Online Workbench Research Articles

DEXTER: A workbench for automatic term extraction with specialized corpora

AbstractAutomatic term extraction has become a priority area of research within corpus processing. Despite the extensive literature in this field, there are still some outstanding issues that should be dealt with during the construction of term extractors, particularly those oriented to support research in terminology and terminography. In this regard, this article describes the design and development of DEXTER, an online workbench for the extraction of simple and complex terms from domain-specific corpora in English, French, Italian and Spanish. In this framework, three issues contribute to placing the most important terms in the foreground. First, unlike the elaborate morphosyntactic patterns proposed by most previous research, shallow lexical filters have been constructed to discard term candidates. Second, a large number of common stopwords are automatically detected by means of a method that relies on the IATE database together with the frequency distribution of the domain-specific corpus and a general corpus. Third, the term-ranking metric, which is grounded on the notions of salience, relevance and cohesion, is guided by the IATE database to display an adequate distribution of terms.

Bridging the gap within text-data analytics: a computer environment for data analysis in linguistic research

Since computer technology became widespread available at universities during the last quarter of the twentieth century, language researchers have been successfully employing software to analyse usage patterns in corpora. However, although there has been a proliferation of software for different disciplines within text-data analytics, e.g. corpus linguistics, statistics, natural language processing and text mining, this article demonstrates that any computer environment intended to support advanced linguistic research more effectively should be grounded on a user-centred approach to holistically integrate cross-disciplinary methods and techniques in a linguist-friendly manner. To this end, I examine not only the tasks that are derived from linguists' needs and goals but also the technologies that appropriately deal with the properties of linguistic data. This research results in the implementation of DAMIEN, an online workbench designed to conduct linguistic experiments on corpora.

A Protocol for Computer-Based Protein Structure and Function Prediction

Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function to improve the understanding of their biological role. Although experimental methods can provide detailed information for a small fraction of these proteins, computational modeling is needed for the majority of protein molecules which are experimentally uncharacterized. The I-TASSER server is an on-line workbench for high-resolution modeling of protein structure and function. Given a protein sequence, a typical output from the I-TASSER server includes secondary structure prediction, predicted solvent accessibility of each residue, homologous template proteins detected by threading and structure alignments, up to five full-length tertiary structural models, and structure-based functional annotations for enzyme classification, Gene Ontology terms and protein-ligand binding sites. All the predictions are tagged with a confidence score which tells how accurate the predictions are without knowing the experimental data. To facilitate the special requests of end users, the server provides channels to accept user-specified inter-residue distance and contact maps to interactively change the I-TASSER modeling; it also allows users to specify any proteins as template, or to exclude any template proteins during the structure assembly simulations. The structural information could be collected by the users based on experimental evidences or biological insights with the purpose of improving the quality of I-TASSER predictions. The server was evaluated as the best programs for protein structure and function predictions in the recent community-wide CASP experiments. There are currently >20,000 registered scientists from over 100 countries who are using the on-line I-TASSER server.

A protocol for computer-based protein structure and function prediction.

Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function to improve the understanding of their biological role. Although experimental methods can provide detailed information for a small fraction of these proteins, computational modeling is needed for the majority of protein molecules which are experimentally uncharacterized. The I-TASSER server is an on-line workbench for high-resolution modeling of protein structure and function. Given a protein sequence, a typical output from the I-TASSER server includes secondary structure prediction, predicted solvent accessibility of each residue, homologous template proteins detected by threading and structure alignments, up to five full-length tertiary structural models, and structure-based functional annotations for enzyme classification, Gene Ontology terms and protein-ligand binding sites. All the predictions are tagged with a confidence score which tells how accurate the predictions are without knowing the experimental data. To facilitate the special requests of end users, the server provides channels to accept user-specified inter-residue distance and contact maps to interactively change the I-TASSER modeling; it also allows users to specify any proteins as template, or to exclude any template proteins during the structure assembly simulations. The structural information could be collected by the users based on experimental evidences or biological insights with the purpose of improving the quality of I-TASSER predictions. The server was evaluated as the best programs for protein structure and function predictions in the recent community-wide CASP experiments. There are currently >20,000 registered scientists from over 100 countries who are using the on-line I-TASSER server.

On Objectives of Instructional Laboratories, Individual Assessment, and Use of Collaborative Remote Laboratories

Three key issues should be addressed to enable universities to deliver engineers who have a solid documented laboratory experience enabling them to design goods and services complying with the requirements of a sustainable society. First, introduce learning objectives of engineering instructional laboratories in courses including laboratory components. Second, implement individual student assessment. Third, introduce free access to online experimental resources as a supplement to the equipment in traditional laboratories. Blekinge Institute of Technology (BTH) in Sweden and the University of South Australia (UniSA) have created online laboratory workbenches for electrical experiments that mimic traditional ones by combining virtual and physical reality. Online workbenches not only supplement traditional ones, but they can also be used for low-cost individual assessment. BTH has started a project disseminating the BTH workbench concept, The Virtual Instrument Systems in Reality (VISIR) Open Laboratory Platform, and invites other universities to set up replicas and participate in further development and standardization. Further, online workbenches offer additional learning possibilities. UniSA has started a project where students located in different countries can perform experiments together as a way to enhance the participants' intercultural competence. This paper discusses online laboratory workbenches and their role in an engineering education appropriate for a sustainable society.