Design theory for innovation of classroom-based information systems

This research used design science research methods to develop, instantiate, implement, and measure the acceptance of a novel software artefact. The primary purpose of this software artefact was to enhance data collection, improve its quality and enable its capture in classroom environments without distracting from the teaching activity. The artefact set is an iOS app, with supporting web services and technologies designed in response to teacher and pastoral care needs. System analysis and design used Enterprise Architecture methods. The novel component of the iOS app implemented proximity detection to identify the student through their iPad and automatically link to that student's data. The use of this novel software artefact and web services was trialled in a school setting, measuring user acceptance and system utility. This integrated system was shown to improve the accuracy, consistency, completeness and timeliness of captured data and the utility of the input and reporting systems.

Using conceptual tool for intuitive interaction to design intuitive website for SME in India : A case study

Statistical reports of SMEs Internet usage from various countries indicate a steady growth. However, deeper investigation of SME’s e-commerce adoption and usage reveals that a number of SMEs fail to realize the full potential of e-commerce. Factors such as lack of tools and models in Information Systems and Information Technology for SMEs, and lack of technical expertise and specialized knowledge within and outside the SME have the most effect. This study aims to address the two important factors in two steps. First, introduce the conceptual tool for intuitive interaction. Second, explain the implementation process of the conceptual tool with the help of a case study. The subject chosen for the case study is a real estate SME from India. The design and development process of the website for the real estate SME was captured in this case study and the duration of the study was four months. Results indicated specific benefits for web designers and SME business owners. Results also indicated that the conceptual tool is easy to use without the need for technical expertise and specialized knowledge.

Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

Service Composition on a Mobile Phone

With the recent increase in interest in service-oriented architectures (SOA) and Web services, developing applications with the Web services paradigm has become feasible. Web services are self-describing, platform-independent computational elements. New applications can be assembled from a set of previously created Web services, which are composed together to make a service that uses its components to perform a certain task. This is the idea of service composition. To bring service composition to a mobile phone, I have created Interactive Service Composer for mobile phones. With Interactive Service Composer, the user is able to build service compositions on his mobile phone, consisting of Web services or services that are available from the mobile phone itself. The service compositions are reusable and can be saved in the phone's memory. Previously saved compositions can also be used in new compositions. While developing applications for mobile phones has been possible for some time, the usability of the solutions is not the same as when developing for desktop computers. When developing for mobile phones, the developer has to more carefully consider the decisions he is going to make with the program he is developing. With the lack of processing power and memory, the applications cannot function as well as on desktop PCs. On the other hand, this does not remove the appeal of developing applications for mobile devices.

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.

Executing SADI services in Galaxy

Background: In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. Results: SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. Conclusions: SADI-Galaxy bridges the gap between Galaxy, an easy to use but "static" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

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

Library Technology Services at Boston University: an un-roadmap

A working paper for discussion

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.