Hugo López-Fernández

Bio: Hugo López-Fernández is an academic researcher from University of Vigo. The author has contributed to research in topics: Medicine & Software. The author has an hindex of 11, co-authored 54 publications receiving 482 citations. Previous affiliations of Hugo López-Fernández include Instituto Politécnico Nacional & Universidade Nova de Lisboa.

Web scraping technologies in an API world

Abstract: 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.

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.

Abstract: Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills. Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Mass-Up software allows data preprocessing, as well as subsequent analysis including (i) biomarker discovery, (ii) clustering, (iii) biclustering, (iv) three-dimensional PCA visualization and (v) classification of large sets of spectra data. Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at http://sing.ei.uvigo.es/mass-up .

LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data.

Abstract: The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution imaging by laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) is an effective technique for qualitative and quantitative imaging due to its high spatial resolution and sensitivity. By applying this technique, vast amounts of raw data are generated to obtain high-quality images, essentially making the use of specific LA–ICP–MS imaging software that can process such data absolutely mandatory. Since existing solutions are usually commercial or hard-to-use for average users, this work introduces LA-iMageS, an open-source, free-to-use multiplatform application for fast and automatic generation of high-quality elemental distribution bioimages from LA–ICP–MS data in the PerkinElmer Elan XL format, whose results can be directly exported to external applications for further analysis. A key strength of LA-iMageS is its substantial added value for users, with particular regard to the customization of the elemental distribution bioimages, which allows, among other features, the ability to change color maps, increase image resolution or toggle between 2D and 3D visualizations.

Integrative Genomics Viewer

Abstract: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Systematic review of research on artificial intelligence applications in higher education – where are the educators?

Abstract: According to various international reports, Artificial Intelligence in Education (AIEd) is one of the currently emerging fields in educational technology. Whilst it has been around for about 30 years, it is still unclear for educators how to make pedagogical advantage of it on a broader scale, and how it can actually impact meaningfully on teaching and learning in higher education. This paper seeks to provide an overview of research on AI applications in higher education through a systematic review. Out of 2656 initially identified publications for the period between 2007 and 2018, 146 articles were included for final synthesis, according to explicit inclusion and exclusion criteria. The descriptive results show that most of the disciplines involved in AIEd papers come from Computer Science and STEM, and that quantitative methods were the most frequently used in empirical studies. The synthesis of results presents four areas of AIEd applications in academic support services, and institutional and administrative services: 1. profiling and prediction, 2. assessment and evaluation, 3. adaptive systems and personalisation, and 4. intelligent tutoring systems. The conclusions reflect on the almost lack of critical reflection of challenges and risks of AIEd, the weak connection to theoretical pedagogical perspectives, and the need for further exploration of ethical and educational approaches in the application of AIEd in higher education.

How to map billions of short reads onto

Abstract: Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?