Methodologies for the Automatic Location of Academic and Educational Texts on the Internet

Traditionally online databases of web resources have been compiled by a human editor, or though the submissions of authors or interested parties. Considerable resources are needed to maintain a constant level of input and relevance in the face of increasing material quantity and quality, and much of what is in databases is of an ephemeral nature. These pressures dictate that many databases stagnate after an initial period of enthusiastic data entry. The solution to this problem would seem to be the automatic harvesting of resources, however, this process necessitates the automatic classification of resources as ‘appropriate’ to a given database, a problem only solved by complex text content analysis. This paper outlines the component methodologies necessary to construct such an automated harvesting system, including a number of novel approaches. In particular this paper looks at the specific problems of automatically identifying academic research work and Higher Education pedagogic materials. Where appropriate, experimental data is presented from searches in the field of Geography as well as the Earth and Environmental Sciences. In addition, appropriate software is reviewed where it exists, and future directions are outlined

Methodologies for the Automatic Location of Academic and Educational Texts on the Internet

Traditionally online databases of web resources have been compiled by a human editor, or though the submissions of authors or interested parties. Considerable resources are needed to maintain a constant level of input and relevance in the face of increasing material quantity and quality, and much of what is in databases is of an ephemeral nature. These pressures dictate that many databases stagnate after an initial period of enthusiastic data entry. The solution to this problem would seem to be the automatic harvesting of resources, however, this process necessitates the automatic classification of resources as ‘appropriate’ to a given database, a problem only solved by complex text content analysis. This paper outlines the component methodologies necessary to construct such an automated harvesting system, including a number of novel approaches. In particular this paper looks at the specific problems of automatically identifying academic research work and Higher Education pedagogic materials. Where appropriate, experimental data is presented from searches in the field of Geography as well as the Earth and Environmental Sciences. In addition, appropriate software is reviewed where it exists, and future directions are outlined

The benefits of in silico modeling to identify possible small-molecule drugs and their off-target interactions

Accepted for publication in a future issue of Future Medicinal Chemistry.The research into the use of small molecules as drugs continues to be a key driver in the development of molecular databases, computer-aided drug design software and collaborative platforms. The evolution of computational approaches is driven by the essential criteria that a drug molecule has to fulfill, from the affinity to targets to minimal side effects while having adequate absorption, distribution, metabolism, and excretion (ADME) properties. A combination of ligand- and structure-based drug development approaches is already used to obtain consensus predictions of small molecule activities and their off-target interactions. Further integration of these methods into easy-to-use workflows informed by systems biology could realize the full potential of available data in the drug discovery and reduce the attrition of drug candidates.Peer reviewe

MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest

Proceedings of the International Workshop on EuroPLOT Persuasive Technology for Learning, Education and Teaching (IWEPLET 2013)

"This book contains the proceedings of the International Workshop on EuroPLOT Persuasive Technology for Learning, Education and Teaching (IWEPLET) 2013 which was held on 16.-17.September 2013 in Paphos (Cyprus) in conjunction with the EC-TEL conference. The workshop and hence the proceedings are divided in two parts: on Day 1 the EuroPLOT project and its results are introduced, with papers about the specific case studies and their evaluation. On Day 2, peer-reviewed papers are presented which address specific topics and issues going beyond the EuroPLOT scope. This workshop is one of the deliverables (D 2.6) of the EuroPLOT project, which has been funded from November 2010 – October 2013 by the Education, Audiovisual and Culture Executive Agency (EACEA) of the European Commission through the Lifelong Learning Programme (LLL) by grant #511633. The purpose of this project was to develop and evaluate Persuasive Learning Objects and Technologies (PLOTS), based on ideas of BJ Fogg. The purpose of this workshop is to summarize the findings obtained during this project and disseminate them to an interested audience. Furthermore, it shall foster discussions about the future of persuasive technology and design in the context of learning, education and teaching. The international community working in this area of research is relatively small. Nevertheless, we have received a number of high-quality submissions which went through a peer-review process before being selected for presentation and publication. We hope that the information found in this book is useful to the reader and that more interest in this novel approach of persuasive design for teaching/education/learning is stimulated. We are very grateful to the organisers of EC-TEL 2013 for allowing to host IWEPLET 2013 within their organisational facilities which helped us a lot in preparing this event. I am also very grateful to everyone in the EuroPLOT team for collaborating so effectively in these three years towards creating excellent outputs, and for being such a nice group with a very positive spirit also beyond work. And finally I would like to thank the EACEA for providing the financial resources for the EuroPLOT project and for being very helpful when needed. This funding made it possible to organise the IWEPLET workshop without charging a fee from the participants.