Search results for "software package"
showing 10 items of 19 documents
iSEE: Interactive SummarizedExperiment Explorer
2018
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproduci…
Validation of ThermoHuman automatic thermographic software for assessing foot temperature before and after running
2020
The aim of the study was to evaluate an automatic thermographic software package (ThermoHuman®) for assessing skin temperature on the soles of the feet before and after running and to compare it with two manual definitions of the regions of interest (ROIs). 120 thermal images of the soles of the feet of 30 participants, at two measurement points (before and after running 30 min) and on two measurement days were analyzed. Three different models of thermographic image analyses were used to obtain the mean temperature of 9 ROIs: A) ThermoHuman (automatic definition of ROIs using ThermoHuman® software), B) Manual (manual delimitation of ROIs by proportion criteria), and C) Manual-TH (manual del…
FMI4j: A Software Package for working with Functional Mock-up Units on the Java Virtual Machine
2018
This paper introduces FMI4j, a software package for working with Functional Mock-up Units (FMUs) on the Java Virtual Machine (JVM). FMI4j is written in Kotlin, which is 100% interoperable with Java, and consists of programming APIs for parsing the meta-data associated with an FMU, as well as running them. FMI4j is compatible with FMI version 2.0 for Model Exchange (ME) and Co-Simulation (CS). Currently, FMI4j is the only software library targeting the JVM supporting ME 2.0. In addition to provide bare-bones access to such FMUs, it provides the means for solving them using a range of bundled fixedand variable-step solvers. A command line tool named FMU2Jar is also provided, which is capable …
A Software Package for a Serum Bank Management
1979
A serum-bank is a collection of human serum samples coming from different locations (in our case Children Hospital, schools, factories, town departemens), allocated in some archives. Principal users of a such data-bank are, of course, physicians and biologists that are mainly interested in statistical analysis (computation of averages, variances factor analysis, etc.) of immunological and epidemiological relevance, in order to investigate about some haematochemical parameters common to some selected subset of the archives [1], [2].
The Detector Control of the PANDA Experiment
2014
The PANDA experiment will be built at the antiproton storage ring HESR, a part of the new accelerator facility FAIR in Darmstadt, Germany. PANDA aims amongst other topics for high precision measurements in hadron spectroscopy and search for exotic matter. To guarantee the high resolution of the different components a detector control system (DCS) monitoring temperatures, humidity, pressure, and controlling chillers and power supplies is needed. The DCS of PANDA is built using the open-source software package EPICS (Experimental Physics and Industrial Control System) with a PANDA specific version of Control-System Studio. In this document the general concepts of the PANDA DCS will be discuss…
Density-functional tight-binding for beginners
2009
This article is a pedagogical introduction to density-functional tight-binding (DFTB) method. We derive it from the density-functional theory, give the details behind the tight-binding formalism, and give practical recipes for parametrization: how to calculate pseudo-atomic orbitals and matrix elements, and especially how to systematically fit the short-range repulsions. Our scope is neither to provide a historical review nor to make performance comparisons, but to give beginner's guide for this approximate, but in many ways invaluable, electronic structure simulation method--now freely available as an open-source software package, hotbit.
An updated version of the computational package SIMPRE that uses the standard conventions for Stevens crystal field parameters
2014
The crystal field approach used by SIMPRE is analyzed, verifying the exactness of the results concerning energy levels and magnetic properties calculated by the package. To coincide with the prevailing conventions, we reformulate the presentation of the crystal field parameters, so that the results are now, also from a formal point of view, strictly correct. New calculations are presented to test the influence of neglecting the excited J states, a common but critical approximation employed by SIMPRE. For that, we examine the case of Er(trensal) complex (H3 trensal = 2,2',2″-tris(salicylideneimino)triethylamine) where the influence of this approximation is found to be minimal. A patched vers…
GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra
2020
As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using s…
On-Line and In-Situ Identification of Air Pollution
2002
The elemental, iron-phase, and oxidation state analysis of urban aerosol samples, collected from different sites in Vitoria metropolitan region, ES, Brazil, was carried out using Mossbauer (MB) Spectroscopy (MBS) and X-ray fluorescence (XRF) techniques. A portable XRF spectrometer for elemental analysis from Na to Fe, and the miniaturized MB spectrometer MIMOS-II have been installed together using a 100 mCi 57 Co(Rh) MB source for XRF excitation. Both measurements can be performed simultaneously. For continuous and fast characterization purposes a software package was developed for Mossbauer and XRF analysis. The software is based on genetic algorithm, fuzzy logic and artificial neural netw…
Particle identification with COMPASS RICH-1
2011
International audience; RICH-1 is a large size RICH detector in operation at the COMPASS experiment since 2001 and recently upgraded implementing a new photon detection system with increased performance.A dedicated software package has been developed to perform RICH-1 data reduction, pattern recognition and particle identification as well as a number of accessory tasks for detector studies.The software package, the algorithms implemented and the detector characterisation and performance are reported in detail.