NTDB: Thermodynamic Database for Nucleic Acids

A new thermodynamic database for normal and modified nucleic acids has been developed. This Thermodynamic Database for Nucleic Acids (NTDB) includes sequence, structure and thermodynamic information as well as experimental methods and conditions. In this release, there are 1851 sequences containing both normal and modified nucleic acids. A user-friendly web-based interface has been developed to allow data searching under different conditions. Useful thermodynamic tools for the study of nucleic acids have been collected and linked for easy usage. NTDB is available at http://ntdb.chem.cuhk.edu.hk.

The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information

The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains 795 full-length homeodomain-containing sequences, 32 experimentally-derived structures and 143 homeo­box loci implicated in human genetic disorders. Entries are fully hyperlinked to facilitate easy retrieval of the original records from source databases. A simple search engine with a graphical user interface is provided to query the component databases and assemble customized data sets. A new feature for this release is the addition of DNA recognition sites for all human homeodomain proteins described in the literature. The Homeodomain Resource is freely available through the World Wide Web at http://genome.nhgri.nih.gov/homeodomain.

An authoring tool for decision support systems in context questions of ecological knowledge

Decision support systems (DSS) support business or organizational decision-making activities, which require the access to information that is internally stored in databases or data warehouses, and externally in the Web accessed by Information Retrieval (IR) or Question Answering (QA) systems. Graphical interfaces to query these sources of information ease to constrain dynamically query formulation based on user selections, but they present a lack of flexibility in query formulation, since the expressivity power is reduced to the user interface design. Natural language interfaces (NLI) are expected as the optimal solution. However, especially for non-expert users, a real natural communication is the most difficult to realize effectively. In this paper, we propose an NLI that improves the interaction between the user and the DSS by means of referencing previous questions or their answers (i.e. anaphora such as the pronoun reference in “What traits are affected by them?”), or by eliding parts of the question (i.e. ellipsis such as “And to glume colour?” after the question “Tell me the QTLs related to awn colour in wheat”). Moreover, in order to overcome one of the main problems of NLIs about the difficulty to adapt an NLI to a new domain, our proposal is based on ontologies that are obtained semi-automatically from a framework that allows the integration of internal and external, structured and unstructured information. Therefore, our proposal can interface with databases, data warehouses, QA and IR systems. Because of the high NL ambiguity of the resolution process, our proposal is presented as an authoring tool that helps the user to query efficiently in natural language. Finally, our proposal is tested on a DSS case scenario about Biotechnology and Agriculture, whose knowledge base is the CEREALAB database as internal structured data, and the Web (e.g. PubMed) as external unstructured information.

How to use WinEdt 5 as an interface for TDA

The text editor WinEdt 5 may be easily configured to provide a user interface for TDA. The configuration described below allows you to launch TDA command files directly from within WinEdt (via menu or shortcut). TDA's standard output will be written to disk and displayed in WinEdt automatically. Furthermore, you may also just execute selected parts of a command file.

Discovering user access pattern based on probabilistic latent factor model

There has been an increased demand for characterizing user access patterns using web mining techniques since the informative knowledge extracted from web server log files can not only offer benefits for web site structure improvement but also for better understanding of user navigational behavior. In this paper, we present a web usage mining method, which utilize web user usage and page linkage information to capture user access pattern based on Probabilistic Latent Semantic Analysis (PLSA) model. A specific probabilistic model analysis algorithm, EM algorithm, is applied to the integrated usage data to infer the latent semantic factors as well as generate user session clusters for revealing user access patterns. Experiments have been conducted on real world data set to validate the effectiveness of the proposed approach. The results have shown that the presented method is capable of characterizing the latent semantic factors and generating user profile in terms of weighted page vectors, which may reflect the common access interest exhibited by users among same session cluster.

A web recommendation technique based on probabilistic latent semantic analysis

Web transaction data between Web visitors and Web functionalities usually convey user task-oriented behavior pattern. Mining such type of click-stream data will lead to capture usage pattern information. Nowadays Web usage mining technique has become one of most widely used methods for Web recommendation, which customizes Web content to user-preferred style. Traditional techniques of Web usage mining, such as Web user session or Web page clustering, association rule and frequent navigational path mining can only discover usage pattern explicitly. They, however, cannot reveal the underlying navigational activities and identify the latent relationships that are associated with the patterns among Web users as well as Web pages. In this work, we propose a Web recommendation framework incorporating Web usage mining technique based on Probabilistic Latent Semantic Analysis (PLSA) model. The main advantages of this method are, not only to discover usage-based access pattern, but also to reveal the underlying latent factor as well. With the discovered user access pattern, we then present user more interested content via collaborative recommendation. To validate the effectiveness of proposed approach, we conduct experiments on real world datasets and make comparisons with some existing traditional techniques. The preliminary experimental results demonstrate the usability of the proposed approach.

Efficient Data Management with Applications to IoT

The Internet of Things (IoT) consists of a worldwide “network of networks,” composed by billions of interconnected heterogeneous devices denoted as things or “Smart Objects” (SOs). Significant research efforts have been dedicated to port the experience gained in the design of the Internet to the IoT, with the goal of maximizing interoperability, using the Internet Protocol (IP) and designing specific protocols like the Constrained Application Protocol (CoAP), which have been widely accepted as drivers for the effective evolution of the IoT. This first wave of standardization can be considered successfully concluded and we can assume that communication with and between SOs is no longer an issue. At this time, to favor the widespread adoption of the IoT, it is crucial to provide mechanisms that facilitate IoT data management and the development of services enabling a real interaction with things. Several reference IoT scenarios have real-time or predictable latency requirements, dealing with billions of device collecting and sending an enormous quantity of data. These features create a new need for architectures specifically designed to handle this scenario, hear denoted as “Big Stream”. In this thesis a new Big Stream Listener-based Graph architecture is proposed. Another important step, is to build more applications around the Web model, bringing about the Web of Things (WoT). As several IoT testbeds have been focused on evaluating lower-layer communication aspects, this thesis proposes a new WoT Testbed aiming at allowing developers to work with a high level of abstraction, without worrying about low-level details. Finally, an innovative SOs-driven User Interface (UI) generation paradigm for mobile applications in heterogeneous IoT networks is proposed, to simplify interactions between users and things.

Design and implementation of graphical user interfaces for complex simulations

The development of increasingly powerful computers, which has enabled the use of windowing software, has also opened the way for the computer study, via simulation, of very complex physical systems. In this study, the main issues related to the implementation of interactive simulations of complex systems are identified and discussed. Most existing simulators are closed in the sense that there is no access to the source code and, even if it were available, adaptation to interaction with other systems would require extensive code re-writing. This work aims to increase the flexibility of such software by developing a set of object-oriented simulation classes, which can be extended, by subclassing, at any level, i.e., at the problem domain, presentation or interaction levels. A strategy, which involves the use of an object-oriented framework, concurrent execution of several simulation modules, use of a networked windowing system and the re-use of existing software written in procedural languages, is proposed. A prototype tool which combines these techniques has been implemented and is presented. It allows the on-line definition of the configuration of the physical system and generates the appropriate graphical user interface. Simulation routines have been developed for the chemical recovery cycle of a paper pulp mill. The application, by creation of new classes, of the prototype to the interactive simulation of this physical system is described. Besides providing visual feedback, the resulting graphical user interface greatly simplifies the interaction with this set of simulation modules. This study shows that considerable benefits can be obtained by application of computer science concepts to the engineering domain, by helping domain experts to tailor interactive tools to suit their needs.

Europeana Creative. EDM Endpoint. Custom Views

The paper discusses the Europeana Creative project which aims to facilitate re-use of cultural heritage metadata and content by the creative industries. The paper focuses on the contribution of Ontotext to the project activities. The Europeana Data Model (EDM) is further discussed as a new proposal for structuring the data that Europeana will ingest, manage and publish. The advantages of using EDM instead of the current ESE metadata set are highlighted. Finally, Ontotext’s EDM Endpoint is presented, based on OWLIM semantic repository and SPARQL query language. A user-friendly RDF view is presented in order to illustrate the possibilities of Forest - an extensible modular user interface framework for creating linked data and semantic web applications.

LAPMv2 - software for underwater large-area photo-mosaicking

LAPMv2 is a research software solution specifically developed to allow marine scientists to produce geo-referenced visual maps of the seafloor, known as mosaics, from a set of underwater images and navigation data. LAPMv2 has a graphical user interface that guides the user through the different steps of the mosaicking workflow. LAPMv2 runs on 64-bit Windows, MacOS X and Linux operating systems. There are two versions for each operating system: (1) the WEB-installers (lightweight but require an internet connection during the installation) and (2) the MCR installers (large files but can be installed on computer without internet-connection). The user manual explains how to install and start the program on the different operating systems. Go to http://www.lapm.eu.com for further information about the latest versions of LAPMv2.

Design de interfaces dinâmicos em sistemas de gestão de conteúdos

Relatório de Estágio para a obtenção do grau de Mestre na área de Educação e Comunicação Multimédia

El consumo tradicional de los nuevos medios. Análisis de la usabilidad de las publicaciones autóctonas para tableta en el contexto universitario español y brasileño

Esta investigación aborda el consumo que los jóvenes universitarios de España y Brasil realizan de las publicaciones para tabletas. A través del estudio de seis casos –las revistas españolas Don, VisàVis y Quality Sport, y los vespertinos brasileños O Globo a Mais, de Río de Janeiro; Estadão Noite, de Sao Paulo; y Diário do Nordeste Plus, de Fortaleza– se aplica una metodología cualitativa, el test de usabilidad, para detectar qué aspectos ralentizan y entorpecen la navegación en las nuevas generaciones de usuarios de medios móviles. A pesar de la influencia de las revistas impresas en la configuración de las publicaciones para tableta, los datos muestran que el usuario necesita “entrenarse” para conocer unas opciones de interacción a veces poco intuitivas o para las que carece de la madurez visual necesaria. Por ello las publicaciones más sencillas obtienen los mejores resultados de usabilidad.

A Stationless Bikeshare Proof of Concept for College Campuses

Bikeshares promote healthy lifestyles and sustainability among commuters, casual riders, and tourists. However, the central pillar of modern systems, the bike station, cannot be easily integrated into a compact college campus. Fixed stations lack the flexibility to meet the needs of college students who make quick, short-distance trips. Additionally, the necessary cost of implementing and maintaining each station prohibits increasing the number of stations for user convenience. Therefore, the team developed a stationless bikeshare based on a smartlock permanently attached to bicycles in the system. The smartlock system design incorporates several innovative approaches to provide usability, security, and reliability that overcome the limitations of a station centered design. A focus group discussion allowed the team to receive feedback on the early lock, system, and website designs, identify improvements and craft a pleasant user experience. The team designed a unique, two-step lock system that is intuitive to operate while mitigating user error. To ensure security, user access is limited through near field ii communications (NFC) technology connected to a mechatronic release system. The said system relied on a NFC module and a servo working through an Arduino microcontroller coded in the Arduino IDE. To track rentals and maintain the system, each bike is fitted with an XBee module to communicate with a scalable ZigBee mesh network. The network allows for bidirectional, real-time communication with a Meteor.js web application, which enables user and administrator functions through an intuitive user interface available on mobile and desktop. The development of an independent smartlock to replace bike stations is essential to meet the needs of the modern college student. With the goal of creating a bikeshare that better serves college students, Team BIKES has laid the framework for a system that is affordable, easily adaptable, and implementable on any university expressing an interest in bringing a bikeshare to its campus.

Online MBPeT dashboard : enabling performance testing as a service in the cloud

In this thesis, tool support is addressed for the combined disciplines of Model-based testing and performance testing. Model-based testing (MBT) utilizes abstract behavioral models to automate test generation, thus decreasing time and cost of test creation. MBT is a functional testing technique, thereby focusing on output, behavior, and functionality. Performance testing, however, is non-functional and is concerned with responsiveness and stability under various load conditions. MBPeT (Model-Based Performance evaluation Tool) is one such tool which utilizes probabilistic models, representing dynamic real-world user behavior patterns, to generate synthetic workload against a System Under Test and in turn carry out performance analysis based on key performance indicators (KPI). Developed at Åbo Akademi University, the MBPeT tool is currently comprised of a downloadable command-line based tool as well as a graphical user interface. The goal of this thesis project is two-fold: 1) to extend the existing MBPeT tool by deploying it as a web-based application, thereby removing the requirement of local installation, and 2) to design a user interface for this web application which will add new user interaction paradigms to the existing feature set of the tool. All phases of the MBPeT process will be realized via this single web deployment location including probabilistic model creation, test configurations, test session execution against a SUT with real-time monitoring of user configurable metric, and final test report generation and display. This web application (MBPeT Dashboard) is implemented with the Java programming language on top of the Vaadin framework for rich internet application development. The Vaadin framework handles the complicated web communications processes and front-end technologies, freeing developers to implement the business logic as well as the user interface in pure Java. A number of experiments are run in a case study environment to validate the functionality of the newly developed Dashboard application as well as the scalability of the solution implemented in handling multiple concurrent users. The results support a successful solution with regards to the functional and performance criteria defined, while improvements and optimizations are suggested to increase both of these factors.

Design de interfaces dinâmicos em sistemas de gestão de conteúdos

Relatório de Estágio para a obtenção do grau de Mestre na área de Educação e Comunicação Multimédia