GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources

GlycoSuiteDB is a relational database that curates information from the scientific literature on glyco­protein derived glycan structures, their biological sources, the references in which the glycan was described and the methods used to determine the glycan structure. To date, the database includes most published O-linked oligosaccharides from the last 50 years and most N-linked oligosaccharides that were published in the 1990s. For each structure, information is available concerning the glycan type, linkage and anomeric configuration, mass and composition. Detailed information is also provided on native and recombinant sources, including tissue and/or cell type, cell line, strain and disease state. Where known, the proteins to which the glycan structures are attached are reported, and cross-references to the SWISS-PROT/TrEMBL protein sequence databases are given if applicable. The GlycoSuiteDB annotations include literature references which are linked to PubMed, and detailed information on the methods used to determine each glycan structure are noted to help the user assess the quality of the structural assignment. GlycoSuiteDB has a user-friendly web interface which allows the researcher to query the database using mono­isotopic or average mass, monosaccharide composition, glycosylation linkages (e.g. N- or O-linked), reducing terminal sugar, attached protein, taxonomy, tissue or cell type and GlycoSuiteDB accession number. Advanced queries using combinations of these parameters are also possible. GlycoSuiteDB can be accessed on the web at http://www.glycosuite.com.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier

Towards a Modeling Environment for Earth Systems Simulations

The developments of models in Earth Sciences, e.g. for earthquake prediction and for the simulation of mantel convection, are fare from being finalized. Therefore there is a need for a modelling environment that allows scientist to implement and test new models in an easy but flexible way. After been verified, the models should be easy to apply within its scope, typically by setting input parameters through a GUI or web services. It should be possible to link certain parameters to external data sources, such as databases and other simulation codes. Moreover, as typically large-scale meshes have to be used to achieve appropriate resolutions, the computational efficiency of the underlying numerical methods is important. Conceptional this leads to a software system with three major layers: the application layer, the mathematical layer, and the numerical algorithm layer. The latter is implemented as a C/C++ library to solve a basic, computational intensive linear problem, such as a linear partial differential equation. The mathematical layer allows the model developer to define his model and to implement high level solution algorithms (e.g. Newton-Raphson scheme, Crank-Nicholson scheme) or choose these algorithms form an algorithm library. The kernels of the model are generic, typically linear, solvers provided through the numerical algorithm layer. Finally, to provide an easy-to-use application environment, a web interface is (semi-automatically) built to edit the XML input file for the modelling code. In the talk, we will discuss the advantages and disadvantages of this concept in more details. We will also present the modelling environment escript which is a prototype implementation toward such a software system in Python (see www.python.org). Key components of escript are the Data class and the PDE class. Objects of the Data class allow generating, holding, accessing, and manipulating data, in such a way that the actual, in the particular context best, representation is transparent to the user. They are also the key to establish connections with external data sources. PDE class objects are describing (linear) partial differential equation objects to be solved by a numerical library. The current implementation of escript has been linked to the finite element code Finley to solve general linear partial differential equations. We will give a few simple examples which will illustrate the usage escript. Moreover, we show the usage of escript together with Finley for the modelling of interacting fault systems and for the simulation of mantel convection.

Internet banking service quality:an investigation of interrelationships between construct dimensions

Service quality measurement in Internet banking services is an area of growing interest to researchers and managers. This research investigates the interrelationships between the dimensions comprising the Internet banking service quality construct through structural equation modelling. Five Internet service quality dimensions are identified: access, web interface, trust, attention and credibility. Credibility is modelled as an outcome of the causal variables of access, web interface, trust and attention. Trust and attention emerges as key dimensions in explaining the credibility dimension. Access is found to be a common antecedent of trust, attention and Web interface dimensions. Implications from the findings are offered.

Issues in creating a corpus for EAP pedagogy and research

UK universities are accepting increasing numbers of students whose L1 is not English on a wide range of programmes at all levels. These students require additional support and training in English, focussing on their academic disciplines. Corpora have been used in EAP since the 1980s, mainly for research, but a growing number of researchers and practitioners have been advocating the use of corpora in EAP pedagogy, and such use is gradually increasing. This paper outlines the processes and factors to be considered in the design and compilation of an EAP corpus (e.g., the selection and acquisition of texts, metadata, data annotation, software tools and outputs, web interface, and screen displays), especially one intended to be used for teaching. Such a corpus would also facilitate EAP research in terms of longitudinal studies, student progression and development, and course and materials design. The paper has been informed by the preparatory work on the EAP subcorpus of the ACORN corpus project at Aston University. © 2007 Elsevier Ltd. All rights reserved.

webComputing Service Framework

Presented is webComputing – a general framework of mathematically oriented services including remote access to hardware and software resources for mathematical computations, and web interface to dynamic interactive computations and visualization in a diversity of contexts: mathematical research and engineering, computer-aided mathematical/technical education and distance learning. webComputing builds on the innovative webMathematica technology connecting technical computing system Mathematica to a web server and providing tools for building dynamic and interactive web-interface to Mathematica-based functionality. Discussed are the conception and some of the major components of webComputing service: Scientific Visualization, Domain- Specific Computations, Interactive Education, and Authoring of Interactive Pages.

Serious Game no tratamento de obesidade infantil: uma proposta de interação natural com monitoramento remoto

The number of overweight people has increased in the last few years. Factors such as attention to diet and changes in lifestyle are crucial in the prevention and control of obesity and diseases related to it. Experts believe that such actions are most effective when initiated during childhood, and that children raised in an environment that encourages physical activity ultimately become healthier adults. However, to arouse and maintain interest in such activities represent a major challenge, which are initially perceived as repetitive and boring, and, thus, soon abandoned. Computer games, traditionally seen as stimulants to a sedentary lifestyle are changing this perception using non-conventional controls that require constant movement of the player. Applications that combine the playfulness of such games to physical activity through devices, like Microsoft Kinect, might become interesting tools in this scenario, by using the familiarity of Natural User Interfaces along with the challenge and the fun of video games, in order to make attractive exercise routines for schoolchildren. The project carried out consists of an exergame composed of several activities designed and implemented with the participation of a Physical Educator, aimed at children between eight and ten years old, whose performance and progress can be remotely monitored by a professional via web interface. The application arising from this work was accompanied by tests with a group of graduating Physical Education students from the University of Rio Verde GO, and subsequently validated through questionnaires whose results are shown on this work.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

Développement et applications d’un outil bio-informatique pour la détection de similarités de champs d’interaction moléculaire

Résumé : Les méthodes de détection de similarités de sites de liaison servent entre autres à la prédiction de fonction et à la prédiction de cibles croisées. Ces méthodes peuvent aider à prévenir les effets secondaires, suggérer le repositionnement de médicament existants, identifier des cibles polypharmacologiques et des remplacements bio-isostériques. La plupart des méthodes utilisent des représentations basées sur les atomes, même si les champs d’interaction moléculaire (MIFs) représentent plus directement ce qui cherche à être identifié. Nous avons développé une méthode bio-informatique, IsoMif, qui détecte les similarités de MIF entre différents sites de liaisons et qui ne nécessite aucun alignement de séquence ou de structure. Sa performance a été comparée à d’autres méthodes avec des bancs d’essais, ce qui n’a jamais été fait pour une méthode basée sur les MIFs. IsoMif performe mieux en moyenne et est plus robuste. Nous avons noté des limites intrinsèques à la méthodologie et d’autres qui proviennent de la nature. L’impact de choix de conception sur la performance est discuté. Nous avons développé une interface en ligne qui permet la détection de similarités entre une protéine et différents ensembles de MIFs précalculés ou à des MIFs choisis par l’utilisateur. Des sessions PyMOL peuvent être téléchargées afin de visualiser les similarités identifiées pour différentes interactions intermoléculaires. Nous avons appliqué IsoMif pour identifier des cibles croisées potentielles de drogues lors d’une analyse à large échelle (5,6 millions de comparaisons). Des simulations d’arrimage moléculaire ont également été effectuées pour les prédictions significatives. L’objectif est de générer des hypothèses de repositionnement et de mécanismes d’effets secondaires observés. Plusieurs exemples sont présentés à cet égard.

EasyInterface: a toolkit for the rapid development of GUIs for research prototype tools

During the lifetime of a research project, different partners develop several research prototype tools that share many common aspects. This is equally true for researchers as individuals and as groups: during a period of time they often develop several related tools to pursue a specific research line. Making research prototype tools easily accessible to the community is of utmost importance to promote the corresponding research, get feedback, and increase the tools’ lifetime beyond the duration of a specific project. One way to achieve this is to build graphical user interfaces (GUIs) that facilitate trying tools; in particular, with web-interfaces one avoids the overhead of downloading and installing the tools. Building GUIs from scratch is a tedious task, in particular for web-interfaces, and thus it typically gets low priority when developing a research prototype. Often we opt for copying the GUI of one tool and modifying it to fit the needs of a new related tool. Apart from code duplication, these tools will “live” separately, even though we might benefit from having them all in a common environment since they are related. This work aims at simplifying the process of building GUIs for research prototypes tools. In particular, we present EasyInterface, a toolkit that is based on novel methodology that provides an easy way to make research prototype tools available via common different environments such as a web-interface, within Eclipse, etc. It includes a novel text-based output language that allows to present results graphically without requiring any knowledge in GUI/Web programming. For example, an output of a tool could be (a structured version of) “highlight line number 10 of file ex.c” and “when the user clicks on line 10, open a dialog box with the text ...”. The environment will interpret this output and converts it to corresponding visual e_ects. The advantage of using this approach is that it will be interpreted equally by all environments of EasyInterface, e.g., the web-interface, the Eclipse plugin, etc. EasyInterface has been developed in the context of the Envisage [5] project, and has been evaluated on tools developed in this project, which include static analyzers, test-case generators, compilers, simulators, etc. EasyInterface is open source and available at GitHub2.

User interface design for social web theme and opinion analysis

The Social Web is a torrent of real-time information and an emerging discipline is now focussed on harnessing this information flow for analysis of themes, opinions and sentiment. This short paper reports on early work on designing better user interfaces for end users in manipulating the outcomes from these analysis engines.

Cross-cultural web user interface design for Indigenous internet users

This project investigated 1) Australian web designers’ cultural perceptions towards Australian Indigenous users and 2) Australian Indigenous cultural features in terms of user interface design. In doing so, it reviews the literature of cross-cultural user interface design by focusing on feasible models and arguments to articulate and integrate Australian Indigenous Internet users’ cultural needs of web user interface. The online survey results collected from 101 Indigenous users and 126 Web designers showed a distinctive difference between them on the integration of Indigenous users' cultural in Web sites. The interview data collected from 14 Indigenous users and 14 web designers suggested practical approaches to the design implications of Indigenous culture.

A Novel Multimodal Interface for Improving Visually Impaired People's Web Accessibility

This paper introduces a novel interface designed to help blind and visually impaired people to explore and navigate on the Web. In contrast to traditionally used assistive tools, such as screen readers and magnifiers, the new interface employs a combination of both audio and haptic features to provide spatial and navigational information to users. The haptic features are presented via a low-cost force feedback mouse allowing blind people to interact with the Web, in a similar fashion to their sighted counterparts. The audio provides navigational and textual information through the use of non-speech sounds and synthesised speech. Interacting with the multimodal interface offers a novel experience to target users, especially to those with total blindness. A series of experiments have been conducted to ascertain the usability of the interface and compare its performance to that of a traditional screen reader. Results have shown the advantages that the new multimodal interface offers blind and visually impaired people. This includes the enhanced perception of the spatial layout of Web pages, and navigation towards elements on a page. Certain issues regarding the design of the haptic and audio features raised in the evaluation are discussed and presented in terms of recommendations for future work.

An Evidential Approach to Query Interface Matching on the Deep Web

Matching query interfaces is a crucial step in data integration across multiple Web databases. The problem is closely related to schema matching that typically exploits different features of schemas. Relying on a particular feature of schemas is not suffcient. We propose an evidential approach to combining multiple matchers using Dempster-Shafer theory of evidence. First, our approach views the match results of an individual matcher as a source of evidence that provides a level of confidence on the validity of each candidate attribute correspondence. Second, it combines multiple sources of evidence to get a combined mass function that represents the overall level of confidence, taking into account the match results of different matchers. Our combination mechanism does not require use of weighing parameters, hence no setting and tuning of them is needed. Third, it selects the top k attribute correspondences of each source attribute from the target schema based on the combined mass function. Finally it uses some heuristics to resolve any conflicts between the attribute correspondences of different source attributes. Our experimental results show that our approach is highly accurate and effective.