19–20, 2006 16.2.4. Tokyo, meeting minutes, October 19–20, 2006 16.3. XML stylesheet conversion crosswalks (pdf, < 0.1 Mb) 16.3.1. FGDCI to DIF stylesheet converter 16.3.2. DIF to FGDCI stylesheet converter 16.3.3. String-modified stylesheet 16.4. FGDC Metadata Standard (pdf, 0.1 Mb) 16.4.1. Overall structure 16.4.2. Section 1: Identification information 16.4.3. Section 2: Data quality information 16.4.4. Section 3: Spatial data organization information 16.4.5. Section 4: Spatial reference information 16.4.6. Section 5: Entity and attribute information 16.4.7. Section 6: Distribution information 16.4.8. Section 7: Metadata reference information 16.4.9. Sections 8, 9 and 10: Citation information, time period information, and contact information 16.5. Images of the Isite server directory structure and the files contained in each subdirectory after Isite installation (pdf, 0.2 Mb) 16.6 Listing of NPEM’s Isite configuration files (pdf, < 0.1 Mb) 16.6.1. zserver.ini 16.6.2. sapi.ini 16.7 Java program to extract records from the NPEM metadatabase and write one XML file for each record (pdf, < 0.1 Mb) 16.8 Java program to execute the metadata extraction program (pdf, < 0.1 Mb) A1 Addendum 1: Instructions for Isite for Windows (pdf, 0.6 Mb) A2 Addendum 2: Instructions for Isite for Windows ADHOST (pdf, 0.3 Mb)

Sistema seguro de votação eletrônica multi-células

Em uso desde a Grécia antiga e atualmente massificado na maioria dos países do mundo, o sistema de votação tradicional baseado em cédulas de papel possui diversos problemas associados à segurança, tais como dificuldades para evitar coerção do eleitor, venda do voto e substituição fraudulenta do eleitor. Além de problemas de usabilidade que acarretam erros de preenchimento da cédula e um processo de apuração lento, que pode durar dias. Ao lado disso, o sistema tradicional não fornece a contraprova do voto, que permite ao eleitor conferir se o seu voto foi corretamente contabilizado na apuração. Inicialmente acreditou-se que a informatização do sistema de votação resolveria todos os problemas do sistema tradicional. Porém, com a sua implantação em alguns países o sistema de votação eletrônica não mostrou-se capaz de fornecer garantias irrefutáveis que não tivesse sido alvo de alterações fraudulentas durante o seu desenvolvimento ou operação. A má reputação do sistema eletrônico está principalmente associada à falta de transparência dos processos que, em sua maioria, não proporcionam a materialização do voto, conferido pelo eleitor para fins de contagem manual, e nem geram evidências (contraprova) da correta contabilização do voto do eleitor. O objetivo deste trabalho é propor uma arquitetura de votação eletrônica que integra, de forma segura, o anonimato e autenticidade do votante, a confidencialidade e integridade do voto/sistema. O sistema aumenta a usabilidade do esquema de votação baseado em "Três Cédulas" de papel, implementando-o computacionalmente. O esquema oferece maior credibilidade ao sistema de votação através da materialização e contraprova do voto, resistência à coerção e ao comércio do voto. Utilizando esquemas de criptografia assimétrica e segurança computacional clássica, associado a um sistema de auditoria eficiente, a proposta garante segurança e transparência nos processos envolvidos. A arquitetura de construção modular distribui a responsabilidade entre suas entidades, agregando-lhe robustez e viabilizando eleições em grande escala. O protótipo do sistema desenvolvido usando serviços web e Election Markup Language mostra a viabilidade da proposta.

Home-Automation System

Nuestro proyecto trata de obtener un sistema centralizado para el manejo y monitorización de un conjunto de aparatos eléctricos del hogar, tales como luces, cámaras, sensores, y otros aparatos mediante una aplicación para dispositivos móviles Android. También se facilita una herramienta web para administrar dichos aparatos. Nuestro sistema da soporte al manejo individual y manual de estos aparatos, por ejemplo encender una lámpara, así como la posibilidad de incluir programas que se ejecuten a una determinada hora, y con una determinada recurrencia. Por ejemplo, se puede programar el encendido de una luz todos los días a las 20:00. Además, también se pueden crear reglas que, dado una determinada situación, realicen una serie de acciones. Por ejemplo, si se detecta que la luminosidad baja de cierto valor (detectado mediante un sensor de luz), se encienda una lámpara. Para conseguir esto se ha realizado una aplicación centralizada, a modo de servidor, que se comunica con los aparatos eléctricos mediante diferentes protocolos de comunicación, así como con el dispositivo móvil Android, y una aplicación web administrativa, a través de un portal de servicios web.

FleSSR project: Sustainable business models for community cloud infrastructure in the UK higher education sector

Cloud-based infrastructure essentially comprises two offerings, cloud-based compute and cloud-based storage. These are perhaps best typified for most people by the two main components of the Amazon Web Services (AWS)1 public cloud offer, the Elastic Compute Cloud (EC2)2 and the Simple Storage Service (S3)3, though, of course, there are many other related services offered by Amazon and many other providers of similar public cloud infrastructure across the Internet.

RESTful Discovery and Eventing for Service Provisioning in Assisted Living Environments

Service provisioning in assisted living environments faces distinct challenges due to the heterogeneity of networks, access technology, and sensing/actuation devices in such an environment. Existing solutions, such as SOAP-based web services, can interconnect heterogeneous devices and services, and can be published, discovered and invoked dynamically. However, it is considered heavier than what is required in the smart environment-like context and hence suffers from performance degradation. Alternatively, REpresentational State Transfer (REST) has gained much attention from the community and is considered as a lighter and cleaner technology compared to the SOAP-based web services. Since it is simple to publish and use a RESTful web service, more and more service providers are moving toward REST-based solutions, which promote a resource-centric conceptualization as opposed to a service-centric conceptualization. Despite such benefits of REST, the dynamic discovery and eventing of RESTful services are yet considered a major hurdle to utilization of the full potential of REST-based approaches. In this paper, we address this issue, by providing a RESTful discovery and eventing specification and demonstrate it in an assisted living healthcare scenario. We envisage that through this approach, the service provisioning in ambient assisted living or other smart environment settings will be more efficient, timely, and less resource-intensive.

Uma infraestrutura para monitoramento de sistemas cientes do contexto.

Aplicações ubíquas e pervasivas são cientes do contexto dos recursos utilizados no que diz respeito à disponibilidade e qualidade. Esta classe de aplicações pode se beneficiar de mecanismos para descobrir recursos que atendam aos requisitos não-funcionais desejados, e mecanismos para monitorar a qualidade destes recursos. Neste trabalho é proposta uma arquitetura para dois serviços que deveriam ser incluídos na infra-estrutura de suporte a ser utilizada pelas aplicações mencionadas: um Serviço de Contexto, que provê acesso a informações de contexto, e um Serviço de Descoberta, que permite a descoberta dinâmica de recursos, levando em conta restrições de contexto a serem satisfeitas. Estes serviços se apóiam em Agentes de Recursos, que efetivamente monitoram os recursos e sensores. Uma implementação de referência foi desenvolvida, oferecendo os serviços mencionados na forma de Serviços Web e implementando os Agentes de Recursos empregando um padrão de projeto simples. Para avaliar os serviços estes foram utilizados como infra-estrutura para o desenvolvimento de um sistema tolerante a falhas e uma aplicação de assistência domiciliar remota (tele-saúde). O desempenho dos serviços também foi avaliado.

Infra-estrutura para informações espaciais.

Atualmente o Brasil conta com um volume imenso de dados sobre o território nacional. Entretanto, grande parte dos dados existentes encontra-se dispersa, fragmentada, sem compatibilização cartográfica e, em alguns casos, duplicada em vários locais. O grande desafio é compartilhar dados geograficamente dispersos e comunicar conceitos importantes entre departamentos dentro da organização ou entre organizações diferentes usando, para isso, tecnologias de informação. Assim, esse trabalho tem como objetivo geral contribuir para o desenvolvimento de uma infra-estrutura para informação geográfica, que possa ser amplamente disseminada via Internet através de Web Services e que atenda os requisitos de interoperabilidade, de modo que diversos usuários possam usufruir dos dados disponíveis, integrando-os quando necessários. Este trabalho incidirá inicialmente nas necessidades de informação geográfica para o Zoneamento Ecológico e Econômico do Brasil. Entretanto, como se trata de um sistema de infra-estrutura de dados espaciais poderá, então, agregar dados para qualquer trabalho que envolva a informação espacial.

支持WSRP 2.0规范的联邦门户的设计与实现

门户（Portal）是基于组件的web应用，它可以集成Internet环境下各种现有应用系统、数据资源和网络信息资源，并为用户形成个性化的访问页面，实现信息的集成和发布。Portlet是门户中的可重用组件，能够提供对web内容、应用程序和其他资源的访问。JSR168规范（Portlet 1.0）和JSR286规范（Portlet 2.0）提供了Portlet的标准。 随着门户的广泛使用，门户已经成为获取信息，巩固和整合IT基础设施的平台。于是来自于同一公司的、自主的、分散的多个部门都部署了自己的门户，但这些门户之间却无法进行内容共享，即Portlet在门户之间的集成。于是出现了联邦门户（Federated Portals），它是由多个分散的门户构成的网络，这些门户基于共同的标准协同工作。联邦门户实现了在异构门户之间共享远程内容，这些远程内容来自于名为生产者的门户，被收集、组合和运行在名为消费者的门户中。 联邦门户的基本特征是基于规范实现跨门户的系统联合。因此联邦门户的关键在于对门户间互操作标准的制定。这个标准就是OASIS推出的WSRP（Web Services for Remote Portlets）规范。WSRP规范提供了门户间互操作标准，成为联邦门户的基础技术。它有1.0和2.0两个版本，分别产生于2003年和2008年。 为了提高联邦门户应用的构建效率，增强异构门户互操作性的能力，完善联邦门户的用户友好性，需要为OncePortal提供支持WSRP 2.0规范的联邦门户。 本文从WSRP 2.0规范和联邦门户的需求出发，设计并实现了支持WSRP 2.0规范的联邦门户。首先根据WSRP 2.0规范对远程Portlet的语法模型、交互模型和生命周期模型三个方面进行特征分析；其次总结了联邦门户的核心功能、系统边界，并给出了联邦门户的设计；然后从Portlet URL的生成与改写、Portlet统一协作框架、远程Portlet资源服务、WSRP容器和代理容器以及Portlet缓存共5个方面介绍了联邦门户的关键技术；最后基于以上分析和设计，实现了联邦门户扩展应用，并将其应用在中科院软件所自主研发的门户产品OncePortal中。

Identyfikacja domen WG/GW zaangażowanych w wiązanie białek Argonaute oraz analiza mechanizmów molekularnych odpowiedzialnych za ich zmienność

Wydział Biologii: Instytut Biologii Molekularnej i Biotechnologii

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.

Powering the virtual university with standard portal technology

This article describes ongoing research on developing a portal framework based on the OASIS Web Services for Remote Portlets (WSRP) standard for integration of Web-based education contents and services made available through a model for a European Networked University. We first identify the requirements for such a framework that supports integration at the presentation level and collaboration in developing and updating study programmes and course materials. We then outline the architecture design, and report on the initial implementation and preliminary evaluation.

WPS orchestration using the Taverna workbench: The eScience approach

eScience is an umbrella concept which covers internet technologies, such as web service orchestration that involves manipulation and processing of high volumes of data, using simple and efficient methodologies. This concept is normally associated with bioinformatics, but nothing prevents the use of an identical approach for geoinfomatics and OGC (Open Geospatial Consortium) web services like WPS (Web Processing Service). In this paper we present an extended WPS implementation based on the PyWPS framework using an automatically generated WSDL (Web Service Description Language) XML document that replicates the WPS input/output document structure used during an Execute request to a server. Services are accessed using a modified SOAP (Simple Object Access Protocol) interface provided by PyWPS, that uses service and input/outputs identifiers as element names. The WSDL XML document is dynamically generated by applying XSLT (Extensible Stylesheet Language Transformation) to the getCapabilities XML document that is generated by PyWPS. The availability of the SOAP interface and WSDL description allows WPS instances to be accessible to workflow development software like Taverna, enabling users to build complex workflows using web services represented by interconnecting graphics. Taverna will transform the visual representation of the workflow into a SCUFL (Simple Conceptual Unified Flow Language) based XML document that can be run internally or sent to a Taverna orchestration server. SCUFL uses a dataflow-centric orchestration model as opposed to the more commonly used orchestration language BPEL (Business Process Execution Language) which is process-centric.

Operational monitoring and forecasting of bathing water quality through exploiting satellite Earth observation and models: The AlgaRisk demonstration service

Coastal zones and shelf-seas are important for tourism, commercial fishing and aquaculture. As a result the importance of good water quality within these regions to support life is recognised worldwide and a number of international directives for monitoring them now exist. This paper describes the AlgaRisk water quality monitoring demonstration service that was developed and operated for the UK Environment Agency in response to the microbiological monitoring needs within the revised European Union Bathing Waters Directive. The AlgaRisk approach used satellite Earth observation to provide a near-real time monitoring of microbiological water quality and a series of nested operational models (atmospheric and hydrodynamic-ecosystem) provided a forecast capability. For the period of the demonstration service (2008–2013) all monitoring and forecast datasets were processed in near-real time on a daily basis and disseminated through a dedicated web portal, with extracted data automatically emailed to agency staff. Near-real time data processing was achieved using a series of supercomputers and an Open Grid approach. The novel web portal and java-based viewer enabled users to visualise and interrogate current and historical data. The system description, the algorithms employed and example results focussing on a case study of an incidence of the harmful algal bloom Karenia mikimotoi are presented. Recommendations and the potential exploitation of web services for future water quality monitoring services are discussed.