Wikipedia como herramienta de aprendizaje en Sistemas Distribuidos (Ingenieria en Informática)

Memoria ID12-0060. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2012-2013

BicOverlapper: a tool for bicluster visualization

BicOverlapper is a tool to visualize biclusters from gene-expression matrices in a way that helps to compare biclustering methods, to unravel trends and to highlight relevant genes and conditions. A visual approach can complement biological and statistical analysis and reduce the time spent by specialists interpreting the results of biclustering algorithms. The technique is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions. AVAILABILITY: The BicOverlapper software and supplementary material are available at http://vis.usal.es/bicoverlappe

Towards an Uncertainty-Aware Visualization in the Digital Humanities

[EN]As visualization becomes widespread in a broad range of cross-disciplinary academic domains, such as the digital humanities (DH), critical voices have been raised on the perils of neglecting the uncertain character of data in the visualization design process. Visualizations that, purposely or not, obscure or remove uncertainty in its different forms from the scholars’ vision may negatively affect the manner in which humanities scholars regard computational methods as useful tools in their daily work. In this paper, we address the issue of uncertainty representation in the context of the humanities from a theoretical perspective, in an attempt to provide the foundations of a framework that allows for the construction of ecological interface designs which are able to expose the computational power of the algorithms at play while, at the same time, respecting the particularities and needs of humanistic research. To this end, we review past uncertainty taxonomies in other domains typically related to the humanities and visualization, such as cartography and GIScience. From this review, we select an uncertainty taxonomy related to the humanities that we link to recent research in visualization for the DH. Finally, we bring a novel analytics method developed by other authors (Progressive Visual Analytics) into question, which we argue can be a good candidate to resolve the aforementioned difficulties in DH practic

Implementación de una arquitectura online para el aprendizaje de la programación en Python

Memoria ID-0006. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2017-2018

Interfaces de usuario imaginadas: el camino de ida y vuelta entre la ciencia y la ficción

Memoria ID-0231. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2016-2017

Asymmetrical nucleosomal DNA signatures regulate transcriptional directionality.

[EN]Despite the symmetrical structure of nucleosomes, in vitro studies have shown that transcription proceeds with different efficiency depending on the orientation of the DNA sequence around them. However, it is unclear whether this functional asymmetry is present in vivo and whether it could regulate transcriptional directionality. Here, we report that the proximal and distal halves of nucleosomal DNA contribute differentially to nucleosome stability in the genome. In +1 nucleosomes, this asymmetry facilitates or hinders transcription depending on the orientation of its underlying DNA, and this difference is associated with an asymmetrical interaction between DNA and histones. These properties are encoded in the DNA signature of +1 nucleosomes, since its incorporation in the two orientations into downstream nucleosomes renders them asymmetrically accessible to MNase and inverts the balance between sense and antisense transcription. Altogether, our results show that nucleosomal DNA endows nucleosomes with asymmetrical properties that modulate the directionality of transcription

Genome-wide search of nucleosome patterns using visual analytics.

[EN]The Burrows-Wheeler transform (BWT) is widely used for the fast alignment of high-throughput sequence data. This method also has potential applications in other areas of bioinformatics, and it can be specially useful for the fast searching of patterns on coverage data from different sources. We present a nucleosome pattern search method that converts levels of nucleosomal occupancy to a sequence-like format to which BWT searches can be applied. The method is embedded in a nucleosome map browser, 'Nucleosee', an interactive visual tool specifically designed to enhance BWT searches, giving them context and making them suitable for visual discourse analysis of the results. The proposed method is fast, flexible and sufficiently generic for the exploration of data in a broad and interactive way. The proposed algorithm and visual browser are available for testing at http://cpg3.der.usal.es/nucleosee. The source code and installation packages are also available at https://github.com/rodrigoSantamaria/nucleosee. Supplementary data are available at Bioinformatics online

A method for the complete analysis of NORM building materials by γ-ray spectrometry using HPGe detectors

[EN] A methodology including software tools for analysing NORM building materials and residues by low-level gamma-ray spectrometry has been developed. It comprises deconvolution of gamma-ray spectra using the software GALEA with focus on the natural radionuclides and Monte Carlo simulations for efficiency and true coincidence summing corrections. The methodology has been tested on a range of building materials and validated against reference materials

Nitric Oxide Metabolism Affects Germination in Botrytiscinerea and Is Connected to Nitrate Assimilation.

[EN]Nitric oxide regulates numerous physiological processes in species from all taxonomic groups. Here, its role in the early developmental stages of the fungal necrotroph Botrytis cinerea was investigated. Pharmacological analysis demonstrated that NO modulated germination, germ tube elongation and nuclear division rate. Experimental evidence indicates that exogenous NO exerts an immediate but transitory negative effect, slowing down germination-associated processes, and that this effect is largely dependent on the flavohemoglobin BCFHG1. The fungus exhibited a "biphasic response" to NO, being more sensitive to low and high concentrations than to intermediate levels of the NO donor. Global gene expression analysis in the wild-type and ΔBcfhg1 strains indicated a situation of strong nitrosative and oxidative stress determined by exogenous NO, which was much more intense in the mutant strain, that the cells tried to alleviate by upregulating several defense mechanisms, including the simultaneous upregulation of the genes encoding the flavohemoglobin BCFHG1, a nitronate monooxygenase (NMO) and a cyanide hydratase. Genetic evidence suggests the coordinated expression of Bcfhg1 and the NMO coding gene, both adjacent and divergently arranged, in response to NO. Nitrate assimilation genes were upregulated upon exposure to NO, and BCFHG1 appeared to be the main enzymatic system involved in the generation of the signal triggering their induction. Comparative expression analysis also showed the influence of NO on other cellular processes, such as mitochondrial respiration or primary and secondary metabolism, whose response could have been mediated by NmrA-like domain proteins

Evolucionando la interacción persona-ordenador mediante el cine y la ciencia ficción

Memoria ID-0116. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2017-2018