Search results for "lcsh:Computer applications to medicine. Medical informatics"
showing 10 items of 130 documents
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
2019
Abstract Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. Results We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify kno…
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
2019
AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…
Job strain in public transport drivers: Data to assess the relationship between demand-control model indicators, traffic accidents and sanctions
2018
This Data in Brief (DiB) article examines the association between the Job Demand-Control (JDC) model of stress and traffic safety outcomes (accidents and sanctions) in public transport drivers (n = 780). The data was collected using a structured self-administrable questionnaire composed of measurements of work stress (Job Content Questionnaire), and demographics (professional driving experience, hours and days working/driving per week). The data contains 4 parts: descriptive statistics, bivariate correlations between the study variables, analysis of variance (ANOVA) and Post-Hoc comparisons between drivers classified different quadrants of the JDC model. For further information, it is conve…
UVPAR: fast detection of functional shifts in duplicate genes.
2006
Abstract Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of t…
Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
2019
Abstract Background Distributed approaches based on the MapReduce programming paradigm have started to be proposed in the Bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. However, the use of MapReduce and related Big Data technologies and frameworks (e.g., Apache Hadoop and Spark) does not necessarily produce satisfactory results, in terms of both efficiency and effectiveness. We discuss how the development of distributed and Big Data management technologies has affected the analysis of large datasets of biological sequences. Moreover, we show how the choice of different parameter configurations and the careful engineering of the …
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
2019
Background Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data. Results In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTfu…
A knowledge-based decision support system in bioinformatics: An application to protein complex extraction
2013
Abstract Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems. Results We briefly present the KDSS' architecture and basic concepts used in the design of the knowl…
Factors Affecting Mobile Diabetes Monitoring Adoption Among Physicians: Questionnaire Study and Path Model
2012
BackgroundPatients with type 1 and type 2 diabetes often find it difficult to control their blood glucose level on a daily basis because of distance or physical incapacity. With the increase in Internet-enabled smartphone use, this problem can be resolved by adopting a mobile diabetes monitoring system. Most existing studies have focused on patients’ usability perceptions, whereas little attention has been paid to physicians’ intentions to adopt this technology. ObjectiveThe aim of the study was to evaluate the perceptions and user acceptance of mobile diabetes monitoring among Japanese physicians. MethodsA questionnaire survey of physicians was conducted in Japan. The structured questionna…
ideal: an R/Bioconductor package for interactive differential expression analysis
2020
AbstractBackgroundRNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.ResultsWe developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpr…
Data concerning the protein absorption and retention properties of xyloglucan-based hydrogel film
2018
In wound dressing applications, exudate absorption and retention are important properties. The data presented here assess the ability of the crosslinked xyloglucan-poly(vinyl alcohol) hydrogel films (XG-PVA), described in "Xyloglucan-based hydrogel films for wound dressing: Structure-property relationships" (Ajovalasit et al., 2018) [1] and "Biocompatibility, hemocompatibility and antimicrobial properties of xyloglucan-based hydrogel film for wound healing application" (Picone et al., 2019), to absorb and retain proteins. These properties were investigated by Comassie blue staining and electrophoresis of Fetal Serum Proteins. (C) 2018 The Authors. Published by Elsevier Inc. This is an open …