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This is the peer reviewed version of the following article: Computer Methods and Programs in Biomedine 138 (2016): 73-81, which has been published in final form at http://dx.doi.org/10.1016/j.cmpb.2016.10.008 ; Background and objective To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines. Methods We have selected well-established software to construct a suite of automated and parallelized workflows to analyse NGS data for DNA-seq (single-nucleotide variants (SNVs) and indels), CNA-seq, bisulfite-seq and ChIP-seq experiments. Results Here, we present RUbioSeq+, an updated and extended version of RUbioSeq, a multiplatform application that incorporates a suite of automated and parallelized workflows to analyse NGS data. This new version includes: (i) an interactive graphical user interface (GUI) that facilitates its use by both biomedical researchers and bioinformaticians, (ii) a new pipeline for ChIP-seq experiments, (iii) pair-wise comparisons (case–control analyses) for DNA-seq experiments, (iv) and improvements in the parallelized and multithreaded execution options. Results generated by our software have been experimentally validated and accepted for publication. Conclusions RUbioSeq+ is free and open to all users at http://rubioseq.bioinfo.cnio.es/. ; M.R-C is funded by the BLUEPRINT Consortium (FP7/ 2007-2013) under grant agreement number 282510. J.M.F is funded by the INB Node 2 - CNIO, a member of Proteored - PRB2-ISCIII and is supported by grant PT13/0001, of the PE I+D+i 2013-2016, funded by ISCIII and FEDER. H.L-F is funded by a postdoctoral fellowship from the Xunta de Galicia. F.F-R and D.G-P are funded by the European Union's Seventh Framework Programme FP7/REGPOT 2012 2013.1 under grant agreement n° 316265 (BIOCAPS) and the "Platform of integration of intelligent techniques for analysis of biomedical information" project (TIN2013-47153-C3-3-R) financed by the Spanish Ministry of Economy and Competitiveness C.FT is funded by the "Spanish National Youth Guarantee Implementation Plan" (2013/2016) financed by the Spanish Ministry of Economy and Competitiveness

Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applications, ranging from simple extraction robots to online meta-servers. This article reviews existing scraping frameworks and tools, identifying their strengths and limitations in terms of extraction capabilities. The main focus is set on showing how straightforward it is today to set up a data scraping pipeline, with minimal programming effort, and answer a number of practical needs. For exemplification purposes, we introduce a biomedical data extraction scenario where the desired data sources, well-known in clinical microbiology and similar domains, do not offer programmatic interfaces yet. Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis. ; This work was partially funded by (i) the [TIN2009-14057-C03-02] project from the Spanish Ministry of Science and Innovation, the Plan E from the Spanish Government and the European Union from the European Regional Development Fund (ERDF), (ii) the Portugal-Spain cooperation action sponsored by the Foundation of Portuguese Universities [E 48/11] and the Spanish Ministry of Science and Innovation [AIB2010PT-00353] and (iii) the Agrupamento INBIOMED [2012/273] from the DXPCTSUG (Direccion Xeral de Promocion Cientifica e Tecnoloxica do Sistema Universitario de Galicia) from the Galician Government and the European Union from the ERDF unha maneira de facer Europa. H. L. F. was supported by a pre-doctoral fellowship from the University of ...

Background: Student participation and the use of active methodologies in classroom learning are being increasingly emphasized. The use of intelligent systems can be of great help when designing and developing these types of activities. Recently, emerging disciplines such as 'educational data mining' and 'learning analytics and knowledge' have provided clear examples of the importance of the use of artificial intelligence techniques in education. Objective: The main objective of this study was to gather expert opinions regarding the benefits of using complementary methods that are supported by intelligent systems, specifically, by intelligent information access systems, when processing texts written in natural language and the benefits of using these methods as companion tools to the learning activities that are employed by biomedical and health sciences teachers. Methods: Eleven teachers of degree courses who belonged to the Faculties of Biomedical Sciences (BS) and Health Sciences (HS) of a Spanish university in Madrid were individually interviewed. These interviews were conducted using a mixed methods questionnaire that included 66 predefined close-ended and open-ended questions. In our study, three intelligent information access systems (i.e., BioAnnote, CLEiM and MedCMap) were successfully used to evaluate the teacher's perceptions regarding the utility of these systems and their different methods in learning activities. Results: All teachers reported using active learning methods in the classroom, most of which were computer programs that were used for initially designing and later executing learning activities. All teachers used case-based learning methods in the classroom, with a specific emphasis on case reports written in Spanish and/or English. In general, few or none of the teachers were familiar with the technical terms related to the technologies used for these activities such as "intelligent systems" or "concept/mental maps". However, they clearly realized the potential applicability of such approaches in both the preparation and the effective use of these activities in the classroom. Specifically, the themes highlighted by a greater number of teachers after analyzing the responses to the open-ended questions were the usefulness of BioAnnote system to provide reliable sources of medical information and the usefulness of the bilingual nature of CLEiM system for learning medical terminology in English. Conclusions: Three intelligent information access systems were successfully used to evaluate the teacher's perceptions regarding the utility of these systems in learning activities. The results of this study showed that integration of reliable sources of information, bilingualism and selective annotation of concepts were the most valued features by the teachers, who also considered the incorporation of these systems into learning activities to be potentially very useful. In addition, in the context of our experimental conditions, our work provides useful insights into the way to appropriately integrate this type of intelligent information access systems into learning activities, revealing key themes to consider when developing such approaches. ; Spanish Ministry of Science and Innovation, European Regional Development Fund (ERDF) (TIN-2013-47153-C03-0X, X=1, 2, 3) and the Regional Government of Madrid under the Research Network MA2VICMR (S2009/TIC-1542). ; 2.731 JCR (2018) Q2, 57/155 Computer Science, Information Systems, 28/98 Health Care Science & Services, 11/26 Medical Informatics ; 0.960 SJR (2018) Q1, 10/163 Health Informatics ; No data IDR 2018 ; UEM