Search results for " software"
showing 10 items of 1178 documents
On the Use of Binary Trees for DNA Hydroxymethylation Analysis
2017
DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. The software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. The binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the perf…
A framework for data-driven adaptive GUI generation based on DICOM
2018
Computer applications for diagnostic medical imaging provide generally a wide range of tools to support physicians in their daily diagnosis activities. Unfortunately, some functionalities are specialized for specific diseases or imaging modalities, while other ones are useless for the images under investigation. Nevertheless, the corresponding Graphical User Interface (GUI) widgets are still present on the screen reducing the image visualization area. As a consequence, the physician may be affected by cognitive overload and visual stress causing a degradation of performances, mainly due to unuseful widgets. In clinical environments, a GUI must represent a sequence of steps for image investi…
Fishing anti-inflammatories from known drugs: In silico repurposing, design, synthesis and biological evaluation of bisacodyl analogues
2017
Herein is described in silico repositioning, design, synthesis, biological evaluation and structure-activity relationship (SAR) of an original class of anti-inflammatory agents based on a polyaromatic pharmacophore structurally related to bisacodyl (BSL) drug used in therapeutic as laxative. We describe the potential of TOMOCOMD-CARDD methods to find out new anti-inflammatory drug-like agents from a diverse series of compounds using the total and local atom based bilinear indices as molecular descriptors. The models obtained were validated by biological studies, identifying BSL as the first anti-inflammatory lead-like using in silico repurposing from commercially available drugs. Several bi…
An android architecture for bio-inspired honest signalling in Human-Humanoid Interaction
2017
Abstract This paper outlines an augmented robotic architecture to study the conditions of successful Human-Humanoid Interaction (HHI). The architecture is designed as a testable model generator for interaction centred on the ability to emit, display and detect honest signals. First we overview the biological theory in which the concept of honest signals has been put forward in order to assess its explanatory power. We reconstruct the application of the concept of honest signalling in accounting for interaction in strategic contexts and in laying bare the foundation for an automated social metrics. We describe the modules of the architecture, which is intended to implement the concept of hon…
Assessing data analysis performance in research contexts: An experiment on accuracy, efficiency, productivity and researchers’ satisfaction
2018
[EN] Any knowledge generation process involves raw data comprehension, evaluation and inferential reasoning. These practices, common to different disciplines, are known as data analysis, and represent the most important set of activities in research contexts. Researchers use data analysis software methods and tools for generating new knowledge in their daily data analysis. In recent years, data analysis software has been incorporating explicit references in modelling of cognitive processes, in order to improve the assistance offered in data analysis tasks. However, data analysis software commercial suites are still resisting this inclusion, and there is little empirical work done in knowing…
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
2017
Abstract: The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, co-chairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing, ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthe…
Digital zenith camera of the University of Latvia
2016
Design of digital zenith camera in Institute of Geodesy and Geoinformatics of the University of Latvia started in 2009. Now, after tests of a prototype, improvements of design and manufacturing of the second version, it has reached operational status. The paper describes construction of camera, features of it‘s control software. Vertical deflection determination results are discussed.
Guidelines for the use of flow cytometry and cell sorting in immunological studies
2017
The marriage between immunology and cytometry is one of the most stable and productive in the recent history of science. A rapid search in PubMed shows that, as of July 2017, using “flow cytometry immunology” as a search term yields more than 68 000 articles, the first of which, interestingly, is not about lymphocytes. It might be stated that, after a short engagement, the exchange of the wedding rings between immunology and cytometry officially occurred when the idea to link fluorochromes to monoclonal antibodies came about. After this, recognizing different types of cells became relatively easy and feasible not only by using a simple fluorescence microscope, but also by a complex and some…
An effective extension of the applicability of alignment-free biological sequence comparison algorithms with Hadoop
2016
Alignment-free methods are one of the mainstays of biological sequence comparison, i.e., the assessment of how similar two biological sequences are to each other, a fundamental and routine task in computational biology and bioinformatics. They have gained popularity since, even on standard desktop machines, they are faster than methods based on alignments. However, with the advent of Next-Generation Sequencing Technologies, datasets whose size, i.e., number of sequences and their total length, is a challenge to the execution of alignment-free methods on those standard machines are quite common. Here, we propose the first paradigm for the computation of k-mer-based alignment-free methods for…
QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computati…
2017
Background In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials…