Arc_Mat: a Matlab-based spatial data analysis toolbox

NASA Astrophysics Data System (ADS)

Liu, Xingjian; Lesage, James

2010-03-01

This article presents an overview of Arc_Mat, a Matlab-based spatial data analysis software package whose source code has been placed in the public domain. An earlier version of the Arc_Mat toolbox was developed to extract map polygon and database information from ESRI shapefiles and provide high quality mapping in the Matlab software environment. We discuss revisions to the toolbox that: utilize enhanced computing and graphing capabilities of more recent versions of Matlab, restructure the toolbox with object-oriented programming features, and provide more comprehensive functions for spatial data analysis. The Arc_Mat toolbox functionality includes basic choropleth mapping; exploratory spatial data analysis that provides exploratory views of spatial data through various graphs, for example, histogram, Moran scatterplot, three-dimensional scatterplot, density distribution plot, and parallel coordinate plots; and more formal spatial data modeling that draws on the extensive Spatial Econometrics Toolbox functions. A brief review of the design aspects of the revised Arc_Mat is described, and we provide some illustrative examples that highlight representative uses of the toolbox. Finally, we discuss programming with and customizing the Arc_Mat toolbox functionalities.

FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

PubMed

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

SIGKit: a New Data-based Software for Learning Introductory Geophysics

NASA Astrophysics Data System (ADS)

Zhang, Y.; Kruse, S.; George, O.; Esmaeili, S.; Papadimitrios, K. S.; Bank, C. G.; Cadmus, A.; Kenneally, N.; Patton, K.; Brusher, J.

2016-12-01

Students of diverse academic backgrounds take introductory geophysics courses to learn the theory of a variety of measurement and analysis methods with the expectation to be able to apply their basic knowledge to real data. Ideally, such data is collected in field courses and also used in lecture-based courses because they provide a critical context for better learning and understanding of geophysical methods. Each method requires a separate software package for the data processing steps, and the complexity and variety of professional software makes the path through data processing to data interpretation a strenuous learning process for students and a challenging teaching task for instructors. SIGKit (Student Investigation of Geophysics Toolkit) being developed as a collaboration between the University of South Florida, the University of Toronto, and MathWorks intends to address these shortcomings by showing the most essential processing steps and allowing students to visualize the underlying physics of the various methods. It is based on MATLAB software and offered as an easy-to-use graphical user interface and packaged so it can run as an executable in the classroom and the field even on computers without MATLAB licenses. An evaluation of the software based on student feedback from focus-group interviews and think-aloud observations helps drive its development and refinement. The toolkit provides a logical gateway into the more sophisticated and costly software students will encounter later in their training and careers by combining essential visualization, modeling, processing, and analysis steps for seismic, GPR, magnetics, gravity, resistivity, and electromagnetic data.

RSEIS and RFOC: Seismic Analysis in R

NASA Astrophysics Data System (ADS)

Lees, J. M.

2015-12-01

Open software is essential for reproducible scientific exchange. R-packages provide a platform for development of seismological investigation software that can be properly documented and traced for data processing. A suite of R packages designed for a wide range of seismic analysis is currently available in the free software platform called R. R is a software platform based on the S-language developed at Bell Labs decades ago. Routines in R can be run as standalone function calls, or developed in object-oriented mode. R comes with a base set of routines, and thousands of user developed packages. The packages developed at UNC include subroutines and interactive codes for processing seismic data, analyzing geographic information (GIS) and inverting data involved in a variety of geophysical applications. On CRAN (Comprehensive R Archive Network, http://www.r-project.org/) currently available packages related to seismic analysis are RSEIS, Rquake, GEOmap, RFOC, zoeppritz, RTOMO, and geophys, Rwave, PEIP, hht, rFDSN. These include signal processing, data management, mapping, earthquake location, deconvolution, focal mechanisms, wavelet transforms, Hilbert-Huang Transforms, tomographic inversion, and Mogi deformation among other useful functionality. All software in R packages is required to have detailed documentation, making the exchange and modification of existing software easy. In this presentation, I will focus on packages RSEIS and RFOC, showing examples from a variety of seismic analyses. The R approach has similarities to the popular (and expensive) MATLAB platform, although R is open source and free to down load.

FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data

PubMed Central

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. PMID:21253357

MATLAB-implemented estimation procedure for model-based assessment of hepatic insulin degradation from standard intravenous glucose tolerance test data.

PubMed

Di Nardo, Francesco; Mengoni, Michele; Morettini, Micaela

2013-05-01

Present study provides a novel MATLAB-based parameter estimation procedure for individual assessment of hepatic insulin degradation (HID) process from standard frequently-sampled intravenous glucose tolerance test (FSIGTT) data. Direct access to the source code, offered by MATLAB, enabled us to design an optimization procedure based on the alternating use of Gauss-Newton's and Levenberg-Marquardt's algorithms, which assures the full convergence of the process and the containment of computational time. Reliability was tested by direct comparison with the application, in eighteen non-diabetic subjects, of well-known kinetic analysis software package SAAM II, and by application on different data. Agreement between MATLAB and SAAM II was warranted by intraclass correlation coefficients ≥0.73; no significant differences between corresponding mean parameter estimates and prediction of HID rate; and consistent residual analysis. Moreover, MATLAB optimization procedure resulted in a significant 51% reduction of CV% for the worst-estimated parameter by SAAM II and in maintaining all model-parameter CV% <20%. In conclusion, our MATLAB-based procedure was suggested as a suitable tool for the individual assessment of HID process. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Optical Excitations and Energy Transfer in Nanoparticle Waveguides

DTIC Science & Technology

2009-03-01

All calculations were performed using our own codes given in the Appendix section. The calculations were performed using Scilab programming package...January 2007, invited Speaker) 12. Scilab is a free software compatible to the famous Matlab package. It can be found at their webpage http

RARtool: A MATLAB Software Package for Designing Response-Adaptive Randomized Clinical Trials with Time-to-Event Outcomes.

PubMed

Ryeznik, Yevgen; Sverdlov, Oleksandr; Wong, Weng Kee

2015-08-01

Response-adaptive randomization designs are becoming increasingly popular in clinical trial practice. In this paper, we present RARtool , a user interface software developed in MATLAB for designing response-adaptive randomized comparative clinical trials with censored time-to-event outcomes. The RARtool software can compute different types of optimal treatment allocation designs, and it can simulate response-adaptive randomization procedures targeting selected optimal allocations. Through simulations, an investigator can assess design characteristics under a variety of experimental scenarios and select the best procedure for practical implementation. We illustrate the utility of our RARtool software by redesigning a survival trial from the literature.

OMPC: an Open-Source MATLAB-to-Python Compiler.

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

InterFace: A software package for face image warping, averaging, and principal components analysis.

PubMed

Kramer, Robin S S; Jenkins, Rob; Burton, A Mike

2017-12-01

We describe InterFace, a software package for research in face recognition. The package supports image warping, reshaping, averaging of multiple face images, and morphing between faces. It also supports principal components analysis (PCA) of face images, along with tools for exploring the "face space" produced by PCA. The package uses a simple graphical user interface, allowing users to perform these sophisticated image manipulations without any need for programming knowledge. The program is available for download in the form of an app, which requires that users also have access to the (freely available) MATLAB Runtime environment.

UQTools: The Uncertainty Quantification Toolbox - Introduction and Tutorial

NASA Technical Reports Server (NTRS)

Kenny, Sean P.; Crespo, Luis G.; Giesy, Daniel P.

2012-01-01

UQTools is the short name for the Uncertainty Quantification Toolbox, a software package designed to efficiently quantify the impact of parametric uncertainty on engineering systems. UQTools is a MATLAB-based software package and was designed to be discipline independent, employing very generic representations of the system models and uncertainty. Specifically, UQTools accepts linear and nonlinear system models and permits arbitrary functional dependencies between the system s measures of interest and the probabilistic or non-probabilistic parametric uncertainty. One of the most significant features incorporated into UQTools is the theoretical development centered on homothetic deformations and their application to set bounding and approximating failure probabilities. Beyond the set bounding technique, UQTools provides a wide range of probabilistic and uncertainty-based tools to solve key problems in science and engineering.

g-PRIME: A Free, Windows Based Data Acquisition and Event Analysis Software Package for Physiology in Classrooms and Research Labs.

PubMed

Lott, Gus K; Johnson, Bruce R; Bonow, Robert H; Land, Bruce R; Hoy, Ronald R

2009-01-01

We present g-PRIME, a software based tool for physiology data acquisition, analysis, and stimulus generation in education and research. This software was developed in an undergraduate neurophysiology course and strongly influenced by instructor and student feedback. g-PRIME is a free, stand-alone, windows application coded and "compiled" in Matlab (does not require a Matlab license). g-PRIME supports many data acquisition interfaces from the PC sound card to expensive high throughput calibrated equipment. The program is designed as a software oscilloscope with standard trigger modes, multi-channel visualization controls, and data logging features. Extensive analysis options allow real time and offline filtering of signals, multi-parameter threshold-and-window based event detection, and two-dimensional display of a variety of parameters including event time, energy density, maximum FFT frequency component, max/min amplitudes, and inter-event rate and intervals. The software also correlates detected events with another simultaneously acquired source (event triggered average) in real time or offline. g-PRIME supports parameter histogram production and a variety of elegant publication quality graphics outputs. A major goal of this software is to merge powerful engineering acquisition and analysis tools with a biological approach to studies of nervous system function.

Software design for analysis of multichannel intracardial and body surface electrocardiograms.

PubMed

Potse, Mark; Linnenbank, André C; Grimbergen, Cornelis A

2002-11-01

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.

Student's Lab Assignments in PDE Course with MAPLE.

ERIC Educational Resources Information Center

Ponidi, B. Alhadi

Computer-aided software has been used intensively in many mathematics courses, especially in computational subjects, to solve initial value and boundary value problems in Partial Differential Equations (PDE). Many software packages were used in student lab assignments such as FORTRAN, PASCAL, MATLAB, MATHEMATICA, and MAPLE in order to accelerate…

PMU Data Event Detection: A User Guide for Power Engineers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, A.; Singh, M.; Muljadi, E.

2014-10-01

This user guide is intended to accompany a software package containing a Matrix Laboratory (MATLAB) script and related functions for processing phasor measurement unit (PMU) data. This package and guide have been developed by the National Renewable Energy Laboratory and the University of Texas at Austin. The objective of this data processing exercise is to discover events in the vast quantities of data collected by PMUs. This document attempts to cover some of the theory behind processing the data to isolate events as well as the functioning of the MATLAB scripts. The report describes (1) the algorithms and mathematical backgroundmore » that the accompanying MATLAB codes use to detect events in PMU data and (2) the inputs required from the user and the outputs generated by the scripts.« less

Wide-field Imaging System and Rapid Direction of Optical Zoom (WOZ)

DTIC Science & Technology

2010-12-24

The modeling tools are based on interaction between three commercial software packages: SolidWorks, COMSOL Multiphysics, and ZEMAX optical design...deformation resulting from the applied voltages. Finally, the deformed surface can be exported to ZEMAX via MatLab. From ZEMAX , various analyses can...results to extract from ZEMAX to support the optimization remains to be determined. Figure 1 shows the deformation calculated using a model of an

TTLEM: Open access tool for building numerically accurate landscape evolution models in MATLAB

NASA Astrophysics Data System (ADS)

Campforts, Benjamin; Schwanghart, Wolfgang; Govers, Gerard

2017-04-01

Despite a growing interest in LEMs, accuracy assessment of the numerical methods they are based on has received little attention. Here, we present TTLEM which is an open access landscape evolution package designed to develop and test your own scenarios and hypothesises. TTLEM uses a higher order flux-limiting finite-volume method to simulate river incision and tectonic displacement. We show that this scheme significantly influences the evolution of simulated landscapes and the spatial and temporal variability of erosion rates. Moreover, it allows the simulation of lateral tectonic displacement on a fixed grid. Through the use of a simple GUI the software produces visible output of evolving landscapes through model run time. In this contribution, we illustrate numerical landscape evolution through a set of movies spanning different spatial and temporal scales. We focus on the erosional domain and use both spatially constant and variable input values for uplift, lateral tectonic shortening, erodibility and precipitation. Moreover, we illustrate the relevance of a stochastic approach for realistic hillslope response modelling. TTLEM is a fully open source software package, written in MATLAB and based on the TopoToolbox platform (topotoolbox.wordpress.com). Installation instructions can be found on this website and the therefore designed GitHub repository.

Wide-field Imaging System and Rapid Direction of Optical Zoom (WOZ)

DTIC Science & Technology

2010-09-25

commercial software packages: SolidWorks, COMSOL Multiphysics, and ZEMAX optical design. SolidWorks is a computer aided design package, which as a live...interface to COMSOL. COMSOL is a finite element analysis/partial differential equation solver. ZEMAX is an optical design package. Both COMSOL and... ZEMAX have live interfaces to MatLab. Our initial investigations have enabled a model in SolidWorks to be updated in COMSOL, an FEA calculation

Gro2mat: a package to efficiently read gromacs output in MATLAB.

PubMed

Dien, Hung; Deane, Charlotte M; Knapp, Bernhard

2014-07-30

Molecular dynamics (MD) simulations are a state-of-the-art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc-format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc. Copyright © 2014 Wiley Periodicals, Inc.

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

Coded Modulation in C and MATLAB

NASA Technical Reports Server (NTRS)

Hamkins, Jon; Andrews, Kenneth S.

2011-01-01

This software, written separately in C and MATLAB as stand-alone packages with equivalent functionality, implements encoders and decoders for a set of nine error-correcting codes and modulators and demodulators for five modulation types. The software can be used as a single program to simulate the performance of such coded modulation. The error-correcting codes implemented are the nine accumulate repeat-4 jagged accumulate (AR4JA) low-density parity-check (LDPC) codes, which have been approved for international standardization by the Consultative Committee for Space Data Systems, and which are scheduled to fly on a series of NASA missions in the Constellation Program. The software implements the encoder and decoder functions, and contains compressed versions of generator and parity-check matrices used in these operations.

Nonstationary Extreme Value Analysis in a Changing Climate: A Software Package

NASA Astrophysics Data System (ADS)

Cheng, L.; AghaKouchak, A.; Gilleland, E.

2013-12-01

Numerous studies show that climatic extremes have increased substantially in the second half of the 20th century. For this reason, analysis of extremes under a nonstationary assumption has received a great deal of attention. This paper presents a software package developed for estimation of return levels, return periods, and risks of climatic extremes in a changing climate. This MATLAB software package offers tools for analysis of climate extremes under both stationary and non-stationary assumptions. The Nonstationary Extreme Value Analysis (hereafter, NEVA) provides an efficient and generalized framework for analyzing extremes using Bayesian inference. NEVA estimates the extreme value parameters using a Differential Evolution Markov Chain (DE-MC) which utilizes the genetic algorithm Differential Evolution (DE) for global optimization over the real parameter space with the Markov Chain Monte Carlo (MCMC) approach and has the advantage of simplicity, speed of calculation and convergence over conventional MCMC. NEVA also offers the confidence interval and uncertainty bounds of estimated return levels based on the sampled parameters. NEVA integrates extreme value design concepts, data analysis tools, optimization and visualization, explicitly designed to facilitate analysis extremes in geosciences. The generalized input and output files of this software package make it attractive for users from across different fields. Both stationary and nonstationary components of the package are validated for a number of case studies using empirical return levels. The results show that NEVA reliably describes extremes and their return levels.

SEDA: A software package for the Statistical Earthquake Data Analysis

NASA Astrophysics Data System (ADS)

Lombardi, A. M.

2017-03-01

In this paper, the first version of the software SEDA (SEDAv1.0), designed to help seismologists statistically analyze earthquake data, is presented. The package consists of a user-friendly Matlab-based interface, which allows the user to easily interact with the application, and a computational core of Fortran codes, to guarantee the maximum speed. The primary factor driving the development of SEDA is to guarantee the research reproducibility, which is a growing movement among scientists and highly recommended by the most important scientific journals. SEDAv1.0 is mainly devoted to produce accurate and fast outputs. Less care has been taken for the graphic appeal, which will be improved in the future. The main part of SEDAv1.0 is devoted to the ETAS modeling. SEDAv1.0 contains a set of consistent tools on ETAS, allowing the estimation of parameters, the testing of model on data, the simulation of catalogs, the identification of sequences and forecasts calculation. The peculiarities of routines inside SEDAv1.0 are discussed in this paper. More specific details on the software are presented in the manual accompanying the program package.

SEDA: A software package for the Statistical Earthquake Data Analysis

PubMed Central

Lombardi, A. M.

2017-01-01

In this paper, the first version of the software SEDA (SEDAv1.0), designed to help seismologists statistically analyze earthquake data, is presented. The package consists of a user-friendly Matlab-based interface, which allows the user to easily interact with the application, and a computational core of Fortran codes, to guarantee the maximum speed. The primary factor driving the development of SEDA is to guarantee the research reproducibility, which is a growing movement among scientists and highly recommended by the most important scientific journals. SEDAv1.0 is mainly devoted to produce accurate and fast outputs. Less care has been taken for the graphic appeal, which will be improved in the future. The main part of SEDAv1.0 is devoted to the ETAS modeling. SEDAv1.0 contains a set of consistent tools on ETAS, allowing the estimation of parameters, the testing of model on data, the simulation of catalogs, the identification of sequences and forecasts calculation. The peculiarities of routines inside SEDAv1.0 are discussed in this paper. More specific details on the software are presented in the manual accompanying the program package. PMID:28290482

Defining Geodetic Reference Frame using Matlab®: PlatEMotion 2.0

NASA Astrophysics Data System (ADS)

Cannavò, Flavio; Palano, Mimmo

2016-03-01

We describe the main features of the developed software tool, namely PlatE-Motion 2.0 (PEM2), which allows inferring the Euler pole parameters by inverting the observed velocities at a set of sites located on a rigid block (inverse problem). PEM2 allows also calculating the expected velocity value for any point located on the Earth providing an Euler pole (direct problem). PEM2 is the updated version of a previous software tool initially developed for easy-to-use file exchange with the GAMIT/GLOBK software package. The software tool is developed in Matlab® framework and, as the previous version, includes a set of MATLAB functions (m-files), GUIs (fig-files), map data files (mat-files) and user's manual as well as some example input files. New changes in PEM2 include (1) some bugs fixed, (2) improvements in the code, (3) improvements in statistical analysis, (4) new input/output file formats. In addition, PEM2 can be now run under the majority of operating systems. The tool is open source and freely available for the scientific community.

TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies.

PubMed

Klein, Johannes; Leupold, Stefan; Biegler, Ilona; Biedendieck, Rebekka; Münch, Richard; Jahn, Dieter

2012-09-01

Time-lapse imaging in combination with fluorescence microscopy techniques enable the investigation of gene regulatory circuits and uncovered phenomena like culture heterogeneity. In this context, computational image processing for the analysis of single cell behaviour plays an increasing role in systems biology and mathematical modelling approaches. Consequently, we developed a software package with graphical user interface for the analysis of single bacterial cell behaviour. A new software called TLM-Tracker allows for the flexible and user-friendly interpretation for the segmentation, tracking and lineage analysis of microbial cells in time-lapse movies. The software package, including manual, tutorial video and examples, is available as Matlab code or executable binaries at http://www.tlmtracker.tu-bs.de.

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

JWST Wavefront Control Toolbox

NASA Technical Reports Server (NTRS)

Shin, Shahram Ron; Aronstein, David L.

2011-01-01

A Matlab-based toolbox has been developed for the wavefront control and optimization of segmented optical surfaces to correct for possible misalignments of James Webb Space Telescope (JWST) using influence functions. The toolbox employs both iterative and non-iterative methods to converge to an optimal solution by minimizing the cost function. The toolbox could be used in either of constrained and unconstrained optimizations. The control process involves 1 to 7 degrees-of-freedom perturbations per segment of primary mirror in addition to the 5 degrees of freedom of secondary mirror. The toolbox consists of a series of Matlab/Simulink functions and modules, developed based on a "wrapper" approach, that handles the interface and data flow between existing commercial optical modeling software packages such as Zemax and Code V. The limitations of the algorithm are dictated by the constraints of the moving parts in the mirrors.

MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

NASA Astrophysics Data System (ADS)

Vergara-Perez, Sandra; Marucho, Marcelo

2016-01-01

One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

PubMed Central

Vergara-Perez, Sandra; Marucho, Marcelo

2015-01-01

One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules. PMID:26924848

MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

PubMed

Vergara-Perez, Sandra; Marucho, Marcelo

2016-01-01

One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

A MATLAB-Aided Method for Teaching Calculus-Based Business Mathematics

ERIC Educational Resources Information Center

Liang, Jiajuan; Pan, William S. Y.

2009-01-01

MATLAB is a powerful package for numerical computation. MATLAB contains a rich pool of mathematical functions and provides flexible plotting functions for illustrating mathematical solutions. The course of calculus-based business mathematics consists of two major topics: 1) derivative and its applications in business; and 2) integration and its…

Using MountainsMap (Digital Surf) surface analysis software as an analysis tool for x-ray mirror optical metrology data

NASA Astrophysics Data System (ADS)

Duffy, Alan; Yates, Brian; Takacs, Peter

2012-09-01

The Optical Metrology Facility at the Canadian Light Source (CLS) has recently purchased MountainsMap surface analysis software from Digital Surf and we report here our experiences with this package and its usefulness as a tool for examining metrology data of synchrotron x-ray mirrors. The package has a number of operators that are useful for determining surface roughness and slope error including compliance with ISO standards (viz. ISO 4287 and ISO 25178). The software is extensible with MATLAB scripts either by loading an m-file or by a user written script. This makes it possible to apply a custom operator to measurement data sets. Using this feature we have applied the simple six-line MATLAB code for the direct least square fitting of ellipses developed by Fitzgibbon et. al. to investigate the residual slope error of elliptical mirrors upon the removal of the best-fit-ellipse. The software includes support for many instruments (e.g. Zygo, MicroMap, etc...) and can import ASCII data (e.g. LTP data). The stitching module allows the user to assemble overlapping images and we report on our experiences with this feature applied to MicroMap surface roughness data. The power spectral density function was determined for the stitched and unstitched data and compared.

HEART: an automated beat-to-beat cardiovascular analysis package using Matlab.

PubMed

Schroeder, M J Mark J; Perreault, Bill; Ewert, D L Daniel L; Koenig, S C Steven C

2004-07-01

A computer program is described for beat-to-beat analysis of cardiovascular parameters from high-fidelity pressure and flow waveforms. The Hemodynamic Estimation and Analysis Research Tool (HEART) is a post-processing analysis software package developed in Matlab that enables scientists and clinicians to document, load, view, calibrate, and analyze experimental data that have been digitally saved in ascii or binary format. Analysis routines include traditional hemodynamic parameter estimates as well as more sophisticated analyses such as lumped arterial model parameter estimation and vascular impedance frequency spectra. Cardiovascular parameter values of all analyzed beats can be viewed and statistically analyzed. An attractive feature of the HEART program is the ability to analyze data with visual quality assurance throughout the process, thus establishing a framework toward which Good Laboratory Practice (GLP) compliance can be obtained. Additionally, the development of HEART on the Matlab platform provides users with the flexibility to adapt or create study specific analysis files according to their specific needs. Copyright 2003 Elsevier Ltd.

CMGTooL user's manual

USGS Publications Warehouse

Xu, Jingping; Lightsom, Fran; Noble, Marlene A.; Denham, Charles

2002-01-01

During the past several years, the sediment transport group in the Coastal and Marine Geology Program (CMGP) of the U. S. Geological Survey has made major revisions to its methodology of processing, analyzing, and maintaining the variety of oceanographic time-series data. First, CMGP completed the transition of the its oceanographic time-series database to a self-documenting NetCDF (Rew et al., 1997) data format. Second, CMGP’s oceanographic data variety and complexity have been greatly expanded from traditional 2-dimensional, single-point time-series measurements (e.g., Electro-magnetic current meters, transmissometers) to more advanced 3-dimensional and profiling time-series measurements due to many new acquisitions of modern instruments such as Acoustic Doppler Current Profiler (RDI, 1996), Acoustic Doppler Velocitimeter, Pulse-Coherence Acoustic Doppler Profiler (SonTek, 2001), Acoustic Bacscatter Sensor (Aquatec, 1001001001001001001). In order to accommodate the NetCDF format of data from the new instruments, a software package of processing, analyzing, and visualizing time-series oceanographic data was developed. It is named CMGTooL. The CMGTooL package contains two basic components: a user-friendly GUI for NetCDF file analysis, processing and manipulation; and a data analyzing program library. Most of the routines in the library are stand-alone programs suitable for batch processing. CMGTooL is written in MATLAB computing language (The Mathworks, 1997), therefore users must have MATLAB installed on their computer in order to use this software package. In addition, MATLAB’s Signal Processing Toolbox is also required by some CMGTooL’s routines. Like most MATLAB programs, all CMGTooL codes are compatible with different computing platforms including PC, MAC, and UNIX machines (Note: CMGTooL has been tested on different platforms that run MATLAB 5.2 (Release 10) or lower versions. Some of the commands related to MAC may not be compatible with later releases of MATLAB). The GUI and some of the library routines call low-level NetCDF file I/O, variable and attribute functions. These NetCDF exclusive functions are supported by a MATLAB toolbox named NetCDF, created by Dr. Charles Denham . This toolbox has to be installed in order to use the CMGTooL GUI. The CMGTooL GUI calls several routines that were initially developed by others. The authors would like to acknowledge the following scientists for their ideas and codes: Dr. Rich Signell (USGS), Dr. Chris Sherwood (USGS), and Dr. Bob Beardsley (WHOI). Many special terms that carry special meanings in either MATLAB or the NetCDF Toolbox are used in this manual. Users are encouraged to read the documents of MATLAB and NetCDF for references.

OSCAR a Matlab based optical FFT code

NASA Astrophysics Data System (ADS)

Degallaix, Jérôme

2010-05-01

Optical simulation softwares are essential tools for designing and commissioning laser interferometers. This article aims to introduce OSCAR, a Matlab based FFT code, to the experimentalist community. OSCAR (Optical Simulation Containing Ansys Results) is used to simulate the steady state electric fields in optical cavities with realistic mirrors. The main advantage of OSCAR over other similar packages is the simplicity of its code requiring only a short time to master. As a result, even for a beginner, it is relatively easy to modify OSCAR to suit other specific purposes. OSCAR includes an extensive manual and numerous detailed examples such as simulating thermal aberration, calculating cavity eigen modes and diffraction loss, simulating flat beam cavities and three mirror ring cavities. An example is also provided about how to run OSCAR on the GPU of modern graphic cards instead of the CPU, making the simulation up to 20 times faster.

A Matlab toolkit for three-dimensional electrical impedance tomography: a contribution to the Electrical Impedance and Diffuse Optical Reconstruction Software project

NASA Astrophysics Data System (ADS)

Polydorides, Nick; Lionheart, William R. B.

2002-12-01

The objective of the Electrical Impedance and Diffuse Optical Reconstruction Software project is to develop freely available software that can be used to reconstruct electrical or optical material properties from boundary measurements. Nonlinear and ill posed problems such as electrical impedance and optical tomography are typically approached using a finite element model for the forward calculations and a regularized nonlinear solver for obtaining a unique and stable inverse solution. Most of the commercially available finite element programs are unsuitable for solving these problems because of their conventional inefficient way of calculating the Jacobian, and their lack of accurate electrode modelling. A complete package for the two-dimensional EIT problem was officially released by Vauhkonen et al at the second half of 2000. However most industrial and medical electrical imaging problems are fundamentally three-dimensional. To assist the development we have developed and released a free toolkit of Matlab routines which can be employed to solve the forward and inverse EIT problems in three dimensions based on the complete electrode model along with some basic visualization utilities, in the hope that it will stimulate further development. We also include a derivation of the formula for the Jacobian (or sensitivity) matrix based on the complete electrode model.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

IB2d: a Python and MATLAB implementation of the immersed boundary method.

PubMed

Battista, Nicholas A; Strickland, W Christopher; Miller, Laura A

2017-03-29

The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an elastic structure immersed in a uniform density fluid. Many existing codes are not publicly available, and the commercial software that exists usually requires expensive licenses and may not be as robust or allow the necessary flexibility that in house codes can provide. We present an open source immersed boundary software package, IB2d, with full implementations in both MATLAB and Python, that is capable of running a vast range of biomechanics models and is accessible to scientists who have experience in high-level programming environments. IB2d contains multiple options for constructing material properties of the fiber structure, as well as the advection-diffusion of a chemical gradient, muscle mechanics models, and artificial forcing to drive boundaries with a preferred motion.

General MACOS Interface for Modeling and Analysis for Controlled Optical Systems

NASA Technical Reports Server (NTRS)

Sigrist, Norbert; Basinger, Scott A.; Redding, David C.

2012-01-01

The General MACOS Interface (GMI) for Modeling and Analysis for Controlled Optical Systems (MACOS) enables the use of MATLAB as a front-end for JPL s critical optical modeling package, MACOS. MACOS is JPL s in-house optical modeling software, which has proven to be a superb tool for advanced systems engineering of optical systems. GMI, coupled with MACOS, allows for seamless interfacing with modeling tools from other disciplines to make possible integration of dynamics, structures, and thermal models with the addition of control systems for deformable optics and other actuated optics. This software package is designed as a tool for analysts to quickly and easily use MACOS without needing to be an expert at programming MACOS. The strength of MACOS is its ability to interface with various modeling/development platforms, allowing evaluation of system performance with thermal, mechanical, and optical modeling parameter variations. GMI provides an improved means for accessing selected key MACOS functionalities. The main objective of GMI is to marry the vast mathematical and graphical capabilities of MATLAB with the powerful optical analysis engine of MACOS, thereby providing a useful tool to anyone who can program in MATLAB. GMI also improves modeling efficiency by eliminating the need to write an interface function for each task/project, reducing error sources, speeding up user/modeling tasks, and making MACOS well suited for fast prototyping.

Gpufit: An open-source toolkit for GPU-accelerated curve fitting.

PubMed

Przybylski, Adrian; Thiel, Björn; Keller-Findeisen, Jan; Stock, Bernd; Bates, Mark

2017-11-16

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.

Using MATLAB Software on the Peregrine System | High-Performance Computing

Science.gov Websites

| NREL MATLAB Software on the Peregrine System Using MATLAB Software on the Peregrine System Learn how to use MATLAB software on the Peregrine system. Running MATLAB in Batch Mode Using the node. Understanding Versions and Licenses Learn about the MATLAB software versions and licenses

An implementation framework for wastewater treatment models requiring a minimum programming expertise.

PubMed

Rodríguez, J; Premier, G C; Dinsdale, R; Guwy, A J

2009-01-01

Mathematical modelling in environmental biotechnology has been a traditionally difficult resource to access for researchers and students without programming expertise. The great degree of flexibility required from model implementation platforms to be suitable for research applications restricts their use to programming expert users. More user friendly software packages however do not normally incorporate the necessary flexibility for most research applications. This work presents a methodology based on Excel and Matlab-Simulink for both flexible and accessible implementation of mathematical models by researchers with and without programming expertise. The models are almost fully defined in an Excel file in which the names and values of the state variables and parameters are easily created. This information is automatically processed in Matlab to create the model structure and almost immediate model simulation, after only a minimum Matlab code definition, is possible. The framework proposed also provides programming expert researchers with a highly flexible and modifiable platform on which to base more complex model implementations. The method takes advantage of structural generalities in most mathematical models of environmental bioprocesses while enabling the integration of advanced elements (e.g. heuristic functions, correlations). The methodology has already been successfully used in a number of research studies.

Software Tools for Developing and Simulating the NASA LaRC CMF Motion Base

NASA Technical Reports Server (NTRS)

Bryant, Richard B., Jr.; Carrelli, David J.

2006-01-01

The NASA Langley Research Center (LaRC) Cockpit Motion Facility (CMF) motion base has provided many design and analysis challenges. In the process of addressing these challenges, a comprehensive suite of software tools was developed. The software tools development began with a detailed MATLAB/Simulink model of the motion base which was used primarily for safety loads prediction, design of the closed loop compensator and development of the motion base safety systems1. A Simulink model of the digital control law, from which a portion of the embedded code is directly generated, was later added to this model to form a closed loop system model. Concurrently, software that runs on a PC was created to display and record motion base parameters. It includes a user interface for controlling time history displays, strip chart displays, data storage, and initializing of function generators used during motion base testing. Finally, a software tool was developed for kinematic analysis and prediction of mechanical clearances for the motion system. These tools work together in an integrated package to support normal operations of the motion base, simulate the end to end operation of the motion base system providing facilities for software-in-the-loop testing, mechanical geometry and sensor data visualizations, and function generator setup and evaluation.

Advanced processing and simulation of MRS data using the FID appliance (FID-A)-An open source, MATLAB-based toolkit.

PubMed

Simpson, Robin; Devenyi, Gabriel A; Jezzard, Peter; Hennessy, T Jay; Near, Jamie

2017-01-01

To introduce a new toolkit for simulation and processing of magnetic resonance spectroscopy (MRS) data, and to demonstrate some of its novel features. The FID appliance (FID-A) is an open-source, MATLAB-based software toolkit for simulation and processing of MRS data. The software is designed specifically for processing data with multiple dimensions (eg, multiple radiofrequency channels, averages, spectral editing dimensions). It is equipped with functions for importing data in the formats of most major MRI vendors (eg, Siemens, Philips, GE, Agilent) and for exporting data into the formats of several common processing software packages (eg, LCModel, jMRUI, Tarquin). This paper introduces the FID-A software toolkit and uses examples to demonstrate its novel features, namely 1) the use of a spectral registration algorithm to carry out useful processing routines automatically, 2) automatic detection and removal of motion-corrupted scans, and 3) the ability to perform several major aspects of the MRS computational workflow from a single piece of software. This latter feature is illustrated through both high-level processing of in vivo GABA-edited MEGA-PRESS MRS data, as well as detailed quantum mechanical simulations to generate an accurate LCModel basis set for analysis of the same data. All of the described processing steps resulted in a marked improvement in spectral quality compared with unprocessed data. Fitting of MEGA-PRESS data using a customized basis set resulted in improved fitting accuracy compared with a generic MEGA-PRESS basis set. The FID-A software toolkit enables high-level processing of MRS data and accurate simulation of in vivo MRS experiments. Magn Reson Med 77:23-33, 2017. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Matlab-Excel Interface for OpenDSS

DOE Office of Scientific and Technical Information (OSTI.GOV)

The software allows users of the OpenDSS grid modeling software to access their load flow models using a GUI interface developed in MATLAB. The circuit definitions are entered into a Microsoft Excel spreadsheet which makes circuit creation and editing a much simpler process than the basic text-based editors used in the native OpenDSS interface. Plot tools have been developed which can be accessed through a MATLAB GUI once the desired parameters have been simulated.

Pedagogical issues for effective teaching of biosignal processing and analysis.

PubMed

Sandham, William A; Hamilton, David J

2010-01-01

Biosignal processing and analysis is generally perceived by many students to be a challenging topic to understand, and to become adept with the necessary analytical skills. This is a direct consequence of the high mathematical content involved, and the many abstract features of the topic. The MATLAB and Mathcad software packages offer an excellent algorithm development environment for teaching biosignal processing and analysis modules, and can also be used effectively in many biosignal, and indeed bioengineering, research areas. In this paper, traditional introductory and advanced biosignal processing (and analysis) syllabi are reviewed, and the use of MATLAB and Mathcad for teaching and research is illustrated with a number of examples.

From MIMO-OFDM Algorithms to a Real-Time Wireless Prototype: A Systematic Matlab-to-Hardware Design Flow

NASA Astrophysics Data System (ADS)

Weijers, Jan-Willem; Derudder, Veerle; Janssens, Sven; Petré, Frederik; Bourdoux, André

2006-12-01

To assess the performance of forthcoming 4th generation wireless local area networks, the algorithmic functionality is usually modelled using a high-level mathematical software package, for instance, Matlab. In order to validate the modelling assumptions against the real physical world, the high-level functional model needs to be translated into a prototype. A systematic system design methodology proves very valuable, since it avoids, or, at least reduces, numerous design iterations. In this paper, we propose a novel Matlab-to-hardware design flow, which allows to map the algorithmic functionality onto the target prototyping platform in a systematic and reproducible way. The proposed design flow is partly manual and partly tool assisted. It is shown that the proposed design flow allows to use the same testbench throughout the whole design flow and avoids time-consuming and error-prone intermediate translation steps.

Integrated software environment based on COMKAT for analyzing tracer pharmacokinetics with molecular imaging.

PubMed

Fang, Yu-Hua Dean; Asthana, Pravesh; Salinas, Cristian; Huang, Hsuan-Ming; Muzic, Raymond F

2010-01-01

An integrated software package, Compartment Model Kinetic Analysis Tool (COMKAT), is presented in this report. COMKAT is an open-source software package with many functions for incorporating pharmacokinetic analysis in molecular imaging research and has both command-line and graphical user interfaces. With COMKAT, users may load and display images, draw regions of interest, load input functions, select kinetic models from a predefined list, or create a novel model and perform parameter estimation, all without having to write any computer code. For image analysis, COMKAT image tool supports multiple image file formats, including the Digital Imaging and Communications in Medicine (DICOM) standard. Image contrast, zoom, reslicing, display color table, and frame summation can be adjusted in COMKAT image tool. It also displays and automatically registers images from 2 modalities. Parametric imaging capability is provided and can be combined with the distributed computing support to enhance computation speeds. For users without MATLAB licenses, a compiled, executable version of COMKAT is available, although it currently has only a subset of the full COMKAT capability. Both the compiled and the noncompiled versions of COMKAT are free for academic research use. Extensive documentation, examples, and COMKAT itself are available on its wiki-based Web site, http://comkat.case.edu. Users are encouraged to contribute, sharing their experience, examples, and extensions of COMKAT. With integrated functionality specifically designed for imaging and kinetic modeling analysis, COMKAT can be used as a software environment for molecular imaging and pharmacokinetic analysis.

Pizza.py Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plimpton, Steve; Jones, Matt; Crozier, Paul

2006-01-01

Pizza.py is a loosely integrated collection of tools, many of which provide support for the LAMMPS molecular dynamics and ChemCell cell modeling packages. There are tools to create input files. convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots. Software packages that are wrapped by Pizza.py. so they can invoked from within Python, include GnuPlot, MatLab, Raster3d. and RasMol. Pizza.py is written in Python and runs on any platform that supports Python. Pizza.py enhances the standard Python interpreter in a few simple ways. Its tools are Python modules which can be invokedmore » interactively, from scripts, or from GUIs when appropriate. Some of the tools require additional Python packages to be installed as part of the users Python. Others are wrappers on software packages (as listed above) which must be available on the users system. It is easy to modify or extend Pizza.py with new functionality or new tools, which need not have anything to do with LAMMPS or ChemCell.« less

An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave.

PubMed

Silva, Ikaro; Moody, George B

The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

Binning in Gaussian Kernel Regularization

DTIC Science & Technology

2005-04-01

OSU-SVM Matlab package, the SVM trained on 966 bins has a comparable test classification rate as the SVM trained on 27,179 samples, but reduces the...71.40%) on 966 randomly sampled data. Using the OSU-SVM Matlab package, the SVM trained on 966 bins has a comparable test classification rate as the...the OSU-SVM Matlab package, the SVM trained on 966 bins has a comparable test classification rate as the SVM trained on 27,179 samples, and reduces

Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy

PubMed Central

Duwé, Sam; Neely, Robert K.; Zhang, Jin

2012-01-01

Abstract. We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. PMID:23208219

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

PubMed Central

Liu, Yijin; Meirer, Florian; Williams, Phillip A.; Wang, Junyue; Andrews, Joy C.; Pianetta, Piero

2012-01-01

Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available. PMID:22338691

Validation of XMALab software for marker-based XROMM.

PubMed

Knörlein, Benjamin J; Baier, David B; Gatesy, Stephen M; Laurence-Chasen, J D; Brainerd, Elizabeth L

2016-12-01

Marker-based XROMM requires software tools for: (1) correcting fluoroscope distortion; (2) calibrating X-ray cameras; (3) tracking radio-opaque markers; and (4) calculating rigid body motion. In this paper we describe and validate XMALab, a new open-source software package for marker-based XROMM (C++ source and compiled versions on Bitbucket). Most marker-based XROMM studies to date have used XrayProject in MATLAB. XrayProject can produce results with excellent accuracy and precision, but it is somewhat cumbersome to use and requires a MATLAB license. We have designed XMALab to accelerate the XROMM process and to make it more accessible to new users. Features include the four XROMM steps (listed above) in one cohesive user interface, real-time plot windows for detecting errors, and integration with an online data management system, XMAPortal. Accuracy and precision of XMALab when tracking markers in a machined object are ±0.010 and ±0.043 mm, respectively. Mean precision for nine users tracking markers in a tutorial dataset of minipig feeding was ±0.062 mm in XMALab and ±0.14 mm in XrayProject. Reproducibility of 3D point locations across nine users was 10-fold greater in XMALab than in XrayProject, and six degree-of-freedom bone motions calculated with a joint coordinate system were 3- to 6-fold more reproducible in XMALab. XMALab is also suitable for tracking white or black markers in standard light videos with optional checkerboard calibration. We expect XMALab to increase both the quality and quantity of animal motion data available for comparative biomechanics research. © 2016. Published by The Company of Biologists Ltd.

TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks

NASA Astrophysics Data System (ADS)

Kazantsev, Daniil; Pickalov, Valery; Nagella, Srikanth; Pasca, Edoardo; Withers, Philip J.

2018-01-01

In the field of computerized tomographic imaging, many novel reconstruction techniques are routinely tested using simplistic numerical phantoms, e.g. the well-known Shepp-Logan phantom. These phantoms cannot sufficiently cover the broad spectrum of applications in CT imaging where, for instance, smooth or piecewise-smooth 3D objects are common. TomoPhantom provides quick access to an external library of modular analytical 2D/3D phantoms with temporal extensions. In TomoPhantom, quite complex phantoms can be built using additive combinations of geometrical objects, such as, Gaussians, parabolas, cones, ellipses, rectangles and volumetric extensions of them. Newly designed phantoms are better suited for benchmarking and testing of different image processing techniques. Specifically, tomographic reconstruction algorithms which employ 2D and 3D scanning geometries, can be rigorously analyzed using the software. TomoPhantom also provides a capability of obtaining analytical tomographic projections which further extends the applicability of software towards more realistic, free from the "inverse crime" testing. All core modules of the package are written in the C-OpenMP language and wrappers for Python and MATLAB are provided to enable easy access. Due to C-based multi-threaded implementation, volumetric phantoms of high spatial resolution can be obtained with computational efficiency.

Kinematic analysis of the finger exoskeleton using MATLAB/Simulink.

PubMed

Nasiłowski, Krzysztof; Awrejcewicz, Jan; Lewandowski, Donat

2014-01-01

A paralyzed and not fully functional part of human body can be supported by the properly designed exoskeleton system with motoric abilities. It can help in rehabilitation, or movement of a disabled/paralyzed limb. Both suitably selected geometry and specialized software are studied applying the MATLAB environment. A finger exoskeleton was the base for MATLAB/Simulink model. Specialized software, such as MATLAB/Simulink give us an opportunity to optimize calculation reaching precise results, which help in next steps of design process. The calculations carried out yield information regarding movement relation between three functionally connected actuators and showed distance and velocity changes during the whole simulation time.

Image processing and pattern recognition with CVIPtools MATLAB toolbox: automatic creation of masks for veterinary thermographic images

NASA Astrophysics Data System (ADS)

Mishra, Deependra K.; Umbaugh, Scott E.; Lama, Norsang; Dahal, Rohini; Marino, Dominic J.; Sackman, Joseph

2016-09-01

CVIPtools is a software package for the exploration of computer vision and image processing developed in the Computer Vision and Image Processing Laboratory at Southern Illinois University Edwardsville. CVIPtools is available in three variants - a) CVIPtools Graphical User Interface, b) CVIPtools C library and c) CVIPtools MATLAB toolbox, which makes it accessible to a variety of different users. It offers students, faculty, researchers and any user a free and easy way to explore computer vision and image processing techniques. Many functions have been implemented and are updated on a regular basis, the library has reached a level of sophistication that makes it suitable for both educational and research purposes. In this paper, the detail list of the functions available in the CVIPtools MATLAB toolbox are presented and how these functions can be used in image analysis and computer vision applications. The CVIPtools MATLAB toolbox allows the user to gain practical experience to better understand underlying theoretical problems in image processing and pattern recognition. As an example application, the algorithm for the automatic creation of masks for veterinary thermographic images is presented.

Error correction and diversity analysis of population mixtures determined by NGS

PubMed Central

Burroughs, Nigel J.; Evans, David J.; Ryabov, Eugene V.

2014-01-01

The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. The error correction method is statistically based and works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. The methods are illustrated using honeybee viral samples. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/, the Warwick University Systems Biology Centre software download site. PMID:25405074

A Compilation of MATLAB Scripts and Functions for MACGMC Analyses

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Bednarcyk, Brett A.; Mital, Subodh K.

2017-01-01

The primary aim of the current effort is to provide scripts that automate many of the repetitive pre- and post-processing tasks associated with composite materials analyses using the Micromechanics Analysis Code with the Generalized Method of Cells. This document consists of a compilation of hundreds of scripts that were developed in MATLAB (The Mathworks, Inc., Natick, MA) programming language and consolidated into 16 MATLAB functions. (MACGMC). MACGMC is a composite material and laminate analysis software code developed at NASA Glenn Research Center. The software package has been built around the generalized method of cells (GMC) family of micromechanics theories. The computer code is developed with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The pre-processing tasks include generation of a multitude of different repeating unit cells (RUCs) for CMCs and PMCs, visualization of RUCs from MACGMC input and output files and generation of the RUC section of a MACGMC input file. The post-processing tasks include visualization of the predicted composite response, such as local stress and strain contours, damage initiation and progression, stress-strain behavior, and fatigue response. In addition to the above, several miscellaneous scripts have been developed that can be used to perform repeated Monte-Carlo simulations to enable probabilistic simulations with minimal manual intervention. This document is formatted to provide MATLAB source files and descriptions of how to utilize them. It is assumed that the user has a basic understanding of how MATLAB scripts work and some MATLAB programming experience.

Design of FPGA ICA for hyperspectral imaging processing

NASA Astrophysics Data System (ADS)

Nordin, Anis; Hsu, Charles C.; Szu, Harold H.

2001-03-01

The remote sensing problem which uses hyperspectral imaging can be transformed into a blind source separation problem. Using this model, hyperspectral imagery can be de-mixed into sub-pixel spectra which indicate the different material present in the pixel. This can be further used to deduce areas which contain forest, water or biomass, without even knowing the sources which constitute the image. This form of remote sensing allows previously blurred images to show the specific terrain involved in that region. The blind source separation problem can be implemented using an Independent Component Analysis algorithm. The ICA Algorithm has previously been successfully implemented using software packages such as MATLAB, which has a downloadable version of FastICA. The challenge now lies in implementing it in a form of hardware, or firmware in order to improve its computational speed. Hardware implementation also solves insufficient memory problem encountered by software packages like MATLAB when employing ICA for high resolution images and a large number of channels. Here, a pipelined solution of the firmware, realized using FPGAs are drawn out and simulated using C. Since C code can be translated into HDLs or be used directly on the FPGAs, it can be used to simulate its actual implementation in hardware. The simulated results of the program is presented here, where seven channels are used to model the 200 different channels involved in hyperspectral imaging.

Design of an ammonia closed-loop storage system in a CSP power plant with a power tower cavity receiver

NASA Astrophysics Data System (ADS)

Abdiwe, Ramadan; Haider, Markus

2017-06-01

In this study the thermochemical system using ammonia as energy storage carrier is investigated and a transient mathematical model using MATLAB software was developed to predict the behavior of the ammonia closed-loop storage system including but not limited to the ammonia solar reactor and the ammonia synthesis reactor. The MATLAB model contains transient mass and energy balances as well as chemical equilibrium model for each relevant system component. For the importance of the dissociation and formation processes in the system, a Computational Fluid Dynamics (CFD) simulation on the ammonia solar and synthesis reactors has been performed. The CFD commercial package FLUENT is used for the simulation study and all the important mechanisms for packed bed reactors are taken into account, such as momentum, heat and mass transfer, and chemical reactions. The FLUENT simulation reveals the profiles inside both reactors and compared them with the profiles from the MATLAB code.

Dynamic optimization case studies in DYNOPT tool

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.

Dispersed Fringe Sensing Analysis - DFSA

NASA Technical Reports Server (NTRS)

Sigrist, Norbert; Shi, Fang; Redding, David C.; Basinger, Scott A.; Ohara, Catherine M.; Seo, Byoung-Joon; Bikkannavar, Siddarayappa A.; Spechler, Joshua A.

2012-01-01

Dispersed Fringe Sensing (DFS) is a technique for measuring and phasing segmented telescope mirrors using a dispersed broadband light image. DFS is capable of breaking the monochromatic light ambiguity, measuring absolute piston errors between segments of large segmented primary mirrors to tens of nanometers accuracy over a range of 100 micrometers or more. The DFSA software tool analyzes DFS images to extract DFS encoded segment piston errors, which can be used to measure piston distances between primary mirror segments of ground and space telescopes. This information is necessary to control mirror segments to establish a smooth, continuous primary figure needed to achieve high optical quality. The DFSA tool is versatile, allowing precise piston measurements from a variety of different optical configurations. DFSA technology may be used for measuring wavefront pistons from sub-apertures defined by adjacent segments (such as Keck Telescope), or from separated sub-apertures used for testing large optical systems (such as sub-aperture wavefront testing for large primary mirrors using auto-collimating flats). An experimental demonstration of the coarse-phasing technology with verification of DFSA was performed at the Keck Telescope. DFSA includes image processing, wavelength and source spectral calibration, fringe extraction line determination, dispersed fringe analysis, and wavefront piston sign determination. The code is robust against internal optical system aberrations and against spectral variations of the source. In addition to the DFSA tool, the software package contains a simple but sophisticated MATLAB model to generate dispersed fringe images of optical system configurations in order to quickly estimate the coarse phasing performance given the optical and operational design requirements. Combining MATLAB (a high-level language and interactive environment developed by MathWorks), MACOS (JPL s software package for Modeling and Analysis for Controlled Optical Systems), and DFSA provides a unique optical development, modeling and analysis package to study current and future approaches to coarse phasing controlled segmented optical systems.

Characterization of fission gas bubbles in irradiated U-10Mo fuel

DOE PAGES

Casella, Andrew M.; Burkes, Douglas E.; MacFarlan, Paul J.; ...

2017-06-06

A simple, repeatable method for characterization of fission gas bubbles in irradiated U-Mo fuels has been developed. This method involves mechanical potting and polishing of samples along with examination with a scanning electron microscope located outside of a hot cell. The commercially available software packages CellProfiler, MATLAB, and Mathematica are used to segment and analyze the captured images. The results are compared and contrasted. Finally, baseline methods for fission gas bubble characterization are suggested for consideration and further development.

Memory-Efficient Analysis of Dense Functional Connectomes.

PubMed

Loewe, Kristian; Donohue, Sarah E; Schoenfeld, Mircea A; Kruse, Rudolf; Borgelt, Christian

2016-01-01

The functioning of the human brain relies on the interplay and integration of numerous individual units within a complex network. To identify network configurations characteristic of specific cognitive tasks or mental illnesses, functional connectomes can be constructed based on the assessment of synchronous fMRI activity at separate brain sites, and then analyzed using graph-theoretical concepts. In most previous studies, relatively coarse parcellations of the brain were used to define regions as graphical nodes. Such parcellated connectomes are highly dependent on parcellation quality because regional and functional boundaries need to be relatively consistent for the results to be interpretable. In contrast, dense connectomes are not subject to this limitation, since the parcellation inherent to the data is used to define graphical nodes, also allowing for a more detailed spatial mapping of connectivity patterns. However, dense connectomes are associated with considerable computational demands in terms of both time and memory requirements. The memory required to explicitly store dense connectomes in main memory can render their analysis infeasible, especially when considering high-resolution data or analyses across multiple subjects or conditions. Here, we present an object-based matrix representation that achieves a very low memory footprint by computing matrix elements on demand instead of explicitly storing them. In doing so, memory required for a dense connectome is reduced to the amount needed to store the underlying time series data. Based on theoretical considerations and benchmarks, different matrix object implementations and additional programs (based on available Matlab functions and Matlab-based third-party software) are compared with regard to their computational efficiency. The matrix implementation based on on-demand computations has very low memory requirements, thus enabling analyses that would be otherwise infeasible to conduct due to insufficient memory. An open source software package containing the created programs is available for download.

Memory-Efficient Analysis of Dense Functional Connectomes

PubMed Central

Loewe, Kristian; Donohue, Sarah E.; Schoenfeld, Mircea A.; Kruse, Rudolf; Borgelt, Christian

2016-01-01

The functioning of the human brain relies on the interplay and integration of numerous individual units within a complex network. To identify network configurations characteristic of specific cognitive tasks or mental illnesses, functional connectomes can be constructed based on the assessment of synchronous fMRI activity at separate brain sites, and then analyzed using graph-theoretical concepts. In most previous studies, relatively coarse parcellations of the brain were used to define regions as graphical nodes. Such parcellated connectomes are highly dependent on parcellation quality because regional and functional boundaries need to be relatively consistent for the results to be interpretable. In contrast, dense connectomes are not subject to this limitation, since the parcellation inherent to the data is used to define graphical nodes, also allowing for a more detailed spatial mapping of connectivity patterns. However, dense connectomes are associated with considerable computational demands in terms of both time and memory requirements. The memory required to explicitly store dense connectomes in main memory can render their analysis infeasible, especially when considering high-resolution data or analyses across multiple subjects or conditions. Here, we present an object-based matrix representation that achieves a very low memory footprint by computing matrix elements on demand instead of explicitly storing them. In doing so, memory required for a dense connectome is reduced to the amount needed to store the underlying time series data. Based on theoretical considerations and benchmarks, different matrix object implementations and additional programs (based on available Matlab functions and Matlab-based third-party software) are compared with regard to their computational efficiency. The matrix implementation based on on-demand computations has very low memory requirements, thus enabling analyses that would be otherwise infeasible to conduct due to insufficient memory. An open source software package containing the created programs is available for download. PMID:27965565

Using MATLAB Software on the Peregrine System | High-Performance Computing

Science.gov Websites

Learn how to run MATLAB software in batch mode on the Peregrine system. Below is an example MATLAB job in batch (non-interactive) mode. To try the example out, create both matlabTest.sub and /$USER. In this example, it is also the directory into which MATLAB will write the output file x.dat

ADFNE: Open source software for discrete fracture network engineering, two and three dimensional applications

NASA Astrophysics Data System (ADS)

Fadakar Alghalandis, Younes

2017-05-01

Rapidly growing topic, the discrete fracture network engineering (DFNE), has already attracted many talents from diverse disciplines in academia and industry around the world to challenge difficult problems related to mining, geothermal, civil, oil and gas, water and many other projects. Although, there are few commercial software capable of providing some useful functionalities fundamental for DFNE, their costs, closed code (black box) distributions and hence limited programmability and tractability encouraged us to respond to this rising demand with a new solution. This paper introduces an open source comprehensive software package for stochastic modeling of fracture networks in two- and three-dimension in discrete formulation. Functionalities included are geometric modeling (e.g., complex polygonal fracture faces, and utilizing directional statistics), simulations, characterizations (e.g., intersection, clustering and connectivity analyses) and applications (e.g., fluid flow). The package is completely written in Matlab scripting language. Significant efforts have been made to bring maximum flexibility to the functions in order to solve problems in both two- and three-dimensions in an easy and united way that is suitable for beginners, advanced and experienced users.

BasinVis 1.0: A MATLAB®-based program for sedimentary basin subsidence analysis and visualization

NASA Astrophysics Data System (ADS)

Lee, Eun Young; Novotny, Johannes; Wagreich, Michael

2016-06-01

Stratigraphic and structural mapping is important to understand the internal structure of sedimentary basins. Subsidence analysis provides significant insights for basin evolution. We designed a new software package to process and visualize stratigraphic setting and subsidence evolution of sedimentary basins from well data. BasinVis 1.0 is implemented in MATLAB®, a multi-paradigm numerical computing environment, and employs two numerical methods: interpolation and subsidence analysis. Five different interpolation methods (linear, natural, cubic spline, Kriging, and thin-plate spline) are provided in this program for surface modeling. The subsidence analysis consists of decompaction and backstripping techniques. BasinVis 1.0 incorporates five main processing steps; (1) setup (study area and stratigraphic units), (2) loading well data, (3) stratigraphic setting visualization, (4) subsidence parameter input, and (5) subsidence analysis and visualization. For in-depth analysis, our software provides cross-section and dip-slip fault backstripping tools. The graphical user interface guides users through the workflow and provides tools to analyze and export the results. Interpolation and subsidence results are cached to minimize redundant computations and improve the interactivity of the program. All 2D and 3D visualizations are created by using MATLAB plotting functions, which enables users to fine-tune the results using the full range of available plot options in MATLAB. We demonstrate all functions in a case study of Miocene sediment in the central Vienna Basin.

SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer.

PubMed

Li, Jiannong; Smalley, Inna; Schell, Michael J; Smalley, Keiran S M; Chen, Y Ann

2017-09-15

Single-cell technologies allow characterization of transcriptomes and epigenomes for individual cells under different conditions and provide unprecedented resolution for researchers to investigate cellular heterogeneity in cancer. The SinCHet ( gle ell erogeneity) toolbox is developed in MATLAB and has a graphical user interface (GUI) for visualization and user interaction. It analyzes both continuous (e.g. mRNA expression) and binary omics data (e.g. discretized methylation data). The toolbox does not only quantify cellular heterogeneity using S hannon P rofile (SP) at different clonal resolutions but also detects heterogeneity differences using a D statistic between two populations. It is defined as the area under the P rofile of S hannon D ifference (PSD). This flexible tool provides a default clonal resolution using the change point of PSD detected by multivariate adaptive regression splines model; it also allows user-defined clonal resolutions for further investigation. This tool provides insights into emerging or disappearing clones between conditions, and enables the prioritization of biomarkers for follow-up experiments based on heterogeneity or marker differences between and/or within cell populations. The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http://labpages2.moffitt.org/chen/software/ . ann.chen@moffitt.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

A menu-driven software package of Bayesian nonparametric (and parametric) mixed models for regression analysis and density estimation.

PubMed

Karabatsos, George

2017-02-01

Most of applied statistics involves regression analysis of data. In practice, it is important to specify a regression model that has minimal assumptions which are not violated by data, to ensure that statistical inferences from the model are informative and not misleading. This paper presents a stand-alone and menu-driven software package, Bayesian Regression: Nonparametric and Parametric Models, constructed from MATLAB Compiler. Currently, this package gives the user a choice from 83 Bayesian models for data analysis. They include 47 Bayesian nonparametric (BNP) infinite-mixture regression models; 5 BNP infinite-mixture models for density estimation; and 31 normal random effects models (HLMs), including normal linear models. Each of the 78 regression models handles either a continuous, binary, or ordinal dependent variable, and can handle multi-level (grouped) data. All 83 Bayesian models can handle the analysis of weighted observations (e.g., for meta-analysis), and the analysis of left-censored, right-censored, and/or interval-censored data. Each BNP infinite-mixture model has a mixture distribution assigned one of various BNP prior distributions, including priors defined by either the Dirichlet process, Pitman-Yor process (including the normalized stable process), beta (two-parameter) process, normalized inverse-Gaussian process, geometric weights prior, dependent Dirichlet process, or the dependent infinite-probits prior. The software user can mouse-click to select a Bayesian model and perform data analysis via Markov chain Monte Carlo (MCMC) sampling. After the sampling completes, the software automatically opens text output that reports MCMC-based estimates of the model's posterior distribution and model predictive fit to the data. Additional text and/or graphical output can be generated by mouse-clicking other menu options. This includes output of MCMC convergence analyses, and estimates of the model's posterior predictive distribution, for selected functionals and values of covariates. The software is illustrated through the BNP regression analysis of real data.

PANDA: a pipeline toolbox for analyzing brain diffusion images.

PubMed

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

PANDA: a pipeline toolbox for analyzing brain diffusion images

PubMed Central

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named “Pipeline for Analyzing braiN Diffusion imAges” (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies. PMID:23439846

Insolation-oriented model of photovoltaic module using Matlab/Simulink

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Huan-Liang

2010-07-15

This paper presents a novel model of photovoltaic (PV) module which is implemented and analyzed using Matlab/Simulink software package. Taking the effect of sunlight irradiance on the cell temperature, the proposed model takes ambient temperature as reference input and uses the solar insolation as a unique varying parameter. The cell temperature is then explicitly affected by the sunlight intensity. The output current and power characteristics are simulated and analyzed using the proposed PV model. The model verification has been confirmed through an experimental measurement. The impact of solar irradiation on cell temperature makes the output characteristic more practical. In addition,more » the insolation-oriented PV model enables the dynamics of PV power system to be analyzed and optimized more easily by applying the environmental parameters of ambient temperature and solar irradiance. (author)« less

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink(Registered TradeMark) (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

An Earthquake Shake Map Routine with Low Cost Accelerometers: Preliminary Results

NASA Astrophysics Data System (ADS)

Alcik, H. A.; Tanircan, G.; Kaya, Y.

2015-12-01

Vast amounts of high quality strong motion data are indispensable inputs of the analyses in the field of geotechnical and earthquake engineering however, high cost of installation of the strong motion systems constitutes the biggest obstacle for worldwide dissemination. In recent years, MEMS based (micro-electro-mechanical systems) accelerometers have been used in seismological research-oriented studies as well as earthquake engineering oriented projects basically due to precision obtained in downsized instruments. In this research our primary goal is to ensure the usage of these low-cost instruments in the creation of shake-maps immediately after a strong earthquake. Second goal is to develop software that will automatically process the real-time data coming from the rapid response network and create shake-map. For those purposes, four MEMS sensors have been set up to deliver real-time data. Data transmission is done through 3G modems. A subroutine was coded in assembler language and embedded into the operating system of each instrument to create MiniSEED files with packages of 1-second instead of 512-byte packages.The Matlab-based software calculates the strong motion (SM) parameters at every second, and they are compared with the user-defined thresholds. A voting system embedded in the software captures the event if the total vote exceeds the threshold. The user interface of the software enables users to monitor the calculated SM parameters either in a table or in a graph (Figure 1). A small scale and affordable rapid response network is created using four MEMS sensors, and the functionality of the software has been tested and validated using shake table tests. The entire system is tested together with a reference sensor under real strong ground motion recordings as well as series of sine waves with varying amplitude and frequency. The successful realization of this software allowed us to set up a test network at Tekirdağ Province, the closest coastal point to the moderate size earthquake activities in the Marmara Sea, Turkey.

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

Multidisciplinary Optimization for Aerospace Using Genetic Optimization

NASA Technical Reports Server (NTRS)

Pak, Chan-gi; Hahn, Edward E.; Herrera, Claudia Y.

2007-01-01

In support of the ARMD guidelines NASA's Dryden Flight Research Center is developing a multidisciplinary design and optimization tool This tool will leverage existing tools and practices, and allow the easy integration and adoption of new state-of-the-art software. Optimization has made its way into many mainstream applications. For example NASTRAN(TradeMark) has its solution sequence 200 for Design Optimization, and MATLAB(TradeMark) has an Optimization Tool box. Other packages, such as ZAERO(TradeMark) aeroelastic panel code and the CFL3D(TradeMark) Navier-Stokes solver have no built in optimizer. The goal of the tool development is to generate a central executive capable of using disparate software packages ina cross platform network environment so as to quickly perform optimization and design tasks in a cohesive streamlined manner. A provided figure (Figure 1) shows a typical set of tools and their relation to the central executive. Optimization can take place within each individual too, or in a loop between the executive and the tool, or both.

Features of control systems analysis with discrete control devices using mathematical packages

NASA Astrophysics Data System (ADS)

Yakovleva, E. M.; Faerman, V. A.

2017-02-01

The article contains presentation of basic provisions of the theory of automatic pulse control systems as well as methods of analysis of such systems using the mathematical software widespread in the academic environment. The pulse systems under research are considered as analogues systems interacting among themselves, including sensors, amplifiers, controlled objects, and discrete parts. To describe such systems, one uses a mathematical apparatus of difference equations as well as discrete transfer functions. To obtain a transfer function of the open-loop system, being important from the point of view of the analysis of control systems, one uses mathematical packages Mathcad and Matlab. Despite identity of the obtained result, the way of its achievement from the point of view of user’s action is various for the specified means. In particular, Matlab uses a structural model of the control system while Mathcad allows only execution of a chain of operator transforms. It is worth noting that distinctions taking place allow considering transformation of signals during interaction of the linear and continuous parts of the control system from different sides. The latter can be used in an educational process for the best assimilation of the course of the control system theory by students.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

Anti-islanding Protection of Distributed Generation Using Rate of Change of Impedance

NASA Astrophysics Data System (ADS)

Shah, Pragnesh; Bhalja, Bhavesh

2013-08-01

Distributed Generation (DG), which is interlinked with distribution system, has inevitable effect on distribution system. Integrating DG with the utility network demands an anti-islanding scheme to protect the system. Failure to trip islanded generators can lead to problems such as threats to personnel safety, out-of-phase reclosing, and degradation of power quality. In this article, a new method for anti-islanding protection based on impedance monitoring of distribution network is carried out in presence of DG. The impedance measured between two phases is used to derive the rate of change of impedance (dz/dt), and its peak values are used for final trip decision. Test data are generated using PSCAD/EMTDC software package and the performance of the proposed method is evaluated in MatLab software. The simulation results show the effectiveness of the proposed scheme as it is capable to detect islanding condition accurately. Subsequently, it is also observed that the proposed scheme does not mal-operate during other disturbances such as short circuit and switching event.

A user-friendly software package to ease the use of VIC hydrologic model for practitioners

NASA Astrophysics Data System (ADS)

Wi, S.; Ray, P.; Brown, C.

2016-12-01

The VIC (Variable Infiltration Capacity) hydrologic and river routing model simulates the water and energy fluxes that occur near the land surface and provides users with useful information regarding the quantity and timing of available water at points of interest within the basin. However, despite its popularity (proved by numerous applications in the literature), its wider adoption is hampered by the considerable effort required to prepare model inputs; e.g., input files storing spatial information related to watershed topography, soil properties, and land cover. This study presents a user-friendly software package (named VIC Setup Toolkit) developed within the MATLAB (matrix laboratory) framework and accessible through an intuitive graphical user interface. The VIC Setup Toolkit enables users to navigate the model building process confidently through prompts and automation, with an intention to promote the use of the model for both practical and academic purposes. The automated processes include watershed delineation, climate and geographical input set-up, model parameter calibration, graph generation and output evaluation. We demonstrate the package's usefulness in various case studies with the American River, Oklahoma River, Feather River and Zambezi River basins.

A versatile software package for inter-subject correlation based analyses of fMRI.

PubMed

Kauppi, Jukka-Pekka; Pajula, Juha; Tohka, Jussi

2014-01-01

In the inter-subject correlation (ISC) based analysis of the functional magnetic resonance imaging (fMRI) data, the extent of shared processing across subjects during the experiment is determined by calculating correlation coefficients between the fMRI time series of the subjects in the corresponding brain locations. This implies that ISC can be used to analyze fMRI data without explicitly modeling the stimulus and thus ISC is a potential method to analyze fMRI data acquired under complex naturalistic stimuli. Despite of the suitability of ISC based approach to analyze complex fMRI data, no generic software tools have been made available for this purpose, limiting a widespread use of ISC based analysis techniques among neuroimaging community. In this paper, we present a graphical user interface (GUI) based software package, ISC Toolbox, implemented in Matlab for computing various ISC based analyses. Many advanced computations such as comparison of ISCs between different stimuli, time window ISC, and inter-subject phase synchronization are supported by the toolbox. The analyses are coupled with re-sampling based statistical inference. The ISC based analyses are data and computation intensive and the ISC toolbox is equipped with mechanisms to execute the parallel computations in a cluster environment automatically and with an automatic detection of the cluster environment in use. Currently, SGE-based (Oracle Grid Engine, Son of a Grid Engine, or Open Grid Scheduler) and Slurm environments are supported. In this paper, we present a detailed account on the methods behind the ISC Toolbox, the implementation of the toolbox and demonstrate the possible use of the toolbox by summarizing selected example applications. We also report the computation time experiments both using a single desktop computer and two grid environments demonstrating that parallelization effectively reduces the computing time. The ISC Toolbox is available in https://code.google.com/p/isc-toolbox/

A versatile software package for inter-subject correlation based analyses of fMRI

PubMed Central

Kauppi, Jukka-Pekka; Pajula, Juha; Tohka, Jussi

2014-01-01

In the inter-subject correlation (ISC) based analysis of the functional magnetic resonance imaging (fMRI) data, the extent of shared processing across subjects during the experiment is determined by calculating correlation coefficients between the fMRI time series of the subjects in the corresponding brain locations. This implies that ISC can be used to analyze fMRI data without explicitly modeling the stimulus and thus ISC is a potential method to analyze fMRI data acquired under complex naturalistic stimuli. Despite of the suitability of ISC based approach to analyze complex fMRI data, no generic software tools have been made available for this purpose, limiting a widespread use of ISC based analysis techniques among neuroimaging community. In this paper, we present a graphical user interface (GUI) based software package, ISC Toolbox, implemented in Matlab for computing various ISC based analyses. Many advanced computations such as comparison of ISCs between different stimuli, time window ISC, and inter-subject phase synchronization are supported by the toolbox. The analyses are coupled with re-sampling based statistical inference. The ISC based analyses are data and computation intensive and the ISC toolbox is equipped with mechanisms to execute the parallel computations in a cluster environment automatically and with an automatic detection of the cluster environment in use. Currently, SGE-based (Oracle Grid Engine, Son of a Grid Engine, or Open Grid Scheduler) and Slurm environments are supported. In this paper, we present a detailed account on the methods behind the ISC Toolbox, the implementation of the toolbox and demonstrate the possible use of the toolbox by summarizing selected example applications. We also report the computation time experiments both using a single desktop computer and two grid environments demonstrating that parallelization effectively reduces the computing time. The ISC Toolbox is available in https://code.google.com/p/isc-toolbox/ PMID:24550818

MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

PubMed

Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

NASA Astrophysics Data System (ADS)

Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C.

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

A system for beach video-monitoring: Beachkeeper plus

NASA Astrophysics Data System (ADS)

Brignone, Massimo; Schiaffino, Chiara F.; Isla, Federico I.; Ferrari, Marco

2012-12-01

A suitable knowledge of coastal systems, of their morphodynamic characteristics and their response to storm events and man-made structures is essential for littoral conservation and management. Nowadays webcams represent a useful device to obtain information from beaches. Video-monitoring techniques are generally site specific and softwares working with any image acquisition system are rare. Therefore, this work aims at submitting theory and applications of an experimental video monitoring software: Beachkeeper plus, a freeware non-profit software, can be employed and redistributed without modifications. A license file is provided inside software package and in the user guide. Beachkeeper plus is based on Matlab® and it can be used for the analysis of images and photos coming from any kind of acquisition system (webcams, digital cameras or images downloaded from internet), without any a-priori information or laboratory study of the acquisition system itself. Therefore, it could become a useful tool for beach planning. Through a simple guided interface, images can be analyzed by performing georeferentiation, rectification, averaging and variance. This software was initially operated in Pietra Ligure (Italy), using images from a tourist webcam, and in Mar del Plata (Argentina) using images from a digital camera. In both cases the reliability in different geomorphologic and morphodynamic conditions was confirmed by the good quality of obtained images after georeferentiation, rectification and averaging.

Echo™ User Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, Dustin Yewell

Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reportingmore » and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.« less

Use of CellNetAnalyzer in biotechnology and metabolic engineering.

PubMed

von Kamp, Axel; Thiele, Sven; Hädicke, Oliver; Klamt, Steffen

2017-11-10

Mathematical models of the cellular metabolism have become an essential tool for the optimization of biotechnological processes. They help to obtain a systemic understanding of the metabolic processes in the used microorganisms and to find suitable genetic modifications maximizing the production performance. In particular, methods of stoichiometric and constraint-based modeling are frequently used in the context of metabolic and bioprocess engineering. Since metabolic networks can be complex and comprise hundreds or even thousands of metabolites and reactions, dedicated software tools are required for an efficient analysis. One such software suite is CellNetAnalyzer, a MATLAB package providing, among others, various methods for analyzing stoichiometric and constraint-based metabolic models. CellNetAnalyzer can be used via command-line based operations or via a graphical user interface with embedded network visualizations. Herein we will present key functionalities of CellNetAnalyzer for applications in biotechnology and metabolic engineering and thereby review constraint-based modeling techniques such as metabolic flux analysis, flux balance analysis, flux variability analysis, metabolic pathway analysis (elementary flux modes) and methods for computational strain design. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

MatchGUI: A Graphical MATLAB-Based Tool for Automatic Image Co-Registration

NASA Technical Reports Server (NTRS)

Ansar, Adnan I.

2011-01-01

MatchGUI software, based on MATLAB, automatically matches two images and displays the match result by superimposing one image on the other. A slider bar allows focus to shift between the two images. There are tools for zoom, auto-crop to overlap region, and basic image markup. Given a pair of ortho-rectified images (focused primarily on Mars orbital imagery for now), this software automatically co-registers the imagery so that corresponding image pixels are aligned. MatchGUI requires minimal user input, and performs a registration over scale and inplane rotation fully automatically

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

Equilibrium-Staged Separations Using Matlab and Mathematica

ERIC Educational Resources Information Center

Binous, Housam

2008-01-01

We show a new approach, based on the utilization of Matlab and Mathematica, for solving liquid-liquid extraction and binary distillation problems. In addition, the author shares his experience using these two softwares to teach equilibrium staged separations at the National Institute of Applied Sciences and Technology. (Contains 7 figures.)

Phenological Parameters Estimation Tool

NASA Technical Reports Server (NTRS)

McKellip, Rodney D.; Ross, Kenton W.; Spruce, Joseph P.; Smoot, James C.; Ryan, Robert E.; Gasser, Gerald E.; Prados, Donald L.; Vaughan, Ronald D.

2010-01-01

The Phenological Parameters Estimation Tool (PPET) is a set of algorithms implemented in MATLAB that estimates key vegetative phenological parameters. For a given year, the PPET software package takes in temporally processed vegetation index data (3D spatio-temporal arrays) generated by the time series product tool (TSPT) and outputs spatial grids (2D arrays) of vegetation phenological parameters. As a precursor to PPET, the TSPT uses quality information for each pixel of each date to remove bad or suspect data, and then interpolates and digitally fills data voids in the time series to produce a continuous, smoothed vegetation index product. During processing, the TSPT displays NDVI (Normalized Difference Vegetation Index) time series plots and images from the temporally processed pixels. Both the TSPT and PPET currently use moderate resolution imaging spectroradiometer (MODIS) satellite multispectral data as a default, but each software package is modifiable and could be used with any high-temporal-rate remote sensing data collection system that is capable of producing vegetation indices. Raw MODIS data from the Aqua and Terra satellites is processed using the TSPT to generate a filtered time series data product. The PPET then uses the TSPT output to generate phenological parameters for desired locations. PPET output data tiles are mosaicked into a Conterminous United States (CONUS) data layer using ERDAS IMAGINE, or equivalent software package. Mosaics of the vegetation phenology data products are then reprojected to the desired map projection using ERDAS IMAGINE

Matlab based Toolkits used to Interface with Optical Design Software for NASA's James Webb Space Telescope

NASA Technical Reports Server (NTRS)

Howard, Joseph

2007-01-01

The viewgraph presentation provides an introduction to the James Webb Space Telescope (JWST). The first part provides a brief overview of Matlab toolkits including CodeV, OSLO, and Zemax Toolkits. The toolkit overview examines purpose, layout, how Matlab gets data from CodeV, function layout, and using cvHELP. The second part provides examples of use with JWST, including wavefront sensitivities and alignment simulations.

Engineering and Scientific Applications: Using MatLab(Registered Trademark) for Data Processing and Visualization

NASA Technical Reports Server (NTRS)

Sen, Syamal K.; Shaykhian, Gholam Ali

2011-01-01

MatLab(TradeMark)(MATrix LABoratory) is a numerical computation and simulation tool that is used by thousands Scientists and Engineers in many countries. MatLab does purely numerical calculations, which can be used as a glorified calculator or interpreter programming language; its real strength is in matrix manipulations. Computer algebra functionalities are achieved within the MatLab environment using "symbolic" toolbox. This feature is similar to computer algebra programs, provided by Maple or Mathematica to calculate with mathematical equations using symbolic operations. MatLab in its interpreter programming language form (command interface) is similar with well known programming languages such as C/C++, support data structures and cell arrays to define classes in object oriented programming. As such, MatLab is equipped with most of the essential constructs of a higher programming language. MatLab is packaged with an editor and debugging functionality useful to perform analysis of large MatLab programs and find errors. We believe there are many ways to approach real-world problems; prescribed methods to ensure foregoing solutions are incorporated in design and analysis of data processing and visualization can benefit engineers and scientist in gaining wider insight in actual implementation of their perspective experiments. This presentation will focus on data processing and visualizations aspects of engineering and scientific applications. Specifically, it will discuss methods and techniques to perform intermediate-level data processing covering engineering and scientific problems. MatLab programming techniques including reading various data files formats to produce customized publication-quality graphics, importing engineering and/or scientific data, organizing data in tabular format, exporting data to be used by other software programs such as Microsoft Excel, data presentation and visualization will be discussed.

Comparison of cyclic correlation algorithm implemented in matlab and python

NASA Astrophysics Data System (ADS)

Carr, Richard; Whitney, James

Simulation is a necessary step for all engineering projects. Simulation gives the engineers an approximation of how their devices will perform under different circumstances, without hav-ing to build, or before building a physical prototype. This is especially true for space bound devices, i.e., space communication systems, where the impact of system malfunction or failure is several orders of magnitude over that of terrestrial applications. Therefore having a reliable simulation tool is key in developing these devices and systems. Math Works Matrix Laboratory (MATLAB) is a matrix based software used by scientists and engineers to solve problems and perform complex simulations. MATLAB has a number of applications in a wide variety of fields which include communications, signal processing, image processing, mathematics, eco-nomics and physics. Because of its many uses MATLAB has become the preferred software for many engineers; it is also very expensive, especially for students and startups. One alternative to MATLAB is Python. The Python is a powerful, easy to use, open source programming environment that can be used to perform many of the same functions as MATLAB. Python programming environment has been steadily gaining popularity in niche programming circles. While there are not as many function included in the software as MATLAB, there are many open source functions that have been developed that are available to be downloaded for free. This paper illustrates how Python can implement the cyclic correlation algorithm and com-pares the results to the cyclic correlation algorithm implemented in the MATLAB environment. Some of the characteristics to be compared are the accuracy and precision of the results, and the length of the programs. The paper will demonstrate that Python is capable of performing simulations of complex algorithms such cyclic correlation.

Development of MATLAB software to control data acquisition from a multichannel systems multi-electrode array.

PubMed

Messier, Erik

2016-08-01

A Multichannel Systems (MCS) microelectrode array data acquisition (DAQ) unit is used to collect multichannel electrograms (EGM) from a Langendorff perfused rabbit heart system to study sudden cardiac death (SCD). MCS provides software through which data being processed by the DAQ unit can be displayed and saved, but this software's combined utility with MATLAB is not very effective. MCSs software stores recorded EGM data in a MathCad (MCD) format, which is then converted to a text file format. These text files are very large, and it is therefore very time consuming to import the EGM data into MATLAB for real-time analysis. Therefore, customized MATLAB software was developed to control the acquisition of data from the MCS DAQ unit, and provide specific laboratory accommodations for this study of SCD. The developed DAQ unit control software will be able to accurately: provide real time display of EGM signals; record and save EGM signals in MATLAB in a desired format; and produce real time analysis of the EGM signals; all through an intuitive GUI.

GOATS Image Projection Component

NASA Technical Reports Server (NTRS)

Haber, Benjamin M.; Green, Joseph J.

2011-01-01

When doing mission analysis and design of an imaging system in orbit around the Earth, answering the fundamental question of imaging performance requires an understanding of the image products that will be produced by the imaging system. GOATS software represents a series of MATLAB functions to provide for geometric image projections. Unique features of the software include function modularity, a standard MATLAB interface, easy-to-understand first-principles-based analysis, and the ability to perform geometric image projections of framing type imaging systems. The software modules are created for maximum analysis utility, and can all be used independently for many varied analysis tasks, or used in conjunction with other orbit analysis tools.

A novel fault location scheme for power distribution system based on injection method and transient line voltage

NASA Astrophysics Data System (ADS)

Huang, Yuehua; Li, Xiaomin; Cheng, Jiangzhou; Nie, Deyu; Wang, Zhuoyuan

2018-02-01

This paper presents a novel fault location method by injecting travelling wave current. The new methodology is based on Time Difference Of Arrival(TDOA)measurement which is available measurements the injection point and the end node of main radial. In other words, TDOA is the maximum correlation time when the signal reflected wave crest of the injected and fault appear simultaneously. Then distance calculation is equal to the wave velocity multiplied by TDOA. Furthermore, in case of some transformers connected to the end of the feeder, it’s necessary to combine with the transient voltage comparison of amplitude. Finally, in order to verify the effectiveness of this method, several simulations have been undertaken by using MATLAB/SIMULINK software packages. The proposed fault location is useful to short the positioning time in the premise of ensuring the accuracy, besides the error is 5.1% and 13.7%.

NLM microcomputer-based tutorials (for microcomputers). Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, M.

1990-04-01

The package consists of TOXLEARN--a microcomputer-based training package for TOXLINE (Toxicology Information Online), CHEMLEARN-a microcomputer-based training package for CHEMLINE (Chemical Information Online), MEDTUTOR--a microcomputer-based training package for MEDLINE (Medical Information Online), and ELHILL LEARN--a microcomputer-based training package for the ELHILL search and retrieval software that supports the above-mentioned databases...Software Description: The programs were developed under PILOTplus using the NLM LEARN Programmer. They run on IBM-PC, XT, AT, PS/2, and fully compatible computers. The programs require 512K RAM memory, one disk drive, and DOS 2.0 or higher. The software supports most monochrome, color graphics, enhanced color graphics, or visual graphics displays.

An open architecture for hybrid force-visual servo control of robotic manipulators in unstructured environments

NASA Astrophysics Data System (ADS)

Hassanzadeh, Iraj; Janabi-Sharifi, Farrokh

2005-12-01

In this paper, a new open architecture for visual servo control tasks is illustrated. A Puma-560 robotic manipulator is used to prove the concept. This design enables doing hybrid forcehisual servo control in an unstructured environment in different modes. Also, it can be controlled through Internet in teleoperation mode using a haptic device. Our proposed structure includes two major parts, hardware and software. In terms of hardware, it consists of a master (host) computer, a slave (target) computer, a Puma 560 manipulator, a CCD camera, a force sensor and a haptic device. There are five DAQ cards, interfacing Puma 560 and a slave computer. An open architecture package is developed using Matlab (R), Simulink (R) and XPC target toolbox. This package has the Hardware-In-the-Loop (HIL) property, i.e., enables one to readily implement different configurations of force, visual or hybrid control in real time. The implementation includes the following stages. First of all, retrofitting of puma was carried out. Then a modular joint controller for Puma 560 was realized using Simulink (R). Force sensor driver and force control implementation were written, using sjknction blocks of Simulink (R). Visual images were captured through Image Acquisition Toolbox of Matlab (R), and processed using Image Processing Toolbox. A haptic device interface was also written in Simulink (R). Thus, this setup could be readily reconfigured and accommodate any other robotic manipulator and/or other sensors without the trouble of the external issues relevant to the control, interface and software, while providing flexibility in components modification.

GRAFLAB 2.3 for UNIX - A MATLAB database, plotting, and analysis tool: User`s guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunn, W.N.

1998-03-01

This report is a user`s manual for GRAFLAB, which is a new database, analysis, and plotting package that has been written entirely in the MATLAB programming language. GRAFLAB is currently used for data reduction, analysis, and archival. GRAFLAB was written to replace GRAFAID, which is a FORTRAN database, analysis, and plotting package that runs on VAX/VMS.

Using Matlab in a Multivariable Calculus Course.

ERIC Educational Resources Information Center

Schlatter, Mark D.

The benefits of high-level mathematics packages such as Matlab include both a computer algebra system and the ability to provide students with concrete visual examples. This paper discusses how both capabilities of Matlab were used in a multivariate calculus class. Graphical user interfaces which display three-dimensional surfaces, contour plots,…

SARA: a software environment for the analysis of relaxation data acquired with accordion spectroscopy

PubMed Central

Harden, Bradley J.

2014-01-01

We present SARA (Software for Accordion Relaxation Analysis), an interactive and user-friendly MATLAB software environment designed for analyzing relaxation data obtained with accordion spectroscopy. Accordion spectroscopy can be used to measure nuclear magnetic resonance (NMR) relaxation rates in a fraction of the time required by traditional methods, yet data analysis can be intimidating and no unified software packages are available to assist investigators. Hence, the technique has not achieved widespread use within the NMR community. SARA offers users a selection of analysis protocols spanning those presented in the literature thus far, with modifications permitting a more general application to crowded spectra such as those of proteins. We discuss the advantages and limitations of each fitting method and suggest a protocol combining the strengths of each procedure to achieve optimal results. In the end, SARA provides an environment for facile extraction of relaxation rates and should promote routine application of accordion relaxation spectroscopy. PMID:24408364

A Digital Control Algorithm for Magnetic Suspension Systems

NASA Technical Reports Server (NTRS)

Britton, Thomas C.

1996-01-01

An ongoing program exists to investigate and develop magnetic suspension technologies and modelling techniques at NASA Langley Research Center. Presently, there is a laboratory-scale large air-gap suspension system capable of five degree-of-freedom (DOF) control that is operational and a six DOF system that is under development. Those systems levitate a cylindrical element containing a permanent magnet core above a planar array of electromagnets, which are used for levitation and control purposes. In order to evaluate various control approaches with those systems, the Generic Real-Time State-Space Controller (GRTSSC) software package was developed. That control software package allows the user to implement multiple control methods and allows for varied input/output commands. The development of the control algorithm is presented. The desired functionality of the software is discussed, including the ability to inject noise on sensor inputs and/or actuator outputs. Various limitations, common issues, and trade-offs are discussed including data format precision; the drawbacks of using either Direct Memory Access (DMA), interrupts, or program control techniques for data acquisition; and platform dependent concerns related to the portability of the software, such as memory addressing formats. Efforts to minimize overall controller loop-rate and a comparison of achievable controller sample rates are discussed. The implementation of a modular code structure is presented. The format for the controller input data file and the noise information file is presented. Controller input vector information is available for post-processing by mathematical analysis software such as MATLAB1.

Development of the CCP-200 mathematical model for Syzran CHPP using the Thermolib software package

NASA Astrophysics Data System (ADS)

Usov, S. V.; Kudinov, A. A.

2016-04-01

Simplified cycle diagram of the CCP-200 power generating unit of Syzran CHPP containing two gas turbines PG6111FA with generators, two steam recovery boilers KUP-110/15-8.0/0.7-540/200, and one steam turbine Siemens SST-600 (one-cylinder with two variable heat extraction units of 60/75 MW in heatextraction and condensing modes, accordingly) with S-GEN5-100 generators was presented. Results of experimental guarantee tests of the CCP-200 steam-gas unit are given. Brief description of the Thermolib application for the MatLab Simulink software package is given. Basic equations used in Thermolib for modeling thermo-technical processes are given. Mathematical models of gas-turbine plant, heat-recovery steam generator, steam turbine and integrated plant for power generating unit CCP-200 of Syzran CHPP were developed with the help of MatLab Simulink and Thermolib. The simulation technique at different ambient temperature values was used in order to get characteristics of the developed mathematical model. Graphic comparison of some characteristics of the CCP-200 simulation model (gas temperature behind gas turbine, gas turbine and combined cycle plant capacity, high and low pressure steam consumption and feed water consumption for high and low pressure economizers) with actual characteristics of the steam-gas unit received at experimental (field) guarantee tests at different ambient temperature are shown. It is shown that the chosen degrees of complexity, characteristics of the CCP-200 simulation model, developed by Thermolib, adequately correspond to the actual characteristics of the steam-gas unit received at experimental (field) guarantee tests; this allows considering the developed mathematical model as adequate and acceptable it for further work.

Blueprint XAS: a Matlab-based toolbox for the fitting and analysis of XAS spectra.

PubMed

Delgado-Jaime, Mario Ulises; Mewis, Craig Philip; Kennepohl, Pierre

2010-01-01

Blueprint XAS is a new Matlab-based program developed to fit and analyse X-ray absorption spectroscopy (XAS) data, most specifically in the near-edge region of the spectrum. The program is based on a methodology that introduces a novel background model into the complete fit model and that is capable of generating any number of independent fits with minimal introduction of user bias [Delgado-Jaime & Kennepohl (2010), J. Synchrotron Rad. 17, 119-128]. The functions and settings on the five panels of its graphical user interface are designed to suit the needs of near-edge XAS data analyzers. A batch function allows for the setting of multiple jobs to be run with Matlab in the background. A unique statistics panel allows the user to analyse a family of independent fits, to evaluate fit models and to draw statistically supported conclusions. The version introduced here (v0.2) is currently a toolbox for Matlab. Future stand-alone versions of the program will also incorporate several other new features to create a full package of tools for XAS data processing.

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

PubMed Central

2013-01-01

The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

PubMed

Hodneland, Erlend; Kögel, Tanja; Frei, Dominik Michael; Gerdes, Hans-Hermann; Lundervold, Arvid

2013-08-09

: The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.

PubMed

Mansouri, Misagh; Reinbolt, Jeffrey A

2012-05-11

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB's variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1s (OpenSim) to 2.9s (MATLAB). For the closed-loop case, a proportional-integral-derivative controller was used to successfully balance a pole on model's hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Updates to FuncLab, a Matlab based GUI for handling receiver functions

NASA Astrophysics Data System (ADS)

Porritt, Robert W.; Miller, Meghan S.

2018-02-01

Receiver functions are a versatile tool commonly used in seismic imaging. Depending on how they are processed, they can be used to image discontinuity structure within the crust or mantle or they can be inverted for seismic velocity either directly or jointly with complementary datasets. However, modern studies generally require large datasets which can be challenging to handle; therefore, FuncLab was originally written as an interactive Matlab GUI to assist in handling these large datasets. This software uses a project database to allow interactive trace editing, data visualization, H-κ stacking for crustal thickness and Vp/Vs ratio, and common conversion point stacking while minimizing computational costs. Since its initial release, significant advances have been made in the implementation of web services and changes in the underlying Matlab platform have necessitated a significant revision to the software. Here, we present revisions to the software, including new features such as data downloading via irisFetch.m, receiver function calculations via processRFmatlab, on-the-fly cross-section tools, interface picking, and more. In the descriptions of the tools, we present its application to a test dataset in Michigan, Wisconsin, and neighboring areas following the passage of USArray Transportable Array. The software is made available online at https://robporritt.wordpress.com/software.

Using the Generic Mapping Tools From Within the MATLAB, Octave and Julia Computing Environments

NASA Astrophysics Data System (ADS)

Luis, J. M. F.; Wessel, P.

2016-12-01

The Generic Mapping Tools (GMT) is a widely used software infrastructure tool set for analyzing and displaying geoscience data. Its power to analyze and process data and produce publication-quality graphics has made it one of several standard processing toolsets used by a large segment of the Earth and Ocean Sciences. GMT's strengths lie in superior publication-quality vector graphics, geodetic-quality map projections, robust data processing algorithms scalable to enormous data sets, and ability to run under all common operating systems. The GMT tool chest offers over 120 modules sharing a common set of command options, file structures, and documentation. GMT modules are command line tools that accept input and write output, and this design allows users to write scripts in which one module's output becomes another module's input, creating highly customized GMT workflows. With the release of GMT 5, these modules are high-level functions with a C API, potentially allowing users access to high-level GMT capabilities from any programmable environment. Many scientists who use GMT also use other computational tools, such as MATLAB® and its clone Octave. We have built a MATLAB/Octave interface on top of the GMT 5 C API. Thus, MATLAB or Octave now has full access to all GMT modules as well as fundamental input/output of GMT data objects via a MEX function. Internally, the GMT/MATLAB C API defines six high-level composite data objects that handle input and output of data via individual GMT modules. These are data tables, grids, text tables (text/data mixed records), color palette tables, raster images (1-4 color bands), and PostScript. The API is responsible for translating between the six GMT objects and the corresponding native MATLAB objects. References to data arrays are passed if transposing of matrices is not required. The GMT and MATLAB/Octave combination is extremely flexible, letting the user harvest the general numerical and graphical capabilities of both systems, and represents a giant step forward in interoperability between GMT and other software package. We will present examples of the symbiotic benefits of combining these platforms. Two other extensions are also in the works: a nearly finished Julia wrapper and an embryonic Python module. Publication supported by FCT- project UID/GEO/50019/2013 - Instituto D. Luiz

Development and validation of a comprehensive model for map of fruits based on enzyme kinetics theory and arrhenius relation.

PubMed

Mangaraj, S; K Goswami, T; Mahajan, P V

2015-07-01

MAP is a dynamic system where respiration of the packaged product and gas permeation through the packaging film takes place simultaneously. The desired level of O2 and CO2 in a package is achieved by matching film permeation rates for O2 and CO2 with respiration rate of the packaged product. A mathematical model for MAP of fresh fruits applying enzyme kinetics based respiration equation coupled with the Arrhenious type model was developed. The model was solved numerically using MATLAB programme. The model was used to determine the time to reach to the equilibrium concentration inside the MA package and the level of O2 and CO2 concentration at equilibrium state. The developed model for prediction of equilibrium O2 and CO2 concentration was validated using experimental data for MA packaging of apple, guava and litchi.

NASA One-Dimensional Combustor Simulation--User Manual for S1D_ML

NASA Technical Reports Server (NTRS)

Stueber, Thomas J.; Paxson, Daniel E.

2014-01-01

The work presented in this paper is to promote research leading to a closed-loop control system to actively suppress thermo-acoustic instabilities. To serve as a model for such a closed-loop control system, a one-dimensional combustor simulation composed using MATLAB software tools has been written. This MATLAB based process is similar to a precursor one-dimensional combustor simulation that was formatted as FORTRAN 77 source code. The previous simulation process requires modification to the FORTRAN 77 source code, compiling, and linking when creating a new combustor simulation executable file. The MATLAB based simulation does not require making changes to the source code, recompiling, or linking. Furthermore, the MATLAB based simulation can be run from script files within the MATLAB environment or with a compiled copy of the executable file running in the Command Prompt window without requiring a licensed copy of MATLAB. This report presents a general simulation overview. Details regarding how to setup and initiate a simulation are also presented. Finally, the post-processing section describes the two types of files created while running the simulation and it also includes simulation results for a default simulation included with the source code.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

PubMed

Markiewicz, Tomasz

2011-03-30

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8 GHz 4 GB RAM server with 768x576 pixel size, 1.28 Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server - 3.5 seconds, at remote analysis - 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

PubMed Central

2011-01-01

Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. Methods In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8GHz 4GB RAM server with 768x576 pixel size, 1.28Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server – 3.5 seconds, at remote analysis – 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. Conclusions The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system. PMID:21489188

Dynamic Modeling and Simulation of an Underactuated System

NASA Astrophysics Data System (ADS)

Libardo Duarte Madrid, Juan; Ospina Henao, P. A.; González Querubín, E.

2017-06-01

In this paper, is used the Lagrangian classical mechanics for modeling the dynamics of an underactuated system, specifically a rotary inverted pendulum that will have two equations of motion. A basic design of the system is proposed in SOLIDWORKS 3D CAD software, which based on the material and dimensions of the model provides some physical variables necessary for modeling. In order to verify the results obtained, a comparison the CAD model simulated in the environment SimMechanics of MATLAB software with the mathematical model who was consisting of Euler-Lagrange’s equations implemented in Simulink MATLAB, solved with the ODE23tb method, included in the MATLAB libraries for the solution of systems of equations of the type and order obtained. This article also has a topological analysis of pendulum trajectories through a phase space diagram, which allows the identification of stable and unstable regions of the system.

Measurement and numerical simulation of high intensity focused ultrasound field in water

NASA Astrophysics Data System (ADS)

Lee, Kang Il

2017-11-01

In the present study, the acoustic field of a high intensity focused ultrasound (HIFU) transducer in water was measured by using a commercially available needle hydrophone intended for HIFU use. To validate the results of hydrophone measurements, numerical simulations of HIFU fields were performed by integrating the axisymmetric Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation from the frequency-domain perspective with the help of a MATLAB-based software package developed for HIFU simulation. Quantitative values for the focal waveforms, the peak pressures, and the size of the focal spot were obtained in various regimes of linear, quasilinear, and nonlinear propagation up to the source pressure levels when the shock front was formed in the waveform. The numerical results with the HIFU simulator solving the KZK equation were compared with the experimental data and found to be in good agreement. This confirms that the numerical simulation based on the KZK equation is capable of capturing the nonlinear pressure field of therapeutic HIFU transducers well enough to make it suitable for HIFU treatment planning.

Prediction and Measurement of Temperature Rise Induced by High Intensity Focused Ultrasound in a Tissue-Mimicking Phantom

NASA Astrophysics Data System (ADS)

Lee, Kang Il

2018-06-01

The present study aims to predict the temperature rise induced by high intensity focused ultrasound (HIFU) in soft tissues to assess tissue damage during HIFU thermal therapies. With the help of a MATLAB-based software package developed for HIFU simulation, the HIFU field was simulated by solving the axisymmetric Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation from the frequency-domain perspective, and the HIFU-induced temperature rise in a tissue-mimicking phantom was simulated by solving Pennes' bioheat transfer (BHT) equation. In order to verify the simulation results, we performed in-vitro heating experiments on a tissue-mimicking phantom by using a 1.1-MHz, single-element, spherically focused HIFU transducer. The temperature rise near the focal spot obtained from the HIFU simulator was in good agreement with that from the in-vitro experiments. This confirms that the HIFU simulator based on the KZK and the BHT equations captures the HIFU-induced temperature rise in soft tissues well enough to make it suitable for HIFU treatment planning.

An overview on real-time control schemes for wheeled mobile robot

NASA Astrophysics Data System (ADS)

Radzak, M. S. A.; Ali, M. A. H.; Sha’amri, S.; Azwan, A. R.

2018-04-01

The purpose of this paper is to review real-time control motion algorithms for wheeled mobile robot (WMR) when navigating in environment such as road. Its need a good controller to avoid collision with any disturbance and maintain a track error at zero level. The controllers are used with other aiding sensors to measure the WMR’s velocities, posture, and interference to estimate the required torque to be applied on the wheels of mobile robot. Four main categories for wheeled mobile robot control systems have been found in literature which are namely: Kinematic based controller, Dynamic based controllers, artificial intelligence based control system, and Active Force control. A MATLAB/Simulink software is the main software to simulate and implement the control system. The real-time toolbox in MATLAB/SIMULINK are used to receive/send data from sensors/to actuator with presence of disturbances, however others software such C, C++ and visual basic are rare to be used.

Control code for laboratory adaptive optics teaching system

NASA Astrophysics Data System (ADS)

Jin, Moonseob; Luder, Ryan; Sanchez, Lucas; Hart, Michael

2017-09-01

By sensing and compensating wavefront aberration, adaptive optics (AO) systems have proven themselves crucial in large astronomical telescopes, retinal imaging, and holographic coherent imaging. Commercial AO systems for laboratory use are now available in the market. One such is the ThorLabs AO kit built around a Boston Micromachines deformable mirror. However, there are limitations in applying these systems to research and pedagogical projects since the software is written with limited flexibility. In this paper, we describe a MATLAB-based software suite to interface with the ThorLabs AO kit by using the MATLAB Engine API and Visual Studio. The software is designed to offer complete access to the wavefront sensor data, through the various levels of processing, to the command signals to the deformable mirror and fast steering mirror. In this way, through a MATLAB GUI, an operator can experiment with every aspect of the AO system's functioning. This is particularly valuable for tests of new control algorithms as well as to support student engagement in an academic environment. We plan to make the code freely available to the community.

FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data.

PubMed

Muir, Dylan R; Kampa, Björn M

2014-01-01

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories.

FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data

PubMed Central

Muir, Dylan R.; Kampa, Björn M.

2015-01-01

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories1. PMID:25653614

CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data

PubMed Central

Weiss, Scott T.

2014-01-01

Bayesian Networks (BN) have been a popular predictive modeling formalism in bioinformatics, but their application in modern genomics has been slowed by an inability to cleanly handle domains with mixed discrete and continuous variables. Existing free BN software packages either discretize continuous variables, which can lead to information loss, or do not include inference routines, which makes prediction with the BN impossible. We present CGBayesNets, a BN package focused around prediction of a clinical phenotype from mixed discrete and continuous variables, which fills these gaps. CGBayesNets implements Bayesian likelihood and inference algorithms for the conditional Gaussian Bayesian network (CGBNs) formalism, one appropriate for predicting an outcome of interest from, e.g., multimodal genomic data. We provide four different network learning algorithms, each making a different tradeoff between computational cost and network likelihood. CGBayesNets provides a full suite of functions for model exploration and verification, including cross validation, bootstrapping, and AUC manipulation. We highlight several results obtained previously with CGBayesNets, including predictive models of wood properties from tree genomics, leukemia subtype classification from mixed genomic data, and robust prediction of intensive care unit mortality outcomes from metabolomic profiles. We also provide detailed example analysis on public metabolomic and gene expression datasets. CGBayesNets is implemented in MATLAB and available as MATLAB source code, under an Open Source license and anonymous download at http://www.cgbayesnets.com. PMID:24922310

CGBayesNets: conditional Gaussian Bayesian network learning and inference with mixed discrete and continuous data.

PubMed

McGeachie, Michael J; Chang, Hsun-Hsien; Weiss, Scott T

2014-06-01

Bayesian Networks (BN) have been a popular predictive modeling formalism in bioinformatics, but their application in modern genomics has been slowed by an inability to cleanly handle domains with mixed discrete and continuous variables. Existing free BN software packages either discretize continuous variables, which can lead to information loss, or do not include inference routines, which makes prediction with the BN impossible. We present CGBayesNets, a BN package focused around prediction of a clinical phenotype from mixed discrete and continuous variables, which fills these gaps. CGBayesNets implements Bayesian likelihood and inference algorithms for the conditional Gaussian Bayesian network (CGBNs) formalism, one appropriate for predicting an outcome of interest from, e.g., multimodal genomic data. We provide four different network learning algorithms, each making a different tradeoff between computational cost and network likelihood. CGBayesNets provides a full suite of functions for model exploration and verification, including cross validation, bootstrapping, and AUC manipulation. We highlight several results obtained previously with CGBayesNets, including predictive models of wood properties from tree genomics, leukemia subtype classification from mixed genomic data, and robust prediction of intensive care unit mortality outcomes from metabolomic profiles. We also provide detailed example analysis on public metabolomic and gene expression datasets. CGBayesNets is implemented in MATLAB and available as MATLAB source code, under an Open Source license and anonymous download at http://www.cgbayesnets.com.

A software package for evaluating the performance of a star sensor operation

NASA Astrophysics Data System (ADS)

Sarpotdar, Mayuresh; Mathew, Joice; Sreejith, A. G.; Nirmal, K.; Ambily, S.; Prakash, Ajin; Safonova, Margarita; Murthy, Jayant

2017-02-01

We have developed a low-cost off-the-shelf component star sensor ( StarSense) for use in minisatellites and CubeSats to determine the attitude of a satellite in orbit. StarSense is an imaging camera with a limiting magnitude of 6.5, which extracts information from star patterns it records in the images. The star sensor implements a centroiding algorithm to find centroids of the stars in the image, a Geometric Voting algorithm for star pattern identification, and a QUEST algorithm for attitude quaternion calculation. Here, we describe the software package to evaluate the performance of these algorithms as a star sensor single operating system. We simulate the ideal case where sky background and instrument errors are omitted, and a more realistic case where noise and camera parameters are added to the simulated images. We evaluate such performance parameters of the algorithms as attitude accuracy, calculation time, required memory, star catalog size, sky coverage, etc., and estimate the errors introduced by each algorithm. This software package is written for use in MATLAB. The testing is parametrized for different hardware parameters, such as the focal length of the imaging setup, the field of view (FOV) of the camera, angle measurement accuracy, distortion effects, etc., and therefore, can be applied to evaluate the performance of such algorithms in any star sensor. For its hardware implementation on our StarSense, we are currently porting the codes in form of functions written in C. This is done keeping in view its easy implementation on any star sensor electronics hardware.

JADA: a graphical user interface for comprehensive internal dose assessment in nuclear medicine.

PubMed

Grimes, Joshua; Uribe, Carlos; Celler, Anna

2013-07-01

The main objective of this work was to design a comprehensive dosimetry package that would keep all aspects of internal dose calculation within the framework of a single software environment and that would be applicable for a variety of dose calculation approaches. Our MATLAB-based graphical user interface (GUI) can be used for processing data obtained using pure planar, pure SPECT, or hybrid planar/SPECT imaging. Time-activity data for source regions are obtained using a set of tools that allow the user to reconstruct SPECT images, load images, coregister a series of planar images, and to perform two-dimensional and three-dimensional image segmentation. Curve fits are applied to the acquired time-activity data to construct time-activity curves, which are then integrated to obtain time-integrated activity coefficients. Subsequently, dose estimates are made using one of three methods. The organ level dose calculation subGUI calculates mean organ doses that are equivalent to dose assessment performed by OLINDA/EXM. Voxelized dose calculation options, which include the voxel S value approach and Monte Carlo simulation using the EGSnrc user code DOSXYZnrc, are available within the process 3D image data subGUI. The developed internal dosimetry software package provides an assortment of tools for every step in the dose calculation process, eliminating the need for manual data transfer between programs. This saves times and minimizes user errors, while offering a versatility that can be used to efficiently perform patient-specific internal dose calculations in a variety of clinical situations.

EEGgui: a program used to detect electroencephalogram anomalies after traumatic brain injury.

PubMed

Sick, Justin; Bray, Eric; Bregy, Amade; Dietrich, W Dalton; Bramlett, Helen M; Sick, Thomas

2013-05-21

Identifying and quantifying pathological changes in brain electrical activity is important for investigations of brain injury and neurological disease. An example is the development of epilepsy, a secondary consequence of traumatic brain injury. While certain epileptiform events can be identified visually from electroencephalographic (EEG) or electrocorticographic (ECoG) records, quantification of these pathological events has proved to be more difficult. In this study we developed MATLAB-based software that would assist detection of pathological brain electrical activity following traumatic brain injury (TBI) and present our MATLAB code used for the analysis of the ECoG. Software was developed using MATLAB(™) and features of the open access EEGLAB. EEGgui is a graphical user interface in the MATLAB programming platform that allows scientists who are not proficient in computer programming to perform a number of elaborate analyses on ECoG signals. The different analyses include Power Spectral Density (PSD), Short Time Fourier analysis and Spectral Entropy (SE). ECoG records used for demonstration of this software were derived from rats that had undergone traumatic brain injury one year earlier. The software provided in this report provides a graphical user interface for displaying ECoG activity and calculating normalized power density using fast fourier transform of the major brain wave frequencies (Delta, Theta, Alpha, Beta1, Beta2 and Gamma). The software further detects events in which power density for these frequency bands exceeds normal ECoG by more than 4 standard deviations. We found that epileptic events could be identified and distinguished from a variety of ECoG phenomena associated with normal changes in behavior. We further found that analysis of spectral entropy was less effective in distinguishing epileptic from normal changes in ECoG activity. The software presented here was a successful modification of EEGLAB in the Matlab environment that allows detection of epileptiform ECoG signals in animals after TBI. The code allows import of large EEG or ECoG data records as standard text files and uses fast fourier transform as a basis for detection of abnormal events. The software can also be used to monitor injury-induced changes in spectral entropy if required. We hope that the software will be useful for other investigators in the field of traumatic brain injury and will stimulate future advances of quantitative analysis of brain electrical activity after neurological injury or disease.

SolTrack: an automatic video processing software for in situ interface tracking.

PubMed

Griesser, S; Pierer, R; Reid, M; Dippenaar, R

2012-10-01

High-Resolution in situ observation of solidification experiments has become a powerful technique to improve the fundamental understanding of solidification processes of metals and alloys. In the present study, high-temperature laser-scanning confocal microscopy (HTLSCM) was utilized to observe and capture in situ solidification and phase transformations of alloys for subsequent post processing and analysis. Until now, this analysis has been very time consuming as frame-by-frame manual evaluation of propagating interfaces was used to determine the interface velocities. SolTrack has been developed using the commercial software package MATLAB and is designed to automatically detect, locate and track propagating interfaces during solidification and phase transformations as well as to calculate interfacial velocities. Different solidification phenomena have been recorded to demonstrate a wider spectrum of applications of this software. A validation, through comparison with manual evaluation, is included where the accuracy is shown to be very high. © 2012 The Authors Journal of Microscopy © 2012 Royal Microscopical Society.

Evaluation of copy number variation detection for a SNP array platform

PubMed Central

2014-01-01

Background Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform. We selected four publicly available software packages designed for CNV calling from an Affymetrix SNP array, including Birdsuite, dChip, Genotyping Console (GTC) and PennCNV. The publicly available dataset generated by Array-based Comparative Genomic Hybridization (CGH), with a resolution of 24 million probes per sample, was considered to be the “gold standard”. Compared with the CGH-based dataset, the success rate, average stability rate, sensitivity, consistence and reproducibility of these four software packages were assessed compared with the “gold standard”. Specially, we also compared the efficiency of detecting CNVs simultaneously by two, three and all of the software packages with that by a single software package. Results Simply from the quantity of the detected CNVs, Birdsuite detected the most while GTC detected the least. We found that Birdsuite and dChip had obvious detecting bias. And GTC seemed to be inferior because of the least amount of CNVs it detected. Thereafter we investigated the detection consistency produced by one certain software package and the rest three software suits. We found that the consistency of dChip was the lowest while GTC was the highest. Compared with the CNVs detecting result of CGH, in the matching group, GTC called the most matching CNVs, PennCNV-Affy ranked second. In the non-overlapping group, GTC called the least CNVs. With regards to the reproducibility of CNV calling, larger CNVs were usually replicated better. PennCNV-Affy shows the best consistency while Birdsuite shows the poorest. Conclusion We found that PennCNV outperformed the other three packages in the sensitivity and specificity of CNV calling. Obviously, each calling method had its own limitations and advantages for different data analysis. Therefore, the optimized calling methods might be identified using multiple algorithms to evaluate the concordance and discordance of SNP array-based CNV calling. PMID:24555668

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fidiani, Elok

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction betweenmore » the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.« less

G-Guidance Interface Design for Small Body Mission Simulation

NASA Technical Reports Server (NTRS)

Acikmese, Behcet; Carson, John; Phan, Linh

2008-01-01

The G-Guidance software implements a guidance and control (G and C) algorithm for small-body, autonomous proximity operations, developed under the Small Body GN and C task at JPL. The software is written in Matlab and interfaces with G-OPT, a JPL-developed optimization package written in C that provides G-Guidance with guaranteed convergence to a solution in a finite computation time with a prescribed accuracy. The resulting program is computationally efficient and is a prototype of an onboard, real-time algorithm for autonomous guidance and control. Two thruster firing schemes are available in G-Guidance, allowing tailoring of the software for specific mission maneuvers. For example, descent, landing, or rendezvous benefit from a thruster firing at the maneuver termination to mitigate velocity errors. Conversely, ascent or separation maneuvers benefit from an immediate firing to avoid potential drift toward a second body. The guidance portion of this software explicitly enforces user-defined control constraints and thruster silence times while minimizing total fuel usage. This program is currently specialized to small-body proximity operations, but the underlying method can be generalized to other applications.

NeuroPG: open source software for optical pattern generation and data acquisition

PubMed Central

Avants, Benjamin W.; Murphy, Daniel B.; Dapello, Joel A.; Robinson, Jacob T.

2015-01-01

Patterned illumination using a digital micromirror device (DMD) is a powerful tool for optogenetics. Compared to a scanning laser, DMDs are inexpensive and can easily create complex illumination patterns. Combining these complex spatiotemporal illumination patterns with optogenetics allows DMD-equipped microscopes to probe neural circuits by selectively manipulating the activity of many individual cells or many subcellular regions at the same time. To use DMDs to study neural activity, scientists must develop specialized software to coordinate optical stimulation patterns with the acquisition of electrophysiological and fluorescence data. To meet this growing need we have developed an open source optical pattern generation software for neuroscience—NeuroPG—that combines, DMD control, sample visualization, and data acquisition in one application. Built on a MATLAB platform, NeuroPG can also process, analyze, and visualize data. The software is designed specifically for the Mightex Polygon400; however, as an open source package, NeuroPG can be modified to incorporate any data acquisition, imaging, or illumination equipment that is compatible with MATLAB’s Data Acquisition and Image Acquisition toolboxes. PMID:25784873

Software and package applicating for network meta-analysis: A usage-based comparative study.

PubMed

Xu, Chang; Niu, Yuming; Wu, Junyi; Gu, Huiyun; Zhang, Chao

2017-12-21

To compare and analyze the characteristics and functions of software applications for network meta-analysis (NMA). PubMed, EMbase, The Cochrane Library, the official websites of Bayesian inference Using Gibbs Sampling (BUGS), Stata and R, and Google were searched to collect the software and packages for performing NMA; software and packages published up to March 2016 were included. After collecting the software, packages, and their user guides, we used the software and packages to calculate a typical example. All characteristics, functions, and computed results were compared and analyzed. Ten types of software were included, including programming and non-programming software. They were developed mainly based on Bayesian or frequentist theory. Most types of software have the characteristics of easy operation, easy mastery, exact calculation, or excellent graphing. However, there was no single software that performed accurate calculations with superior graphing; this could only be achieved through the combination of two or more types of software. This study suggests that the user should choose the appropriate software according to personal programming basis, operational habits, and financial ability. Then, the choice of the combination of BUGS and R (or Stata) software to perform the NMA is considered. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Investigation of an alternative generic model for predicting pharmacokinetic changes during physiological stress.

PubMed

Peng, Henry T; Edginton, Andrea N; Cheung, Bob

2013-10-01

Physiologically based pharmacokinetic models were developed using MATLAB Simulink® and PK-Sim®. We compared the capability and usefulness of these two models by simulating pharmacokinetic changes of midazolam under exercise and heat stress to verify the usefulness of MATLAB Simulink® as a generic PBPK modeling software. Although both models show good agreement with experimental data obtained under resting condition, their predictions of pharmacokinetics changes are less accurate in the stressful conditions. However, MATLAB Simulink® may be more flexible to include physiologically based processes such as oral absorption and simulate various stress parameters such as stress intensity, duration and timing of drug administration to improve model performance. Further work will be conducted to modify algorithms in our generic model developed using MATLAB Simulink® and to investigate pharmacokinetics under other physiological stress such as trauma. © The Author(s) 2013.

Matpar: Parallel Extensions for MATLAB

NASA Technical Reports Server (NTRS)

Springer, P. L.

1998-01-01

Matpar is a set of client/server software that allows a MATLAB user to take advantage of a parallel computer for very large problems. The user can replace calls to certain built-in MATLAB functions with calls to Matpar functions.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB

PubMed Central

Mansouri, Misagh; Reinbolt, Jeffrey A.

2013-01-01

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB’s variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1 s (OpenSim) to 2.9 s (MATLAB). For the closed-loop case, a proportional–integral–derivative controller was used to successfully balance a pole on model’s hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. PMID:22464351

Detection and Classification of Objects in Synthetic Aperture Radar Imagery

DTIC Science & Technology

2006-02-01

a higher False Alarm Rate (FAR). Currently, a standard edge detector is the Canny algorithm, which is available with the mathematics package MATLAB ...the algorithm used to calculate the Radon transform. The MATLAB implementation uses the built in Radon transform procedure, which is extremely... MATLAB code for a faster forward-backwards selection process has also been provided. In both cases, the feature selection was accomplished by using

The Kepler Science Operations Center Pipeline Framework Extensions

NASA Technical Reports Server (NTRS)

Klaus, Todd C.; Cote, Miles T.; McCauliff, Sean; Girouard, Forrest R.; Wohler, Bill; Allen, Christopher; Chandrasekaran, Hema; Bryson, Stephen T.; Middour, Christopher; Caldwell, Douglas A.;

Simulated Analysis of Linear Reversible Enzyme Inhibition with SCILAB

ERIC Educational Resources Information Center

Antuch, Manuel; Ramos, Yaquelin; Álvarez, Rubén

2014-01-01

SCILAB is a lesser-known program (than MATLAB) for numeric simulations and has the advantage of being free software. A challenging software-based activity to analyze the most common linear reversible inhibition types with SCILAB is described. Students establish typical values for the concentration of enzyme, substrate, and inhibitor to simulate…

Astronomical Software Directory Service

NASA Technical Reports Server (NTRS)

Hanisch, R. J.; Payne, H.; Hayes, J.

1998-01-01

This is the final report on the development of the Astronomical Software Directory Service (ASDS), a distributable, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URL's indexed for full-text searching.

Kinetic modeling and fitting software for interconnected reaction schemes: VisKin.

PubMed

Zhang, Xuan; Andrews, Jared N; Pedersen, Steen E

2007-02-15

Reaction kinetics for complex, highly interconnected kinetic schemes are modeled using analytical solutions to a system of ordinary differential equations. The algorithm employs standard linear algebra methods that are implemented using MatLab functions in a Visual Basic interface. A graphical user interface for simple entry of reaction schemes facilitates comparison of a variety of reaction schemes. To ensure microscopic balance, graph theory algorithms are used to determine violations of thermodynamic cycle constraints. Analytical solutions based on linear differential equations result in fast comparisons of first order kinetic rates and amplitudes as a function of changing ligand concentrations. For analysis of higher order kinetics, we also implemented a solution using numerical integration. To determine rate constants from experimental data, fitting algorithms that adjust rate constants to fit the model to imported data were implemented using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno methods. We have included the ability to carry out global fitting of data sets obtained at varying ligand concentrations. These tools are combined in a single package, which we have dubbed VisKin, to guide and analyze kinetic experiments. The software is available online for use on PCs.

MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.

PubMed

Wade, Matthew J; Oakley, Jordan; Harbisher, Sophie; Parker, Nicholas G; Dolfing, Jan

2017-01-01

Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.

Dust Tsunamis, Blackouts and 50 deg C: Teaching MATLAB in East Africa

NASA Astrophysics Data System (ADS)

Trauth, M. H.

2016-12-01

MATLAB is the tool of choice when analyzing earth and environmental data from East Africa. The software and companion toolboxes helps to process satellite images and digital elevation models, to detect trends, cycles, and recurrent, characteristic types of climate transitions in climate time series, and to model the hydrological balance of ancient lakes. The advantage of MATLAB is that the user can do many different types of analyses with the same software, making the software very attractive for young scientists at African universities. Since 2009 we are organizing summer schools on the subject of data analysis with various tools including MATLAB in Ethiopia, Kenya and Tanzania. Throughout the summerschool, participants are instructed by teams of senior researchers, together with young scientists, some of which were participants of an earlier summerschool. The participants are themselves integrated in teaching, depending on previous knowledge, so that the boundary between teachers and learners constantly shifts or even dissolves. From the extraordinarily positive experience, but also the difficulties in teaching data analysis methods with MATLAB in East Africa is reported.

SPSS and SAS programs for generalizability theory analyses.

PubMed

Mushquash, Christopher; O'Connor, Brian P

2006-08-01

The identification and reduction of measurement errors is a major challenge in psychological testing. Most investigators rely solely on classical test theory for assessing reliability, whereas most experts have long recommended using generalizability theory instead. One reason for the common neglect of generalizability theory is the absence of analytic facilities for this purpose in popular statistical software packages. This article provides a brief introduction to generalizability theory, describes easy to use SPSS, SAS, and MATLAB programs for conducting the recommended analyses, and provides an illustrative example, using data (N = 329) for the Rosenberg Self-Esteem Scale. Program output includes variance components, relative and absolute errors and generalizability coefficients, coefficients for D studies, and graphs of D study results.

Closing the loop on improvement: Packaging experience in the Software Engineering Laboratory

NASA Technical Reports Server (NTRS)

Waligora, Sharon R.; Landis, Linda C.; Doland, Jerry T.

1994-01-01

As part of its award-winning software process improvement program, the Software Engineering Laboratory (SEL) has developed an effective method for packaging organizational best practices based on real project experience into useful handbooks and training courses. This paper shares the SEL's experience over the past 12 years creating and updating software process handbooks and training courses. It provides cost models and guidelines for successful experience packaging derived from SEL experience.

Validation of thermal effects of LED package by using Elmer finite element simulation method

NASA Astrophysics Data System (ADS)

Leng, Lai Siang; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Taniselass, Steven; Bin Ab Aziz, Muhamad Hafiz; Vairavan, Rajendaran; Kirtsaeng, Supap

2017-02-01

The overall performance of the Light-emitting diode, LED package is critically affected by the heat attribution. In this study, open source software - Elmer FEM has been utilized to study the thermal analysis of the LED package. In order to perform a complete simulation study, both Salome software and ParaView software were introduced as Pre and Postprocessor. The thermal effect of the LED package was evaluated by this software. The result has been validated with commercially licensed software based on previous work. The percentage difference from both simulation results is less than 5% which is tolerable and comparable.

An Integrated Software Package to Enable Predictive Simulation Capabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yousu; Fitzhenry, Erin B.; Jin, Shuangshuang

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package,more » as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.« less

The application of MATLAB-based analytic hierarchy process in Hainan residential quarter function factor evaluation

NASA Astrophysics Data System (ADS)

Qiu, Dongdong; Liu, Peiqi

2017-04-01

Since being designated as an international tourist island, Hainan has become an overwhelmingly favored choice of real estate investment. This paper first constructed Hainan residential quarter function factor index system, then evaluated relevant factors, and finally solved the problem of factor importance ranking. In this specific case, the software MATLAB was used to facilitate AHP calculation. The evaluation results have guiding and referential value to both real estate developers and residential consumers.

Arduino-Based Data Acquisition into Excel, LabVIEW, and MATLAB

ERIC Educational Resources Information Center

Nichols, Daniel

2017-01-01

Data acquisition equipment for physics can be quite expensive. As an alternative, data can be acquired using a low-cost Arduino microcontroller. The Arduino has been used in physics labs where the data are acquired using the Arduino software. The Arduino software, however, does not contain a suite of tools for data fitting and analysis. The data…

Engineering and Scientific Applications: Using MatLab(Registered Trademark) for Data Processing and Visualization

NASA Technical Reports Server (NTRS)

Sen, Syamal K.; Shaykhian, Gholam Ali

2011-01-01

MatLab(R) (MATrix LABoratory) is a numerical computation and simulation tool that is used by thousands Scientists and Engineers in many cou ntries. MatLab does purely numerical calculations, which can be used as a glorified calculator or interpreter programming language; its re al strength is in matrix manipulations. Computer algebra functionalities are achieved within the MatLab environment using "symbolic" toolbo x. This feature is similar to computer algebra programs, provided by Maple or Mathematica to calculate with mathematical equations using s ymbolic operations. MatLab in its interpreter programming language fo rm (command interface) is similar with well known programming languag es such as C/C++, support data structures and cell arrays to define c lasses in object oriented programming. As such, MatLab is equipped with most ofthe essential constructs of a higher programming language. M atLab is packaged with an editor and debugging functionality useful t o perform analysis of large MatLab programs and find errors. We belie ve there are many ways to approach real-world problems; prescribed methods to ensure foregoing solutions are incorporated in design and ana lysis of data processing and visualization can benefit engineers and scientist in gaining wider insight in actual implementation of their perspective experiments. This presentation will focus on data processing and visualizations aspects of engineering and scientific applicati ons. Specifically, it will discuss methods and techniques to perform intermediate-level data processing covering engineering and scientifi c problems. MatLab programming techniques including reading various data files formats to produce customized publication-quality graphics, importing engineering and/or scientific data, organizing data in tabu lar format, exporting data to be used by other software programs such as Microsoft Excel, data presentation and visualization will be discussed. The presentation will emphasize creating practIcal scripts (pro grams) that extend the basic features of MatLab TOPICS mclude (1) Ma trix and vector analysis and manipulations (2) Mathematical functions (3) Symbolic calculations & functions (4) Import/export data files (5) Program lOgic and flow control (6) Writing function and passing parameters (7) Test application programs

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

DTIC Science & Technology

2011-01-01

open-source BMI software solu- tions are currently available, we feel that the Craniux software package fills a specific need in the realm of BMI...data, such as cortical source imaging using EEG or MEG recordings. It is with these characteristics in mind that we feel the Craniux software package...S. Adee, “Dean Kamen’s ‘luke arm’ prosthesis readies for clinical trials,” IEEE Spectrum, February 2008, http://spectrum .ieee.org/biomedical

CPMC-Lab: A MATLAB package for Constrained Path Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Nguyen, Huy; Shi, Hao; Xu, Jie; Zhang, Shiwei

2014-12-01

We describe CPMC-Lab, a MATLAB program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to ab initio calculations in molecules and solids. The present package implements the full ground-state constrained-path Monte Carlo (CPMC) method in MATLAB with a graphical interface, using the Hubbard model as an example. The package can perform calculations in finite supercells in any dimensions, under periodic or twist boundary conditions. Importance sampling and all other algorithmic details of a total energy calculation are included and illustrated. This open-source tool allows users to experiment with various model and run parameters and visualize the results. It provides a direct and interactive environment to learn the method and study the code with minimal overhead for setup. Furthermore, the package can be easily generalized for auxiliary-field quantum Monte Carlo (AFQMC) calculations in many other models for correlated electron systems, and can serve as a template for developing a production code for AFQMC total energy calculations in real materials. Several illustrative studies are carried out in one- and two-dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps.

High-Speed GPU-Based Fully Three-Dimensional Diffuse Optical Tomographic System

PubMed Central

Saikia, Manob Jyoti; Kanhirodan, Rajan; Mohan Vasu, Ram

2014-01-01

We have developed a graphics processor unit (GPU-) based high-speed fully 3D system for diffuse optical tomography (DOT). The reduction in execution time of 3D DOT algorithm, a severely ill-posed problem, is made possible through the use of (1) an algorithmic improvement that uses Broyden approach for updating the Jacobian matrix and thereby updating the parameter matrix and (2) the multinode multithreaded GPU and CUDA (Compute Unified Device Architecture) software architecture. Two different GPU implementations of DOT programs are developed in this study: (1) conventional C language program augmented by GPU CUDA and CULA routines (C GPU), (2) MATLAB program supported by MATLAB parallel computing toolkit for GPU (MATLAB GPU). The computation time of the algorithm on host CPU and the GPU system is presented for C and Matlab implementations. The forward computation uses finite element method (FEM) and the problem domain is discretized into 14610, 30823, and 66514 tetrahedral elements. The reconstruction time, so achieved for one iteration of the DOT reconstruction for 14610 elements, is 0.52 seconds for a C based GPU program for 2-plane measurements. The corresponding MATLAB based GPU program took 0.86 seconds. The maximum number of reconstructed frames so achieved is 2 frames per second. PMID:24891848

High-Speed GPU-Based Fully Three-Dimensional Diffuse Optical Tomographic System.

PubMed

Saikia, Manob Jyoti; Kanhirodan, Rajan; Mohan Vasu, Ram

2014-01-01

We have developed a graphics processor unit (GPU-) based high-speed fully 3D system for diffuse optical tomography (DOT). The reduction in execution time of 3D DOT algorithm, a severely ill-posed problem, is made possible through the use of (1) an algorithmic improvement that uses Broyden approach for updating the Jacobian matrix and thereby updating the parameter matrix and (2) the multinode multithreaded GPU and CUDA (Compute Unified Device Architecture) software architecture. Two different GPU implementations of DOT programs are developed in this study: (1) conventional C language program augmented by GPU CUDA and CULA routines (C GPU), (2) MATLAB program supported by MATLAB parallel computing toolkit for GPU (MATLAB GPU). The computation time of the algorithm on host CPU and the GPU system is presented for C and Matlab implementations. The forward computation uses finite element method (FEM) and the problem domain is discretized into 14610, 30823, and 66514 tetrahedral elements. The reconstruction time, so achieved for one iteration of the DOT reconstruction for 14610 elements, is 0.52 seconds for a C based GPU program for 2-plane measurements. The corresponding MATLAB based GPU program took 0.86 seconds. The maximum number of reconstructed frames so achieved is 2 frames per second.

Edge detection and mathematic fitting for corneal surface with Matlab software.

PubMed

Di, Yue; Li, Mei-Yan; Qiao, Tong; Lu, Na

2017-01-01

To select the optimal edge detection methods to identify the corneal surface, and compare three fitting curve equations with Matlab software. Fifteen subjects were recruited. The corneal images from optical coherence tomography (OCT) were imported into Matlab software. Five edge detection methods (Canny, Log, Prewitt, Roberts, Sobel) were used to identify the corneal surface. Then two manual identifying methods (ginput and getpts) were applied to identify the edge coordinates respectively. The differences among these methods were compared. Binomial curve (y=Ax 2 +Bx+C), Polynomial curve [p(x)=p1x n +p2x n-1 +....+pnx+pn+1] and Conic section (Ax 2 +Bxy+Cy 2 +Dx+Ey+F=0) were used for curve fitting the corneal surface respectively. The relative merits among three fitting curves were analyzed. Finally, the eccentricity (e) obtained by corneal topography and conic section were compared with paired t -test. Five edge detection algorithms all had continuous coordinates which indicated the edge of the corneal surface. The ordinates of manual identifying were close to the inside of the actual edges. Binomial curve was greatly affected by tilt angle. Polynomial curve was lack of geometrical properties and unstable. Conic section could calculate the tilted symmetry axis, eccentricity, circle center, etc . There were no significant differences between 'e' values by corneal topography and conic section ( t =0.9143, P =0.3760 >0.05). It is feasible to simulate the corneal surface with mathematical curve with Matlab software. Edge detection has better repeatability and higher efficiency. The manual identifying approach is an indispensable complement for detection. Polynomial and conic section are both the alternative methods for corneal curve fitting. Conic curve was the optimal choice based on the specific geometrical properties.

Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging

PubMed Central

Patel, Tapan P.; Man, Karen; Firestein, Bonnie L.; Meaney, David F.

2017-01-01

Background Recent advances in genetically engineered calcium and membrane potential indicators provide the potential to estimate the activation dynamics of individual neurons within larger, mesoscale networks (100s–1000 +neurons). However, a fully integrated automated workflow for the analysis and visualization of neural microcircuits from high speed fluorescence imaging data is lacking. New method Here we introduce FluoroSNNAP, Fluorescence Single Neuron and Network Analysis Package. FluoroSNNAP is an open-source, interactive software developed in MATLAB for automated quantification of numerous biologically relevant features of both the calcium dynamics of single-cells and network activity patterns. FluoroSNNAP integrates and improves upon existing tools for spike detection, synchronization analysis, and inference of functional connectivity, making it most useful to experimentalists with little or no programming knowledge. Results We apply FluoroSNNAP to characterize the activity patterns of neuronal microcircuits undergoing developmental maturation in vitro. Separately, we highlight the utility of single-cell analysis for phenotyping a mixed population of neurons expressing a human mutant variant of the microtubule associated protein tau and wild-type tau. Comparison with existing method(s) We show the performance of semi-automated cell segmentation using spatiotemporal independent component analysis and significant improvement in detecting calcium transients using a template-based algorithm in comparison to peak-based or wavelet-based detection methods. Our software further enables automated analysis of microcircuits, which is an improvement over existing methods. Conclusions We expect the dissemination of this software will facilitate a comprehensive analysis of neuronal networks, promoting the rapid interrogation of circuits in health and disease. PMID:25629800

NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data

PubMed Central

Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

2010-01-01

A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware. PMID:21344013

NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data.

PubMed

Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

2011-01-01

A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware.

The Relationship between Gender and Students' Attitude and Experience of Using a Mathematical Software Program (MATLAB)

ERIC Educational Resources Information Center

Ocak, Mehmet A.

2006-01-01

This correlation study examined the relationship between gender and the students' attitude and prior knowledge of using one of the mathematical software programs (MATLAB). Participants were selected from one community college, one state university and one private college. Students were volunteers from three Calculus I classrooms (one class from…

Photogrammetric 3d Reconstruction in Matlab: Development of a Free Tool

NASA Astrophysics Data System (ADS)

Masiero, A.

2017-11-01

This paper presents the current state of development of a free Matlab tool for photogrammetric reconstruction developed at the University of Padova, Italy. The goal of this software is mostly educational, i.e. allowing students to have a close look to the specific steps which lead to the computation of a dense point cloud. As most of recently developed photogrammetric softwares, it is based on a Structure from Motion approach. Despite being mainly motivated by educational purposes, certain implementation details are clearly inspired by recent research works, e.g. limiting the computational burden of the feature matching by determining a suboptimal set of features to be considered, using information provided by external sensors to ease the matching process.

Collaborative Software Development Approach Used to Deliver the New Shuttle Telemetry Ground Station

NASA Technical Reports Server (NTRS)

Kirby, Randy L.; Mann, David; Prenger, Stephen G.; Craig, Wayne; Greenwood, Andrew; Morsics, Jonathan; Fricker, Charles H.; Quach, Son; Lechese, Paul

2003-01-01

United Space Alliance (USA) developed and used a new software development method to meet technical, schedule, and budget challenges faced during the development and delivery of the new Shuttle Telemetry Ground Station at Kennedy Space Center. This method, called Collaborative Software Development, enabled KSC to effectively leverage industrial software and build additional capabilities to meet shuttle system and operational requirements. Application of this method resulted in reduced time to market, reduced development cost, improved product quality, and improved programmer competence while developing technologies of benefit to a small company in California (AP Labs Inc.). Many modifications were made to the baseline software product (VMEwindow), which improved its quality and functionality. In addition, six new software capabilities were developed, which are the subject of this article and add useful functionality to the VMEwindow environment. These new software programs are written in C or VXWorks and are used in conjunction with other ground station software packages, such as VMEwindow, Matlab, Dataviews, and PVWave. The Space Shuttle Telemetry Ground Station receives frequency-modulation (FM) and pulse-code-modulated (PCM) signals from the shuttle and support equipment. The hardware architecture (see figure) includes Sun workstations connected to multiple PCM- and FM-processing VersaModule Eurocard (VME) chassis. A reflective memory network transports raw data from PCM Processors (PCMPs) to the programmable digital-to-analog (D/A) converters, strip chart recorders, and analysis and controller workstations.

The Hidden Cost of Buying a Computer.

ERIC Educational Resources Information Center

Johnson, Michael

1983-01-01

In order to process data in a computer, application software must be either developed or purchased. Costs for modifications of the software package and maintenance are often hidden. The decision to buy or develop software packages should be based upon factors of time and maintenance. (MLF)

Multivariate and repeated measures (MRM): A new toolbox for dependent and multimodal group-level neuroimaging data

PubMed Central

McFarquhar, Martyn; McKie, Shane; Emsley, Richard; Suckling, John; Elliott, Rebecca; Williams, Stephen

2016-01-01

Repeated measurements and multimodal data are common in neuroimaging research. Despite this, conventional approaches to group level analysis ignore these repeated measurements in favour of multiple between-subject models using contrasts of interest. This approach has a number of drawbacks as certain designs and comparisons of interest are either not possible or complex to implement. Unfortunately, even when attempting to analyse group level data within a repeated-measures framework, the methods implemented in popular software packages make potentially unrealistic assumptions about the covariance structure across the brain. In this paper, we describe how this issue can be addressed in a simple and efficient manner using the multivariate form of the familiar general linear model (GLM), as implemented in a new MATLAB toolbox. This multivariate framework is discussed, paying particular attention to methods of inference by permutation. Comparisons with existing approaches and software packages for dependent group-level neuroimaging data are made. We also demonstrate how this method is easily adapted for dependency at the group level when multiple modalities of imaging are collected from the same individuals. Follow-up of these multimodal models using linear discriminant functions (LDA) is also discussed, with applications to future studies wishing to integrate multiple scanning techniques into investigating populations of interest. PMID:26921716

Development of Airport Noise Mapping using Matlab Software (Case Study: Adi Soemarmo Airport - Boyolali, Indonesia)

NASA Astrophysics Data System (ADS)

Andarani, Pertiwi; Setiyo Huboyo, Haryono; Setyanti, Diny; Budiawan, Wiwik

2018-02-01

Noise is considered as one of the main environmental impact of Adi Soemarmo International Airport (ASIA), the second largest airport in Central Java Province, Indonesia. In order to manage the noise of airport, airport noise mapping is necessary. However, a model that requires simple input but still reliable was not available in ASIA. Therefore, the objective of this study are to develop model using Matlab software, to verify its reliability by measuring actual noise exposure, and to analyze the area of noise levels‥ The model was developed based on interpolation or extrapolation of identified Noise-Power-Distance (NPD) data. In accordance with Indonesian Government Ordinance No.40/2012, the noise metric used is WECPNL (Weighted Equivalent Continuous Perceived Noise Level). Based on this model simulation, there are residence area in the region of noise level II (1.912 km2) and III (1.16 km2) and 18 school buildings in the area of noise levels I, II, and III. These land-uses are actually prohibited unless noise insulation is equipped. The model using Matlab in the case of Adi Soemarmo International Airport is valid based on comparison of the field measurement (6 sampling points). However, it is important to validate the model again once the case study (the airport) is changed.

Academic Web Authoring Mulitmedia Development and Course Management Tools

ERIC Educational Resources Information Center

Halloran, Margaret E.

2005-01-01

Course management software enables faculty members to learn one software package for web-based curriculum, assessment, synchronous and asynchronous discussions, collaborative work, multimedia and interactive resource development. There are as many as 109 different course management software packages on the market and several studies have evaluated…

Strategies for Sharing Seismic Data Among Multiple Computer Platforms

NASA Astrophysics Data System (ADS)

Baker, L. M.; Fletcher, J. B.

2001-12-01

Seismic waveform data is readily available from a variety of sources, but it often comes in a distinct, instrument-specific data format. For example, data may be from portable seismographs, such as those made by Refraction Technology or Kinemetrics, from permanent seismograph arrays, such as the USGS Parkfield Dense Array, from public data centers, such as the IRIS Data Center, or from personal communication with other researchers through e-mail or ftp. A computer must be selected to import the data - usually whichever is the most suitable for reading the originating format. However, the computer best suited for a specific analysis may not be the same. When copies of the data are then made for analysis, a proliferation of copies of the same data results, in possibly incompatible, computer-specific formats. In addition, if an error is detected and corrected in one copy, or some other change is made, all the other copies must be updated to preserve their validity. Keeping track of what data is available, where it is located, and which copy is authoritative requires an effort that is easy to neglect. We solve this problem by importing waveform data to a shared network file server that is accessible to all our computers on our campus LAN. We use a Network Appliance file server running Sun's Network File System (NFS) software. Using an NFS client software package on each analysis computer, waveform data can then be read by our MatLab or Fortran applications without first copying the data. Since there is a single copy of the waveform data in a single location, the NFS file system hierarchy provides an implicit complete waveform data catalog and the single copy is inherently authoritative. Another part of our solution is to convert the original data into a blocked-binary format (known historically as USGS DR100 or VFBB format) that is interpreted by MatLab or Fortran library routines available on each computer so that the idiosyncrasies of each machine are not visible to the user. Commercial software packages, such as MatLab, also have the ability to share data in their own formats across multiple computer platforms. Our Fortran applications can create plot files in Adobe PostScript, Illustrator, and Portable Document Format (PDF) formats. Vendor support for reading these files is readily available on multiple computer platforms. We will illustrate by example our strategies for sharing seismic data among our multiple computer platforms, and we will discuss our positive and negative experiences. We will include our solutions for handling the different byte ordering, floating-point formats, and text file ``end-of-line'' conventions on the various computer platforms we use (6 different operating systems on 5 processor architectures).

The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data

PubMed Central

Hebart, Martin N.; Görgen, Kai; Haynes, John-Dylan

2015-01-01

The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns. PMID:25610393

Orbit Determination Toolbox

NASA Technical Reports Server (NTRS)

Carpenter, James R.; Berry, Kevin; Gregpru. Late; Speckman, Keith; Hur-Diaz, Sun; Surka, Derek; Gaylor, Dave

2010-01-01

The Orbit Determination Toolbox is an orbit determination (OD) analysis tool based on MATLAB and Java that provides a flexible way to do early mission analysis. The toolbox is primarily intended for advanced mission analysis such as might be performed in concept exploration, proposal, early design phase, or rapid design center environments. The emphasis is on flexibility, but it has enough fidelity to produce credible results. Insight into all flight dynamics source code is provided. MATLAB is the primary user interface and is used for piecing together measurement and dynamic models. The Java Astrodynamics Toolbox is used as an engine for things that might be slow or inefficient in MATLAB, such as high-fidelity trajectory propagation, lunar and planetary ephemeris look-ups, precession, nutation, polar motion calculations, ephemeris file parsing, and the like. The primary analysis functions are sequential filter/smoother and batch least-squares commands that incorporate Monte-Carlo data simulation, linear covariance analysis, measurement processing, and plotting capabilities at the generic level. These functions have a user interface that is based on that of the MATLAB ODE suite. To perform a specific analysis, users write MATLAB functions that implement truth and design system models. The user provides his or her models as inputs to the filter commands. The software provides a capability to publish and subscribe to a software bus that is compliant with the NASA Goddard Mission Services Evolution Center (GMSEC) standards, to exchange data with other flight dynamics tools to simplify the flight dynamics design cycle. Using the publish and subscribe approach allows for analysts in a rapid design center environment to seamlessly incorporate changes in spacecraft and mission design into navigation analysis and vice versa.

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

Recent technological advances and new software packages put unprecedented power for experimenting and theory-building in the hands of students at all levels. Microcomputer-based laboratory (MBL) and model-solving tools illustrate the educational potential of the technology. These tools include modeling software and three MBL packages (which are…

Machining Chatter Analysis for High Speed Milling Operations

NASA Astrophysics Data System (ADS)

Sekar, M.; Kantharaj, I.; Amit Siddhappa, Savale

2017-10-01

Chatter in high speed milling is characterized by time delay differential equations (DDE). Since closed form solution exists only for simple cases, the governing non-linear DDEs of chatter problems are solved by various numerical methods. Custom codes to solve DDEs are tedious to build, implement and not error free and robust. On the other hand, software packages provide solution to DDEs, however they are not straight forward to implement. In this paper an easy way to solve DDE of chatter in milling is proposed and implemented with MATLAB. Time domain solution permits the study and model of non-linear effects of chatter vibration with ease. Time domain results are presented for various stable and unstable conditions of cut and compared with stability lobe diagrams.

ATLAS software configuration and build tool optimisation

NASA Astrophysics Data System (ADS)

Rybkin, Grigory; Atlas Collaboration

2014-06-01

ATLAS software code base is over 6 million lines organised in about 2000 packages. It makes use of some 100 external software packages, is developed by more than 400 developers and used by more than 2500 physicists from over 200 universities and laboratories in 6 continents. To meet the challenge of configuration and building of this software, the Configuration Management Tool (CMT) is used. CMT expects each package to describe its build targets, build and environment setup parameters, dependencies on other packages in a text file called requirements, and each project (group of packages) to describe its policies and dependencies on other projects in a text project file. Based on the effective set of configuration parameters read from the requirements files of dependent packages and project files, CMT commands build the packages, generate the environment for their use, or query the packages. The main focus was on build time performance that was optimised within several approaches: reduction of the number of reads of requirements files that are now read once per package by a CMT build command that generates cached requirements files for subsequent CMT build commands; introduction of more fine-grained build parallelism at package task level, i.e., dependent applications and libraries are compiled in parallel; code optimisation of CMT commands used for build; introduction of package level build parallelism, i. e., parallelise the build of independent packages. By default, CMT launches NUMBER-OF-PROCESSORS build commands in parallel. The other focus was on CMT commands optimisation in general that made them approximately 2 times faster. CMT can generate a cached requirements file for the environment setup command, which is especially useful for deployment on distributed file systems like AFS or CERN VMFS. The use of parallelism, caching and code optimisation significantly-by several times-reduced software build time, environment setup time, increased the efficiency of multi-core computing resources utilisation, and considerably improved software developer and user experience.

MATLAB algorithm to implement soil water data assimilation with the Ensemble Kalman Filter using HYDRUS.

PubMed

Valdes-Abellan, Javier; Pachepsky, Yakov; Martinez, Gonzalo

2018-01-01

Data assimilation is becoming a promising technique in hydrologic modelling to update not only model states but also to infer model parameters, specifically to infer soil hydraulic properties in Richard-equation-based soil water models. The Ensemble Kalman Filter method is one of the most widely employed method among the different data assimilation alternatives. In this study the complete Matlab© code used to study soil data assimilation efficiency under different soil and climatic conditions is shown. The code shows the method how data assimilation through EnKF was implemented. Richards equation was solved by the used of Hydrus-1D software which was run from Matlab. •MATLAB routines are released to be used/modified without restrictions for other researchers•Data assimilation Ensemble Kalman Filter method code.•Soil water Richard equation flow solved by Hydrus-1D.

Antropometric parameters problem solving of shoe lasts by deforming membranes with medium weight

NASA Astrophysics Data System (ADS)

Albu, A. V.; Anghel Drugarin, C. V.; Barla, E. M.; Porav, V.

2018-01-01

The paper presents research results into getting a virtual model of shoe last and anthropometric parameters change. The most important change occurs in the fingers region. Alternatives CAD-CAM technology for next generation is based on DELCAM software for the CAM procedure and simulation of MATLAB software. This research has led to the virtual changes of the last, anthropometric parameter - the width of the fingers (ld) and shoe last length - (Lp) and images have been achieved with the representation in section of the shoe last changed from the original shoe lasts by FEM method (Finite element method) in MATLAB environment. The results are applied in the textile industry and in the elaboration of linings consumption or in the development of leather substitutes on fabric, knitted or woven material type.

Dill: an algorithm and a symbolic software package for doing classical supersymmetry calculations

NASA Astrophysics Data System (ADS)

Luc̆ić, Vladan

1995-11-01

An algorithm is presented that formalizes different steps in a classical Supersymmetric (SUSY) calculation. Based on the algorithm Dill, a symbolic software package, that can perform the calculations, is developed in the Mathematica programming language. While the algorithm is quite general, the package is created for the 4 - D, N = 1 model. Nevertheless, with little modification, the package could be used for other SUSY models. The package has been tested and some of the results are presented.

A MATLAB Library for Rapid Prototyping of Wireless Communications Algorithms with the Universal Software Radio Peripheral (USRP) Radio Family

DTIC Science & Technology

2013-06-01

Radio is a software development toolkit that provides signal processing blocks to drive the SDR. GNU Radio has many strong points – it is actively...maintained with a large user base, new capabilities are constantly being added, and compiled C code is fast for many real-time applications such as...programming interface (API) makes learning the architecture a daunting task, even for the experienced software developer. This requirement poses many

PSAMM: A Portable System for the Analysis of Metabolic Models

PubMed Central

Steffensen, Jon Lund; Dufault-Thompson, Keith; Zhang, Ying

2016-01-01

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies. PMID:26828591

Basic analysis of reflectometry data software package for the analysis of multilayered structures according to reflectometry data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Astaf'ev, S. B., E-mail: bard@ns.crys.ras.ru; Shchedrin, B. M.; Yanusova, L. G.

2012-01-15

The main principles of developing the Basic Analysis of Reflectometry Data (BARD) software package, which is aimed at obtaining a unified (standardized) tool for analyzing the structure of thin multilayer films and nanostructures of different nature based on reflectometry data, are considered. This software package contains both traditionally used procedures for processing reflectometry data and the authors' original developments on the basis of new methods for carrying out and analyzing reflectometry experiments. The structure of the package, its functional possibilities, examples of application, and prospects of development are reviewed.

Using an architectural approach to integrate heterogeneous, distributed software components

NASA Technical Reports Server (NTRS)

Callahan, John R.; Purtilo, James M.

1995-01-01

Many computer programs cannot be easily integrated because their components are distributed and heterogeneous, i.e., they are implemented in diverse programming languages, use different data representation formats, or their runtime environments are incompatible. In many cases, programs are integrated by modifying their components or interposing mechanisms that handle communication and conversion tasks. For example, remote procedure call (RPC) helps integrate heterogeneous, distributed programs. When configuring such programs, however, mechanisms like RPC must be used explicitly by software developers in order to integrate collections of diverse components. Each collection may require a unique integration solution. This paper describes improvements to the concepts of software packaging and some of our experiences in constructing complex software systems from a wide variety of components in different execution environments. Software packaging is a process that automatically determines how to integrate a diverse collection of computer programs based on the types of components involved and the capabilities of available translators and adapters in an environment. Software packaging provides a context that relates such mechanisms to software integration processes and reduces the cost of configuring applications whose components are distributed or implemented in different programming languages. Our software packaging tool subsumes traditional integration tools like UNIX make by providing a rule-based approach to software integration that is independent of execution environments.

A SIMULINK environment for flight dynamics and control analysis: Application to the DHC-2 Beaver. Part 1: Implementation of a model library in SIMULINK. Part 2: Nonlinear analysis of the Beaver autopilot

NASA Technical Reports Server (NTRS)

Rauw, Marc O.

1993-01-01

The design of advanced Automatic Aircraft Control Systems (AACS's) can be improved upon considerably if the designer can access all models and tools required for control system design and analysis through a graphical user interface, from within one software environment. This MSc-thesis presents the first step in the development of such an environment, which is currently being done at the Section for Stability and Control of Delft University of Technology, Faculty of Aerospace Engineering. The environment is implemented within the commercially available software package MATLAB/SIMULINK. The report consists of two parts. Part 1 gives a detailed description of the AACS design environment. The heart of this environment is formed by the SIMULINK implementation of a nonlinear aircraft model in block-diagram format. The model has been worked out for the old laboratory aircraft of the Faculty, the DeHavilland DHC-2 'Beaver', but due to its modular structure, it can easily be adapted for other aircraft. Part 1 also describes MATLAB programs which can be applied for finding steady-state trimmed-flight conditions and for linearization of the aircraft model, and it shows how the built-in simulation routines of SIMULINK have been used for open-loop analysis of the aircraft dynamics. Apart from the implementation of the models and tools, a thorough treatment of the theoretical backgrounds is presented. Part 2 of this report presents a part of an autopilot design process for the 'Beaver' aircraft, which clearly demonstrates the power and flexibility of the AACS design environment from part 1. Evaluations of all longitudinal and lateral control laws by means of nonlinear simulations are treated in detail. A floppy disk containing all relevant MATLAB programs and SIMULINK models is provided as a supplement.

Frequency Domain Identification Toolbox

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Juang, Jer-Nan; Chen, Chung-Wen

1996-01-01

This report documents software written in MATLAB programming language for performing identification of systems from frequency response functions. MATLAB is a commercial software environment which allows easy manipulation of data matrices and provides other intrinsic matrix functions capabilities. Algorithms programmed in this collection of subroutines have been documented elsewhere but all references are provided in this document. A main feature of this software is the use of matrix fraction descriptions and system realization theory to identify state space models directly from test data. All subroutines have templates for the user to use as guidelines.

Control Strategies for the DAB Based PV Interface System

PubMed Central

El-Helw, Hadi M.; Al-Hasheem, Mohamed; Marei, Mostafa I.

2016-01-01

This paper presents an interface system based on the Dual Active Bridge (DAB) converter for Photovoltaic (PV) arrays. Two control strategies are proposed for the DAB converter to harvest the maximum power from the PV array. The first strategy is based on a simple PI controller to regulate the terminal PV voltage through the phase shift angle of the DAB converter. The Perturb and Observe (P&O) Maximum Power Point Tracking (MPPT) technique is utilized to set the reference of the PV terminal voltage. The second strategy presented in this paper employs the Artificial Neural Network (ANN) to directly set the phase shift angle of the DAB converter that results in harvesting maximum power. This feed-forward strategy overcomes the stability issues of the feedback strategy. The proposed PV interface systems are modeled and simulated using MATLAB/SIMULINK and the EMTDC/PSCAD software packages. The simulation results reveal accurate and fast response of the proposed systems. The dynamic performance of the proposed feed-forward strategy outdoes that of the feedback strategy in terms of accuracy and response time. Moreover, an experimental prototype is built to test and validate the proposed PV interface system. PMID:27560138

PETSc Users Manual Revision 3.3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Brown, J.; Buschelman, K.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

PETSc Users Manual Revision 3.4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Brown, J.; Buschelman, K.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

PETSc Users Manual Revision 3.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. ;For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

Automatic landslide detection from LiDAR DTM derivatives by geographic-object-based image analysis based on open-source software

NASA Astrophysics Data System (ADS)

Knevels, Raphael; Leopold, Philip; Petschko, Helene

2017-04-01

With high-resolution airborne Light Detection and Ranging (LiDAR) data more commonly available, many studies have been performed to facilitate the detailed information on the earth surface and to analyse its limitation. Specifically in the field of natural hazards, digital terrain models (DTM) have been used to map hazardous processes such as landslides mainly by visual interpretation of LiDAR DTM derivatives. However, new approaches are striving towards automatic detection of landslides to speed up the process of generating landslide inventories. These studies usually use a combination of optical imagery and terrain data, and are designed in commercial software packages such as ESRI ArcGIS, Definiens eCognition, or MathWorks MATLAB. The objective of this study was to investigate the potential of open-source software for automatic landslide detection based only on high-resolution LiDAR DTM derivatives in a study area within the federal state of Burgenland, Austria. The study area is very prone to landslides which have been mapped with different methodologies in recent years. The free development environment R was used to integrate open-source geographic information system (GIS) software, such as SAGA (System for Automated Geoscientific Analyses), GRASS (Geographic Resources Analysis Support System), or TauDEM (Terrain Analysis Using Digital Elevation Models). The implemented geographic-object-based image analysis (GEOBIA) consisted of (1) derivation of land surface parameters, such as slope, surface roughness, curvature, or flow direction, (2) finding optimal scale parameter by the use of an objective function, (3) multi-scale segmentation, (4) classification of landslide parts (main scarp, body, flanks) by k-mean thresholding, (5) assessment of the classification performance using a pre-existing landslide inventory, and (6) post-processing analysis for the further use in landslide inventories. The results of the developed open-source approach demonstrated good success rates to objectively detect landslides in high-resolution topography data by GEOBIA.

Reliability and accuracy of three imaging software packages used for 3D analysis of the upper airway on cone beam computed tomography images.

PubMed

Chen, Hui; van Eijnatten, Maureen; Wolff, Jan; de Lange, Jan; van der Stelt, Paul F; Lobbezoo, Frank; Aarab, Ghizlane

2017-08-01

The aim of this study was to assess the reliability and accuracy of three different imaging software packages for three-dimensional analysis of the upper airway using CBCT images. To assess the reliability of the software packages, 15 NewTom 5G ® (QR Systems, Verona, Italy) CBCT data sets were randomly and retrospectively selected. Two observers measured the volume, minimum cross-sectional area and the length of the upper airway using Amira ® (Visage Imaging Inc., Carlsbad, CA), 3Diagnosys ® (3diemme, Cantu, Italy) and OnDemand3D ® (CyberMed, Seoul, Republic of Korea) software packages. The intra- and inter-observer reliability of the upper airway measurements were determined using intraclass correlation coefficients and Bland & Altman agreement tests. To assess the accuracy of the software packages, one NewTom 5G ® CBCT data set was used to print a three-dimensional anthropomorphic phantom with known dimensions to be used as the "gold standard". This phantom was subsequently scanned using a NewTom 5G ® scanner. Based on the CBCT data set of the phantom, one observer measured the volume, minimum cross-sectional area, and length of the upper airway using Amira ® , 3Diagnosys ® , and OnDemand3D ® , and compared these measurements with the gold standard. The intra- and inter-observer reliability of the measurements of the upper airway using the different software packages were excellent (intraclass correlation coefficient ≥0.75). There was excellent agreement between all three software packages in volume, minimum cross-sectional area and length measurements. All software packages underestimated the upper airway volume by -8.8% to -12.3%, the minimum cross-sectional area by -6.2% to -14.6%, and the length by -1.6% to -2.9%. All three software packages offered reliable volume, minimum cross-sectional area and length measurements of the upper airway. The length measurements of the upper airway were the most accurate results in all software packages. All software packages underestimated the upper airway dimensions of the anthropomorphic phantom.

Reviews.

ERIC Educational Resources Information Center

Radcliffe, George; And Others

1988-01-01

Reviews three software packages: 1) a package containing 68 programs covering general topics in chemistry; 2) a package dealing with acid-base titration curves and allows for variables to be changed; 3) a chemistry tutorial and drill package. (MVL)

Evaluation of interaction dynamics of concurrent processes

NASA Astrophysics Data System (ADS)

Sobecki, Piotr; Białasiewicz, Jan T.; Gross, Nicholas

2017-03-01

The purpose of this paper is to present the wavelet tools that enable the detection of temporal interactions of concurrent processes. In particular, the determination of interaction coherence of time-varying signals is achieved using a complex continuous wavelet transform. This paper has used electrocardiogram (ECG) and seismocardiogram (SCG) data set to show multiple continuous wavelet analysis techniques based on Morlet wavelet transform. MATLAB Graphical User Interface (GUI), developed in the reported research to assist in quick and simple data analysis, is presented. These software tools can discover the interaction dynamics of time-varying signals, hence they can reveal their correlation in phase and amplitude, as well as their non-linear interconnections. The user-friendly MATLAB GUI enables effective use of the developed software what enables to load two processes under investigation, make choice of the required processing parameters, and then perform the analysis. The software developed is a useful tool for researchers who have a need for investigation of interaction dynamics of concurrent processes.

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

Educational Software for Interference and Optical Diffraction Analysis in Fresnel and Fraunhofer Regions Based on MATLAB GUIs and the FDTD Method

ERIC Educational Resources Information Center

Frances, J.; Perez-Molina, M.; Bleda, S.; Fernandez, E.; Neipp, C.; Belendez, A.

2012-01-01

Interference and diffraction of light are elementary topics in optics. The aim of the work presented here is to develop an accurate and cheap optical-system simulation software that provides a virtual laboratory for studying the effects of propagation in both time and space for the near- and far-field regions. In laboratory sessions, this software…

4D BADA-based Trajectory Generator and 3D Guidance Algorithm

NASA Technical Reports Server (NTRS)

Palacios, Eduardo Sepulveda; Johnson, Marcus A.

2013-01-01

This paper presents a hybrid integration between aerodynamic, airline procedures and other BADA-based (Base of Aircraft Data) coefficients with a classical aircraft dynamic model. This paper also describes a three-dimensional guidance algorithm implemented in order to produce commands for the aircraft to follow a flight plan. The software chosen for this work is MATLAB.

Investigation into the development of computer aided design software for space based sensors

NASA Technical Reports Server (NTRS)

Pender, C. W.; Clark, W. L.

1987-01-01

The described effort is phase one of the development of a Computer Aided Design (CAD) software to be used to perform radiometric sensor design. The software package will be referred to as SCAD and is directed toward the preliminary phase of the design of space based sensor system. The approach being followed is to develop a modern, graphic intensive, user friendly software package using existing software as building blocks. The emphasis will be directed toward the development of a shell containing menus, smart defaults, and interfaces, which can accommodate a wide variety of existing application software packages. The shell will offer expected utilities such as graphics, tailored menus, and a variety of drivers for I/O devices. Following the development of the shell, the development of SCAD is planned as chiefly selection and integration of appropriate building blocks. The phase one development activities have included: the selection of hardware which will be used with SCAD; the determination of the scope of SCAD; the preliminary evaluation of a number of software packages for applicability to SCAD; determination of a method for achieving required capabilities where voids exist; and then establishing a strategy for binding the software modules into an easy to use tool kit.

Performance Improvements to the Naval Postgraduate School Turbopropulsion Labs Transonic Axially Splittered Rotor

DTIC Science & Technology

2013-12-01

Implementation of current NPS TPL design procedure that uses COTS software (MATLAB, SolidWorks, and ANSYS - CFX ) for the geometric rendering and...procedure that uses commercial-off-the-shelf software (MATLAB, SolidWorks, and ANSYS - CFX ) for the geometric rendering and analysis was modified and... CFX The CFD simulation program in ANSYS Workbench. CFX -Pre CFX boundary conditions and solver settings module. CFX -Solver CFX solver program. CFX

Modern software approaches applied to a Hydrological model: the GEOtop Open-Source Software Project

NASA Astrophysics Data System (ADS)

Cozzini, Stefano; Endrizzi, Stefano; Cordano, Emanuele; Bertoldi, Giacomo; Dall'Amico, Matteo

2017-04-01

The GEOtop hydrological scientific package is an integrated hydrological model that simulates the heat and water budgets at and below the soil surface. It describes the three-dimensional water flow in the soil and the energy exchange with the atmosphere, considering the radiative and turbulent fluxes. Furthermore, it reproduces the highly non-linear interactions between the water and energy balance during soil freezing and thawing, and simulates the temporal evolution of snow cover, soil temperature and moisture. The core components of the package were presented in the 2.0 version (Endrizzi et al, 2014), which was released as Free Software Open-source project. However, despite the high scientific quality of the project, a modern software engineering approach was still missing. Such weakness hindered its scientific potential and its use both as a standalone package and, more importantly, in an integrate way with other hydrological software tools. In this contribution we present our recent software re-engineering efforts to create a robust and stable scientific software package open to the hydrological community, easily usable by researchers and experts, and interoperable with other packages. The activity takes as a starting point the 2.0 version, scientifically tested and published. This version, together with several test cases based on recent published or available GEOtop applications (Cordano and Rigon, 2013, WRR, Kollet et al, 2016, WRR) provides the baseline code and a certain number of referenced results as benchmark. Comparison and scientific validation can then be performed for each software re-engineering activity performed on the package. To keep track of any single change the package is published on its own github repository geotopmodel.github.io/geotop/ under GPL v3.0 license. A Continuous Integration mechanism by means of Travis-CI has been enabled on the github repository on master and main development branches. The usage of CMake configuration tool and the suite of tests (easily manageable by means of ctest tools) greatly reduces the burden of the installation and allows us to enhance portability on different compilers and Operating system platforms. The package was also complemented by several software tools which provide web-based visualization of results based on R plugins, in particular "shiny" (Chang at al, 2016), "geotopbricks" and "geotopOptim2" (Cordano et al, 2016) packages, which allow rapid and efficient scientific validation of new examples and tests. The software re-engineering activities are still under development. However, our first results are promising enough to eventually reach a robust and stable software project that manages in a flexible way a complex state-of-the-art hydrological model like GEOtop and integrates it into wider workflows.

INTERFACING SAS TO ORACLE IN THE UNIX ENVIRONMENT

EPA Science Inventory

SAS is an EPA standard data and statistical analysis software package while ORACLE is EPA's standard data base management system software package. RACLE has the advantage over SAS in data retrieval and storage capabilities but has limited data and statistical analysis capability....

RxGen General Optical Model Prescription Generator

NASA Technical Reports Server (NTRS)

Sigrist, Norbert

2012-01-01

RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

Multivariate and repeated measures (MRM): A new toolbox for dependent and multimodal group-level neuroimaging data.

PubMed

McFarquhar, Martyn; McKie, Shane; Emsley, Richard; Suckling, John; Elliott, Rebecca; Williams, Stephen

2016-05-15

Repeated measurements and multimodal data are common in neuroimaging research. Despite this, conventional approaches to group level analysis ignore these repeated measurements in favour of multiple between-subject models using contrasts of interest. This approach has a number of drawbacks as certain designs and comparisons of interest are either not possible or complex to implement. Unfortunately, even when attempting to analyse group level data within a repeated-measures framework, the methods implemented in popular software packages make potentially unrealistic assumptions about the covariance structure across the brain. In this paper, we describe how this issue can be addressed in a simple and efficient manner using the multivariate form of the familiar general linear model (GLM), as implemented in a new MATLAB toolbox. This multivariate framework is discussed, paying particular attention to methods of inference by permutation. Comparisons with existing approaches and software packages for dependent group-level neuroimaging data are made. We also demonstrate how this method is easily adapted for dependency at the group level when multiple modalities of imaging are collected from the same individuals. Follow-up of these multimodal models using linear discriminant functions (LDA) is also discussed, with applications to future studies wishing to integrate multiple scanning techniques into investigating populations of interest. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Modeling of Habitat and Foraging Behavior of Beaked Whales in the Southern California Bight

DTIC Science & Technology

2014-09-30

preference. APPROACH High-Frequency Acoustic Recording Packages ( HARPs , Wiggins & Hildebrand 2007) have collected acoustic data at 17 sites...signal processing for HARP data is performed using the MATLAB (Mathworks, Natick, MA) based custom program Triton (Wiggins & Hildebrand 2007) and... HARP data are stored with the remainder of metadata (e.g. project name, instrument location, detection settings, detection effort) in the database

A graphic user interface for efficient 3D photo-reconstruction based on free software

NASA Astrophysics Data System (ADS)

Castillo, Carlos; James, Michael; Gómez, Jose A.

2015-04-01

Recently, different studies have stressed the applicability of 3D photo-reconstruction based on Structure from Motion algorithms in a wide range of geoscience applications. For the purpose of image photo-reconstruction, a number of commercial and freely available software packages have been developed (e.g. Agisoft Photoscan, VisualSFM). The workflow involves typically different stages such as image matching, sparse and dense photo-reconstruction, point cloud filtering and georeferencing. For approaches using open and free software, each of these stages usually require different applications. In this communication, we present an easy-to-use graphic user interface (GUI) developed in Matlab® code as a tool for efficient 3D photo-reconstruction making use of powerful existing software: VisualSFM (Wu, 2015) for photo-reconstruction and CloudCompare (Girardeau-Montaut, 2015) for point cloud processing. The GUI performs as a manager of configurations and algorithms, taking advantage of the command line modes of existing software, which allows an intuitive and automated processing workflow for the geoscience user. The GUI includes several additional features: a) a routine for significantly reducing the duration of the image matching operation, normally the most time consuming stage; b) graphical outputs for understanding the overall performance of the algorithm (e.g. camera connectivity, point cloud density); c) a number of useful options typically performed before and after the photo-reconstruction stage (e.g. removal of blurry images, image renaming, vegetation filtering); d) a manager of batch processing for the automated reconstruction of different image datasets. In this study we explore the advantages of this new tool by testing its performance using imagery collected in several soil erosion applications. References Girardeau-Montaut, D. 2015. CloudCompare documentation accessed at http://cloudcompare.org/ Wu, C. 2015. VisualSFM documentation access at http://ccwu.me/vsfm/doc.html#.

System Simulation of Nuclear Power Plant by Coupling RELAP5 and Matlab/Simulink

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng Lin; Dong Hou; Zhihong Xu

2006-07-01

Since RELAP5 code has general and advanced features in thermal-hydraulic computation, it has been widely used in transient and accident safety analysis, experiment planning analysis, and system simulation, etc. So we wish to design, analyze, verify a new Instrumentation And Control (I and C) system of Nuclear Power Plant (NPP) based on the best-estimated code, and even develop our engineering simulator. But because of limited function of simulating control and protection system in RELAP5, it is necessary to expand the function for high efficient, accurate, flexible design and simulation of I and C system. Matlab/Simulink, a scientific computation software, justmore » can compensate the limitation, which is a powerful tool in research and simulation of plant process control. The software is selected as I and C part to be coupled with RELAP5 code to realize system simulation of NPPs. There are two key techniques to be solved. One is the dynamic data exchange, by which Matlab/Simulink receives plant parameters and returns control results. Database is used to communicate the two codes. Accordingly, Dynamic Link Library (DLL) is applied to link database in RELAP5, while DLL and S-Function is applied in Matlab/Simulink. The other problem is synchronization between the two codes for ensuring consistency in global simulation time. Because Matlab/Simulink always computes faster than RELAP5, the simulation time is sent by RELAP5 and received by Matlab/Simulink. A time control subroutine is added into the simulation procedure of Matlab/Simulink to control its simulation advancement. Through these ways, Matlab/Simulink is dynamically coupled with RELAP5. Thus, in Matlab/Simulink, we can freely design control and protection logic of NPPs and test it with best-estimated plant model feedback. A test will be shown to illuminate that results of coupling calculation are nearly the same with one of single RELAP5 with control logic. In practice, a real Pressurized Water Reactor (PWR) is modeled by RELAP5 code, and its main control and protection system is duplicated by Matlab/Simulink. Some steady states and transients are calculated under control of these I and C systems, and the results are compared with the plant test curves. The application showed that it can do exact system simulation of NPPs by coupling RELAP5 and Matlab/Simulink. This paper will mainly focus on the coupling method, plant thermal-hydraulic model, main control logics, test and application results. (authors)« less

User's Guide for MapIMG 2: Map Image Re-projection Software Package

USGS Publications Warehouse

Finn, Michael P.; Trent, Jason R.; Buehler, Robert A.

2006-01-01

BACKGROUND Scientists routinely accomplish small-scale geospatial modeling in the raster domain, using high-resolution datasets for large parts of continents and low-resolution to high-resolution datasets for the entire globe. Direct implementation of point-to-point transformation with appropriate functions yields the variety of projections available in commercial software packages, but implementation with data other than points requires specific adaptation of the transformation equations or prior preparation of the data to allow the transformation to succeed. It seems that some of these packages use the U.S. Geological Survey's (USGS) General Cartographic Transformation Package (GCTP) or similar point transformations without adaptation to the specific characteristics of raster data (Usery and others, 2003a). Usery and others (2003b) compiled and tabulated the accuracy of categorical areas in projected raster datasets of global extent. Based on the shortcomings identified in these studies, geographers and applications programmers at the USGS expanded and evolved a USGS software package, MapIMG, for raster map projection transformation (Finn and Trent, 2004). Daniel R. Steinwand of Science Applications International Corporation, National Center for Earth Resources Observation and Science, originally developed MapIMG for the USGS, basing it on GCTP. Through previous and continuing efforts at the USGS' National Geospatial Technical Operations Center, this program has been transformed from an application based on command line input into a software package based on a graphical user interface for Windows, Linux, and other UNIX machines.

MATLAB Software Versions and Licenses for the Peregrine System |

Science.gov Websites

: Feature usage info: Users of MATLAB: (Total of 6 licenses issued; Total of ... licenses in use) Users of Compiler: (Total of 1 license issued; Total of ... licenses in use) Users of Distrib_Computing_Toolbox : (Total of 4 licenses issued; Total of ... licenses in use) Users of MATLAB_Distrib_Comp_Engine: (Total of

Trick Simulation Environment 07

NASA Technical Reports Server (NTRS)

Lin, Alexander S.; Penn, John M.

2012-01-01

The Trick Simulation Environment is a generic simulation toolkit used for constructing and running simulations. This release includes a Monte Carlo analysis simulation framework and a data analysis package. It produces all auto documentation in XML. Also, the software is capable of inserting a malfunction at any point during the simulation. Trick 07 adds variable server output options and error messaging and is capable of using and manipulating wide characters for international support. Wide character strings are available as a fundamental type for variables processed by Trick. A Trick Monte Carlo simulation uses a statistically generated, or predetermined, set of inputs to iteratively drive the simulation. Also, there is a framework in place for optimization and solution finding where developers may iteratively modify the inputs per run based on some analysis of the outputs. The data analysis package is capable of reading data from external simulation packages such as MATLAB and Octave, as well as the common comma-separated values (CSV) format used by Excel, without the use of external converters. The file formats for MATLAB and Octave were obtained from their documentation sets, and Trick maintains generic file readers for each format. XML tags store the fields in the Trick header comments. For header files, XML tags for structures and enumerations, and the members within are stored in the auto documentation. For source code files, XML tags for each function and the calling arguments are stored in the auto documentation. When a simulation is built, a top level XML file, which includes all of the header and source code XML auto documentation files, is created in the simulation directory. Trick 07 provides an XML to TeX converter. The converter reads in header and source code XML documentation files and converts the data to TeX labels and tables suitable for inclusion in TeX documents. A malfunction insertion capability allows users to override the value of any simulation variable, or call a malfunction job, at any time during the simulation. Users may specify conditions, use the return value of a malfunction trigger job, or manually activate a malfunction. The malfunction action may consist of executing a block of input file statements in an action block, setting simulation variable values, call a malfunction job, or turn on/off simulation jobs.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

cit: hypothesis testing software for mediation analysis in genomic applications.

PubMed

Millstein, Joshua; Chen, Gary K; Breton, Carrie V

2016-08-01

The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). joshua.millstein@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

NASA Astrophysics Data System (ADS)

Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

Nuclear Fuel Depletion Analysis Using Matlab Software

NASA Astrophysics Data System (ADS)

Faghihi, F.; Nematollahi, M. R.

Coupled first order IVPs are frequently used in many parts of engineering and sciences. In this article, we presented a code including three computer programs which are joint with the Matlab software to solve and plot the solutions of the first order coupled stiff or non-stiff IVPs. Some engineering and scientific problems related to IVPs are given and fuel depletion (production of the 239Pu isotope) in a Pressurized Water Nuclear Reactor (PWR) are computed by the present code.

Developing a Virtual Physics World

ERIC Educational Resources Information Center

Wegener, Margaret; McIntyre, Timothy J.; McGrath, Dominic; Savage, Craig M.; Williamson, Michael

2012-01-01

In this article, the successful implementation of a development cycle for a physics teaching package based on game-like virtual reality software is reported. The cycle involved several iterations of evaluating students' use of the package followed by instructional and software development. The evaluation used a variety of techniques, including…

Develop a Model Component

NASA Technical Reports Server (NTRS)

Ensey, Tyler S.

2013-01-01

During my internship at NASA, I was a model developer for Ground Support Equipment (GSE). The purpose of a model developer is to develop and unit test model component libraries (fluid, electrical, gas, etc.). The models are designed to simulate software for GSE (Ground Special Power, Crew Access Arm, Cryo, Fire and Leak Detection System, Environmental Control System (ECS), etc. .) before they are implemented into hardware. These models support verifying local control and remote software for End-Item Software Under Test (SUT). The model simulates the physical behavior (function, state, limits and 110) of each end-item and it's dependencies as defined in the Subsystem Interface Table, Software Requirements & Design Specification (SRDS), Ground Integrated Schematic (GIS), and System Mechanical Schematic.(SMS). The software of each specific model component is simulated through MATLAB's Simulink program. The intensiv model development life cycle is a.s follows: Identify source documents; identify model scope; update schedule; preliminary design review; develop model requirements; update model.. scope; update schedule; detailed design review; create/modify library component; implement library components reference; implement subsystem components; develop a test script; run the test script; develop users guide; send model out for peer review; the model is sent out for verifictionlvalidation; if there is empirical data, a validation data package is generated; if there is not empirical data, a verification package is generated; the test results are then reviewed; and finally, the user. requests accreditation, and a statement of accreditation is prepared. Once each component model is reviewed and approved, they are intertwined together into one integrated model. This integrated model is then tested itself, through a test script and autotest, so that it can be concluded that all models work conjointly, for a single purpose. The component I was assigned, specifically, was a fluid component, a discrete pressure switch. The switch takes a fluid pressure input, and if the pressure is greater than a designated cutoff pressure, the switch would stop fluid flow.

pyam: Python Implementation of YaM

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan

2012-01-01

pyam is a software development framework with tools for facilitating the rapid development of software in a concurrent software development environment. pyam provides solutions for development challenges associated with software reuse, managing multiple software configurations, developing software product lines, and multiple platform development and build management. pyam uses release-early, release-often development cycles to allow developers to integrate their changes incrementally into the system on a continual basis. It facilitates the creation and merging of branches to support the isolated development of immature software to avoid impacting the stability of the development effort. It uses modules and packages to organize and share software across multiple software products, and uses the concepts of link and work modules to reduce sandbox setup times even when the code-base is large. One sidebenefit is the enforcement of a strong module-level encapsulation of a module s functionality and interface. This increases design transparency, system stability, and software reuse. pyam is written in Python and is organized as a set of utilities on top of the open source SVN software version control package. All development software is organized into a collection of modules. pyam packages are defined as sub-collections of the available modules. Developers can set up private sandboxes for module/package development. All module/package development takes place on private SVN branches. High-level pyam commands support the setup, update, and release of modules and packages. Released and pre-built versions of modules are available to developers. Developers can tailor the source/link module mix for their sandboxes so that new sandboxes (even large ones) can be built up easily and quickly by pointing to pre-existing module releases. All inter-module interfaces are publicly exported via links. A minimal, but uniform, convention is used for building modules.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

Upgrading Custom Simulink Library Components for Use in Newer Versions of Matlab

NASA Technical Reports Server (NTRS)

Stewart, Camiren L.

2014-01-01

The Spaceport Command and Control System (SCCS) at Kennedy Space Center (KSC) is a control system for monitoring and launching manned launch vehicles. Simulations of ground support equipment (GSE) and the launch vehicle systems are required throughout the life cycle of SCCS to test software, hardware, and procedures to train the launch team. The simulations of the GSE at the launch site in conjunction with off-line processing locations are developed using Simulink, a piece of Commercial Off-The-Shelf (COTS) software. The simulations that are built are then converted into code and ran in a simulation engine called Trick, a Government off-the-shelf (GOTS) piece of software developed by NASA. In the world of hardware and software, it is not uncommon to see the products that are utilized be upgraded and patched or eventually fade away into an obsolete status. In the case of SCCS simulation software, Matlab, a MathWorks product, has released a number of stable versions of Simulink since the deployment of the software on the Development Work Stations in the Linux environment (DWLs). The upgraded versions of Simulink has introduced a number of new tools and resources that, if utilized fully and correctly, will save time and resources during the overall development of the GSE simulation and its correlating documentation. Unfortunately, simply importing the already built simulations into the new Matlab environment will not suffice as it will produce results that may not be expected as they were in the version that is currently being utilized. Thus, an upgrade execution plan was developed and executed to fully upgrade the simulation environment to one of the latest versions of Matlab.

Development of a UNIX network compatible reactivity computer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez, R.F.; Edwards, R.M.

1996-12-31

A state-of-the-art UNIX network compatible controller and UNIX host workstation with MATLAB/SIMULINK software were used to develop, implement, and validate a digital reactivity calculation. An objective of the development was to determine why a Macintosh-based reactivity computer reactivity output drifted intolerably.

A Software Development Approach for Computer Assisted Language Learning

ERIC Educational Resources Information Center

Cushion, Steve

2005-01-01

Over the last 5 years we have developed, produced, tested, and evaluated an authoring software package to produce web-based, interactive, audio-enhanced language-learning material. That authoring package has been used to produce language-learning material in French, Spanish, German, Arabic, and Tamil. We are currently working on increasing…

A Multi-User Microcomputer System for Small Libraries.

ERIC Educational Resources Information Center

Leggate, Peter

1988-01-01

Describes the development of Bookshelf, a multi-user microcomputer system for small libraries that uses an integrated software package. The discussion covers the design parameters of the package, which were based on a survey of seven small libraries, and some characteristics of the software. (three notes with references) (CLB)

Large Scale Software Building with CMake in ATLAS

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The offline software of the ATLAS experiment at the Large Hadron Collider (LHC) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector’s trigger system to select LHC collision events during data taking. The ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows, many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications also require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the above mentioned software packages. This also makes it possible to develop and test new and modified packages on top of existing releases. The system also allows one to detect and execute partial rebuilds of the release based on single package changes. The build system makes use of CPack for building RPM packages out of the software releases, and CTest for running unit and integration tests. We report on the migration and integration of the ATLAS software to CMake and show working examples of this large scale project in production.

A Study of Visualization for Mathematics Education

NASA Technical Reports Server (NTRS)

Daugherty, Sarah C.

2008-01-01

Graphical representations such as figures, illustrations, and diagrams play a critical role in mathematics and they are equally important in mathematics education. However, graphical representations in mathematics textbooks are static, Le. they are used to illustrate only a specific example or a limited set. of examples. By using computer software to visualize mathematical principles, virtually there is no limit to the number of specific cases and examples that can be demonstrated. However, we have not seen widespread adoption of visualization software in mathematics education. There are currently a number of software packages that provide visualization of mathematics for research and also software packages specifically developed for mathematics education. We conducted a survey of mathematics visualization software packages, summarized their features and user bases, and analyzed their limitations. In this survey, we focused on evaluating the software packages for their use with mathematical subjects adopted by institutions of secondary education in the United States (middle schools and high schools), including algebra, geometry, trigonometry, and calculus. We found that cost, complexity, and lack of flexibility are the major factors that hinder the widespread use of mathematics visualization software in education.

Object-oriented design of medical imaging software.

PubMed

Ligier, Y; Ratib, O; Logean, M; Girard, C; Perrier, R; Scherrer, J R

1994-01-01

A special software package for interactive display and manipulation of medical images was developed at the University Hospital of Geneva, as part of a hospital wide Picture Archiving and Communication System (PACS). This software package, called Osiris, was especially designed to be easily usable and adaptable to the needs of noncomputer-oriented physicians. The Osiris software has been developed to allow the visualization of medical images obtained from any imaging modality. It provides generic manipulation tools, processing tools, and analysis tools more specific to clinical applications. This software, based on an object-oriented paradigm, is portable and extensible. Osiris is available on two different operating systems: the Unix X-11/OSF-Motif based workstations, and the Macintosh family.

A SOFTWARE PACKAGE FOR UNSUPERVISED PATTERN RECOGNITION AND SYNOPTIC REPRESENTATION OF RESULTS: APPLICATION TO VOLCANIC TREMOR DATA OF MT ETNA

NASA Astrophysics Data System (ADS)

Langer, H. K.; Falsaperla, S. M.; Behncke, B.; Messina, A.; Spampinato, S.

2009-12-01

Artificial Intelligence (AI) has found broad applications in volcano observatories worldwide with the aim of reducing volcanic hazard. The need to process larger and larger quantity of data makes indeed AI techniques appealing for monitoring purposes. Tools based on Artificial Neural Networks and Support Vector Machine have proved to be particularly successful in the classification of seismic events and volcanic tremor changes heralding eruptive activity, such as paroxysmal explosions and lava fountaining at Stromboli and Mt Etna, Italy (e.g., Falsaperla et al., 1996; Langer et al., 2009). Moving on from the excellent results obtained from these applications, we present KKAnalysis, a MATLAB based software which combines several unsupervised pattern classification methods, exploiting routines of the SOM Toolbox 2 for MATLAB (http://www.cis.hut.fi/projects/somtoolbox). KKAnalysis is based on Self Organizing Maps (SOM) and clustering methods consisting of K-Means, Fuzzy C-Means, and a scheme based on a metrics accounting for correlation between components of the feature vector. We show examples of applications of this tool to volcanic tremor data recorded at Mt Etna between 2007 and 2009. This time span - during which Strombolian explosions, 7 episodes of lava fountaining and effusive activity occurred - is particularly interesting, as it encompassed different states of volcanic activity (i.e., non-eruptive, eruptive according to different styles) for the unsupervised classifier to identify, highlighting their development in time. Even subtle changes in the signal characteristics allow the unsupervised classifier to recognize features belonging to the different classes and stages of volcanic activity. A convenient color-code representation shows up the temporal development of the different classes of signal, making this method extremely helpful for monitoring purposes and surveillance. Though being developed for volcanic tremor classification, KKAnalysis is generally applicable to any type of physical or chemical pattern, provided that feature vectors are given in numerical form. References: Falsaperla, S., S. Graziani, G. Nunnari, and S. Spampinato (1996). Automatic classification of volcanic earthquakes by using multy-layered neural networks. Natural Hazard, 13, 205-228. Langer, H., S. Falsaperla, M. Masotti, R. Campanini, S. Spampinato, and A. Messina (2008). Synopsis of supervised and unsupervised pattern classification techniques applied to volcanic tremor data at Mt Etna, Italy. Geophys. J. Int., doi:10.1111/j.1365-246X.2009.04179.x.

Accelerated rescaling of single Monte Carlo simulation runs with the Graphics Processing Unit (GPU).

PubMed

Yang, Owen; Choi, Bernard

2013-01-01

To interpret fiber-based and camera-based measurements of remitted light from biological tissues, researchers typically use analytical models, such as the diffusion approximation to light transport theory, or stochastic models, such as Monte Carlo modeling. To achieve rapid (ideally real-time) measurement of tissue optical properties, especially in clinical situations, there is a critical need to accelerate Monte Carlo simulation runs. In this manuscript, we report on our approach using the Graphics Processing Unit (GPU) to accelerate rescaling of single Monte Carlo runs to calculate rapidly diffuse reflectance values for different sets of tissue optical properties. We selected MATLAB to enable non-specialists in C and CUDA-based programming to use the generated open-source code. We developed a software package with four abstraction layers. To calculate a set of diffuse reflectance values from a simulated tissue with homogeneous optical properties, our rescaling GPU-based approach achieves a reduction in computation time of several orders of magnitude as compared to other GPU-based approaches. Specifically, our GPU-based approach generated a diffuse reflectance value in 0.08ms. The transfer time from CPU to GPU memory currently is a limiting factor with GPU-based calculations. However, for calculation of multiple diffuse reflectance values, our GPU-based approach still can lead to processing that is ~3400 times faster than other GPU-based approaches.

Advanced Software Development Workstation Project

NASA Technical Reports Server (NTRS)

Lee, Daniel

1989-01-01

The Advanced Software Development Workstation Project, funded by Johnson Space Center, is investigating knowledge-based techniques for software reuse in NASA software development projects. Two prototypes have been demonstrated and a third is now in development. The approach is to build a foundation that provides passive reuse support, add a layer that uses domain-independent programming knowledge, add a layer that supports the acquisition of domain-specific programming knowledge to provide active support, and enhance maintainability and modifiability through an object-oriented approach. The development of new application software would use specification-by-reformulation, based on a cognitive theory of retrieval from very long-term memory in humans, and using an Ada code library and an object base. Current tasks include enhancements to the knowledge representation of Ada packages and abstract data types, extensions to support Ada package instantiation knowledge acquisition, integration with Ada compilers and relational databases, enhancements to the graphical user interface, and demonstration of the system with a NASA contractor-developed trajectory simulation package. Future work will focus on investigating issues involving scale-up and integration.

Optical Modeling Activities for NASA's James Webb Space Telescope (JWST). 4; Overview and Introduction of Matlab Based Toolkits used to Interface with Optical Design Software

NASA Technical Reports Server (NTRS)

Howard, Joseph

2007-01-01

This is part four of a series on the ongoing optical modeling activities for James Webb Space Telescope (JWST). The first two discussed modeling JWST on-orbit performance using wavefront sensitivities to predict line of sight motion induced blur, and stability during thermal transients. The third investigates the aberrations resulting from alignment and figure compensation of the controllable degrees of freedom (primary and secondary mirrors), which may be encountered during ground alignment and on-orbit commissioning of the observatory. The work here introduces some of the math software tools used to perform the work of the previous three papers of this series. NASA has recently approved these in-house tools for public release as open source, so this presentation also serves as a quick tutorial on their use. The tools are collections of functions written in Matlab, which interface with optical design software (CodeV, OSLO, and Zemax) using either COM or DDE communication protocol. The functions are discussed, and examples are given.

Optical modeling activities for NASA's James Webb Space Telescope (JWST): IV. Overview and introduction of MATLAB based toolkits used to interface with optical design software

NASA Astrophysics Data System (ADS)

Howard, Joseph M.

2007-09-01

This paper is part four of a series on the ongoing optical modeling activities for the James Webb Space Telescope (JWST). The first two papers discussed modeling JWST on-orbit performance using wavefront sensitivities to predict line of sight motion induced blur, and stability during thermal transients. The third paper investigates the aberrations resulting from alignment and figure compensation of the controllable degrees of freedom (primary and secondary mirrors), which may be encountered during ground alignment and on-orbit commissioning of the observatory. The work here introduces some of the math software tools used to perform the work of the previous three papers of this series. NASA has recently approved these in-house tools for public release as open source, so this presentation also serves as a quick tutorial on their use. The tools are collections of functions written for use in MATLAB to interface with optical design software (CODE V, OSLO, and ZEMAX) using either COM or DDE communication protocol. The functions are discussed, and examples are given.

Tricuspid Annular Geometry: A Three-Dimensional Transesophageal Echocardiographic Study

PubMed Central

Mahmood, Feroze; Kim, Han; Chaudary, Bilal; Bergman, Remco; Matyal, Robina; Gerstle, Jeniffer; Gorman, Joseph H.; Gorman, Robert C.; Khabbaz, Kamal R.

2013-01-01

Objective To demonstrate the clinical feasibility of accurately measuring tricuspid annular area by 3-dimensional (3D) transesophageal echocardiography (TEE) and to assess the geometric differences based on the presence of tricuspid regurgitation (TR). Also, the shape of the tricuspid annulus was compared with previous descriptions in the literature. Design Prospective. Setting Tertiary care university hospital. Interventions Three-dimensional TEE. Participants Patients undergoing cardiac surgery. Measurements and Main Results Volumetric data sets from 20 patients were acquired by 3D TEE and prospectively analyzed. Comparisons in annular geometry were made between groups based on the presence of TR. The QLab (Philips Medical Systems, Andover, MA) software package was used to calculate tricuspid annular area by both linear elliptical dimensions and planimetry. Further analyses were performed in the 4D Cardio-View (TomTec Corporation GmBH, Munich, Germany) and MATLAB (Natick, MA) software environments to accurately assess annular shape. It was found that patients with greater TR had an eccentrically dilated annulus with a larger annular area. Also, the area as measured by the linear ellipse method was overestimated as compared to the planimetry method. Furthermore, the irregular saddle-shaped geometry of the tricuspid annulus was confirmed through the mathematic model developed by the authors. Conclusions Three-dimensional TEE can be used to measure the tricuspid annular area in a clinically feasible fashion, with an eccentric dilation seen in patients with TR. The tricuspid annulus shape is complex, with annular high and low points, and annular area calculation based on linear measurements significantly overestimates 3D planimetered area. PMID:23725682

Statistical tools for analysis and modeling of cosmic populations and astronomical time series: CUDAHM and TSE

NASA Astrophysics Data System (ADS)

Loredo, Thomas; Budavari, Tamas; Scargle, Jeffrey D.

2018-01-01

This presentation provides an overview of open-source software packages addressing two challenging classes of astrostatistics problems. (1) CUDAHM is a C++ framework for hierarchical Bayesian modeling of cosmic populations, leveraging graphics processing units (GPUs) to enable applying this computationally challenging paradigm to large datasets. CUDAHM is motivated by measurement error problems in astronomy, where density estimation and linear and nonlinear regression must be addressed for populations of thousands to millions of objects whose features are measured with possibly complex uncertainties, potentially including selection effects. An example calculation demonstrates accurate GPU-accelerated luminosity function estimation for simulated populations of $10^6$ objects in about two hours using a single NVIDIA Tesla K40c GPU. (2) Time Series Explorer (TSE) is a collection of software in Python and MATLAB for exploratory analysis and statistical modeling of astronomical time series. It comprises a library of stand-alone functions and classes, as well as an application environment for interactive exploration of times series data. The presentation will summarize key capabilities of this emerging project, including new algorithms for analysis of irregularly-sampled time series.

A Non-linear Lifting Line Model for Design and Analysis of Trochoidal Propulsors

NASA Astrophysics Data System (ADS)

Roesler, Bernard; Epps, Brenden

2014-11-01

Flapping wing propulsors may increase the propulsive efficiency of large shipping vessels. A comparison of the design of a notional propulsor for a large shipping vessel with (a) a conventional ducted propeller versus (b) a flapping wing propulsor is presented. Calculations for flapping wing propulsors are performed using an open-source MATLAB software suite developed by the authors, CyROD, implementing an unsteady lifting-line model with free vortex wake roll-up to study the non-linear effects of foil-wake, and foil-foil interactions. Improvements to the traditional lifting line theory are made using further discretization of the wake vortex ring spacing near the trailing edge. Considerations of packaging options for a flapping wing propulsor on a large shipping vessel are presented, and compared with those for a conventional ducted propeller.

On the release of cppxfel for processing X-ray free-electron laser images.

PubMed

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K; Stuart, David Ian

2016-06-01

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel , a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

On the release of cppxfel for processing X-ray free-electron laser images

DOE PAGES

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K.; ...

2016-05-11

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed formore » existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.« less

PETOOL: MATLAB-based one-way and two-way split-step parabolic equation tool for radiowave propagation over variable terrain

NASA Astrophysics Data System (ADS)

Ozgun, Ozlem; Apaydin, Gökhan; Kuzuoglu, Mustafa; Sevgi, Levent

2011-12-01

A MATLAB-based one-way and two-way split-step parabolic equation software tool (PETOOL) has been developed with a user-friendly graphical user interface (GUI) for the analysis and visualization of radio-wave propagation over variable terrain and through homogeneous and inhomogeneous atmosphere. The tool has a unique feature over existing one-way parabolic equation (PE)-based codes, because it utilizes the two-way split-step parabolic equation (SSPE) approach with wide-angle propagator, which is a recursive forward-backward algorithm to incorporate both forward and backward waves into the solution in the presence of variable terrain. First, the formulation of the classical one-way SSPE and the relatively-novel two-way SSPE is presented, with particular emphasis on their capabilities and the limitations. Next, the structure and the GUI capabilities of the PETOOL software tool are discussed in detail. The calibration of PETOOL is performed and demonstrated via analytical comparisons and/or representative canonical tests performed against the Geometric Optic (GO) + Uniform Theory of Diffraction (UTD). The tool can be used for research and/or educational purposes to investigate the effects of a variety of user-defined terrain and range-dependent refractivity profiles in electromagnetic wave propagation. Program summaryProgram title: PETOOL (Parabolic Equation Toolbox) Catalogue identifier: AEJS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 143 349 No. of bytes in distributed program, including test data, etc.: 23 280 251 Distribution format: tar.gz Programming language: MATLAB (MathWorks Inc.) 2010a. Partial Differential Toolbox and Curve Fitting Toolbox required Computer: PC Operating system: Windows XP and Vista Classification: 10 Nature of problem: Simulation of radio-wave propagation over variable terrain on the Earth's surface, and through homogeneous and inhomogeneous atmosphere. Solution method: The program implements one-way and two-way Split-Step Parabolic Equation (SSPE) algorithm, with wide-angle propagator. The SSPE is, in general, an initial-value problem starting from a reference range (typically from an antenna), and marching out in range by obtaining the field along the vertical direction at each range step, through the use of step-by-step Fourier transformations. The two-way algorithm incorporates the backward-propagating waves into the standard one-way SSPE by utilizing an iterative forward-backward scheme for modeling multipath effects over a staircase-approximated terrain. Unusual features: This is the first software package implementing a recursive forward-backward SSPE algorithm to account for the multipath effects during radio-wave propagation, and enabling the user to easily analyze and visualize the results of the two-way propagation with GUI capabilities. Running time: Problem dependent. Typically, it is about 1.5 ms (for conducting ground) and 4 ms (for lossy ground) per range step for a vertical field profile of vector length 1500, on Intel Core 2 Duo 1.6 GHz with 2 GB RAM under Windows Vista.

Two-Photon Processor and SeNeCA: a freely available software package to process data from two-photon calcium imaging at speeds down to several milliseconds per frame.

PubMed

Tomek, Jakub; Novak, Ondrej; Syka, Josef

2013-07-01

Two-Photon Processor (TPP) is a versatile, ready-to-use, and freely available software package in MATLAB to process data from in vivo two-photon calcium imaging. TPP includes routines to search for cell bodies in full-frame (Search for Neural Cells Accelerated; SeNeCA) and line-scan acquisition, routines for calcium signal calculations, filtering, spike-mining, and routines to construct parametric fields. Searching for somata in artificial in vivo data, our algorithm achieved better performance than human annotators. SeNeCA copes well with uneven background brightness and in-plane motion artifacts, the major problems in simple segmentation methods. In the fast mode, artificial in vivo images with a resolution of 256 × 256 pixels containing ≈ 100 neurons can be processed at a rate up to 175 frames per second (tested on Intel i7, 8 threads, magnetic hard disk drive). This speed of a segmentation algorithm could bring new possibilities into the field of in vivo optophysiology. With such a short latency (down to 5-6 ms on an ordinary personal computer) and using some contemporary optogenetic tools, it will allow experiments in which a control program can continuously evaluate the occurrence of a particular spatial pattern of activity (a possible correlate of memory or cognition) and subsequently inhibit/stimulate the entire area of the circuit or inhibit/stimulate a different part of the neuronal system. TPP will be freely available on our public web site. Similar all-in-one and freely available software has not yet been published.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging.

PubMed

Bonekamp, S; Ghosh, P; Crawford, S; Solga, S F; Horska, A; Brancati, F L; Diehl, A M; Smith, S; Clark, J M

2008-01-01

To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Feature evaluation and test-retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. A random sample of 15 obese adults with type 2 diabetes. Axial T1-weighted spin echo images centered at vertebral bodies of L2-L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test-retest reliability. Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test-retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging

PubMed Central

Bonekamp, S; Ghosh, P; Crawford, S; Solga, SF; Horska, A; Brancati, FL; Diehl, AM; Smith, S; Clark, JM

2009-01-01

Objective To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Design Feature evaluation and test–retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. Subjects A random sample of 15 obese adults with type 2 diabetes. Measurements Axial T1-weighted spin echo images centered at vertebral bodies of L2–L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test–retest reliability. Results Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test–retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Conclusion Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages. PMID:17700582

Is liver perfusion CT reproducible? A study on intra- and interobserver agreement of normal hepatic haemodynamic parameters obtained with two different software packages.

PubMed

Bretas, Elisa Almeida Sathler; Torres, Ulysses S; Torres, Lucas Rios; Bekhor, Daniel; Saito Filho, Celso Fernando; Racy, Douglas Jorge; Faggioni, Lorenzo; D'Ippolito, Giuseppe

2017-10-01

To evaluate the agreement between the measurements of perfusion CT parameters in normal livers by using two different software packages. This retrospective study was based on 78 liver perfusion CT examinations acquired for detecting suspected liver metastasis. Patients with any morphological or functional hepatic abnormalities were excluded. The final analysis included 37 patients (59.7 ± 14.9 y). Two readers (1 and 2) independently measured perfusion parameters using different software packages from two major manufacturers (A and B). Arterial perfusion (AP) and portal perfusion (PP) were determined using the dual-input vascular one-compartmental model. Inter-reader agreement for each package and intrareader agreement between both packages were assessed with intraclass correlation coefficients (ICC) and Bland-Altman statistics. Inter-reader agreement was substantial for AP using software A (ICC = 0.82) and B (ICC = 0.85-0.86), fair for PP using software A (ICC = 0.44) and fair to moderate for PP using software B (ICC = 0.56-0.77). Intrareader agreement between software A and B ranged from slight to moderate (ICC = 0.32-0.62) for readers 1 and 2 considering the AP parameters, and from fair to moderate (ICC = 0.40-0.69) for readers 1 and 2 considering the PP parameters. At best there was only moderate agreement between both software packages, resulting in some uncertainty and suboptimal reproducibility. Advances in knowledge: Software-dependent factors may contribute to variance in perfusion measurements, demanding further technical improvements. AP measurements seem to be the most reproducible parameter to be adopted when evaluating liver perfusion CT.

OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

PubMed

Purvis, Lucian A B; Clarke, William T; Biasiolli, Luca; Valkovič, Ladislav; Robson, Matthew D; Rodgers, Christopher T

2017-01-01

In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA) toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM) standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

Image enhancement using MCNP5 code and MATLAB in neutron radiography.

PubMed

Tharwat, Montaser; Mohamed, Nader; Mongy, T

2014-07-01

This work presents a method that can be used to enhance the neutron radiography (NR) image for objects with high scattering materials like hydrogen, carbon and other light materials. This method used Monte Carlo code, MCNP5, to simulate the NR process and get the flux distribution for each pixel of the image and determines the scattered neutron distribution that caused image blur, and then uses MATLAB to subtract this scattered neutron distribution from the initial image to improve its quality. This work was performed before the commissioning of digital NR system in Jan. 2013. The MATLAB enhancement method is quite a good technique in the case of static based film neutron radiography, while in neutron imaging (NI) technique, image enhancement and quantitative measurement were efficient by using ImageJ software. The enhanced image quality and quantitative measurements were presented in this work. Copyright © 2014 Elsevier Ltd. All rights reserved.

Neutrino oscillation parameter sampling with MonteCUBES

NASA Astrophysics Data System (ADS)

Blennow, Mattias; Fernandez-Martinez, Enrique

2010-01-01

We present MonteCUBES ("Monte Carlo Utility Based Experiment Simulator"), a software package designed to sample the neutrino oscillation parameter space through Markov Chain Monte Carlo algorithms. MonteCUBES makes use of the GLoBES software so that the existing experiment definitions for GLoBES, describing long baseline and reactor experiments, can be used with MonteCUBES. MonteCUBES consists of two main parts: The first is a C library, written as a plug-in for GLoBES, implementing the Markov Chain Monte Carlo algorithm to sample the parameter space. The second part is a user-friendly graphical Matlab interface to easily read, analyze, plot and export the results of the parameter space sampling. Program summaryProgram title: MonteCUBES (Monte Carlo Utility Based Experiment Simulator) Catalogue identifier: AEFJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 69 634 No. of bytes in distributed program, including test data, etc.: 3 980 776 Distribution format: tar.gz Programming language: C Computer: MonteCUBES builds and installs on 32 bit and 64 bit Linux systems where GLoBES is installed Operating system: 32 bit and 64 bit Linux RAM: Typically a few MBs Classification: 11.1 External routines: GLoBES [1,2] and routines/libraries used by GLoBES Subprograms used:Cat Id ADZI_v1_0, Title GLoBES, Reference CPC 177 (2007) 439 Nature of problem: Since neutrino masses do not appear in the standard model of particle physics, many models of neutrino masses also induce other types of new physics, which could affect the outcome of neutrino oscillation experiments. In general, these new physics imply high-dimensional parameter spaces that are difficult to explore using classical methods such as multi-dimensional projections and minimizations, such as those used in GLoBES [1,2]. Solution method: MonteCUBES is written as a plug-in to the GLoBES software [1,2] and provides the necessary methods to perform Markov Chain Monte Carlo sampling of the parameter space. This allows an efficient sampling of the parameter space and has a complexity which does not grow exponentially with the parameter space dimension. The integration of the MonteCUBES package with the GLoBES software makes sure that the experimental definitions already in use by the community can also be used with MonteCUBES, while also lowering the learning threshold for users who already know GLoBES. Additional comments: A Matlab GUI for interpretation of results is included in the distribution. Running time: The typical running time varies depending on the dimensionality of the parameter space, the complexity of the experiment, and how well the parameter space should be sampled. The running time for our simulations [3] with 15 free parameters at a Neutrino Factory with O(10) samples varied from a few hours to tens of hours. References:P. Huber, M. Lindner, W. Winter, Comput. Phys. Comm. 167 (2005) 195, hep-ph/0407333. P. Huber, J. Kopp, M. Lindner, M. Rolinec, W. Winter, Comput. Phys. Comm. 177 (2007) 432, hep-ph/0701187. S. Antusch, M. Blennow, E. Fernandez-Martinez, J. Lopez-Pavon, arXiv:0903.3986 [hep-ph].

Diagnosis diagrams for passing signals on an automatic block signaling railway section

NASA Astrophysics Data System (ADS)

Spunei, E.; Piroi, I.; Chioncel, C. P.; Piroi, F.

2018-01-01

This work presents a diagnosis method for railway traffic security installations. More specifically, the authors present a series of diagnosis charts for passing signals on a railway block equipped with an automatic block signaling installation. These charts are based on the exploitation electric schemes, and are subsequently used to develop a diagnosis software package. The thus developed software package contributes substantially to a reduction of failure detection and remedy for these types of installation faults. The use of the software package eliminates making wrong decisions in the fault detection process, decisions that may result in longer remedy times and, sometimes, to railway traffic events.

Design Method for Numerical Function Generators Based on Polynomial Approximation for FPGA Implementation

DTIC Science & Technology

2007-08-01

with a Design Specification de- scribed by Scilab [26], a MATLAB-like software applica- tion, and ends up with HDL code. The Design Specifica- tion...Conf. on Field Programmable Logic and Applications (FPL’05), Tampere, Finland, pp. 118–123, Aug. 2005. [26] Scilab 3.0, INRIA-ENPC, France, http

A Microcomputer-Based Software Package for Eye-Monitoring Research. Technical Report No. 434.

ERIC Educational Resources Information Center

McConkie, George W.; And Others

A software package is described that collects and reduces eye behavior data (eye position and pupil size) using an IBM-PC compatible computer. Written in C language for speed and portability, it includes several features: (1) data can be simultaneously collected from other sources (such as electroencephalography and electromyography); (2)…

The Package-Based Development Process in the Flight Dynamics Division

NASA Technical Reports Server (NTRS)

Parra, Amalia; Seaman, Carolyn; Basili, Victor; Kraft, Stephen; Condon, Steven; Burke, Steven; Yakimovich, Daniil

1997-01-01

The Software Engineering Laboratory (SEL) has been operating for more than two decades in the Flight Dynamics Division (FDD) and has adapted to the constant movement of the software development environment. The SEL's Improvement Paradigm shows that process improvement is an iterative process. Understanding, Assessing and Packaging are the three steps that are followed in this cyclical paradigm. As the improvement process cycles back to the first step, after having packaged some experience, the level of understanding will be greater. In the past, products resulting from the packaging step have been large process documents, guidebooks, and training programs. As the technical world moves toward more modularized software, we have made a move toward more modularized software development process documentation, as such the products of the packaging step are becoming smaller and more frequent. In this manner, the QIP takes on a more spiral approach rather than a waterfall. This paper describes the state of the FDD in the area of software development processes, as revealed through the understanding and assessing activities conducted by the COTS study team. The insights presented include: (1) a characterization of a typical FDD Commercial Off the Shelf (COTS) intensive software development life-cycle process, (2) lessons learned through the COTS study interviews, and (3) a description of changes in the SEL due to the changing and accelerating nature of software development in the FDD.

Diagnostic evaluation of three cardiac software packages using a consecutive group of patients

PubMed Central

2011-01-01

Purpose The aim of this study was to compare the diagnostic performance of the three software packages 4DMSPECT (4DM), Emory Cardiac Toolbox (ECTb), and Cedars Quantitative Perfusion SPECT (QPS) for quantification of myocardial perfusion scintigram (MPS) using a large group of consecutive patients. Methods We studied 1,052 consecutive patients who underwent 2-day stress/rest 99mTc-sestamibi MPS studies. The reference/gold-standard classifications for the MPS studies were obtained from three physicians, with more than 25 years each of experience in nuclear cardiology, who re-evaluated all MPS images. Automatic processing was carried out using 4DM, ECTb, and QPS software packages. Total stress defect extent (TDE) and summed stress score (SSS) based on a 17-segment model were obtained from the software packages. Receiver-operating characteristic (ROC) analysis was performed. Results A total of 734 patients were classified as normal and the remaining 318 were classified as having infarction and/or ischemia. The performance of the software packages calculated as the area under the SSS ROC curve were 0.87 for 4DM, 0.80 for QPS, and 0.76 for ECTb (QPS vs. ECTb p = 0.03; other differences p < 0.0001). The area under the TDE ROC curve were 0.87 for 4DM, 0.82 for QPS, and 0.76 for ECTb (QPS vs. ECTb p = 0.0005; other differences p < 0.0001). Conclusion There are considerable differences in performance between the three software packages with 4DM showing the best performance and ECTb the worst. These differences in performance should be taken in consideration when software packages are used in clinical routine or in clinical studies. PMID:22214226

ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

PubMed

Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. Copyright © 2011 Elsevier Inc. All rights reserved.

GENERAL PURPOSE ADA PACKAGES

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

Ten families of subprograms are bundled together for the General-Purpose Ada Packages. The families bring to Ada many features from HAL/S, PL/I, FORTRAN, and other languages. These families are: string subprograms (INDEX, TRIM, LOAD, etc.); scalar subprograms (MAX, MIN, REM, etc.); array subprograms (MAX, MIN, PROD, SUM, GET, and PUT); numerical subprograms (EXP, CUBIC, etc.); service subprograms (DATE_TIME function, etc.); Linear Algebra II; Runge-Kutta integrators; and three text I/O families of packages. In two cases, a family consists of a single non-generic package. In all other cases, a family comprises a generic package and its instances for a selected group of scalar types. All generic packages are designed to be easily instantiated for the types declared in the user facility. The linear algebra package is LINRAG2. This package includes subprograms supplementing those in NPO-17985, An Ada Linear Algebra Package Modeled After HAL/S (LINRAG). Please note that LINRAG2 cannot be compiled without LINRAG. Most packages have widespread applicability, although some are oriented for avionics applications. All are designed to facilitate writing new software in Ada. Several of the packages use conventions introduced by other programming languages. A package of string subprograms is based on HAL/S (a language designed for the avionics software in the Space Shuttle) and PL/I. Packages of scalar and array subprograms are taken from HAL/S or generalized current Ada subprograms. A package of Runge-Kutta integrators is patterned after a built-in MAC (MIT Algebraic Compiler) integrator. Those packages modeled after HAL/S make it easy to translate existing HAL/S software to Ada. The General-Purpose Ada Packages program source code is available on two 360K 5.25" MS-DOS format diskettes. The software was developed using VAX Ada v1.5 under DEC VMS v4.5. It should be portable to any validated Ada compiler and it should execute either interactively or in batch. The largest package requires 205K of main memory on a DEC VAX running VMS. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

A Comparison of Four Software Programs for Implementing Decision Analytic Cost-Effectiveness Models.

PubMed

Hollman, Chase; Paulden, Mike; Pechlivanoglou, Petros; McCabe, Christopher

2017-08-01

The volume and technical complexity of both academic and commercial research using decision analytic modelling has increased rapidly over the last two decades. The range of software programs used for their implementation has also increased, but it remains true that a small number of programs account for the vast majority of cost-effectiveness modelling work. We report a comparison of four software programs: TreeAge Pro, Microsoft Excel, R and MATLAB. Our focus is on software commonly used for building Markov models and decision trees to conduct cohort simulations, given their predominance in the published literature around cost-effectiveness modelling. Our comparison uses three qualitative criteria as proposed by Eddy et al.: "transparency and validation", "learning curve" and "capability". In addition, we introduce the quantitative criterion of processing speed. We also consider the cost of each program to academic users and commercial users. We rank the programs based on each of these criteria. We find that, whilst Microsoft Excel and TreeAge Pro are good programs for educational purposes and for producing the types of analyses typically required by health technology assessment agencies, the efficiency and transparency advantages of programming languages such as MATLAB and R become increasingly valuable when more complex analyses are required.

MatSeis and the GNEM R&E regional seismic anaylsis tools.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chael, Eric Paul; Hart, Darren M.; Young, Christopher John

2003-08-01

To improve the nuclear event monitoring capability of the U.S., the NNSA Ground-based Nuclear Explosion Monitoring Research & Engineering (GNEM R&E) program has been developing a collection of products known as the Knowledge Base (KB). Though much of the focus for the KB has been on the development of calibration data, we have also developed numerous software tools for various purposes. The Matlab-based MatSeis package and the associated suite of regional seismic analysis tools were developed to aid in the testing and evaluation of some Knowledge Base products for which existing applications were either not available or ill-suited. This presentationmore » will provide brief overviews of MatSeis and each of the tools, emphasizing features added in the last year. MatSeis was begun in 1996 and is now a fairly mature product. It is a highly flexible seismic analysis package that provides interfaces to read data from either flatfiles or an Oracle database. All of the standard seismic analysis tasks are supported (e.g. filtering, 3 component rotation, phase picking, event location, magnitude calculation), as well as a variety of array processing algorithms (beaming, FK, coherency analysis, vespagrams). The simplicity of Matlab coding and the tremendous number of available functions make MatSeis/Matlab an ideal environment for developing new monitoring research tools (see the regional seismic analysis tools below). New MatSeis features include: addition of evid information to events in MatSeis, options to screen picks by author, input and output of origerr information, improved performance in reading flatfiles, improved speed in FK calculations, and significant improvements to Measure Tool (filtering, multiple phase display), Free Plot (filtering, phase display and alignment), Mag Tool (maximum likelihood options), and Infra Tool (improved calculation speed, display of an F statistic stream). Work on the regional seismic analysis tools (CodaMag, EventID, PhaseMatch, and Dendro) began in 1999 and the tools vary in their level of maturity. All rely on MatSeis to provide necessary data (waveforms, arrivals, origins, and travel time curves). CodaMag Tool implements magnitude calculation by scaling to fit the envelope shape of the coda for a selected phase type (Mayeda, 1993; Mayeda and Walter, 1996). New tool features include: calculation of a yield estimate based on the source spectrum, display of a filtered version of the seismogram based on the selected band, and the output of codamag data records for processed events. EventID Tool implements event discrimination using phase ratios of regional arrivals (Hartse et al., 1997; Walter et al., 1999). New features include: bandpass filtering of displayed waveforms, screening of reference events based on SNR, multivariate discriminants, use of libcgi to access correction surfaces, and the output of discrim{_}data records for processed events. PhaseMatch Tool implements match filtering to isolate surface waves (Herrin and Goforth, 1977). New features include: display of the signal's observed dispersion and an option to use a station-based dispersion surface. Dendro Tool implements agglomerative hierarchical clustering using dendrograms to identify similar events based on waveform correlation (Everitt, 1993). New features include: modifications to include arrival information within the tool, and the capability to automatically add/re-pick arrivals based on the picked arrivals for similar events.« less

GRAVTool, a Package to Compute Geoid Model by Remove-Compute-Restore Technique

NASA Astrophysics Data System (ADS)

Marotta, G. S.; Blitzkow, D.; Vidotti, R. M.

2015-12-01

Currently, there are several methods to determine geoid models. They can be based on terrestrial gravity data, geopotential coefficients, astro-geodetic data or a combination of them. Among the techniques to compute a precise geoid model, the Remove-Compute-Restore (RCR) has been widely applied. It considers short, medium and long wavelengths derived from altitude data provided by Digital Terrain Models (DTM), terrestrial gravity data and global geopotential coefficients, respectively. In order to apply this technique, it is necessary to create procedures that compute gravity anomalies and geoid models, by the integration of different wavelengths, and that adjust these models to one local vertical datum. This research presents a developed package called GRAVTool based on MATLAB software to compute local geoid models by RCR technique and its application in a study area. The studied area comprehends the federal district of Brazil, with ~6000 km², wavy relief, heights varying from 600 m to 1340 m, located between the coordinates 48.25ºW, 15.45ºS and 47.33ºW, 16.06ºS. The results of the numerical example on the studied area show the local geoid model computed by the GRAVTool package (Figure), using 1377 terrestrial gravity data, SRTM data with 3 arc second of resolution, and geopotential coefficients of the EIGEN-6C4 model to degree 360. The accuracy of the computed model (σ = ± 0.071 m, RMS = 0.069 m, maximum = 0.178 m and minimum = -0.123 m) matches the uncertainty (σ =± 0.073) of 21 points randomly spaced where the geoid was computed by geometrical leveling technique supported by positioning GNSS. The results were also better than those achieved by Brazilian official regional geoid model (σ = ± 0.099 m, RMS = 0.208 m, maximum = 0.419 m and minimum = -0.040 m).

Three-Dimensional (3D) Nanometrology Based on Scanning Electron Microscope (SEM) Stereophotogrammetry.

PubMed

Tondare, Vipin N; Villarrubia, John S; Vlada R, András E

2017-10-01

Three-dimensional (3D) reconstruction of a sample surface from scanning electron microscope (SEM) images taken at two perspectives has been known for decades. Nowadays, there exist several commercially available stereophotogrammetry software packages. For testing these software packages, in this study we used Monte Carlo simulated SEM images of virtual samples. A virtual sample is a model in a computer, and its true dimensions are known exactly, which is impossible for real SEM samples due to measurement uncertainty. The simulated SEM images can be used for algorithm testing, development, and validation. We tested two stereophotogrammetry software packages and compared their reconstructed 3D models with the known geometry of the virtual samples used to create the simulated SEM images. Both packages performed relatively well with simulated SEM images of a sample with a rough surface. However, in a sample containing nearly uniform and therefore low-contrast zones, the height reconstruction error was ≈46%. The present stereophotogrammetry software packages need further improvement before they can be used reliably with SEM images with uniform zones.

Improving the quality of EHR recording in primary care: a data quality feedback tool.

PubMed

van der Bij, Sjoukje; Khan, Nasra; Ten Veen, Petra; de Bakker, Dinny H; Verheij, Robert A

2017-01-01

Electronic health record (EHR) data are used to exchange information among health care providers. For this purpose, the quality of the data is essential. We developed a data quality feedback tool that evaluates differences in EHR data quality among practices and software packages as part of a larger intervention. The tool was applied in 92 practices in the Netherlands using different software packages. Practices received data quality feedback in 2010 and 2012. We observed large differences in the quality of recording. For example, the percentage of episodes of care that had a meaningful diagnostic code ranged from 30% to 100%. Differences were highly related to the software package. A year after the first measurement, the quality of recording had improved significantly and differences decreased, with 67% of the physicians indicating that they had actively changed their recording habits based on the results of the first measurement. About 80% found the feedback helpful in pinpointing recording problems. One of the software vendors made changes in functionality as a result of the feedback. Our EHR data quality feedback tool is capable of highlighting differences among practices and software packages. As such, it also stimulates improvements. As substantial variability in recording is related to the software package, our study strengthens the evidence that data quality can be improved substantially by standardizing the functionalities of EHR software packages. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software

PubMed Central

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong

2017-01-01

Abstract Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. PMID:28327936

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

PubMed

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2017-04-01

Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line-based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. © The Authors 2017. Published by Oxford University Press.

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

Scilab and Maxima Environment: Towards Free Software in Numerical Analysis

ERIC Educational Resources Information Center

Mora, Angel; Galan, Jose Luis; Aguilera, Gabriel; Fernandez, Alvaro; Merida, Enrique; Rodriguez, Pedro

2010-01-01

In this work we will present the ScilabUMA environment we have developed as an alternative to Matlab. This environment connects Scilab (for numerical analysis) and Maxima (for symbolic computations). Furthermore, the developed interface is, in our opinion at least, as powerful as the interface of Matlab. (Contains 3 figures.)

VAVUQ, Python and Matlab freeware for Verification and Validation, Uncertainty Quantification

NASA Astrophysics Data System (ADS)

Courtney, J. E.; Zamani, K.; Bombardelli, F. A.; Fleenor, W. E.

2015-12-01

A package of scripts is presented for automated Verification and Validation (V&V) and Uncertainty Quantification (UQ) for engineering codes that approximate Partial Differential Equations (PDFs). The code post-processes model results to produce V&V and UQ information. This information can be used to assess model performance. Automated information on code performance can allow for a systematic methodology to assess the quality of model approximations. The software implements common and accepted code verification schemes. The software uses the Method of Manufactured Solutions (MMS), the Method of Exact Solution (MES), Cross-Code Verification, and Richardson Extrapolation (RE) for solution (calculation) verification. It also includes common statistical measures that can be used for model skill assessment. Complete RE can be conducted for complex geometries by implementing high-order non-oscillating numerical interpolation schemes within the software. Model approximation uncertainty is quantified by calculating lower and upper bounds of numerical error from the RE results. The software is also able to calculate the Grid Convergence Index (GCI), and to handle adaptive meshes and models that implement mixed order schemes. Four examples are provided to demonstrate the use of the software for code and solution verification, model validation and uncertainty quantification. The software is used for code verification of a mixed-order compact difference heat transport solver; the solution verification of a 2D shallow-water-wave solver for tidal flow modeling in estuaries; the model validation of a two-phase flow computation in a hydraulic jump compared to experimental data; and numerical uncertainty quantification for 3D CFD modeling of the flow patterns in a Gust erosion chamber.

DEVELOPMENT OF A PORTABLE SOFTWARE LANGUAGE FOR PHYSIOLOGICALLY-BASED PHARMACOKINETIC (PBPK) MODELS

EPA Science Inventory

The PBPK modeling community has had a long-standing problem with modeling software compatibility. The numerous software packages used for PBPK models are, at best, minimally compatible. This creates problems ranging from model obsolescence due to software support discontinuation...

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaenko, Alexander; Windus, Theresa L.; Sosonkina, Masha

2012-10-19

The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecularmore » systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.« less

ibex: An open infrastructure software platform to facilitate collaborative work in radiomics

PubMed Central

Zhang, Lifei; Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E.

2015-01-01

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (ibex), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The ibex software package was developed using the matlab and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, ibex is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, ibex provides an integrated development environment on top of matlab and c/c++, so users are not limited to its built-in functions. In the ibex developer studio, users can plug in, debug, and test new algorithms, extending ibex’s functionality. ibex also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the ibex workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the ibex software to be intuitive, powerful, and easy to use. ibex can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone ibex and ibex’s source code can be downloaded. Conclusions: The authors successfully implemented ibex, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation. PMID:25735289

IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.

PubMed

Zhang, Lifei; Fried, David V; Fave, Xenia J; Hunter, Luke A; Yang, Jinzhong; Court, Laurence E

2015-03-01

Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX's source code can be downloaded. The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

The AIROPA software package: milestones for testing general relativity in the strong gravity regime with AO

NASA Astrophysics Data System (ADS)

Witzel, Gunther; Lu, Jessica R.; Ghez, Andrea M.; Martinez, Gregory D.; Fitzgerald, Michael P.; Britton, Matthew; Sitarski, Breann N.; Do, Tuan; Campbell, Randall D.; Service, Maxwell; Matthews, Keith; Morris, Mark R.; Becklin, E. E.; Wizinowich, Peter L.; Ragland, Sam; Doppmann, Greg; Neyman, Chris; Lyke, James; Kassis, Marc; Rizzi, Luca; Lilley, Scott; Rampy, Rachel

2016-07-01

General relativity can be tested in the strong gravity regime by monitoring stars orbiting the supermassive black hole at the Galactic Center with adaptive optics. However, the limiting source of uncertainty is the spatial PSF variability due to atmospheric anisoplanatism and instrumental aberrations. The Galactic Center Group at UCLA has completed a project developing algorithms to predict PSF variability for Keck AO images. We have created a new software package (AIROPA), based on modified versions of StarFinder and Arroyo, that takes atmospheric turbulence profiles, instrumental aberration maps, and images as inputs and delivers improved photometry and astrometry on crowded fields. This software package will be made publicly available soon.

Use of symbolic computation in robotics education

NASA Technical Reports Server (NTRS)

Vira, Naren; Tunstel, Edward

1992-01-01

An application of symbolic computation in robotics education is described. A software package is presented which combines generality, user interaction, and user-friendliness with the systematic usage of symbolic computation and artificial intelligence techniques. The software utilizes MACSYMA, a LISP-based symbolic algebra language, to automatically generate closed-form expressions representing forward and inverse kinematics solutions, the Jacobian transformation matrices, robot pose error-compensation models equations, and Lagrange dynamics formulation for N degree-of-freedom, open chain robotic manipulators. The goal of such a package is to aid faculty and students in the robotics course by removing burdensome tasks of mathematical manipulations. The software package has been successfully tested for its accuracy using commercially available robots.

Numerical simulation of water hammer in low pressurized pipe: comparison of SimHydraulics and Lax-Wendroff method with experiment

NASA Astrophysics Data System (ADS)

Himr, D.

2013-04-01

Article describes simulation of unsteady flow during water hammer with two programs, which use different numerical approaches to solve ordinary one dimensional differential equations describing the dynamics of hydraulic elements and pipes. First one is Matlab-Simulink-SimHydraulics, which is a commercial software developed to solve the dynamics of general hydraulic systems. It defines them with block elements. The other software is called HYDRA and it is based on the Lax-Wendrff numerical method, which serves as a tool to solve the momentum and continuity equations. This program was developed in Matlab by Brno University of Technology. Experimental measurements were performed on a simple test rig, which consists of an elastic pipe with strong damping connecting two reservoirs. Water hammer is induced with fast closing the valve. Physical properties of liquid and pipe elasticity parameters were considered in both simulations, which are in very good agreement and differences in comparison with experimental data are minimal.

The Virtual Brain: a simulator of primate brain network dynamics.

PubMed

Sanz Leon, Paula; Knock, Stuart A; Woodman, M Marmaduke; Domide, Lia; Mersmann, Jochen; McIntosh, Anthony R; Jirsa, Viktor

2013-01-01

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications.

The Virtual Brain: a simulator of primate brain network dynamics

PubMed Central

Sanz Leon, Paula; Knock, Stuart A.; Woodman, M. Marmaduke; Domide, Lia; Mersmann, Jochen; McIntosh, Anthony R.; Jirsa, Viktor

2013-01-01

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications. PMID:23781198

NLSEmagic: Nonlinear Schrödinger equation multi-dimensional Matlab-based GPU-accelerated integrators using compact high-order schemes

NASA Astrophysics Data System (ADS)

Caplan, R. M.

2013-04-01

We present a simple to use, yet powerful code package called NLSEmagic to numerically integrate the nonlinear Schrödinger equation in one, two, and three dimensions. NLSEmagic is a high-order finite-difference code package which utilizes graphic processing unit (GPU) parallel architectures. The codes running on the GPU are many times faster than their serial counterparts, and are much cheaper to run than on standard parallel clusters. The codes are developed with usability and portability in mind, and therefore are written to interface with MATLAB utilizing custom GPU-enabled C codes with the MEX-compiler interface. The packages are freely distributed, including user manuals and set-up files. Catalogue identifier: AEOJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOJ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 124453 No. of bytes in distributed program, including test data, etc.: 4728604 Distribution format: tar.gz Programming language: C, CUDA, MATLAB. Computer: PC, MAC. Operating system: Windows, MacOS, Linux. Has the code been vectorized or parallelized?: Yes. Number of processors used: Single CPU, number of GPU processors dependent on chosen GPU card (max is currently 3072 cores on GeForce GTX 690). Supplementary material: Setup guide, Installation guide. RAM: Highly dependent on dimensionality and grid size. For typical medium-large problem size in three dimensions, 4GB is sufficient. Keywords: Nonlinear Schröodinger Equation, GPU, high-order finite difference, Bose-Einstien condensates. Classification: 4.3, 7.7. Nature of problem: Integrate solutions of the time-dependent one-, two-, and three-dimensional cubic nonlinear Schrödinger equation. Solution method: The integrators utilize a fully-explicit fourth-order Runge-Kutta scheme in time and both second- and fourth-order differencing in space. The integrators are written to run on NVIDIA GPUs and are interfaced with MATLAB including built-in visualization and analysis tools. Restrictions: The main restriction for the GPU integrators is the amount of RAM on the GPU as the code is currently only designed for running on a single GPU. Unusual features: Ability to visualize real-time simulations through the interaction of MATLAB and the compiled GPU integrators. Additional comments: Setup guide and Installation guide provided. Program has a dedicated web site at www.nlsemagic.com. Running time: A three-dimensional run with a grid dimension of 87×87×203 for 3360 time steps (100 non-dimensional time units) takes about one and a half minutes on a GeForce GTX 580 GPU card.

Compact Numerical Function Generators Based on Quadratic Approximation: Architecture and Synthesis Method

DTIC Science & Technology

2006-12-01

Specifi- cation described by Scilab [19], a MATLAB-like software, into HDL code. The Design Specification consists of a func- tion f (x), a domain over x...In- ter. Conf. on Field Programmable Logic and Applications (FPL’05), pp.118–123, Tampere, Finland, Aug. 2005. [19] Scilab 3.0, INRIA-ENPC, France

Programmable Numerical Function Generators Based on Quadratic Approximation: Architecture and Synthesis Method

DTIC Science & Technology

2006-01-01

experts. Fig. 1 shows the synthesis flow for the NFG. It converts the Design Specification described by Scilab [18], a MATLAB-like software, into HDL...Tam- pare, Finland, pp. 118–123, Aug. 2005. [18] Scilab 3.0, INRIA-ENPC, France, http://scilabsoft.inria.fr/ [19] M. J. Schulte and J. E. Stine

E-Learning Technologies: Employing Matlab Web Server to Facilitate the Education of Mathematical Programming

ERIC Educational Resources Information Center

Karagiannis, P.; Markelis, I.; Paparrizos, K.; Samaras, N.; Sifaleras, A.

2006-01-01

This paper presents new web-based educational software (webNetPro) for "Linear Network Programming." It includes many algorithms for "Network Optimization" problems, such as shortest path problems, minimum spanning tree problems, maximum flow problems and other search algorithms. Therefore, webNetPro can assist the teaching process of courses such…

A globally convergent LCL method for nonlinear optimization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedlander, M. P.; Saunders, M. A.; Mathematics and Computer Science

2005-01-01

For optimization problems with nonlinear constraints, linearly constrained Lagrangian (LCL) methods solve a sequence of subproblems of the form 'minimize an augmented Lagrangian function subject to linearized constraints.' Such methods converge rapidly near a solution but may not be reliable from arbitrary starting points. Nevertheless, the well-known software package MINOS has proved effective on many large problems. Its success motivates us to derive a related LCL algorithm that possesses three important properties: it is globally convergent, the subproblem constraints are always feasible, and the subproblems may be solved inexactly. The new algorithm has been implemented in Matlab, with an optionmore » to use either MINOS or SNOPT (Fortran codes) to solve the linearly constrained subproblems. Only first derivatives are required. We present numerical results on a subset of the COPS, HS, and CUTE test problems, which include many large examples. The results demonstrate the robustness and efficiency of the stabilized LCL procedure.« less

A Model-based Approach to Controlling the ST-5 Constellation Lights-Out Using the GMSEC Message Bus and Simulink

NASA Technical Reports Server (NTRS)

Witt, Kenneth J.; Stanley, Jason; Shendock, Robert; Mandl, Daniel

2005-01-01

Space Technology 5 (ST-5) is a three-satellite constellation, technology validation mission under the New Millennium Program at NASA to be launched in March 2006. One of the key technologies to be validated is a lights-out, model-based operations approach to be used for one week to control the ST-5 constellation with no manual intervention. The ground architecture features the GSFC Mission Services Evolution Center (GMSEC) middleware, which allows easy plugging in of software components and a standardized messaging protocol over a software bus. A predictive modeling tool built on MatLab's Simulink software package makes use of the GMSEC standard messaging protocol to interface to the Advanced Mission Planning System (AMPS) Scenario Scheduler which controls all activities, resource allocation and real-time re-profiling of constellation resources when non-nominal events occur. The key features of this system, which we refer to as the ST-5 Simulink system, are as follows: Original daily plan is checked to make sure that predicted resources needed are available by comparing the plan against the model. As the plan is run in real-time, the system re-profiles future activities in real-time if planned activities do not occur in the predicted timeframe or fashion. Alert messages are sent out on the GMSEC bus by the system if future predicted problems are detected. This will allow the Scenario Scheduler to correct the situation before the problem happens. The predictive model is evolved automatically over time via telemetry updates thus reducing the cost of implementing and maintaining the models by an order of magnitude from previous efforts at GSFC such as the model-based system built for MAP in the mid-1990's. This paper will describe the key features, lessons learned and implications for future missions once this system is successfully validated on-orbit in 2006.

Fitting model-based psychometric functions to simultaneity and temporal-order judgment data: MATLAB and R routines.

PubMed

Alcalá-Quintana, Rocío; García-Pérez, Miguel A

2013-12-01

Research on temporal-order perception uses temporal-order judgment (TOJ) tasks or synchrony judgment (SJ) tasks in their binary SJ2 or ternary SJ3 variants. In all cases, two stimuli are presented with some temporal delay, and observers judge the order of presentation. Arbitrary psychometric functions are typically fitted to obtain performance measures such as sensitivity or the point of subjective simultaneity, but the parameters of these functions are uninterpretable. We describe routines in MATLAB and R that fit model-based functions whose parameters are interpretable in terms of the processes underlying temporal-order and simultaneity judgments and responses. These functions arise from an independent-channels model assuming arrival latencies with exponential distributions and a trichotomous decision space. Different routines fit data separately for SJ2, SJ3, and TOJ tasks, jointly for any two tasks, or also jointly for the three tasks (for common cases in which two or even the three tasks were used with the same stimuli and participants). Additional routines provide bootstrap p-values and confidence intervals for estimated parameters. A further routine is included that obtains performance measures from the fitted functions. An R package for Windows and source code of the MATLAB and R routines are available as Supplementary Files.

MOCASSIN-prot software

USDA-ARS?s Scientific Manuscript database

MOCASSIN-prot is a software, implemented in Perl and Matlab, for constructing protein similarity networks to classify proteins. Both domain composition and quantitative sequence similarity information are utilized in constructing the directed protein similarity networks. For each reference protein i...

Light Curve Simulation Using Spacecraft CAD Models and Empirical Material Spectral BRDFS

NASA Astrophysics Data System (ADS)

Willison, A.; Bedard, D.

This paper presents a Matlab-based light curve simulation software package that uses computer-aided design (CAD) models of spacecraft and the spectral bidirectional reflectance distribution function (sBRDF) of their homogenous surface materials. It represents the overall optical reflectance of objects as a sBRDF, a spectrometric quantity, obtainable during an optical ground truth experiment. The broadband bidirectional reflectance distribution function (BRDF), the basis of a broadband light curve, is produced by integrating the sBRDF over the optical wavelength range. Colour-filtered BRDFs, the basis of colour-filtered light curves, are produced by first multiplying the sBRDF by colour filters, and integrating the products. The software package's validity is established through comparison of simulated reflectance spectra and broadband light curves with those measured of the CanX-1 Engineering Model (EM) nanosatellite, collected during an optical ground truth experiment. It is currently being extended to simulate light curves of spacecraft in Earth orbit, using spacecraft Two-Line-Element (TLE) sets, yaw/pitch/roll angles, and observer coordinates. Measured light curves of the NEOSSat spacecraft will be used to validate simulated quantities. The sBRDF was chosen to represent material reflectance as it is spectrometric and a function of illumination and observation geometry. Homogeneous material sBRDFs were obtained using a goniospectrometer for a range of illumination and observation geometries, collected in a controlled environment. The materials analyzed include aluminum alloy, two types of triple-junction photovoltaic (TJPV) cell, white paint, and multi-layer insulation (MLI). Interpolation and extrapolation methods were used to determine the sBRDF for all possible illumination and observation geometries not measured in the laboratory, resulting in empirical look-up tables. These look-up tables are referenced when calculating the overall sBRDF of objects, where the contribution of each facet is proportionally integrated.

Comparison of four software packages for CT lung volumetry in healthy individuals.

PubMed

Nemec, Stefan F; Molinari, Francesco; Dufresne, Valerie; Gosset, Natacha; Silva, Mario; Bankier, Alexander A

2015-06-01

To compare CT lung volumetry (CTLV) measurements provided by different software packages, and to provide normative data for lung densitometric measurements in healthy individuals. This retrospective study included 51 chest CTs of 17 volunteers (eight men and nine women; mean age, 30 ± 6 years), who underwent spirometrically monitored CT at total lung capacity (TLC), functional residual capacity (FRC), and mean inspiratory capacity (MIC). Volumetric differences assessed by four commercial software packages were compared with analysis of variance (ANOVA) for repeated measurements and benchmarked against the threshold for acceptable variability between spirometric measurements. Mean lung density (MLD) and parenchymal heterogeneity (MLD-SD) were also compared with ANOVA. Volumetric differences ranged from 12 to 213 ml (0.20 % to 6.45 %). Although 16/18 comparisons (among four software packages at TLC, MIC, and FRC) were statistically significant (P < 0.001 to P = 0.004), only 3/18 comparisons, one at MIC and two at FRC, exceeded the spirometry variability threshold. MLD and MLD-SD significantly increased with decreasing volumes, and were significantly larger in lower compared to upper lobes (P < 0.001). Lung volumetric differences provided by different software packages are small. These differences should not be interpreted based on statistical significance alone, but together with absolute volumetric differences. • Volumetric differences, assessed by different CTLV software, are small but statistically significant. • Volumetric differences are smaller at TLC than at MIC and FRC. • Volumetric differences rarely exceed spirometric repeatability thresholds at MIC and FRC. • Differences between CTLV measurements should be interpreted based on comparison of absolute differences. • MLD increases with decreasing volumes, and is larger in lower compared to upper lobes.

A comparative study of programming languages for next-generation astrodynamics systems

NASA Astrophysics Data System (ADS)

Eichhorn, Helge; Cano, Juan Luis; McLean, Frazer; Anderl, Reiner

2018-03-01

Due to the computationally intensive nature of astrodynamics tasks, astrodynamicists have relied on compiled programming languages such as Fortran for the development of astrodynamics software. Interpreted languages such as Python, on the other hand, offer higher flexibility and development speed thereby increasing the productivity of the programmer. While interpreted languages are generally slower than compiled languages, recent developments such as just-in-time (JIT) compilers or transpilers have been able to close this speed gap significantly. Another important factor for the usefulness of a programming language is its wider ecosystem which consists of the available open-source packages and development tools such as integrated development environments or debuggers. This study compares three compiled languages and three interpreted languages, which were selected based on their popularity within the scientific programming community and technical merit. The three compiled candidate languages are Fortran, C++, and Java. Python, Matlab, and Julia were selected as the interpreted candidate languages. All six languages are assessed and compared to each other based on their features, performance, and ease-of-use through the implementation of idiomatic solutions to classical astrodynamics problems. We show that compiled languages still provide the best performance for astrodynamics applications, but JIT-compiled dynamic languages have reached a competitive level of speed and offer an attractive compromise between numerical performance and programmer productivity.

Solar power plant performance evaluation: simulation and experimental validation

NASA Astrophysics Data System (ADS)

Natsheh, E. M.; Albarbar, A.

2012-05-01

In this work the performance of solar power plant is evaluated based on a developed model comprise photovoltaic array, battery storage, controller and converters. The model is implemented using MATLAB/SIMULINK software package. Perturb and observe (P&O) algorithm is used for maximizing the generated power based on maximum power point tracker (MPPT) implementation. The outcome of the developed model are validated and supported by a case study carried out using operational 28.8kW grid-connected solar power plant located in central Manchester. Measurements were taken over 21 month's period; using hourly average irradiance and cell temperature. It was found that system degradation could be clearly monitored by determining the residual (the difference) between the output power predicted by the model and the actual measured power parameters. It was found that the residual exceeded the healthy threshold, 1.7kW, due to heavy snow in Manchester last winter. More important, the developed performance evaluation technique could be adopted to detect any other reasons that may degrade the performance of the P V panels such as shading and dirt. Repeatability and reliability of the developed system performance were validated during this period. Good agreement was achieved between the theoretical simulation and the real time measurement taken the online grid connected solar power plant.

Data Packages for the Hanford Immobilized Low Activity Tank Waste Performance Assessment 2001 Version [SEC 1 THRU 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

MANN, F.M.

Data package supporting the 2001 Immobilized Low-Activity Waste Performance Analysis. Geology, hydrology, geochemistry, facility, waste form, and dosimetry data based on recent investigation are provided. Verification and benchmarking packages for selected software codes are provided.

An Automated Weather Research and Forecasting (WRF)-Based Nowcasting System: Software Description

DTIC Science & Technology

2013-10-01

14. ABSTRACT A Web service /Web interface software package has been engineered to address the need for an automated means to run the Weather Research...An Automated Weather Research and Forecasting (WRF)- Based Nowcasting System: Software Description by Stephen F. Kirby, Brian P. Reen, and...Based Nowcasting System: Software Description Stephen F. Kirby, Brian P. Reen, and Robert E. Dumais Jr. Computational and Information Sciences

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB.

PubMed

Lee, Leng-Feng; Umberger, Brian R

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1-2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility.

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB

PubMed Central

Lee, Leng-Feng

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1–2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility. PMID:26835184

Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

PubMed Central

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

Background An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use. PMID:25825906

Reference gene validation for RT-qPCR, a note on different available software packages.

PubMed

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use.

Evolution of a modular software network

PubMed Central

Fortuna, Miguel A.; Bonachela, Juan A.; Levin, Simon A.

2011-01-01

“Evolution behaves like a tinkerer” (François Jacob, Science, 1977). Software systems provide a singular opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to explore the evolution of a complex network in a unique way. The modular design detected during its growth is based on the reuse of existing code in order to minimize costs during programming. The increase of modularity experienced by the system over time has not counterbalanced the increase in incompatibilities between software packages within modules. This negative effect is far from being a failure of design. A random process of package installation shows that the higher the modularity, the larger the fraction of packages working properly in a local computer. The decrease in the relative number of conflicts between packages from different modules avoids a failure in the functionality of one package spreading throughout the entire system. Some potential analogies with the evolutionary and ecological processes determining the structure of ecological networks of interacting species are discussed. PMID:22106260

Imperial College near infrared spectroscopy neuroimaging analysis framework.

PubMed

Orihuela-Espina, Felipe; Leff, Daniel R; James, David R C; Darzi, Ara W; Yang, Guang-Zhong

2018-01-01

This paper describes the Imperial College near infrared spectroscopy neuroimaging analysis (ICNNA) software tool for functional near infrared spectroscopy neuroimaging data. ICNNA is a MATLAB-based object-oriented framework encompassing an application programming interface and a graphical user interface. ICNNA incorporates reconstruction based on the modified Beer-Lambert law and basic processing and data validation capabilities. Emphasis is placed on the full experiment rather than individual neuroimages as the central element of analysis. The software offers three types of analyses including classical statistical methods based on comparison of changes in relative concentrations of hemoglobin between the task and baseline periods, graph theory-based metrics of connectivity and, distinctively, an analysis approach based on manifold embedding. This paper presents the different capabilities of ICNNA in its current version.

Development of advanced fermentor control applications for use in an industrial automation environment.

PubMed

Hamilton, Ryan; Tamminana, Krishna; Boyd, John; Sasaki, Gen; Toda, Alex; Haskell, Sid; Danbe, Elizabeth

2013-04-01

We present a software platform developed by Genentech and MathWorks Consulting Group that allows arbitrary MATLAB (MATLAB is a registered trademark of The MathWorks, Inc.) functions to perform supervisory control of process equipment (in this case, fermentors) via the OLE for process control (OPC) communication protocol, under the direction of an industrial automation layer. The software features automated synchronization and deployment of server control code and has been proven to be tolerant of OPC communication interruptions. Since deployment in the spring of 2010, this software has successfully performed supervisory control of more than 700 microbial fermentations in the Genentech pilot plant and has enabled significant reductions in the time required to develop and implement novel control strategies (months reduced to days). The software is available for download at the MathWorks File Exchange Web site at http://www.mathworks.com/matlabcentral/fileexchange/36866.

Tool for Generation of MAC/GMC Representative Unit Cell for CMC/PMC Analysis

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Pineda, Evan J.

2016-01-01

This document describes a recently developed analysis tool that enhances the resident capabilities of the Micromechanics Analysis Code with the Generalized Method of Cells (MAC/GMC) 4.0. This tool is especially useful in analyzing ceramic matrix composites (CMCs), where higher fidelity with improved accuracy of local response is needed. The tool, however, can be used for analyzing polymer matrix composites (PMCs) as well. MAC/GMC 4.0 is a composite material and laminate analysis software developed at NASA Glenn Research Center. The software package has been built around the concept of the generalized method of cells (GMC). The computer code is developed with a user friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermomechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The primary focus of the current effort is to provide a graphical user interface (GUI) capability that generates a number of different user-defined repeating unit cells (RUCs). In addition, the code has provisions for generation of a MAC/GMC-compatible input text file that can be merged with any MAC/GMC input file tailored to analyze composite materials. Although the primary intention was to address the three different constituents and phases that are usually present in CMCs-namely, fibers, matrix, and interphase-it can be easily modified to address two-phase polymer matrix composite (PMC) materials where an interphase is absent. Currently, the tool capability includes generation of RUCs for square packing, hexagonal packing, and random fiber packing as well as RUCs based on actual composite micrographs. All these options have the fibers modeled as having a circular cross-sectional area. In addition, a simplified version of RUC is provided where the fibers are treated as having a square cross section and are distributed randomly. This RUC facilitates a speedy analysis using the higher fidelity version of GMC known as HFGMC. The first four mentioned options above support uniform subcell discretization. The last one has variable subcell sizes due to the primary intention of keeping the RUC size to a minimum to gain the speed ups using the higher fidelity version of MAC. The code is implemented within the MATLAB (The Mathworks, Inc., Natick, MA) developmental framework; however, a standalone application that does not need a priori MATLAB installation is also created with the aid of the MATLAB compiler.

Hydratools, a MATLAB® based data processing package for Sontek Hydra data

USGS Publications Warehouse

Martini, M.; Lightsom, F.L.; Sherwood, C.R.; Xu, Jie; Lacy, J.R.; Ramsey, A.; Horwitz, R.

2005-01-01

The U.S. Geological Survey (USGS) has developed a set of MATLAB tools to process and convert data collected by Sontek Hydra instruments to netCDF, which is a format used by the USGS to process and archive oceanographic time-series data. The USGS makes high-resolution current measurements within 1.5 meters of the bottom. These data are used in combination with other instrument data from sediment transport studies to develop sediment transport models. Instrument manufacturers provide software which outputs unique binary data formats. Multiple data formats are cumbersome. The USGS solution is to translate data streams into a common data format: netCDF. The Hydratools toolbox is written to create netCDF format files following EPIC conventions, complete with embedded metadata. Data are accepted from both the ADV and the PCADP. The toolbox will detect and remove bad data, substitute other sources of heading and tilt measurements if necessary, apply ambiguity corrections, calculate statistics, return information about data quality, and organize metadata. Standardized processing and archiving makes these data more easily and routinely accessible locally and over the Internet. In addition, documentation of the techniques used in the toolbox provides a baseline reference for others utilizing the data.

Increasing Accessibility by Pooling Digital Resources

ERIC Educational Resources Information Center

Cushion, Steve

2004-01-01

There are now many CALL authoring packages that can create interactive websites and a large number of language teachers are writing materials for the whole range of such packages. Currently, each product stores its data in different formats thus hindering interoperability, pooling of digital resources and moving between software packages based in…

Multiple-Group Analysis Using the sem Package in the R System

ERIC Educational Resources Information Center

Evermann, Joerg

2010-01-01

Multiple-group analysis in covariance-based structural equation modeling (SEM) is an important technique to ensure the invariance of latent construct measurements and the validity of theoretical models across different subpopulations. However, not all SEM software packages provide multiple-group analysis capabilities. The sem package for the R…

LANZ: Software solving the large sparse symmetric generalized eigenproblem

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1990-01-01

A package, LANZ, for solving the large symmetric generalized eigenproblem is described. The package was tested on four different architectures: Convex 200, CRAY Y-MP, Sun-3, and Sun-4. The package uses a Lanczos' method and is based on recent research into solving the generalized eigenproblem.

A general spectral method for the numerical simulation of one-dimensional interacting fermions

NASA Astrophysics Data System (ADS)

Clason, Christian; von Winckel, Gregory

2012-08-01

This software implements a general framework for the direct numerical simulation of systems of interacting fermions in one spatial dimension. The approach is based on a specially adapted nodal spectral Galerkin method, where the basis functions are constructed to obey the antisymmetry relations of fermionic wave functions. An efficient Matlab program for the assembly of the stiffness and potential matrices is presented, which exploits the combinatorial structure of the sparsity pattern arising from this discretization to achieve optimal run-time complexity. This program allows the accurate discretization of systems with multiple fermions subject to arbitrary potentials, e.g., for verifying the accuracy of multi-particle approximations such as Hartree-Fock in the few-particle limit. It can be used for eigenvalue computations or numerical solutions of the time-dependent Schrödinger equation. The new version includes a Python implementation of the presented approach. New version program summaryProgram title: assembleFermiMatrix Catalogue identifier: AEKO_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKO_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 332 No. of bytes in distributed program, including test data, etc.: 5418 Distribution format: tar.gz Programming language: MATLAB/GNU Octave, Python Computer: Any architecture supported by MATLAB, GNU Octave or Python Operating system: Any supported by MATLAB, GNU Octave or Python RAM: Depends on the data Classification: 4.3, 2.2. External routines: Python 2.7+, NumPy 1.3+, SciPy 0.10+ Catalogue identifier of previous version: AEKO_v1_0 Journal reference of previous version: Comput. Phys. Commun. 183 (2012) 405 Does the new version supersede the previous version?: Yes Nature of problem: The direct numerical solution of the multi-particle one-dimensional Schrödinger equation in a quantum well is challenging due to the exponential growth in the number of degrees of freedom with increasing particles. Solution method: A nodal spectral Galerkin scheme is used where the basis functions are constructed to obey the antisymmetry relations of the fermionic wave function. The assembly of these matrices is performed efficiently by exploiting the combinatorial structure of the sparsity patterns. Reasons for new version: A Python implementation is now included. Summary of revisions: Added a Python implementation; small documentation fixes in Matlab implementation. No change in features of the package. Restrictions: Only one-dimensional computational domains with homogeneous Dirichlet or periodic boundary conditions are supported. Running time: Seconds to minutes.

Packaging Software Assets for Reuse

NASA Astrophysics Data System (ADS)

Mattmann, C. A.; Marshall, J. J.; Downs, R. R.

2010-12-01

The reuse of existing software assets such as code, architecture, libraries, and modules in current software and systems development projects can provide many benefits, including reduced costs, in time and effort, and increased reliability. Many reusable assets are currently available in various online catalogs and repositories, usually broken down by disciplines such as programming language (Ibiblio for Maven/Java developers, PyPI for Python developers, CPAN for Perl developers, etc.). The way these assets are packaged for distribution can play a role in their reuse - an asset that is packaged simply and logically is typically easier to understand, install, and use, thereby increasing its reusability. A well-packaged asset has advantages in being more reusable and thus more likely to provide benefits through its reuse. This presentation will discuss various aspects of software asset packaging and how they can affect the reusability of the assets. The characteristics of well-packaged software will be described. A software packaging domain model will be introduced, and some existing packaging approaches examined. An example case study of a Reuse Enablement System (RES), currently being created by near-term Earth science decadal survey missions, will provide information about the use of the domain model. Awareness of these factors will help software developers package their reusable assets so that they can provide the most benefits for software reuse.

BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.

PubMed

Shi, Xu; Barnes, Robert O; Chen, Li; Shajahan-Haq, Ayesha N; Hilakivi-Clarke, Leena; Clarke, Robert; Wang, Yue; Xuan, Jianhua

2015-07-15

Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence. The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

GenoMatrix: A Software Package for Pedigree-Based and Genomic Prediction Analyses on Complex Traits.

PubMed

Nazarian, Alireza; Gezan, Salvador Alejandro

2016-07-01

Genomic and pedigree-based best linear unbiased prediction methodologies (G-BLUP and P-BLUP) have proven themselves efficient for partitioning the phenotypic variance of complex traits into its components, estimating the individuals' genetic merits, and predicting unobserved (or yet-to-be observed) phenotypes in many species and fields of study. The GenoMatrix software, presented here, is a user-friendly package to facilitate the process of using genome-wide marker data and parentage information for G-BLUP and P-BLUP analyses on complex traits. It provides users with a collection of applications which help them on a set of tasks from performing quality control on data to constructing and manipulating the genomic and pedigree-based relationship matrices and obtaining their inverses. Such matrices will be then used in downstream analyses by other statistical packages. The package also enables users to obtain predicted values for unobserved individuals based on the genetic values of observed related individuals. GenoMatrix is available to the research community as a Windows 64bit executable and can be downloaded free of charge at: http://compbio.ufl.edu/software/genomatrix/. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Constitutive modeling of the human Anterior Cruciate Ligament (ACL) under uniaxial loading using viscoelastic prony series and hyperelastic five parameter Mooney-Rivlin model

NASA Astrophysics Data System (ADS)

Chakraborty, Souvik; Mondal, Debabrata; Motalab, Mohammad

2016-07-01

In this present study, the stress-strain behavior of the Human Anterior Cruciate Ligament (ACL) is studied under uniaxial loads applied with various strain rates. Tensile testing of the human ACL samples requires state of the art test facilities. Furthermore, difficulty in finding human ligament for testing purpose results in very limited archival data. Nominal Stress vs. deformation gradient plots for different strain rates, as found in literature, is used to model the material behavior either as a hyperelastic or as a viscoelastic material. The well-known five parameter Mooney-Rivlin constitutivemodel for hyperelastic material and the Prony Series model for viscoelastic material are used and the objective of the analyses comprises of determining the model constants and their variation-trend with strain rates for the Human Anterior Cruciate Ligament (ACL) material using the non-linear curve fitting tool. The relationship between the model constants and strain rate, using the Hyperelastic Mooney-Rivlin model, has been obtained. The variation of the values of each coefficient with strain rates, obtained using Hyperelastic Mooney-Rivlin model are then plotted and variation of the values with strain rates are obtained for all the model constants. These plots are again fitted using the software package MATLAB and a power law relationship between the model constants and strain rates is obtained for each constant. The obtained material model for Human Anterior Cruciate Ligament (ACL) material can be implemented in any commercial finite element software package for stress analysis.

Canputer Science and Technology: Introduction to Software Packages

DTIC Science & Technology

1984-04-01

Table 5 Sources of Software Packages.20 Table 6 Reference Services Matrix . 33 Table 7 Reference Matrix.40 LIST OF FIGURES Figure 1 Document...consideration should be given to the acquisition of appropriate software packages to replace or upgrade existing services and to provide services not...Consequently, there are many companies that produce only software packages, and are committed to providing training, service , and support. These vendors

Acoustic Doppler Current Profiler Data Processing System manual [ADCP

USGS Publications Warehouse

Cote, Jessica M.; Hotchkiss, Frances S.; Martini, Marinna A.; Denham, Charles R.; revisions by Ramsey, Andree L.; Ruane, Stephen

2000-01-01

This open-file report describes the data processing software currently in use by the U.S. Geological Survey (USGS), Woods Hole Coastal and Marine Science Center (WHCMSC), to process time series of acoustic Doppler current data obtained by Teledyne RD Instruments Workhorse model ADCPs. The Sediment Transport Instrumentation Group (STG) at the WHCMSC has a long-standing commitment to providing scientists high quality oceanographic data published in a timely manner. To meet this commitment, STG has created this software to aid personnel in processing and reviewing data as well as evaluating hardware for signs of instrument malfunction. The output data format for the data is network Common Data Form (netCDF), which meets USGS publication standards. Typically, ADCP data are recorded in beam coordinates. This conforms to the USGS philosophy to post-process rather than internally process data. By preserving the original data quality indicators as well as the initial data set, data can be evaluated and reprocessed for different types of analyses. Beam coordinate data are desirable for internal and surface wave experiments, for example. All the code in this software package is intended to run using the MATLAB program available from The Mathworks, Inc. As such, it is platform independent and can be adapted by the USGS and others for specialized experiments with non-standard requirements. The software is continuously being updated and revised as improvements are required. The most recent revision may be downloaded from: http://woodshole.er.usgs.gov/operations/stg/Pubs/ADCPtools/adcp_index.htm The USGS makes this software available at the user?s discretion and responsibility.

Computer-Aided Teaching Using MATLAB/Simulink for Enhancing an IM Course With Laboratory Tests

ERIC Educational Resources Information Center

Bentounsi, A.; Djeghloud, H.; Benalla, H.; Birem, T.; Amiar, H.

2011-01-01

This paper describes an automatic procedure using MATLAB software to plot the circle diagram for two induction motors (IMs), with wound and squirrel-cage rotors, from no-load and blocked-rotor tests. The advantage of this approach is that it avoids the need for a direct load test in predetermining the IM characteristics under reduced power.…

Software Tools for Development on the Peregrine System | High-Performance

Science.gov Websites

Computing | NREL Software Tools for Development on the Peregrine System Software Tools for and manage software at the source code level. Cross-Platform Make and SCons The "Cross-Platform Make" (CMake) package is from Kitware, and SCons is a modern software build tool based on Python

Flight simulation software at NASA Dryden Flight Research Center

NASA Technical Reports Server (NTRS)

Norlin, Ken A.

1995-01-01

The NASA Dryden Flight Research Center has developed a versatile simulation software package that is applicable to a broad range of fixed-wing aircraft. This package has evolved in support of a variety of flight research programs. The structure is designed to be flexible enough for use in batch-mode, real-time pilot-in-the-loop, and flight hardware-in-the-loop simulation. Current simulations operate on UNIX-based platforms and are coded with a FORTRAN shell and C support routines. This paper discusses the features of the simulation software design and some basic model development techniques. The key capabilities that have been included in the simulation are described. The NASA Dryden simulation software is in use at other NASA centers, within industry, and at several universities. The straightforward but flexible design of this well-validated package makes it especially useful in an engineering environment.

The Ettention software package.

PubMed

Dahmen, Tim; Marsalek, Lukas; Marniok, Nico; Turoňová, Beata; Bogachev, Sviatoslav; Trampert, Patrick; Nickels, Stefan; Slusallek, Philipp

2016-02-01

We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Copyright © 2015 Elsevier B.V. All rights reserved.

MOPEX: a software package for astronomical image processing and visualization

NASA Astrophysics Data System (ADS)

Makovoz, David; Roby, Trey; Khan, Iffat; Booth, Hartley

2006-06-01

We present MOPEX - a software package for astronomical image processing and display. The package is a combination of command-line driven image processing software written in C/C++ with a Java-based GUI. The main image processing capabilities include creating mosaic images, image registration, background matching, point source extraction, as well as a number of minor image processing tasks. The combination of the image processing and display capabilities allows for much more intuitive and efficient way of performing image processing. The GUI allows for the control over the image processing and display to be closely intertwined. Parameter setting, validation, and specific processing options are entered by the user through a set of intuitive dialog boxes. Visualization feeds back into further processing by providing a prompt feedback of the processing results. The GUI also allows for further analysis by accessing and displaying data from existing image and catalog servers using a virtual observatory approach. Even though originally designed for the Spitzer Space Telescope mission, a lot of functionalities are of general usefulness and can be used for working with existing astronomical data and for new missions. The software used in the package has undergone intensive testing and benefited greatly from effective software reuse. The visualization part has been used for observation planning for both the Spitzer and Herschel Space Telescopes as part the tool Spot. The visualization capabilities of Spot have been enhanced and integrated with the image processing functionality of the command-line driven MOPEX. The image processing software is used in the Spitzer automated pipeline processing, which has been in operation for nearly 3 years. The image processing capabilities have also been tested in off-line processing by numerous astronomers at various institutions around the world. The package is multi-platform and includes automatic update capabilities. The software package has been developed by a small group of software developers and scientists at the Spitzer Science Center. It is available for distribution at the Spitzer Science Center web page.

Diagnostic Testing Package DX v 2.0 Technical Specification. Methodology Project.

ERIC Educational Resources Information Center

McArthur, David

This paper contains the technical specifications, schematic diagrams, and program printout for a computer software package for the development and administration of diagnostic tests. The second version of the Diagnostic Testing Package DX consists of a PASCAL-based set of modules located in two main programs: (1) EDITTEST creates, modifies, and…

Computer Aided Design Parameters for Forward Basing

DTIC Science & Technology

1988-12-01

21 meters. Systematic errors within limits stated for absolute accuracy are tolerated at this level. DEM data acquired photogrammetrically using manual ...This is a professional drawing package, 19 capable of the manipulation required for this project. With the AutoLISP programming language (a variation on...Table 2). 0 25 Data Conversion Package II GWN System’s Digital Terrain Modeling (DTM) package was used. This AutoLISP -based third party software is

Selection of software for mechanical engineering undergraduates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheah, C. T.; Yin, C. S.; Halim, T.

A major problem with the undergraduate mechanical course is the limited exposure of students to software packages coupled with the long learning curve on the existing software packages. This work proposes the use of appropriate software packages for the entire mechanical engineering curriculum to ensure students get sufficient exposure real life design problems. A variety of software packages are highlighted as being suitable for undergraduate work in mechanical engineering, e.g. simultaneous non-linear equations; uncertainty analysis; 3-D modeling software with the FEA; analysis tools for the solution of problems in thermodynamics, fluid mechanics, mechanical system design, and solid mechanics.

Model-Based GN and C Simulation and Flight Software Development for Orion Missions beyond LEO

NASA Technical Reports Server (NTRS)

Odegard, Ryan; Milenkovic, Zoran; Henry, Joel; Buttacoli, Michael

2014-01-01

For Orion missions beyond low Earth orbit (LEO), the Guidance, Navigation, and Control (GN&C) system is being developed using a model-based approach for simulation and flight software. Lessons learned from the development of GN&C algorithms and flight software for the Orion Exploration Flight Test One (EFT-1) vehicle have been applied to the development of further capabilities for Orion GN&C beyond EFT-1. Continuing the use of a Model-Based Development (MBD) approach with the Matlab®/Simulink® tool suite, the process for GN&C development and analysis has been largely improved. Furthermore, a model-based simulation environment in Simulink, rather than an external C-based simulation, greatly eases the process for development of flight algorithms. The benefits seen by employing lessons learned from EFT-1 are described, as well as the approach for implementing additional MBD techniques. Also detailed are the key enablers for improvements to the MBD process, including enhanced configuration management techniques for model-based software systems, automated code and artifact generation, and automated testing and integration.

Visualizing the inner product space ℝm×n in a MATLAB-assisted linear algebra classroom

NASA Astrophysics Data System (ADS)

Caglayan, Günhan

2018-05-01

This linear algebra note offers teaching and learning ideas in the treatment of the inner product space ? in a technology-supported learning environment. Classroom activities proposed in this note demonstrate creative ways of integrating MATLAB technology into various properties of Frobenius inner product as visualization tools that complement the algebraic approach. As implemented in linear algebra lessons in a university in the Unites States, the article also incorporates algebraic and visual work of students who experienced these activities with MATLAB software. The connection between the Frobenius norm and the Euclidean norm is also emphasized.

Development of high performance scientific components for interoperability of computing packages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Campus Energy Model for Control and Performance Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

The Waveform Suite: A robust platform for accessing and manipulating seismic waveforms in MATLAB

NASA Astrophysics Data System (ADS)

Reyes, C. G.; West, M. E.; McNutt, S. R.

2009-12-01

The Waveform Suite, developed at the University of Alaska Geophysical Institute, is an open-source collection of MATLAB classes that provide a means to import, manipulate, display, and share waveform data while ensuring integrity of the data and stability for programs that incorporate them. Data may be imported from a variety of sources, such as Antelope, Winston databases, SAC files, SEISAN, .mat files, or other user-defined file formats. The waveforms being manipulated in MATLAB are isolated from their stored representations, relieving the overlying programs from the responsibility of understanding the specific format in which data is stored or retrieved. The waveform class provides an object oriented framework that simplifies manipulations to waveform data. Playing with data becomes easier because the tedious aspects of data manipulation have been automated. The user is able to change multiple waveforms simultaneously using standard mathematical operators and other syntactically familiar functions. Unlike MATLAB structs or workspace variables, the data stored within waveform class objects are protected from modification, and instead are accessed through standardized functions, such as get and set; these are already familiar to users of MATLAB’s graphical features. This prevents accidental or nonsensical modifications to the data, which in turn simplifies troubleshooting of complex programs. Upgrades to the internal structure of the waveform class are invisible to applications which use it, making maintenance easier. We demonstrate the Waveform Suite’s capabilities on seismic data from Okmok and Redoubt volcanoes. Years of data from Okmok were retrieved from Antelope and Winston databases. Using the Waveform Suite, we built a tremor-location program. Because the program was built on the Waveform Suite, modifying it to operate on real-time data from Redoubt involved only minimal code changes. The utility of the Waveform Suite as a foundation for large developments is demonstrated with the Correlation Toolbox for MATLAB. This mature package contains 50+ codes for carrying out various type of waveform correlation analyses (multiplet analysis, clustering, interferometry, …) This package is greatly strengthened by delegating numerous book-keeping and signal processing tasks to the underlying Waveform Suite. The Waveform Suite’s built-in tools for searching arbitrary directory/file structures is demonstrated with matched video and audio from the recent eruption of Redoubt Volcano. These tools were used to find subsets of photo images corresponding to specific seismic traces. Using Waveform’s audio file routines, matched video and audio were assembled to produce outreach-quality eruption products. The Waveform Suite is not designed as a ready-to-go replacement for more comprehensive packages such as SAC or AH. Rather, it is a suite of classes which provide core time series functionality in a MATLAB environment. It is designed to be a more robust alternative to the numerous ad hoc MATLAB formats that exist. Complex programs may be created upon the Waveform Suite’s framework, while existing programs may be modified to take advantage of the Waveform Suites capabilities.

Lightweight robotic mobility: template-based modeling for dynamics and controls using ADAMS/car and MATLAB

NASA Astrophysics Data System (ADS)

Adamczyk, Peter G.; Gorsich, David J.; Hudas, Greg R.; Overholt, James

2003-09-01

The U.S. Army is seeking to develop autonomous off-road mobile robots to perform tasks in the field such as supply delivery and reconnaissance in dangerous territory. A key problem to be solved with these robots is off-road mobility, to ensure that the robots can accomplish their tasks without loss or damage. We have developed a computer model of one such concept robot, the small-scale "T-1" omnidirectional vehicle (ODV), to study the effects of different control strategies on the robot's mobility in off-road settings. We built the dynamic model in ADAMS/Car and the control system in Matlab/Simulink. This paper presents the template-based method used to construct the ADAMS model of the T-1 ODV. It discusses the strengths and weaknesses of ADAMS/Car software in such an application, and describes the benefits and challenges of the approach as a whole. The paper also addresses effective linking of ADAMS/Car and Matlab for complete control system development. Finally, this paper includes a section describing the extension of the T-1 templates to other similar ODV concepts for rapid development.

MultiElec: A MATLAB Based Application for MEA Data Analysis.

PubMed

Georgiadis, Vassilis; Stephanou, Anastasis; Townsend, Paul A; Jackson, Thomas R

2015-01-01

We present MultiElec, an open source MATLAB based application for data analysis of microelectrode array (MEA) recordings. MultiElec displays an extremely user-friendly graphic user interface (GUI) that allows the simultaneous display and analysis of voltage traces for 60 electrodes and includes functions for activation-time determination, the production of activation-time heat maps with activation time and isoline display. Furthermore, local conduction velocities are semi-automatically calculated along with their corresponding vector plots. MultiElec allows ad hoc signal suppression, enabling the user to easily and efficiently handle signal artefacts and for incomplete data sets to be analysed. Voltage traces and heat maps can be simply exported for figure production and presentation. In addition, our platform is able to produce 3D videos of signal progression over all 60 electrodes. Functions are controlled entirely by a single GUI with no need for command line input or any understanding of MATLAB code. MultiElec is open source under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. Both the program and source code are available to download from http://www.cancer.manchester.ac.uk/MultiElec/.

Nuclear Data Online Services at Peking University

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, T.S.; Guo, Z.Y.; Ye, W.G.

2005-05-24

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

Fan, T. S.; Guo, Z. Y.; Ye, W. G.; Liu, W. L.; Liu, T. J.; Liu, C. X.; Chen, J. X.; Tang, G. Y.; Shi, Z. M.; Huang, X. L.; Chen, J. E.

2005-05-01

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

General Tool for Evaluating High-Contrast Coronagraphic Telescope Performance Error Budgets

NASA Technical Reports Server (NTRS)

Marchen, Luis F.

2011-01-01

The Coronagraph Performance Error Budget (CPEB) tool automates many of the key steps required to evaluate the scattered starlight contrast in the dark hole of a space-based coronagraph. The tool uses a Code V prescription of the optical train, and uses MATLAB programs to call ray-trace code that generates linear beam-walk and aberration sensitivity matrices for motions of the optical elements and line-of-sight pointing, with and without controlled fine-steering mirrors (FSMs). The sensitivity matrices are imported by macros into Excel 2007, where the error budget is evaluated. The user specifies the particular optics of interest, and chooses the quality of each optic from a predefined set of PSDs. The spreadsheet creates a nominal set of thermal and jitter motions, and combines that with the sensitivity matrices to generate an error budget for the system. CPEB also contains a combination of form and ActiveX controls with Visual Basic for Applications code to allow for user interaction in which the user can perform trade studies such as changing engineering requirements, and identifying and isolating stringent requirements. It contains summary tables and graphics that can be instantly used for reporting results in view graphs. The entire process to obtain a coronagraphic telescope performance error budget has been automated into three stages: conversion of optical prescription from Zemax or Code V to MACOS (in-house optical modeling and analysis tool), a linear models process, and an error budget tool process. The first process was improved by developing a MATLAB package based on the Class Constructor Method with a number of user-defined functions that allow the user to modify the MACOS optical prescription. The second process was modified by creating a MATLAB package that contains user-defined functions that automate the process. The user interfaces with the process by utilizing an initialization file where the user defines the parameters of the linear model computations. Other than this, the process is fully automated. The third process was developed based on the Terrestrial Planet Finder coronagraph Error Budget Tool, but was fully automated by using VBA code, form, and ActiveX controls.

Analytical and Experimental Evaluation of Digital Control Systems for the Semi-Span Super-Sonic Transport (S4T) Wind Tunnel Model

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Christhilf, David; Perry, Boyd, III

2012-01-01

An important objective of the Semi-Span Super-Sonic Transport (S4T) wind tunnel model program was the demonstration of Flutter Suppression (FS), Gust Load Alleviation (GLA), and Ride Quality Enhancement (RQE). It was critical to evaluate the stability and robustness of these control laws analytically before testing them and experimentally while testing them to ensure safety of the model and the wind tunnel. MATLAB based software was applied to evaluate the performance of closed-loop systems in terms of stability and robustness. Existing software tools were extended to use analytical representations of the S4T and the control laws to analyze and evaluate the control laws prior to testing. Lessons were learned about the complex windtunnel model and experimental testing. The open-loop flutter boundary was determined from the closed-loop systems. A MATLAB/Simulink Simulation developed under the program is available for future work to improve the CPE process. This paper is one of a series of that comprise a special session, which summarizes the S4T wind-tunnel program.

Computer Center: Software Review.

ERIC Educational Resources Information Center

Duhrkopf, Richard, Ed.; Belshe, John F., Ed.

1988-01-01

Reviews a software package, "Mitosis-Meiosis," available for Apple II or IBM computers with colorgraphics capabilities. Describes the documentation, presentation and flexibility of the program. Rates the program based on graphics and usability in a biology classroom. (CW)

Using the DOE Knowledge Base for Special Event Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armstrong, H.M.; Harris, J.M.; Young, C.J.

1998-10-20

The DOE Knowledge Base is a library of detailed information whose purpose is to support the United States National Data Center (USNDC) in its mission to monitor compliance with the Comprehensive Test Ban Treaty (CTBT). One of the important tasks which the USNDC must accomplish is to periodically perform detailed analysis of events of high interest, so-called "Special Events", to provide the national authority with information needed to make policy decisions. In this paper we investigate some possible uses of the Knowledge Base for Special Event Analysis (SEA), and make recommendations for improving Knowledge Base support for SEA. To analyzemore » an event in detail, there are two basic types of data which must be used sensor-derived data (wave- forms, arrivals, events, etc.) and regiohalized contextual data (known sources, geological characteristics, etc.). Cur- rently there is no single package which can provide full access to both types of data, so for our study we use a separate package for each MatSeis, the Sandia Labs-developed MATLAB-based seismic analysis package, for wave- form data analysis, and ArcView, an ESRI product, for contextual data analysis. Both packages are well-suited to pro- totyping because they provide a rich set of currently available functionality and yet are also flexible and easily extensible, . Using these tools and Phase I Knowledge Base data sets, we show how the Knowledge Base can improve both the speed and the quality of SEA. Empirically-derived interpolated correction information can be accessed to improve both location estimates and associated error estimates. This information can in turn be used to identi~ any known nearby sources (e.g. mines, volcanos), which may then trigger specialized processing of the sensor data. Based on the location estimate, preferred magnitude formulas and discriminants can be retrieved, and any known blockages can be identified to prevent miscalculations. Relevant historic events can be identilled either by spatial proximity searches or through waveform correlation processing. The locations and waveforms of these events can then be made available for side-by-side comparison and processing. If synthetic modeling is thought to be warranted, a wide variety of rele- vant contextu~l information (e.g. crustal thickness and layering, seismic velocities, attenuation factors) can be retrieved and sent to the appropriate applications. Once formedj the synthetics can then be brought in for side-by-side comparison and fhrther processing. Based on our study, we make two general recommendations. First, proper inter-process communication between sensor data analysis software and contextual data analysis sofisvare should be developed. Second, some of the Knowl- edge Base data sets should be prioritized or winnowed to streamline comparison with observed quantities.« less

EEGVIS: A MATLAB Toolbox for Browsing, Exploring, and Viewing Large Datasets.

PubMed

Robbins, Kay A

2012-01-01

Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug-in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/eegvis.

A Review of DIMPACK Version 1.0: Conditional Covariance-Based Test Dimensionality Analysis Package

ERIC Educational Resources Information Center

Deng, Nina; Han, Kyung T.; Hambleton, Ronald K.

2013-01-01

DIMPACK Version 1.0 for assessing test dimensionality based on a nonparametric conditional covariance approach is reviewed. This software was originally distributed by Assessment Systems Corporation and now can be freely accessed online. The software consists of Windows-based interfaces of three components: DIMTEST, DETECT, and CCPROX/HAC, which…

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

Carr, Francis; Evans, Antony; Feron, Eric; Clarke, John-Paul

2003-01-01

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

Reality versus Simulation

ERIC Educational Resources Information Center

Srinivasan, Srilekha; Perez, Lance C.; Palmer, Robert D.; Brooks, David W.; Wilson, Kathleen; Fowler, David

2006-01-01

A systematic study of the implementation of simulation hardware (TIMS) replacing software (MATLAB) was undertaken for advanced undergraduate and early graduate courses in electrical engineering. One outcome of the qualitative component of the study was remarkable: most students interviewed (4/4 and 6/9) perceived the software simulations as…

A parameterization of nuclear track profiles in CR-39 detector

NASA Astrophysics Data System (ADS)

Azooz, A. A.; Al-Nia'emi, S. H.; Al-Jubbori, M. A.

2012-11-01

In this work, the empirical parameterization describing the alpha particles’ track depth in CR-39 detectors is extended to describe longitudinal track profiles against etching time for protons and alpha particles. MATLAB based software is developed for this purpose. The software calculates and plots the depth, diameter, range, residual range, saturation time, and etch rate versus etching time. The software predictions are compared with other experimental data and with results of calculations using the original software, TRACK_TEST, developed for alpha track calculations. The software related to this work is freely downloadable and performs calculations for protons in addition to alpha particles. Program summary Program title: CR39 Catalog identifier: AENA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENA_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Copyright (c) 2011, Aasim Azooz Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met • Redistributions of source code must retain the above copyright, this list of conditions and the following disclaimer. • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution This software is provided by the copyright holders and contributors “as is” and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the copyright owner or contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. No. of lines in distributed program, including test data, etc.: 15598 No. of bytes in distributed program, including test data, etc.: 3933244 Distribution format: tar.gz Programming language: MATLAB. Computer: Any Desktop or Laptop. Operating system: Windows 1998 or above (with MATLAB R13 or above installed). RAM: 512 Megabytes or higher Classification: 17.5. Nature of problem: A new semispherical parameterization of charged particle tracks in CR-39 SSNTD is carried out in a previous paper. This parameterization is developed here into a MATLAB based software to calculate the track length and track profile for any proton or alpha particle energy or etching time. This software is intended to compete with the TRACK_TEST [1] and TRACK_VISION [2] software currently in use by all people working in the field of SSNTD. Solution method: Based on fitting of experimental results of protons and alpha particles track lengths for various energies and etching times to a new semispherical formula with four free fitting parameters, the best set of energy independent parameters were found. These parameters are introduced into the software and the software is programmed to solve the set of equations to calculate the track depth, track etching rate as a function of both time and residual range for particles of normal and oblique incidence, the track longitudinal profile at both normal and oblique incidence, and the three dimensional track profile at normal incidence. Running time: 1-8 s on Pentium (4) 2 GHz CPU, 3 GB of RAM depending on the etching time value References: [1] ADWT_v1_0 Track_Test Computer program TRACK_TEST for calculating parameters and plotting profiles for etch pits in nuclear track materials. D. Nikezic, K.N. Yu Comput. Phys. Commun. 174(2006)160 [2] AEAF_v1_0 TRACK_VISION Computer program TRACK_VISION for simulating optical appearance of etched tracks in CR-39 nuclear track detectors. D. Nikezic, K.N. Yu Comput. Phys. Commun. 178(2008)591

Methods and Software for Building Bibliographic Data Bases.

ERIC Educational Resources Information Center

Daehn, Ralph M.

1985-01-01

This in-depth look at database management systems (DBMS) for microcomputers covers data entry, information retrieval, security, DBMS software and design, and downloading of literature search results. The advantages of in-house systems versus online search vendors are discussed, and specifications of three software packages and 14 sources are…

Design requirements for SRB production control system. Volume 3: Package evaluation, modification and hardware

NASA Technical Reports Server (NTRS)

1981-01-01

The software package evaluation was designed to analyze commercially available, field-proven, production control or manufacturing resource planning management technology and software package. The analysis was conducted by comparing SRB production control software requirements and conceptual system design to software package capabilities. The methodology of evaluation and the findings at each stage of evaluation are described. Topics covered include: vendor listing; request for information (RFI) document; RFI response rate and quality; RFI evaluation process; and capabilities versus requirements.

RNAbrowse: RNA-Seq de novo assembly results browser.

PubMed

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.

Mesoscale and severe storms (Mass) data management and analysis system

NASA Technical Reports Server (NTRS)

Hickey, J. S.; Karitani, S.; Dickerson, M.

1984-01-01

Progress on the Mesoscale and Severe Storms (MASS) data management and analysis system is described. An interactive atmospheric data base management software package to convert four types of data (Sounding, Single Level, Grid, Image) into standard random access formats is implemented and integrated with the MASS AVE80 Series general purpose plotting and graphics display data analysis software package. An interactive analysis and display graphics software package (AVE80) to analyze large volumes of conventional and satellite derived meteorological data is enhanced to provide imaging/color graphics display utilizing color video hardware integrated into the MASS computer system. Local and remote smart-terminal capability is provided by installing APPLE III computer systems within individual scientist offices and integrated with the MASS system, thus providing color video display, graphics, and characters display of the four data types.

Hearing the Signal in the Noise: A Software-Based Content Analysis of Patterns in Responses by Experts and Students to a New Venture Investment Proposal

ERIC Educational Resources Information Center

Hostager, Todd J.; Voiovich, Jason; Hughes, Raymond K.

2013-01-01

The authors apply a software-based content analysis method to uncover differences in responses by expert entrepreneurs and undergraduate entrepreneur majors to a new venture investment proposal. Data analyzed via the Leximancer software package yielded conceptual maps highlighting key differences in the nature of these responses. Study methods and…

Matlab as a robust control design tool

NASA Technical Reports Server (NTRS)

Gregory, Irene M.

1994-01-01

This presentation introduces Matlab as a tool used in flight control research. The example used to illustrate some of the capabilities of this software is a robust controller designed for a single stage to orbit air breathing vehicles's ascent to orbit. The global requirements of the controller are to stabilize the vehicle and follow a trajectory in the presence of atmospheric disturbances and strong dynamic coupling between airframe and propulsion.

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation

PubMed Central

Sherfey, Jason S.; Soplata, Austin E.; Ardid, Salva; Roberts, Erik A.; Stanley, David A.; Pittman-Polletta, Benjamin R.; Kopell, Nancy J.

2018-01-01

DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community. PMID:29599715

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

PubMed

Sherfey, Jason S; Soplata, Austin E; Ardid, Salva; Roberts, Erik A; Stanley, David A; Pittman-Polletta, Benjamin R; Kopell, Nancy J

2018-01-01

DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

Spectrum image analysis tool - A flexible MATLAB solution to analyze EEL and CL spectrum images.

PubMed

Schmidt, Franz-Philipp; Hofer, Ferdinand; Krenn, Joachim R

2017-02-01

Spectrum imaging techniques, gaining simultaneously structural (image) and spectroscopic data, require appropriate and careful processing to extract information of the dataset. In this article we introduce a MATLAB based software that uses three dimensional data (EEL/CL spectrum image in dm3 format (Gatan Inc.'s DigitalMicrograph ® )) as input. A graphical user interface enables a fast and easy mapping of spectral dependent images and position dependent spectra. First, data processing such as background subtraction, deconvolution and denoising, second, multiple display options including an EEL/CL moviemaker and, third, the applicability on a large amount of data sets with a small work load makes this program an interesting tool to visualize otherwise hidden details. Copyright © 2016 Elsevier Ltd. All rights reserved.

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

Reviews six software packages for use with school age children ranging from grade 3 to grade 12. Includes "The Microcomputer Based Lab Project: Motion, Sound"; "Genetics"; "Geologic History"; "The Microscope Simulator"; and "Wiz Works" all for Apple II and "Reading for Information: Level…

Framework for multi-resolution analyses of advanced traffic management strategies [summary].

DOT National Transportation Integrated Search

2017-01-01

Transportation planning relies extensively on software that can simulate and predict travel behavior in response to alternative transportation networks. However, different software packages view traffic at different scales. Some programs are based on...

Software development to implement the TxDOT culvert rating guide.

DOT National Transportation Integrated Search

2013-05-01

This implementation project created CULVLR: Culvert Load Rating, Version 1.0.0, a Windows-based : desktop application software package that automates the process by which Texas Department of Transportation : (TxDOT) engineers and their consultants ...

Woods Hole Image Processing System Software implementation; using NetCDF as a software interface for image processing

USGS Publications Warehouse

Paskevich, Valerie F.

1992-01-01

The Branch of Atlantic Marine Geology has been involved in the collection, processing and digital mosaicking of high, medium and low-resolution side-scan sonar data during the past 6 years. In the past, processing and digital mosaicking has been accomplished with a dedicated, shore-based computer system. With the need to process sidescan data in the field with increased power and reduced cost of major workstations, a need to have an image processing package on a UNIX based computer system which could be utilized in the field as well as be more generally available to Branch personnel was identified. This report describes the initial development of that package referred to as the Woods Hole Image Processing System (WHIPS). The software was developed using the Unidata NetCDF software interface to allow data to be more readily portable between different computer operating systems.

A New PC and LabVIEW Package Based System for Electrochemical Investigations

PubMed Central

Stević, Zoran; Andjelković, Zoran; Antić, Dejan

2008-01-01

The paper describes a new PC and LabVIEW software package based system for electrochemical research. An overview of well known electrochemical methods, such as potential measurements, galvanostatic and potentiostatic method, cyclic voltammetry and EIS is given. Electrochemical impedance spectroscopy has been adapted for systems containing large capacitances. For signal generation and recording of the response of investigated electrochemical cell, a measurement and control system was developed, based on a PC P4. The rest of the hardware consists of a commercially available AD-DA converter and an external interface for analog signal processing. The interface is a result of authors own research. The software platform for desired measurement methods is LabVIEW 8.2 package, which is regarded as a high standard in the area of modern virtual instruments. The developed system was adjusted, tested and compared with commercially available system and ORCAD simulation. PMID:27879794

Does Your Graphing Software Real-ly Work?

ERIC Educational Resources Information Center

Marchand, R. J.; McDevitt, T. J.; Bosse, Michael J.; Nandakumar, N. R.

2007-01-01

Many popular mathematical software products including Maple, Mathematica, Derive, Mathcad, Matlab, and some of the TI calculators produce incorrect graphs because they use complex arithmetic instead of "real" arithmetic. This article expounds on this issue, provides possible remedies for instructors to share with their students, and demonstrates…

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools. PMID:24833336

Transverse emittance and phase space program developed for use at the Fermilab A0 Photoinjector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thurman-Keup, R.; Johnson, A.S.; Lumpkin, A.H.

2011-03-01

The Fermilab A0 Photoinjector is a 16 MeV high intensity, high brightness electron linac developed for advanced accelerator R&D. One of the key parameters for the electron beam is the transverse beam emittance. Here we report on a newly developed MATLAB based GUI program used for transverse emittance measurements using the multi-slit technique. This program combines the image acquisition and post-processing tools for determining the transverse phase space parameters with uncertainties. An integral part of accelerator research is a measurement of the beam phase space. Measurements of the transverse phase space can be accomplished by a variety of methods includingmore » multiple screens separated by drift spaces, or by sampling phase space via pepper pots or slits. In any case, the measurement of the phase space parameters, in particular the emittance, can be drastically simplified and sped up by automating the measurement in an intuitive fashion utilizing a graphical interface. At the A0 Photoinjector (A0PI), the control system is DOOCS, which originated at DESY. In addition, there is a library for interfacing to MATLAB, a graphically capable numerical analysis package sold by The Mathworks. It is this graphical package which was chosen as the basis for a graphical phase space measurement system due to its combination of analysis and display capabilities.« less

INDOOR AIR QUALITY AND INHALATION EXPOSURE - SIMULATION TOOL KIT

EPA Science Inventory

A Microsoft Windows-based indoor air quality (IAQ) simulation software package is presented. Named Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short, this package complements and supplements existing IAQ simulation programs and is desi...

An open-source software package for multivariate modeling and clustering: applications to air quality management.

PubMed

Wang, Xiuquan; Huang, Guohe; Zhao, Shan; Guo, Junhong

2015-09-01

This paper presents an open-source software package, rSCA, which is developed based upon a stepwise cluster analysis method and serves as a statistical tool for modeling the relationships between multiple dependent and independent variables. The rSCA package is efficient in dealing with both continuous and discrete variables, as well as nonlinear relationships between the variables. It divides the sample sets of dependent variables into different subsets (or subclusters) through a series of cutting and merging operations based upon the theory of multivariate analysis of variance (MANOVA). The modeling results are given by a cluster tree, which includes both intermediate and leaf subclusters as well as the flow paths from the root of the tree to each leaf subcluster specified by a series of cutting and merging actions. The rSCA package is a handy and easy-to-use tool and is freely available at http://cran.r-project.org/package=rSCA . By applying the developed package to air quality management in an urban environment, we demonstrate its effectiveness in dealing with the complicated relationships among multiple variables in real-world problems.

scraps: An open-source Python-based analysis package for analyzing and plotting superconducting resonator data

DOE PAGES

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn; ...

2016-11-07

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

Software requirements flow-down and preliminary software design for the G-CLEF spectrograph

NASA Astrophysics Data System (ADS)

Evans, Ian N.; Budynkiewicz, Jamie A.; DePonte Evans, Janet; Miller, Joseph B.; Onyuksel, Cem; Paxson, Charles; Plummer, David A.

2016-08-01

The Giant Magellan Telescope (GMT)-Consortium Large Earth Finder (G-CLEF) is a fiber-fed, precision radial velocity (PRV) optical echelle spectrograph that will be the first light instrument on the GMT. The G-CLEF instrument device control subsystem (IDCS) provides software control of the instrument hardware, including the active feedback loops that are required to meet the G-CLEF PRV stability requirements. The IDCS is also tasked with providing operational support packages that include data reduction pipelines and proposal preparation tools. A formal, but ultimately pragmatic approach is being used to establish a complete and correct set of requirements for both the G-CLEF device control and operational support packages. The device control packages must integrate tightly with the state-machine driven software and controls reference architecture designed by the GMT Organization. A model-based systems engineering methodology is being used to develop a preliminary design that meets these requirements. Through this process we have identified some lessons that have general applicability to the development of software for ground-based instrumentation. For example, tasking an individual with overall responsibility for science/software/hardware integration is a key step to ensuring effective integration between these elements. An operational concept document that includes detailed routine and non- routine operational sequences should be prepared in parallel with the hardware design process to tie together these elements and identify any gaps. Appropriate time-phasing of the hardware and software design phases is important, but revisions to driving requirements that impact software requirements and preliminary design are inevitable. Such revisions must be carefully managed to ensure efficient use of resources.

A comparison of six software packages for evaluation of solid lung nodules using semi-automated volumetry: what is the minimum increase in size to detect growth in repeated CT examinations.

PubMed

de Hoop, Bartjan; Gietema, Hester; van Ginneken, Bram; Zanen, Pieter; Groenewegen, Gerard; Prokop, Mathias

2009-04-01

We compared interexamination variability of CT lung nodule volumetry with six currently available semi-automated software packages to determine the minimum change needed to detect the growth of solid lung nodules. We had ethics committee approval. To simulate a follow-up examination with zero growth, we performed two low-dose unenhanced CT scans in 20 patients referred for pulmonary metastases. Between examinations, patients got off and on the table. Volumes of all pulmonary nodules were determined on both examinations using six nodule evaluation software packages. Variability (upper limit of the 95% confidence interval of the Bland-Altman plot) was calculated for nodules for which segmentation was visually rated as adequate. We evaluated 214 nodules (mean diameter 10.9 mm, range 3.3 mm-30.0 mm). Software packages provided adequate segmentation in 71% to 86% of nodules (p < 0.001). In case of adequate segmentation, variability in volumetry between scans ranged from 16.4% to 22.3% for the various software packages. Variability with five to six software packages was significantly less for nodules >or=8 mm in diameter (range 12.9%-17.1%) than for nodules <8 mm (range 18.5%-25.6%). Segmented volumes of each package were compared to each of the other packages. Systematic volume differences were detected in 11/15 comparisons. This hampers comparison of nodule volumes between software packages.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

Extraction of CT dose information from DICOM metadata: automated Matlab-based approach.

PubMed

Dave, Jaydev K; Gingold, Eric L

2013-01-01

The purpose of this study was to extract exposure parameters and dose-relevant indexes of CT examinations from information embedded in DICOM metadata. DICOM dose report files were identified and retrieved from a PACS. An automated software program was used to extract from these files information from the structured elements in the DICOM metadata relevant to exposure. Extracting information from DICOM metadata eliminated potential errors inherent in techniques based on optical character recognition, yielding 100% accuracy.

Ground-Based GPS Sensing of Azimuthal Variations in Precipitable Water Vapor

NASA Technical Reports Server (NTRS)

Kroger, P. M.; Bar-Sever, Y. E.

1997-01-01

Current models for troposphere delay employed by GPS software packages map the total zenith delay to the line-of-sight delay of the individual satellite-receiver link under the assumption of azimuthal homogeneity. This could be a poor approximation for many sites, in particular, those located at an ocean front or next to a mountain range. We have modified the GIPSY-OASIS II software package to include a simple non-symmetric mapping function (MacMillan, 1995) which introduces two new parameters.

Development of an Ada package library

NASA Technical Reports Server (NTRS)

Burton, Bruce; Broido, Michael

1986-01-01

A usable prototype Ada package library was developed and is currently being evaluated for use in large software development efforts. The library system is comprised of an Ada-oriented design language used to facilitate the collection of reuse information, a relational data base to store reuse information, a set of reusable Ada components and tools, and a set of guidelines governing the system's use. The prototyping exercise is discussed and the lessons learned from it have led to the definition of a comprehensive tool set to facilitate software reuse.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

Parallel and Preemptable Dynamically Dimensioned Search Algorithms for Single and Multi-objective Optimization in Water Resources

NASA Astrophysics Data System (ADS)

Tolson, B.; Matott, L. S.; Gaffoor, T. A.; Asadzadeh, M.; Shafii, M.; Pomorski, P.; Xu, X.; Jahanpour, M.; Razavi, S.; Haghnegahdar, A.; Craig, J. R.

2015-12-01

We introduce asynchronous parallel implementations of the Dynamically Dimensioned Search (DDS) family of algorithms including DDS, discrete DDS, PA-DDS and DDS-AU. These parallel algorithms are unique from most existing parallel optimization algorithms in the water resources field in that parallel DDS is asynchronous and does not require an entire population (set of candidate solutions) to be evaluated before generating and then sending a new candidate solution for evaluation. One key advance in this study is developing the first parallel PA-DDS multi-objective optimization algorithm. The other key advance is enhancing the computational efficiency of solving optimization problems (such as model calibration) by combining a parallel optimization algorithm with the deterministic model pre-emption concept. These two efficiency techniques can only be combined because of the asynchronous nature of parallel DDS. Model pre-emption functions to terminate simulation model runs early, prior to completely simulating the model calibration period for example, when intermediate results indicate the candidate solution is so poor that it will definitely have no influence on the generation of further candidate solutions. The computational savings of deterministic model preemption available in serial implementations of population-based algorithms (e.g., PSO) disappear in synchronous parallel implementations as these algorithms. In addition to the key advances above, we implement the algorithms across a range of computation platforms (Windows and Unix-based operating systems from multi-core desktops to a supercomputer system) and package these for future modellers within a model-independent calibration software package called Ostrich as well as MATLAB versions. Results across multiple platforms and multiple case studies (from 4 to 64 processors) demonstrate the vast improvement over serial DDS-based algorithms and highlight the important role model pre-emption plays in the performance of parallel, pre-emptable DDS algorithms. Case studies include single- and multiple-objective optimization problems in water resources model calibration and in many cases linear or near linear speedups are observed.

Neo: an object model for handling electrophysiology data in multiple formats

PubMed Central

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L.; Rodgers, Chris C.; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P.

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology. PMID:24600386

Neo: an object model for handling electrophysiology data in multiple formats.

PubMed

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L; Rodgers, Chris C; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named "Neo," suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.

A non-axial superconducting magnet design for optimized patient access and minimal SAD for use in a Linac-MR hybrid: proof of concept.

PubMed

Yaghoobpour Tari, Shima; Wachowicz, Keith; Gino Fallone, B

2017-04-21

A prototype rotating hybrid magnetic resonance imaging system and linac has been developed to allow for simultaneous imaging and radiation delivery parallel to B 0 . However, the design of a compact magnet capable of rotation in a small vault with sufficient patient access and a typical clinical source-to-axis distance (SAD) is challenging. This work presents a novel superconducting magnet design as a proof of concept that allows for a reduced SAD and ample patient access by moving the superconducting coils to the side of the yoke. The yoke and pole-plate structures are shaped to direct the magnetic flux appropriately. The outer surface of the pole plate is optimized subject to the minimization of a cost function, which evaluates the uniformity of the magnetic field over an ellipsoid. The magnetic field calculations required in this work are performed with the 3D finite element method software package Opera-3D. Each tentative design strategy is virtually modeled in this software package, which is externally controlled by MATLAB, with its key geometries defined as variables. The optimization variables are the thickness of the pole plate at control points distributed over the pole plate surface. A novel design concept as a superconducting non-axial magnet is introduced, which could create a large uniform B 0 magnetic field with fewer geometric restriction. This non-axial 0.5 T superconducting magnet has a moderately reduced SAD of 123 cm and a vertical patient opening of 68 cm. This work is presented as a proof of principle to investigate the feasibility of a non-axial magnet with the coils located around the yoke, and the results encourage future design optimizations to maximize the benefits of this non-axial design.

A non-axial superconducting magnet design for optimized patient access and minimal SAD for use in a Linac-MR hybrid: proof of concept

NASA Astrophysics Data System (ADS)

Yaghoobpour Tari, Shima; Wachowicz, Keith; Fallone, B. Gino

2017-04-01

A prototype rotating hybrid magnetic resonance imaging system and linac has been developed to allow for simultaneous imaging and radiation delivery parallel to B 0. However, the design of a compact magnet capable of rotation in a small vault with sufficient patient access and a typical clinical source-to-axis distance (SAD) is challenging. This work presents a novel superconducting magnet design as a proof of concept that allows for a reduced SAD and ample patient access by moving the superconducting coils to the side of the yoke. The yoke and pole-plate structures are shaped to direct the magnetic flux appropriately. The outer surface of the pole plate is optimized subject to the minimization of a cost function, which evaluates the uniformity of the magnetic field over an ellipsoid. The magnetic field calculations required in this work are performed with the 3D finite element method software package Opera-3D. Each tentative design strategy is virtually modeled in this software package, which is externally controlled by MATLAB, with its key geometries defined as variables. The optimization variables are the thickness of the pole plate at control points distributed over the pole plate surface. A novel design concept as a superconducting non-axial magnet is introduced, which could create a large uniform B 0 magnetic field with fewer geometric restriction. This non-axial 0.5 T superconducting magnet has a moderately reduced SAD of 123 cm and a vertical patient opening of 68 cm. This work is presented as a proof of principle to investigate the feasibility of a non-axial magnet with the coils located around the yoke, and the results encourage future design optimizations to maximize the benefits of this non-axial design.

Volumetric neuroimage analysis extensions for the MIPAV software package.

PubMed

Bazin, Pierre-Louis; Cuzzocreo, Jennifer L; Yassa, Michael A; Gandler, William; McAuliffe, Matthew J; Bassett, Susan S; Pham, Dzung L

2007-09-15

We describe a new collection of publicly available software tools for performing quantitative neuroimage analysis. The tools perform semi-automatic brain extraction, tissue classification, Talairach alignment, and atlas-based measurements within a user-friendly graphical environment. They are implemented as plug-ins for MIPAV, a freely available medical image processing software package from the National Institutes of Health. Because the plug-ins and MIPAV are implemented in Java, both can be utilized on nearly any operating system platform. In addition to the software plug-ins, we have also released a digital version of the Talairach atlas that can be used to perform regional volumetric analyses. Several studies are conducted applying the new tools to simulated and real neuroimaging data sets.

UWB Tracking Software Development

NASA Technical Reports Server (NTRS)

Gross, Julia; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dusl, John; Ni, Jianjun; Rafford, Melinda

2006-01-01

An Ultra-Wideband (UWB) two-cluster Angle of Arrival (AOA) tracking prototype system is currently being developed and tested at NASA Johnson Space Center for space exploration applications. This talk discusses the software development efforts for this UWB two-cluster AOA tracking system. The role the software plays in this system is to take waveform data from two UWB radio receivers as an input, feed this input into an AOA tracking algorithm, and generate the target position as an output. The architecture of the software (Input/Output Interface and Algorithm Core) will be introduced in this talk. The development of this software has three phases. In Phase I, the software is mostly Matlab driven and calls C++ socket functions to provide the communication links to the radios. This is beneficial in the early stage when it is necessary to frequently test changes in the algorithm. Phase II of the development is to have the software mostly C++ driven and call a Matlab function for the AOA tracking algorithm. This is beneficial in order to send the tracking results to other systems and also to improve the tracking update rate of the system. The third phase is part of future work and is to have the software completely C++ driven with a graphics user interface. This software design enables the fine resolution tracking of the UWB two-cluster AOA tracking system.

Novel optimization technique of isolated microgrid with hydrogen energy storage.

PubMed

Beshr, Eman Hassan; Abdelghany, Hazem; Eteiba, Mahmoud

2018-01-01

This paper presents a novel optimization technique for energy management studies of an isolated microgrid. The system is supplied by various Distributed Energy Resources (DERs), Diesel Generator (DG), a Wind Turbine Generator (WTG), Photovoltaic (PV) arrays and supported by fuel cell/electrolyzer Hydrogen storage system for short term storage. Multi-objective optimization is used through non-dominated sorting genetic algorithm to suit the load requirements under the given constraints. A novel multi-objective flower pollination algorithm is utilized to check the results. The Pros and cons of the two optimization techniques are compared and evaluated. An isolated microgrid is modelled using MATLAB software package, dispatch of active/reactive power, optimal load flow analysis with slack bus selection are carried out to be able to minimize fuel cost and line losses under realistic constraints. The performance of the system is studied and analyzed during both summer and winter conditions and three case studies are presented for each condition. The modified IEEE 15 bus system is used to validate the proposed algorithm.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Novel optimization technique of isolated microgrid with hydrogen energy storage

PubMed Central

Abdelghany, Hazem; Eteiba, Mahmoud

2018-01-01

This paper presents a novel optimization technique for energy management studies of an isolated microgrid. The system is supplied by various Distributed Energy Resources (DERs), Diesel Generator (DG), a Wind Turbine Generator (WTG), Photovoltaic (PV) arrays and supported by fuel cell/electrolyzer Hydrogen storage system for short term storage. Multi-objective optimization is used through non-dominated sorting genetic algorithm to suit the load requirements under the given constraints. A novel multi-objective flower pollination algorithm is utilized to check the results. The Pros and cons of the two optimization techniques are compared and evaluated. An isolated microgrid is modelled using MATLAB software package, dispatch of active/reactive power, optimal load flow analysis with slack bus selection are carried out to be able to minimize fuel cost and line losses under realistic constraints. The performance of the system is studied and analyzed during both summer and winter conditions and three case studies are presented for each condition. The modified IEEE 15 bus system is used to validate the proposed algorithm. PMID:29466433

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

NDE Software Developed at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Roth, Donald J.; Martin, Richard E.; Rauser, Richard W.; Nichols, Charles; Bonacuse, Peter J.

2014-01-01

NASA Glenn Research Center has developed several important Nondestructive Evaluation (NDE) related software packages for different projects in the last 10 years. Three of the software packages have been created with commercial-grade user interfaces and are available to United States entities for download on the NASA Technology Transfer and Partnership Office server (https://sr.grc.nasa.gov/). This article provides brief overviews of the software packages.

PScan 1.0: flexible software framework for polygon based multiphoton microscopy

NASA Astrophysics Data System (ADS)

Li, Yongxiao; Lee, Woei Ming

2016-12-01

Multiphoton laser scanning microscopes exhibit highly localized nonlinear optical excitation and are powerful instruments for in-vivo deep tissue imaging. Customized multiphoton microscopy has a significantly superior performance for in-vivo imaging because of precise control over the scanning and detection system. To date, there have been several flexible software platforms catered to custom built microscopy systems i.e. ScanImage, HelioScan, MicroManager, that perform at imaging speeds of 30-100fps. In this paper, we describe a flexible software framework for high speed imaging systems capable of operating from 5 fps to 1600 fps. The software is based on the MATLAB image processing toolbox. It has the capability to communicate directly with a high performing imaging card (Matrox Solios eA/XA), thus retaining high speed acquisition. The program is also designed to communicate with LabVIEW and Fiji for instrument control and image processing. Pscan 1.0 can handle high imaging rates and contains sufficient flexibility for users to adapt to their high speed imaging systems.

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses.

PubMed

Desai, Trunil S; Srivastava, Shireesh

2018-01-01

13 C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13 C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13 C-MFA software that works in various operating systems will enable more researchers to perform 13 C-MFA and to further modify and develop the package.

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses

PubMed Central

Desai, Trunil S.

2018-01-01

13C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13C-MFA software that works in various operating systems will enable more researchers to perform 13C-MFA and to further modify and develop the package. PMID:29736347

A New PC and LabVIEW Package Based System for Electrochemical Investigations.

PubMed

Stević, Zoran; Andjelković, Zoran; Antić, Dejan

2008-03-15

The paper describes a new PC and LabVIEW software package based system forelectrochemical research. An overview of well known electrochemical methods, such aspotential measurements, galvanostatic and potentiostatic method, cyclic voltammetry andEIS is given. Electrochemical impedance spectroscopy has been adapted for systemscontaining large capacitances. For signal generation and recording of the response ofinvestigated electrochemical cell, a measurement and control system was developed, basedon a PC P4. The rest of the hardware consists of a commercially available AD-DA converterand an external interface for analog signal processing. The interface is a result of authorsown research. The software platform for desired measurement methods is LabVIEW 8.2package, which is regarded as a high standard in the area of modern virtual instruments. Thedeveloped system was adjusted, tested and compared with commercially available systemand ORCAD simulation.

Flight Dynamics and Control of a Morphing UAV: Bio inspired by Natural Fliers

DTIC Science & Technology

2017-02-17

Approved for public release: distribution unlimited. IV Modelling and Sizing Tornado Vortex Lattice Method (VLM) was used for aerodynamic prediction... Tornado is a Vortex Lattice Method software programmed in MATLAB; it was selected due to its fast solving time and ability to be controlled through...custom MATLAB scripts. Tornado VLM models the wing as thin sheet of discrete vortices and computes the pressure and force distributions around the

MathBrowser: Web-Enabled Mathematical Software with Application to the Chemistry Curriculum, v 1.0

NASA Astrophysics Data System (ADS)

Goldsmith, Jack G.

1997-10-01

MathSoft: Cambridge, MA, 1996; free via ftp from www.mathsoft.com. The movement to provide computer-based applications in chemistry has come to focus on three main areas: software aimed at specific applications (drawing, simulation, data analysis, etc.), multimedia applications designed to assist in the presentation of conceptual information, and packages to be used in conjunction with a particular textbook at a specific point in the chemistry curriculum. The result is a situation where no single software package devoted to problem solving can be used across a large segment of the curriculum. Adoption of World Wide Web (WWW) technology by a manufacturer of mathematical software, however, has produced software that provides an attractive means of providing a problem-solving resource to students in courses from freshman through senior level.

MINDS: A microcomputer interactive data system for 8086-based controllers

NASA Technical Reports Server (NTRS)

Soeder, J. F.

1985-01-01

A microcomputer interactive data system (MINDS) software package for the 8086 family of microcomputers is described. To enhance program understandability and ease of code maintenance, the software is written in PL/M-86, Intel Corporation's high-level system implementation language. The MINDS software is intended to run in residence with real-time digital control software to provide displays of steady-state and transient data. In addition, the MINDS package provides classic monitor capabilities along with extended provisions for debugging an executing control system. The software uses the CP/M-86 operating system developed by Digital Research, Inc., to provide program load capabilities along with a uniform file structure for data and table storage. Finally, a library of input and output subroutines to be used with consoles equipped with PL/M-86 and assembly language is described.

ELRIS2D: A MATLAB Package for the 2D Inversion of DC Resistivity/IP Data

NASA Astrophysics Data System (ADS)

Akca, Irfan

2016-04-01

ELRIS2D is an open source code written in MATLAB for the two-dimensional inversion of direct current resistivity (DCR) and time domain induced polarization (IP) data. The user interface of the program is designed for functionality and ease of use. All available settings of the program can be reached from the main window. The subsurface is discre-tized using a hybrid mesh generated by the combination of structured and unstructured meshes, which reduces the computational cost of the whole inversion procedure. The inversion routine is based on the smoothness constrained least squares method. In order to verify the program, responses of two test models and field data sets were inverted. The models inverted from the synthetic data sets are consistent with the original test models in both DC resistivity and IP cases. A field data set acquired in an archaeological site is also used for the verification of outcomes of the program in comparison with the excavation results.

Forecasting the mortality rates of Malaysian population using Heligman-Pollard model

NASA Astrophysics Data System (ADS)

Ibrahim, Rose Irnawaty; Mohd, Razak; Ngataman, Nuraini; Abrisam, Wan Nur Azifah Wan Mohd

2017-08-01

Actuaries, demographers and other professionals have always been aware of the critical importance of mortality forecasting due to declining trend of mortality and continuous increases in life expectancy. Heligman-Pollard model was introduced in 1980 and has been widely used by researchers in modelling and forecasting future mortality. This paper aims to estimate an eight-parameter model based on Heligman and Pollard's law of mortality. Since the model involves nonlinear equations that are explicitly difficult to solve, the Matrix Laboratory Version 7.0 (MATLAB 7.0) software will be used in order to estimate the parameters. Statistical Package for the Social Sciences (SPSS) will be applied to forecast all the parameters according to Autoregressive Integrated Moving Average (ARIMA). The empirical data sets of Malaysian population for period of 1981 to 2015 for both genders will be considered, which the period of 1981 to 2010 will be used as "training set" and the period of 2011 to 2015 as "testing set". In order to investigate the accuracy of the estimation, the forecast results will be compared against actual data of mortality rates. The result shows that Heligman-Pollard model fit well for male population at all ages while the model seems to underestimate the mortality rates for female population at the older ages.

Further Development, Support and Enhancement of CONDUIT

NASA Technical Reports Server (NTRS)

Veronica, Moldoveanu; Levine, William S.

1999-01-01

From the first airplanes steered by handles, wheels, and pedals to today's advanced aircraft, there has been a century of revolutionary inventions, all of them contributing to flight quality. The stability and controllability of aircraft as they appear to a pilot are called flying or handling qualities. Many years after the first airplanes flew, flying qualities were identified and ranked from desirable to unsatisfactory. Later on engineers developed design methods to satisfy these practical criteria. CONDUIT, which stands for Control Designer's Unified Interface, is a modern software package that provides a methodology for optimization of flight control systems in order to improve the flying qualities. CONDUIT is dependent on an the optimization engine called CONSOL-OPTCAD (C-O). C-O performs multicriterion parametric optimization. C-O was successfully tested on a variety of control problems. The optimization-based computational system, C-O, requires a particular control system description as a MATLAB file and possesses the ability to modify the vector of design parameters in an attempt to satisfy performance objectives and constraints specified by the designer, in a C-type file. After the first optimization attempts on the UH-60A control system, an early interface system, named GIFCORCODE (Graphical Interface for CONSOL-OPTCAD for Rotorcraft Controller Design) was created.

Design and implementation of a software package to control a network of robotic observatories

NASA Astrophysics Data System (ADS)

Tuparev, G.; Nicolova, I.; Zlatanov, B.; Mihova, D.; Popova, I.; Hessman, F. V.

2006-09-01

We present a description of a reusable software package able to control a large, heterogeneous network of fully and semi-robotic observatories initially developed to run the MONET network of two 1.2 m telescopes. Special attention is given to the design of a robust, long-term observation scheduler which also allows the trading of observation time and facilities within various networks. The handling of the ``Phase I&II" project-development process, the time-accounting between complex organizational structures, and usability issues for making the package accessible not only to professional astronomers, but also to amateurs and high-school students is discussed. A simple RTML-based solution to link multiple networks is demonstrated.

FRAME (Force Review Automation Environment): MATLAB-based AFM data processor.

PubMed

Partola, Kostyantyn R; Lykotrafitis, George

2016-05-03

Data processing of force-displacement curves generated by atomic force microscopes (AFMs) for elastic moduli and unbinding event measurements is very time consuming and susceptible to user error or bias. There is an evident need for consistent, dependable, and easy-to-use AFM data processing software. We have developed an open-source software application, the force review automation environment (or FRAME), that provides users with an intuitive graphical user interface, automating data processing, and tools for expediting manual processing. We did not observe a significant difference between manually processed and automatically processed results from the same data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

Non-Contact Technique for Determining the Mechanical Stress in thin Films on Wafers by Profiler

NASA Astrophysics Data System (ADS)

Djuzhev, N. A.; Dedkova, A. A.; E Gusev, E.; Makhiboroda, M. A.; Glagolev, P. Y.

2017-04-01

This paper presents an algorithm for analysis of relief for the purpose of calculating mechanical stresses in a selected direction on the plate in the form of software package Matlab. The method allows for the measurement sample in the local area. It provides a visual representation of the data and allows to get stress distribution on wafer surface. Automated analysis process reduces the likelihood of errors researcher. Achieved time saving during processing results. In carrying out several measurements possible drawing card plate to predict yield crystals. According to this technique done in measurement of mechanical stresses of thermal silicon oxide film on a silicon substrate. Analysis of the results showed objectivity and reliability calculations. This method can be used for selecting the optimal parameters of the material deposition conditions. In software of device-technological simulation TCAD defined process time, temperature and oxidation of the operation of the sample environment for receiving the set value of the dielectric film thickness. Calculated thermal stresses are in the system silicon-silicon oxide. There is a good correlation between numerical simulations and analytical calculation. It is shown that the nature of occurrence of mechanical stress is not limited to the difference of thermal expansion coefficients of materials.

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Renke; Jin, Shuangshuang; Chen, Yousu

This paper presents a faster-than-real-time dynamic simulation software package that is designed for large-size power system dynamic simulation. It was developed on the GridPACKTM high-performance computing (HPC) framework. The key features of the developed software package include (1) faster-than-real-time dynamic simulation for a WECC system (17,000 buses) with different types of detailed generator, controller, and relay dynamic models, (2) a decoupled parallel dynamic simulation algorithm with optimized computation architecture to better leverage HPC resources and technologies, (3) options for HPC-based linear and iterative solvers, (4) hidden HPC details, such as data communication and distribution, to enable development centered on mathematicalmore » models and algorithms rather than on computational details for power system researchers, and (5) easy integration of new dynamic models and related algorithms into the software package.« less

Digital Model Ofwalls of Padua Lowrelief

NASA Astrophysics Data System (ADS)

Fissore, F.; Guarnieri, A.; Vettore, A.

2017-11-01

Photogrammetry has been widely used in the recent years in a number of applications, e.g. cultural heritage, surveying buildings and infrastructures. Despite nowadays its use is quite common, most of the used photogrammetric softwares are commercial. This paper aims at comparing the use of a free Matlab tool that is being developed at the University of Padova mostly for educational purposes with that of a commercial (and widely used) software (Agisoft PhotoScan). Despite the above mentioned free Matlab tool is designed to work for airborne photogrammetric, in this work it is used in a slightly different case: the 3D reconstruction of a low relief of the walls of Padova, which is on the façade of the church Santa Maria del Giglio, Venice, Italy.

Evaluating Process Sustainability Using Flowsheet Monitoring

EPA Science Inventory

Environmental metric software can be used to evaluate the sustainability of a chemical based on data from the chemical process that is used to manufacture it. One problem in developing environmental metric software is that chemical process simulation packages typically do not rea...

RNAbrowse: RNA-Seq De Novo Assembly Results Browser

PubMed Central

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

Astronomical Software Directory Service

NASA Astrophysics Data System (ADS)

Hanisch, Robert J.; Payne, Harry; Hayes, Jeffrey

1997-01-01

With the support of NASA's Astrophysics Data Program (NRA 92-OSSA-15), we have developed the Astronomical Software Directory Service (ASDS): a distributed, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URLs indexed for full-text searching. Users are performing about 400 searches per month. A new aspect of our service is the inclusion of telescope and instrumentation manuals, which prompted us to change the name to the Astronomical Software and Documentation Service. ASDS was originally conceived to serve two purposes: to provide a useful Internet service in an area of expertise of the investigators (astronomical software), and as a research project to investigate various architectures for searching through a set of documents distributed across the Internet. Two of the co-investigators were then installing and maintaining astronomical software as their primary job responsibility. We felt that a service which incorporated our experience in this area would be more useful than a straightforward listing of software packages. The original concept was for a service based on the client/server model, which would function as a directory/referral service rather than as an archive. For performing the searches, we began our investigation with a decision to evaluate the Isite software from the Center for Networked Information Discovery and Retrieval (CNIDR). This software was intended as a replacement for Wide-Area Information Service (WAIS), a client/server technology for performing full-text searches through a set of documents. Isite had some additional features that we considered attractive, and we enjoyed the cooperation of the Isite developers, who were happy to have ASDS as a demonstration project. We ended up staying with the software throughout the project, making modifications to take advantage of new features as they came along, as well as influencing the software development. The Web interface to the search engine is provided by a gateway program written in C++ by a consultant to the project (A. Warnock).

NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies.

PubMed

Sauk, Martin; Žilina, Olga; Kurg, Ants; Ustav, Eva-Liina; Peters, Maire; Paluoja, Priit; Roost, Anne Mari; Teder, Hindrek; Palta, Priit; Brison, Nathalie; Vermeesch, Joris R; Krjutškov, Kaarel; Salumets, Andres; Kaplinski, Lauris

2018-04-04

Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/ .

The equipment access software for a distributed UNIX-based accelerator control system

NASA Astrophysics Data System (ADS)

Trofimov, Nikolai; Zelepoukine, Serguei; Zharkov, Eugeny; Charrue, Pierre; Gareyte, Claire; Poirier, Hervé

1994-12-01

This paper presents a generic equipment access software package for a distributed control system using computers with UNIX or UNIX-like operating systems. The package consists of three main components, an application Equipment Access Library, Message Handler and Equipment Data Base. An application task, which may run in any computer in the network, sends requests to access equipment through Equipment Library calls. The basic request is in the form Equipment-Action-Data and is routed via a remote procedure call to the computer to which the given equipment is connected. In this computer the request is received by the Message Handler. According to the type of the equipment connection, the Message Handler either passes the request to the specific process software in the same computer or forwards it to a lower level network of equipment controllers using MIL1553B, GPIB, RS232 or BITBUS communication. The answer is then returned to the calling application. Descriptive information required for request routing and processing is stored in the real-time Equipment Data Base. The package has been written to be portable and is currently available on DEC Ultrix, LynxOS, HPUX, XENIX, OS-9 and Apollo domain.

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

PubMed

Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

1997-12-01

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

The experience factory: Can it make you a 5? or what is its relationship to other quality and improvement concepts?

NASA Technical Reports Server (NTRS)

Basili, Victor R.

1992-01-01

The concepts of quality improvements have permeated many businesses. It is clear that the nineties will be the quality era for software and there is a growing need to develop or adapt quality improvement approaches to the software business. Thus we must understand software as an artifact and software as a business. Since the business we are dealing with is software, we must understand the nature of software and software development. The software discipline is evolutionary and experimental; it is a laboratory science. Software is development not production. The technologies of the discipline are human based. There is a lack of models that allow us to reason about the process and the product. All software is not the same; process is a variable, goals are variable, etc. Packaged, reusable, experiences require additional resources in the form of organization, processes, people, etc. There have been a variety of organizational frameworks proposed to improve quality for various businesses. The ones discussed in this presentation include: Plan-Do-Check-Act, a quality improvement process based upon a feedback cycle for optimizing a single process model/production line; the Experience Factory/Quality Improvement Paradigm, continuous improvements through the experimentation, packaging, and reuse of experiences based upon a business's needs; Total Quality Management, a management approach to long term success through customer satisfaction based on the participation of all members of an organization; the SEI capability maturity model, a staged process improvement based upon assessment with regard to a set of key process areas until you reach a level 5 which represents a continuous process improvement; and Lean (software) Development, a principle supporting the concentration of the production on 'value added' activities and the elimination of reduction of 'not value added' activities.

The STARLINK software collection

NASA Astrophysics Data System (ADS)

Penny, A. J.; Wallace, P. T.; Sherman, J. C.; Terret, D. L.

1993-12-01

A demonstration will be given of some recent Starlink software. STARLINK is: a network of computers used by UK astronomers; a collection of programs for the calibration and analysis of astronomical data; a team of people giving hardware, software and administrative support. The Starlink Project has been in operation since 1980 to provide UK astronomers with interactive image processing and data reduction facilities. There are now Starlink computer systems at 25 UK locations, serving about 1500 registered users. The Starlink software collection now has about 25 major packages covering a wide range of astronomical data reduction and analysis techniques, as well as many smaller programs and utilities. At the core of most of the packages is a common `software environment', which provides many of the functions which applications need and offers standardized methods of structuring and accessing data. The software environment simplifies programming and support, and makes it easy to use different packages for different stages of the data reduction. Users see a consistent style, and can mix applications without hitting problems of differing data formats. The Project group coordinates the writing and distribution of this software collection, which is Unix based. Outside the UK, Starlink is used at a large number of places, which range from installations at major UK telescopes, which are Starlink-compatible and managed like Starlink sites, to individuals who run only small parts of the Starlink software collection.

NMRbox: A Resource for Biomolecular NMR Computation.

PubMed

Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

2017-04-25

Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

Software Defined GPS API: Development and Implementation of GPS Correlator Architectures Using MATLAB with Focus on SDR Implementations

DTIC Science & Technology

2014-05-18

intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved techniques...with the intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved...intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved techniques to

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.

PubMed

Hill, Jon; Davis, Katie E

2014-01-01

Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.

SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells.

PubMed

Stylianidou, Stella; Brennan, Connor; Nissen, Silas B; Kuwada, Nathan J; Wiggins, Paul A

2016-11-01

Many quantitative cell biology questions require fast yet reliable automated image segmentation to identify and link cells from frame-to-frame, and characterize the cell morphology and fluorescence. We present SuperSegger, an automated MATLAB-based image processing package well-suited to quantitative analysis of high-throughput live-cell fluorescence microscopy of bacterial cells. SuperSegger incorporates machine-learning algorithms to optimize cellular boundaries and automated error resolution to reliably link cells from frame-to-frame. Unlike existing packages, it can reliably segment microcolonies with many cells, facilitating the analysis of cell-cycle dynamics in bacteria as well as cell-contact mediated phenomena. This package has a range of built-in capabilities for characterizing bacterial cells, including the identification of cell division events, mother, daughter and neighbouring cells, and computing statistics on cellular fluorescence, the location and intensity of fluorescent foci. SuperSegger provides a variety of postprocessing data visualization tools for single cell and population level analysis, such as histograms, kymographs, frame mosaics, movies and consensus images. Finally, we demonstrate the power of the package by analyzing lag phase growth with single cell resolution. © 2016 John Wiley & Sons Ltd.

User's Guide for the MapImage Reprojection Software Package, Version 1.01

USGS Publications Warehouse

Finn, Michael P.; Trent, Jason R.

2004-01-01

Scientists routinely accomplish small-scale geospatial modeling in the raster domain, using high-resolution datasets (such as 30-m data) for large parts of continents and low-resolution to high-resolution datasets for the entire globe. Recently, Usery and others (2003a) expanded on the previously limited empirical work with real geographic data by compiling and tabulating the accuracy of categorical areas in projected raster datasets of global extent. Geographers and applications programmers at the U.S. Geological Survey's (USGS) Mid-Continent Mapping Center (MCMC) undertook an effort to expand and evolve an internal USGS software package, MapImage, or mapimg, for raster map projection transformation (Usery and others, 2003a). Daniel R. Steinwand of Science Applications International Corporation, Earth Resources Observation Systems Data Center in Sioux Falls, S. Dak., originally developed mapimg for the USGS, basing it on the USGS's General Cartographic Transformation Package (GCTP). It operated as a command line program on the Unix operating system. Through efforts at MCMC, and in coordination with Mr. Steinwand, this program has been transformed from an application based on a command line into a software package based on a graphic user interface for Windows, Linux, and Unix machines. Usery and others (2003b) pointed out that many commercial software packages do not use exact projection equations and that even when exact projection equations are used, the software often results in error and sometimes does not complete the transformation for specific projections, at specific resampling resolutions, and for specific singularities. Direct implementation of point-to-point transformation with appropriate functions yields the variety of projections available in these software packages, but implementation with data other than points requires specific adaptation of the equations or prior preparation of the data to allow the transformation to succeed. Additional constraints apply to global raster data. It appears that some packages use the USGS's GCTP or similar point transformations without adaptation to the specific characteristics of raster data (Usery and others, 2003b). It is most common for programs to compute transformations of raster data in an inverse fashion. Such mapping can result in an erroneous position and replicate data or create pixels not in the original space. As Usery and others (2003a) indicated, mapimg performs a corresponding forward transformation to ensure the same location results from both methods. The primary benefit of this function is to mask cells outside the domain. MapImage 1.01 is now on the Web. You can download the User's Guide, source, and binaries from the following site: http://mcmcweb.er.usgs.gov/carto_research/projection/acc_proj_data.html

The Predicting Model of E-commerce Site Based on the Ideas of Curve Fitting

NASA Astrophysics Data System (ADS)

Tao, Zhang; Li, Zhang; Dingjun, Chen

On the basis of the idea of the second multiplication curve fitting, the number and scale of Chinese E-commerce site is analyzed. A preventing increase model is introduced in this paper, and the model parameters are solved by the software of Matlab. The validity of the preventing increase model is confirmed though the numerical experiment. The experimental results show that the precision of preventing increase model is ideal.

A multimedia adult literacy program: Combining NASA technology, instructional design theory, and authentic literacy concepts

NASA Technical Reports Server (NTRS)

Willis, Jerry W.

1993-01-01

For a number of years, the Software Technology Branch of the Information Systems Directorate has been involved in the application of cutting edge hardware and software technologies to instructional tasks related to NASA projects. The branch has developed intelligent computer aided training shells, instructional applications of virtual reality and multimedia, and computer-based instructional packages that use fuzzy logic for both instructional and diagnostic decision making. One outcome of the work on space-related technology-supported instruction has been the creation of a significant pool of human talent in the branch with current expertise on the cutting edges of instructional technologies. When the human talent is combined with advanced technologies for graphics, sound, video, CD-ROM, and high speed computing, the result is a powerful research and development group that both contributes to the applied foundations of instructional technology and creates effective instructional packages that take advantage of a range of advanced technologies. Several branch projects are currently underway that combine NASA-developed expertise to significant instructional problems in public education. The branch, for example, has developed intelligent computer aided software to help high school students learn physics and staff are currently working on a project to produce educational software for young children with language deficits. This report deals with another project, the adult literacy tutor. Unfortunately, while there are a number of computer-based instructional packages available for adult literacy instruction, most of them are based on the same instructional models that failed these students when they were in school. The teacher-centered, discrete skill and drill-oriented, instructional strategies, even when they are supported by color computer graphics and animation, that form the foundation for most of the computer-based literacy packages currently on the market may not be the most effective or most desirable way to use computer technology in literacy programs. This project is developing a series of instructional packages that are based on a different instructional model - authentic instruction. The instructional development model used to create these packages is also different. Instead of using the traditional five stage linear, sequential model based on behavioral learning theory, the project uses the recursive, reflective design and development model (R2D2) that is based on cognitive learning theory, particularly the social constructivism of Vygotsky, and an epistemology based on critical theory. Using alternative instructional and instructional development theories, the result of the summer faculty fellowship is LiteraCity, a multimedia adult literacy instructional package that is a simulation of finding and applying for a job. The program, which is about 120 megabytes, is distributed on CD-ROM.

An Elementary Algorithm to Evaluate Trigonometric Functions to High Precision

ERIC Educational Resources Information Center

Johansson, B. Tomas

2018-01-01

Evaluation of the cosine function is done via a simple Cordic-like algorithm, together with a package for handling arbitrary-precision arithmetic in the computer program Matlab. Approximations to the cosine function having hundreds of correct decimals are presented with a discussion around errors and implementation.

Dynamic Modeling and Simulation of a Rotational Inverted Pendulum

NASA Astrophysics Data System (ADS)

Duart, J. L.; Montero, B.; Ospina, P. A.; González, E.

2017-01-01

This paper presents an alternative way to the dynamic modeling of a rotational inverted pendulum using the classic mechanics known as Euler-Lagrange allows to find motion equations that describe our model. It also has a design of the basic model of the system in SolidWorks software, which based on the material and dimensions of the model provides some physical variables necessary for modeling. In order to verify the theoretical results, It was made a contrast between the solutions obtained by simulation SimMechanics-Matlab and the system of equations Euler-Lagrange, solved through ODE23tb method included in Matlab bookstores for solving equations systems of the type and order obtained. This article comprises a pendulum trajectory analysis by a phase space diagram that allows the identification of stable and unstable regions of the system.

Alternatives for jet engine control

NASA Technical Reports Server (NTRS)

Sain, M. K.

1983-01-01

Tensor model order reduction, recursive tensor model identification, input design for tensor model identification, software development for nonlinear feedback control laws based upon tensors, and development of the CATNAP software package for tensor modeling, identification and simulation were studied. The last of these are discussed.

Computer Aided Teaching of Digital Signal Processing.

ERIC Educational Resources Information Center

Castro, Ian P.

1990-01-01

Describes a microcomputer-based software package developed at the University of Surrey for teaching digital signal processing to undergraduate science and engineering students. Menu-driven software capabilities are explained, including demonstration of qualitative concepts and experimentation with quantitative data, and examples are given of…

Evaluating Process Sustainability Using Flowsheet Monitoring (Abstract)

EPA Science Inventory

Environmental metric software can be used to evaluate the sustainability of a chemical based upon data from the chemical process that is used to manufacture it. One problem in developing environmental metric software is that chemical process simulation packages typically do not p...

Note: A simple image processing based fiducial auto-alignment method for sample registration.

PubMed

Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

2015-08-01

A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

Automatic Rock Detection and Mapping from HiRISE Imagery

NASA Technical Reports Server (NTRS)

Huertas, Andres; Adams, Douglas S.; Cheng, Yang

2008-01-01

This system includes a C-code software program and a set of MATLAB software tools for statistical analysis and rock distribution mapping. The major functions include rock detection and rock detection validation. The rock detection code has been evolved into a production tool that can be used by engineers and geologists with minor training.

Visual NNet: An Educational ANN's Simulation Environment Reusing Matlab Neural Networks Toolbox

ERIC Educational Resources Information Center

Garcia-Roselló, Emilio; González-Dacosta, Jacinto; Lado, Maria J.; Méndez, Arturo J.; Garcia Pérez-Schofield, Baltasar; Ferrer, Fátima

2011-01-01

Artificial Neural Networks (ANN's) are nowadays a common subject in different curricula of graduate and postgraduate studies. Due to the complex algorithms involved and the dynamic nature of ANN's, simulation software has been commonly used to teach this subject. This software has usually been developed specifically for learning purposes, because…

The Use of the Software MATLAB To Improve Chemical Engineering Education.

ERIC Educational Resources Information Center

Damatto, T.; Maegava, L. M.; Filho, R. Maciel

In all the Brazilian Universities involved with the project "Prodenge-Reenge", the main objective is to improve teaching and learning procedures for the engineering disciplines. The Chemical Engineering College of Campinas State University focused its effort on the use of engineering softwares. The work developed by this project has…

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

Reports on a study that compares the performance of students enrolled in two sections of a Web-based computer networking course: one utilizing a simulation package and the second utilizing a static, graphical software package. Analysis shows statistically significant improvements in performance in the simulation group compared to the…

Health Physics Positions Data Base: Revision 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerr, G.D.; Borges, T.; Stafford, R.S.

1994-02-01

The Health Physics Positions (HPPOS) Data Base of the Nuclear Regulatory Commission (NRC) is a collection of NRC staff positions on a wide range of topics involving radiation protection (health physics). It consists of 328 documents in the form of letters, memoranda, and excerpts from technical reports. The HPPOS Data Base was developed by the NRC Headquarters and Regional Offices to help ensure uniformity in inspections, enforcement, and licensing actions. Staff members of the Oak Ridge National Laboratory (ORNL) have assisted the NRC staff in summarizing the documents during the preparation of this NUREG report. These summaries are also beingmore » made available as a {open_quotes}stand alone{close_quotes} software package for IBM and IBM-compatible personal computers. The software package for this report is called HPPOS Version 2.0. A variety of indexing schemes were used to increase the usefulness of the NUREG report and its associated software. The software package and the summaries in the report are written in the context of the {open_quotes}new{close_quotes} 10 CFR Part 20 ({section}{section}20.1001--20.2401). The purpose of this NUREG report is to allow interested individuals to familiarize themselves with the contents of the HPPOS Data Base and with the basis of many NRC decisions and regulations. The HPPOS summaries and original documents are intended to serve as a source of information for radiation protection programs at nuclear research and power reactors, nuclear medicine, and other industries that either process or use nuclear materials.« less

Piezoelectric Actuator Modeling Using MSC/NASTRAN and MATLAB

NASA Technical Reports Server (NTRS)

Reaves, Mercedes C.; Horta, Lucas G.

2003-01-01

This paper presents a procedure for modeling structures containing piezoelectric actuators using MSCMASTRAN and MATLAB. The paper describes the utility and functionality of one set of validated modeling tools. The tools described herein use MSCMASTRAN to model the structure with piezoelectric actuators and a thermally induced strain to model straining of the actuators due to an applied voltage field. MATLAB scripts are used to assemble the dynamic equations and to generate frequency response functions. The application of these tools is discussed using a cantilever aluminum beam with a surface mounted piezoelectric actuator as a sample problem. Software in the form of MSCINASTRAN DMAP input commands, MATLAB scripts, and a step-by-step procedure to solve the example problem are provided. Analysis results are generated in terms of frequency response functions from deflection and strain data as a function of input voltage to the actuator.

Introduction to multifractal detrended fluctuation analysis in matlab.

PubMed

Ihlen, Espen A F

2012-01-01

Fractal structures are found in biomedical time series from a wide range of physiological phenomena. The multifractal spectrum identifies the deviations in fractal structure within time periods with large and small fluctuations. The present tutorial is an introduction to multifractal detrended fluctuation analysis (MFDFA) that estimates the multifractal spectrum of biomedical time series. The tutorial presents MFDFA step-by-step in an interactive Matlab session. All Matlab tools needed are available in Introduction to MFDFA folder at the website www.ntnu.edu/inm/geri/software. MFDFA are introduced in Matlab code boxes where the reader can employ pieces of, or the entire MFDFA to example time series. After introducing MFDFA, the tutorial discusses the best practice of MFDFA in biomedical signal processing. The main aim of the tutorial is to give the reader a simple self-sustained guide to the implementation of MFDFA and interpretation of the resulting multifractal spectra.

Introduction to Multifractal Detrended Fluctuation Analysis in Matlab

PubMed Central

Ihlen, Espen A. F.

2012-01-01

Fractal structures are found in biomedical time series from a wide range of physiological phenomena. The multifractal spectrum identifies the deviations in fractal structure within time periods with large and small fluctuations. The present tutorial is an introduction to multifractal detrended fluctuation analysis (MFDFA) that estimates the multifractal spectrum of biomedical time series. The tutorial presents MFDFA step-by-step in an interactive Matlab session. All Matlab tools needed are available in Introduction to MFDFA folder at the website www.ntnu.edu/inm/geri/software. MFDFA are introduced in Matlab code boxes where the reader can employ pieces of, or the entire MFDFA to example time series. After introducing MFDFA, the tutorial discusses the best practice of MFDFA in biomedical signal processing. The main aim of the tutorial is to give the reader a simple self-sustained guide to the implementation of MFDFA and interpretation of the resulting multifractal spectra. PMID:22675302

Matlab Based LOCO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Portmann, Greg; /LBL, Berkeley; Safranek, James

The LOCO algorithm has been used by many accelerators around the world. Although the uses for LOCO vary, the most common use has been to find calibration errors and correct the optics functions. The light source community in particular has made extensive use of the LOCO algorithms to tightly control the beta function and coupling. Maintaining high quality beam parameters requires constant attention so a relatively large effort was put into software development for the LOCO application. The LOCO code was originally written in FORTRAN. This code worked fine but it was somewhat awkward to use. For instance, the FORTRANmore » code itself did not calculate the model response matrix. It required a separate modeling code such as MAD to calculate the model matrix then one manually loads the data into the LOCO code. As the number of people interested in LOCO grew, it required making it easier to use. The decision to port LOCO to Matlab was relatively easy. It's best to use a matrix programming language with good graphics capability; Matlab was also being used for high level machine control; and the accelerator modeling code AT, [5], was already developed for Matlab. Since LOCO requires collecting and processing a relative large amount of data, it is very helpful to have the LOCO code compatible with the high level machine control, [3]. A number of new features were added while porting the code from FORTRAN and new methods continue to evolve, [7][9]. Although Matlab LOCO was written with AT as the underlying tracking code, a mechanism to connect to other modeling codes has been provided.« less

Solving PDEs with Intrepid

DOE PAGES

Bochev, P.; Edwards, H. C.; Kirby, R. C.; ...

2012-01-01

Intrepid is a Trilinos package for advanced discretizations of Partial Differential Equations (PDEs). The package provides a comprehensive set of tools for local, cell-based construction of a wide range of numerical methods for PDEs. This paper describes the mathematical ideas and software design principles incorporated in the package. We also provide representative examples showcasing the use of Intrepid both in the context of numerical PDEs and the more general context of data analysis.

Gas flow calculation method of a ramjet engine

NASA Astrophysics Data System (ADS)

Kostyushin, Kirill; Kagenov, Anuar; Eremin, Ivan; Zhiltsov, Konstantin; Shuvarikov, Vladimir

2017-11-01

At the present study calculation methodology of gas dynamics equations in ramjet engine is presented. The algorithm is based on Godunov`s scheme. For realization of calculation algorithm, the system of data storage is offered, the system does not depend on mesh topology, and it allows using the computational meshes with arbitrary number of cell faces. The algorithm of building a block-structured grid is given. Calculation algorithm in the software package "FlashFlow" is implemented. Software package is verified on the calculations of simple configurations of air intakes and scramjet models.

3CCD image segmentation and edge detection based on MATLAB

NASA Astrophysics Data System (ADS)

He, Yong; Pan, Jiazhi; Zhang, Yun

2006-09-01

This research aimed to identify weeds from crops in early stage in the field operation by using image-processing technology. As 3CCD images offer greater binary value difference between weed and crop section than ordinary digital images taken by common cameras. It has 3 channels (green, red, ifred) which takes a snap-photo of the same area, and the three images can be composed into one image, which facilitates the segmentation of different areas. By the application of image-processing toolkit on MATLAB, the different areas in the image can be segmented clearly. As edge detection technique is the first and very important step in image processing, The different result of different processing method was compared. Especially, by using the wavelet packet transform toolkit on MATLAB, An image was preprocessed and then the edge was extracted, and getting more clearly cut image of edge. The segmentation methods include operations as erosion, dilation and other algorithms to preprocess the images. It is of great importance to segment different areas in digital images in field real time, so as to be applied in precision farming, to saving energy and herbicide and many other materials. At present time Large scale software as MATLAB on PC was used, but the computation can be reduced and integrated into a small embed system, which means that the application of this technique in agricultural engineering is feasible and of great economical value.

Medical knowledge packages and their integration into health-care information systems and the World Wide Web.

PubMed

Adlassnig, Klaus-Peter; Rappelsberger, Andrea

2008-01-01

Software-based medical knowledge packages (MKPs) are packages of highly structured medical knowledge that can be integrated into various health-care information systems or the World Wide Web. They have been established to provide different forms of clinical decision support such as textual interpretation of combinations of laboratory rest results, generating diagnostic hypotheses as well as confirmed and excluded diagnoses to support differential diagnosis in internal medicine, or for early identification and automatic monitoring of hospital-acquired infections. Technically, an MKP may consist of a number of inter-connected Arden Medical Logic Modules. Several MKPs have been integrated thus far into hospital, laboratory, and departmental information systems. This has resulted in useful and widely accepted software-based clinical decision support for the benefit of the patient, the physician, and the organization funding the health care system.

The software-defined fast post-processing for GEM soft x-ray diagnostics in the Tungsten Environment in Steady-state Tokamak thermal fusion reactor

NASA Astrophysics Data System (ADS)

Krawczyk, Rafał Dominik; Czarski, Tomasz; Linczuk, Paweł; Wojeński, Andrzej; Kolasiński, Piotr; GÄ ska, Michał; Chernyshova, Maryna; Mazon, Didier; Jardin, Axel; Malard, Philippe; Poźniak, Krzysztof; Kasprowicz, Grzegorz; Zabołotny, Wojciech; Kowalska-Strzeciwilk, Ewa; Malinowski, Karol

2018-06-01

This article presents a novel software-defined server-based solutions that were introduced in the fast, real-time computation systems for soft X-ray diagnostics for the WEST (Tungsten Environment in Steady-state Tokamak) reactor in Cadarache, France. The objective of the research was to provide a fast processing of data at high throughput and with low latencies for investigating the interplay between the particle transport and magnetohydrodynamic activity. The long-term objective is to implement in the future a fast feedback signal in the reactor control mechanisms to sustain the fusion reaction. The implemented electronic measurement device is anticipated to be deployed in the WEST. A standalone software-defined computation engine was designed to handle data collected at high rates in the server back-end of the system. Signals are obtained from the front-end field-programmable gate array mezzanine cards that acquire and perform a selection from the gas electron multiplier detector. A fast, authorial library for plasma diagnostics was written in C++. It originated from reference offline MATLAB implementations. They were redesigned for runtime analysis during the experiment in the novel online modes of operation. The implementation allowed the benchmarking, evaluation, and optimization of plasma processing algorithms with the possibility to check the consistency with reference computations written in MATLAB. The back-end software and hardware architecture are presented with data evaluation mechanisms. The online modes of operation for the WEST are discussed. The results concerning the performance of the processing and the introduced functionality are presented.

Dexterity: A MATLAB-based analysis software suite for processing and visualizing data from tasks that measure arm or forelimb function.

PubMed

Butensky, Samuel D; Sloan, Andrew P; Meyers, Eric; Carmel, Jason B

2017-07-15

Hand function is critical for independence, and neurological injury often impairs dexterity. To measure hand function in people or forelimb function in animals, sensors are employed to quantify manipulation. These sensors make assessment easier and more quantitative and allow automation of these tasks. While automated tasks improve objectivity and throughput, they also produce large amounts of data that can be burdensome to analyze. We created software called Dexterity that simplifies data analysis of automated reaching tasks. Dexterity is MATLAB software that enables quick analysis of data from forelimb tasks. Through a graphical user interface, files are loaded and data are identified and analyzed. These data can be annotated or graphed directly. Analysis is saved, and the graph and corresponding data can be exported. For additional analysis, Dexterity provides access to custom scripts created by other users. To determine the utility of Dexterity, we performed a study to evaluate the effects of task difficulty on the degree of impairment after injury. Dexterity analyzed two months of data and allowed new users to annotate the experiment, visualize results, and save and export data easily. Previous analysis of tasks was performed with custom data analysis, requiring expertise with analysis software. Dexterity made the tools required to analyze, visualize and annotate data easy to use by investigators without data science experience. Dexterity increases accessibility to automated tasks that measure dexterity by making analysis of large data intuitive, robust, and efficient. Copyright © 2017 Elsevier B.V. All rights reserved.

tscvh R Package: Computational of the two samples test on microarray-sequencing data

NASA Astrophysics Data System (ADS)

Fajriyah, Rohmatul; Rosadi, Dedi

2017-12-01

We present a new R package, a tscvh (two samples cross-variance homogeneity), as we called it. This package is a software of the cross-variance statistical test which has been proposed and introduced by Fajriyah ([3] and [4]), based on the cross-variance concept. The test can be used as an alternative test for the significance difference between two means when sample size is small, the situation which is usually appeared in the bioinformatics research. Based on its statistical distribution, the p-value can be also provided. The package is built under a homogeneity of variance between samples.

Mold heating and cooling microprocessor conversion. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffman, D.P.

Conversion of the microprocessors and software for the Mold Heating and Cooling (MHAC) pump package control systems was initiated to allow required system enhancements and provide data communications capabilities with the Plastics Information and Control System (PICS). The existing microprocessor-based control systems for the pump packages use an Intel 8088-based microprocessor board with a maximum of 64 Kbytes of program memory. The requirements for the system conversion were developed, and hardware has been selected to allow maximum reuse of existing hardware and software while providing the required additional capabilities and capacity. The new hardware will incorporate an Intel 80286-based microprocessormore » board with an 80287 math coprocessor, the system includes additional memory, I/O, and RS232 communication ports.« less

WinTRAX: A raytracing software package for the design of multipole focusing systems

NASA Astrophysics Data System (ADS)

Grime, G. W.

2013-07-01

The software package TRAX was a simulation tool for modelling the path of charged particles through linear cylindrical multipole fields described by analytical expressions and was a development of the earlier OXRAY program (Grime and Watt, 1983; Grime et al., 1982) [1,2]. In a 2005 comparison of raytracing software packages (Incerti et al., 2005) [3], TRAX/OXRAY was compared with Geant4 and Zgoubi and was found to give close agreement with the more modern codes. TRAX was a text-based program which was only available for operation in a now rare VMS workstation environment, so a new program, WinTRAX, has been developed for the Windows operating system. This implements the same basic computing strategy as TRAX, and key sections of the code are direct translations from FORTRAN to C++, but the Windows environment is exploited to make an intuitive graphical user interface which simplifies and enhances many operations including system definition and storage, optimisation, beam simulation (including with misaligned elements) and aberration coefficient determination. This paper describes the program and presents comparisons with other software and real installations.

ICEG2D: An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils with Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson, David S.; Soni, Bharat K.

2000-01-01

An integrated software package, ICEG2D, was developed to automate computational fluid dynamics (CFD) simulations for single-element airfoils with ice accretion. ICEG2D is designed to automatically perform three primary functions: (1) generating a grid-ready, surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generating a high-quality grid using the generated surface point distribution, and (3) generating the input and restart files needed to run the general purpose CFD solver NPARC. ICEG2D can be executed in batch mode using a script file or in an interactive mode by entering directives from a command line. This report summarizes activities completed in the first year of a three-year research and development program to address issues related to CFD simulations for aircraft components with ice accretion. Specifically, this document describes the technology employed in the software, the installation procedure, and a description of the operation of the software package. Validation of the geometry and grid generation modules of ICEG2D is also discussed.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

Student Development of Educational Software: Spin-Offs from Classroom Use of DIAS.

ERIC Educational Resources Information Center

Harrington, John A., Jr.; And Others

1988-01-01

Describes several college courses which encourage students to develop computer software programs in the areas of remote sensing and geographic information systems. A microcomputer-based tutorial package, the Digital Image Analysis System (DAIS), teaches the principles of digital processing. (LS)

Quantitative evaluation of software packages for single-molecule localization microscopy.

PubMed

Sage, Daniel; Kirshner, Hagai; Pengo, Thomas; Stuurman, Nico; Min, Junhong; Manley, Suliana; Unser, Michael

2015-08-01

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

Development of program package for investigation and modeling of carbon nanostructures in diamond like carbon films with the help of Raman scattering and infrared absorption spectra line resolving

NASA Astrophysics Data System (ADS)

Hayrapetyan, David B.; Hovhannisyan, Levon; Mantashyan, Paytsar A.

2013-04-01

The analysis of complex spectra is an actual problem for modern science. The work is devoted to the creation of a software package, which analyzes spectrum in the different formats, possesses by dynamic knowledge database and self-study mechanism, performs automated analysis of the spectra compound based on knowledge database by application of certain algorithms. In the software package as searching systems, hyper-spherical random search algorithms, gradient algorithms and genetic searching algorithms were used. The analysis of Raman and IR spectrum of diamond-like carbon (DLC) samples were performed by elaborated program. After processing the data, the program immediately displays all the calculated parameters of DLC.

Mold Heating and Cooling Pump Package Operator Interface Controls Upgrade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Josh A. Salmond

2009-08-07

The modernization of the Mold Heating and Cooling Pump Package Operator Interface (MHC PP OI) consisted of upgrading the antiquated single board computer with a proprietary operating system to off-the-shelf hardware and off-the-shelf software with customizable software options. The pump package is the machine interface between a central heating and cooling system that pumps heat transfer fluid through an injection or compression mold base on a local plastic molding machine. The operator interface provides the intelligent means of controlling this pumping process. Strict temperature control of a mold allows the production of high quality parts with tight tolerances and lowmore » residual stresses. The products fabricated are used on multiple programs.« less

Browndye: A Software Package for Brownian Dynamics

PubMed Central

McCammon, J. Andrew

2010-01-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. PMID:21132109

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

PubMed Central

Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

2008-01-01

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

Development of a software package for solid-angle calculations using the Monte Carlo method

NASA Astrophysics Data System (ADS)

Zhang, Jie; Chen, Xiulian; Zhang, Changsheng; Li, Gang; Xu, Jiayun; Sun, Guangai

2014-02-01

Solid-angle calculations play an important role in the absolute calibration of radioactivity measurement systems and in the determination of the activity of radioactive sources, which are often complicated. In the present paper, a software package is developed to provide a convenient tool for solid-angle calculations in nuclear physics. The proposed software calculates solid angles using the Monte Carlo method, in which a new type of variance reduction technique was integrated. The package, developed under the environment of Microsoft Foundation Classes (MFC) in Microsoft Visual C++, has a graphical user interface, in which, the visualization function is integrated in conjunction with OpenGL. One advantage of the proposed software package is that it can calculate the solid angle subtended by a detector with different geometric shapes (e.g., cylinder, square prism, regular triangular prism or regular hexagonal prism) to a point, circular or cylindrical source without any difficulty. The results obtained from the proposed software package were compared with those obtained from previous studies and calculated using Geant4. It shows that the proposed software package can produce accurate solid-angle values with a greater computation speed than Geant4.

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. K.

FTOOLS, a highly modular collection of over 110 utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Science Archive Research Center) at NASA's Goddard Space Flight Center. Each utility performs a single simple task such as presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual utilities can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. The collection of utilities provides both generic processing and analysis utilities and utilities specific to high energy astrophysics data sets used for the ASCA, ROSAT, GRO, and XTE missions. A core set of FTOOLS providing support for generic FITS data processing, FITS image analysis and timing analysis can easily be split out of the full software package for users not needing the high energy astrophysics mission utilities. The FTOOLS software package is designed to be both compatible with IRAF and completely stand alone in a UNIX or VMS environment. The user interface is controlled by standard IRAF parameter files. The package is self documenting through the IRAF help facility and a stand alone help task. Software is written in ANSI C and \\fortran to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

Real-time visual simulation of APT system based on RTW and Vega

NASA Astrophysics Data System (ADS)

Xiong, Shuai; Fu, Chengyu; Tang, Tao

2012-10-01

The Matlab/Simulink simulation model of APT (acquisition, pointing and tracking) system is analyzed and established. Then the model's C code which can be used for real-time simulation is generated by RTW (Real-Time Workshop). Practical experiments show, the simulation result of running the C code is the same as running the Simulink model directly in the Matlab environment. MultiGen-Vega is a real-time 3D scene simulation software system. With it and OpenGL, the APT scene simulation platform is developed and used to render and display the virtual scenes of the APT system. To add some necessary graphics effects to the virtual scenes real-time, GLSL (OpenGL Shading Language) shaders are used based on programmable GPU. By calling the C code, the scene simulation platform can adjust the system parameters on-line and get APT system's real-time simulation data to drive the scenes. Practical application shows that this visual simulation platform has high efficiency, low charge and good simulation effect.

An image-processing software package: UU and Fig for optical metrology applications

NASA Astrophysics Data System (ADS)

Chen, Lujie

2013-06-01

Modern optical metrology applications are largely supported by computational methods, such as phase shifting [1], Fourier Transform [2], digital image correlation [3], camera calibration [4], etc, in which image processing is a critical and indispensable component. While it is not too difficult to obtain a wide variety of image-processing programs from the internet; few are catered for the relatively special area of optical metrology. This paper introduces an image-processing software package: UU (data processing) and Fig (data rendering) that incorporates many useful functions to process optical metrological data. The cross-platform programs UU and Fig are developed based on wxWidgets. At the time of writing, it has been tested on Windows, Linux and Mac OS. The userinterface is designed to offer precise control of the underline processing procedures in a scientific manner. The data input/output mechanism is designed to accommodate diverse file formats and to facilitate the interaction with other independent programs. In terms of robustness, although the software was initially developed for personal use, it is comparably stable and accurate to most of the commercial software of similar nature. In addition to functions for optical metrology, the software package has a rich collection of useful tools in the following areas: real-time image streaming from USB and GigE cameras, computational geometry, computer vision, fitting of data, 3D image processing, vector image processing, precision device control (rotary stage, PZT stage, etc), point cloud to surface reconstruction, volume rendering, batch processing, etc. The software package is currently used in a number of universities for teaching and research.

The NOD3 software package: A graphical user interface-supported reduction package for single-dish radio continuum and polarisation observations

NASA Astrophysics Data System (ADS)

Müller, Peter; Krause, Marita; Beck, Rainer; Schmidt, Philip

2017-10-01

Context. The venerable NOD2 data reduction software package for single-dish radio continuum observations, which was developed for use at the 100-m Effelsberg radio telescope, has been successfully applied over many decades. Modern computing facilities, however, call for a new design. Aims: We aim to develop an interactive software tool with a graphical user interface for the reduction of single-dish radio continuum maps. We make a special effort to reduce the distortions along the scanning direction (scanning effects) by combining maps scanned in orthogonal directions or dual- or multiple-horn observations that need to be processed in a restoration procedure. The package should also process polarisation data and offer the possibility to include special tasks written by the individual user. Methods: Based on the ideas of the NOD2 package we developed NOD3, which includes all necessary tasks from the raw maps to the final maps in total intensity and linear polarisation. Furthermore, plot routines and several methods for map analysis are available. The NOD3 package is written in Python, which allows the extension of the package via additional tasks. The required data format for the input maps is FITS. Results: The NOD3 package is a sophisticated tool to process and analyse maps from single-dish observations that are affected by scanning effects from clouds, receiver instabilities, or radio-frequency interference. The "basket-weaving" tool combines orthogonally scanned maps into a final map that is almost free of scanning effects. The new restoration tool for dual-beam observations reduces the noise by a factor of about two compared to the NOD2 version. Combining single-dish with interferometer data in the map plane ensures the full recovery of the total flux density. Conclusions: This software package is available under the open source license GPL for free use at other single-dish radio telescopes of the astronomical community. The NOD3 package is designed to be extendable to multi-channel data represented by data cubes in Stokes I, Q, and U.

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action

PubMed Central

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels—from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures. PMID:27920748

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action.

PubMed

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels-from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures.

International Inventory of Software Packages in the Information Field.

ERIC Educational Resources Information Center

Keren, Carl, Ed.; Sered, Irina, Ed.

Designed to provide guidance in selecting appropriate software for library automation, information storage and retrieval, or management of bibliographic databases, this inventory describes 188 computer software packages. The information was obtained through a questionnaire survey of 600 software suppliers and developers who were asked to describe…

GCE Data Toolbox for MATLAB - a software framework for automating environmental data processing, quality control and documentation

NASA Astrophysics Data System (ADS)

Sheldon, W.; Chamblee, J.; Cary, R. H.

2013-12-01

Environmental scientists are under increasing pressure from funding agencies and journal publishers to release quality-controlled data in a timely manner, as well as to produce comprehensive metadata for submitting data to long-term archives (e.g. DataONE, Dryad and BCO-DMO). At the same time, the volume of digital data that researchers collect and manage is increasing rapidly due to advances in high frequency electronic data collection from flux towers, instrumented moorings and sensor networks. However, few pre-built software tools are available to meet these data management needs, and those tools that do exist typically focus on part of the data management lifecycle or one class of data. The GCE Data Toolbox has proven to be both a generalized and effective software solution for environmental data management in the Long Term Ecological Research Network (LTER). This open source MATLAB software library, developed by the Georgia Coastal Ecosystems LTER program, integrates metadata capture, creation and management with data processing, quality control and analysis to support the entire data lifecycle. Raw data can be imported directly from common data logger formats (e.g. SeaBird, Campbell Scientific, YSI, Hobo), as well as delimited text files, MATLAB files and relational database queries. Basic metadata are derived from the data source itself (e.g. parsed from file headers) and by value inspection, and then augmented using editable metadata templates containing boilerplate documentation, attribute descriptors, code definitions and quality control rules. Data and metadata content, quality control rules and qualifier flags are then managed together in a robust data structure that supports database functionality and ensures data validity throughout processing. A growing suite of metadata-aware editing, quality control, analysis and synthesis tools are provided with the software to support managing data using graphical forms and command-line functions, as well as developing automated workflows for unattended processing. Finalized data and structured metadata can be exported in a wide variety of text and MATLAB formats or uploaded to a relational database for long-term archiving and distribution. The GCE Data Toolbox can be used as a complete, light-weight solution for environmental data and metadata management, but it can also be used in conjunction with other cyber infrastructure to provide a more comprehensive solution. For example, newly acquired data can be retrieved from a Data Turbine or Campbell LoggerNet Database server for quality control and processing, then transformed to CUAHSI Observations Data Model format and uploaded to a HydroServer for distribution through the CUAHSI Hydrologic Information System. The GCE Data Toolbox can also be leveraged in analytical workflows developed using Kepler or other systems that support MATLAB integration or tool chaining. This software can therefore be leveraged in many ways to help researchers manage, analyze and distribute the data they collect.

Glioblastoma Segmentation: Comparison of Three Different Software Packages.

PubMed

Fyllingen, Even Hovig; Stensjøen, Anne Line; Berntsen, Erik Magnus; Solheim, Ole; Reinertsen, Ingerid

2016-01-01

To facilitate a more widespread use of volumetric tumor segmentation in clinical studies, there is an urgent need for reliable, user-friendly segmentation software. The aim of this study was therefore to compare three different software packages for semi-automatic brain tumor segmentation of glioblastoma; namely BrainVoyagerTM QX, ITK-Snap and 3D Slicer, and to make data available for future reference. Pre-operative, contrast enhanced T1-weighted 1.5 or 3 Tesla Magnetic Resonance Imaging (MRI) scans were obtained in 20 consecutive patients who underwent surgery for glioblastoma. MRI scans were segmented twice in each software package by two investigators. Intra-rater, inter-rater and between-software agreement was compared by using differences of means with 95% limits of agreement (LoA), Dice's similarity coefficients (DSC) and Hausdorff distance (HD). Time expenditure of segmentations was measured using a stopwatch. Eighteen tumors were included in the analyses. Inter-rater agreement was highest for BrainVoyager with difference of means of 0.19 mL and 95% LoA from -2.42 mL to 2.81 mL. Between-software agreement and 95% LoA were very similar for the different software packages. Intra-rater, inter-rater and between-software DSC were ≥ 0.93 in all analyses. Time expenditure was approximately 41 min per segmentation in BrainVoyager, and 18 min per segmentation in both 3D Slicer and ITK-Snap. Our main findings were that there is a high agreement within and between the software packages in terms of small intra-rater, inter-rater and between-software differences of means and high Dice's similarity coefficients. Time expenditure was highest for BrainVoyager, but all software packages were relatively time-consuming, which may limit usability in an everyday clinical setting.

Fluidica CFD software for fluids instruction

NASA Astrophysics Data System (ADS)

Colonius, Tim

2008-11-01

Fluidica is an open-source freely available Matlab graphical user interface (GUI) to to an immersed-boundary Navier- Stokes solver. The algorithm is programmed in Fortran and compiled into Matlab as mex-function. The user can create external flows about arbitrarily complex bodies and collections of free vortices. The code runs fast enough for complex 2D flows to be computed and visualized in real-time on the screen. This facilitates its use in homework and in the classroom for demonstrations of various potential-flow and viscous flow phenomena. The GUI has been written with the goal of allowing the student to learn how to use the software as she goes along. The user can select which quantities are viewed on the screen, including contours of various scalars, velocity vectors, streamlines, particle trajectories, streaklines, and finite-time Lyapunov exponents. In this talk, we demonstrate the software in the context of worked classroom examples demonstrating lift and drag, starting vortices, separation, and vortex dynamics.

The Application of COMSOL Multiphysics Package on the Modelling of Complex 3-D Lithospheric Electrical Resistivity Structures - A Case Study from the Proterozoic Orogenic belt within the North China Craton

NASA Astrophysics Data System (ADS)

Guo, L.; Yin, Y.; Deng, M.; Guo, L.; Yan, J.

2017-12-01

At present, most magnetotelluric (MT) forward modelling and inversion codes are based on finite difference method. But its structured mesh gridding cannot be well adapted for the conditions with arbitrary topography or complex tectonic structures. By contrast, the finite element method is more accurate in calculating complex and irregular 3-D region and has lower requirement of function smoothness. However, the complexity of mesh gridding and limitation of computer capacity has been affecting its application. COMSOL Multiphysics is a cross-platform finite element analysis, solver and multiphysics full-coupling simulation software. It achieves highly accurate numerical simulations with high computational performance and outstanding multi-field bi-directional coupling analysis capability. In addition, its AC/DC and RF module can be used to easily calculate the electromagnetic responses of complex geological structures. Using the adaptive unstructured grid, the calculation is much faster. In order to improve the discretization technique of computing area, we use the combination of Matlab and COMSOL Multiphysics to establish a general procedure for calculating the MT responses for arbitrary resistivity models. The calculated responses include the surface electric and magnetic field components, impedance components, magnetic transfer functions and phase tensors. Then, the reliability of this procedure is certificated by 1-D, 2-D and 3-D and anisotropic forward modeling tests. Finally, we establish the 3-D lithospheric resistivity model for the Proterozoic Wutai-Hengshan Mts. within the North China Craton by fitting the real MT data collected there. The reliability of the model is also verified by induced vectors and phase tensors. Our model shows more details and better resolution, compared with the previously published 3-D model based on the finite difference method. In conclusion, COMSOL Multiphysics package is suitable for modeling the 3-D lithospheric resistivity structures under complex tectonic deformation backgrounds, which could be a good complement to the existing finite-difference inversion algorithms.

Pedagogical Approach to the Modeling and Simulation of Oscillating Chemical Systems with Modern Software: The Brusselator Model

ERIC Educational Resources Information Center

Lozano-Parada, Jaime H.; Burnham, Helen; Martinez, Fiderman Machuca

2018-01-01

A classical nonlinear system, the "Brusselator", was used to illustrate the modeling and simulation of oscillating chemical systems using stability analysis techniques with modern software tools such as Comsol Multiphysics, Matlab, and Excel. A systematic approach is proposed in order to establish a regime of parametric conditions that…

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose volume outcome relationships

NASA Astrophysics Data System (ADS)

El Naqa, I.; Suneja, G.; Lindsay, P. E.; Hope, A. J.; Alaly, J. R.; Vicic, M.; Bradley, J. D.; Apte, A.; Deasy, J. O.

2006-11-01

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

GIS based model interfacing : incorporating existing software and new techniques into a streamlined interface package

DOT National Transportation Integrated Search

2000-01-01

The ability to visualize data has grown immensely as the speed and functionality of Geographic Information Systems (GIS) have increased. Now, with modeling software and GIS, planners are able to view a prediction of the future traffic demands in thei...

From Workstation to Teacher Support System: A Tool to Increase Productivity.

ERIC Educational Resources Information Center

Chen, J. Wey

1989-01-01

Describes a teacher support system which is a computer-based workstation that provides support for teachers and administrators by integrating teacher utility programs, instructional management software, administrative packages, and office automation tools. Hardware is described and software components are explained, including database managers,…

Sci—Thur AM: YIS - 11: Estimation of Bladder-Wall Cumulative Dose in Multi-Fraction Image-Based Gynaecological Brachytherapy Using Deformable Point Set Registration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakariaee, R; Brown, C J; Hamarneh, G

2014-08-15

Dosimetric parameters based on dose-volume histograms (DVH) of contoured structures are routinely used to evaluate dose delivered to target structures and organs at risk. However, the DVH provides no information on the spatial distribution of the dose in situations of repeated fractions with changes in organ shape or size. The aim of this research was to develop methods to more accurately determine geometrically localized, cumulative dose to the bladder wall in intracavitary brachytherapy for cervical cancer. The CT scans and treatment plans of 20 cervical cancer patients were used. Each patient was treated with five high-dose-rate (HDR) brachytherapy fractions ofmore » 600cGy prescribed dose. The bladder inner and outer surfaces were delineated using MIM Maestro software (MIM Software Inc.) and were imported into MATLAB (MathWorks) as 3-dimensional point clouds constituting the “bladder wall”. A point-set registration toolbox for MATLAB, Coherent Point Drift (CPD), was used to non-rigidly transform the bladder-wall points from four of the fractions to the coordinate system of the remaining (reference) fraction, which was chosen to be the emptiest bladder for each patient. The doses were accumulated on the reference fraction and new cumulative dosimetric parameters were calculated. The LENT-SOMA toxicity scores of these patients were studied against the cumulative dose parameters. Based on this study, there was no significant correlation between the toxicity scores and the determined cumulative dose parameters.« less

OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

PubMed

Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

2017-08-01

Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Features of free software packages in flow cytometry: a comparison between four non-commercial software sources.

PubMed

Sahraneshin Samani, Fazel; Moore, Jodene K; Khosravani, Pardis; Ebrahimi, Marzieh

2014-08-01

Flow cytometers designed to analyze large particles are enabling new applications in biology. Data analysis is a critical component of the process FCM. In this article we compare features of four free software packages including WinMDI, Cyflogic, Flowing software, and Cytobank.

Development of a Nevada Statewide Database for Safety Analyst Software

DOT National Transportation Integrated Search

2017-02-02

Safety Analyst is a software package developed by the Federal Highway Administration (FHWA) and twenty-seven participating state and local agencies including the Nevada Department of Transportation (NDOT). The software package implemented many of the...

Propulsion Diagnostic Method Evaluation Strategy (ProDiMES) User's Guide

NASA Technical Reports Server (NTRS)

Simon, Donald L.

2010-01-01

This report is a User's Guide for the Propulsion Diagnostic Method Evaluation Strategy (ProDiMES). ProDiMES is a standard benchmarking problem and a set of evaluation metrics to enable the comparison of candidate aircraft engine gas path diagnostic methods. This Matlab (The Mathworks, Inc.) based software tool enables users to independently develop and evaluate diagnostic methods. Additionally, a set of blind test case data is also distributed as part of the software. This will enable the side-by-side comparison of diagnostic approaches developed by multiple users. The Users Guide describes the various components of ProDiMES, and provides instructions for the installation and operation of the tool.

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction

PubMed Central

2014-01-01

Abstract Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work. PMID:24891820

Rotational Analysis of FTIR Spectra from Cigarette Smoke: An Application of Chem Spec II Software in the Undergraduate Laboratory

ERIC Educational Resources Information Center

Ford, Alan R.; Burns, William A.; Reeve, Scott W.

2004-01-01

A version of the classic gas phase infrared experiment was developed for students at Arkansas State University based on the shortcomings of the rotationally resolved infrared experiment. Chem Spec II is a noncommercial Windows-based software package developed to aid in the potentially complicated problem of assigning quantum numbers to observed…

Probabilistic commodity-flow-based focusing of monitoring activities to facilitate early detection of Phytophthora ramorum outbreaks

Treesearch

Steven C. McKelvey; William D. Smith; Frank Koch

2012-01-01

This project summary describes a probabilistic model developed with funding support from the Forest Health Monitoring Program of the Forest Service, U.S. Department of Agriculture (BaseEM Project SO-R-08-01). The model has been implemented in SODBuster, a standalone software package developed using the Java software development kit from Sun Microsystems.

Computer Aided Drafting Packages for Secondary Education. Edition 2. PC DOS Compatible Programs. A MicroSIFT Quarterly Report.

ERIC Educational Resources Information Center

Pollard, Jim

This report reviews eight IBM-compatible software packages that are available to secondary schools to teach computer-aided drafting (CAD). Software packages to be considered were selected following reviews of CAD periodicals, computers in education periodicals, advertisements, and recommendations of teachers. The packages were then rated by…

WGCNA: an R package for weighted correlation network analysis.

PubMed

Langfelder, Peter; Horvath, Steve

2008-12-29

Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA.

WGCNA: an R package for weighted correlation network analysis

PubMed Central

Langfelder, Peter; Horvath, Steve

2008-01-01

Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at . PMID:19114008

Model Based Optimal Sensor Network Design for Condition Monitoring in an IGCC Plant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Rajeeva; Kumar, Aditya; Dai, Dan

2012-12-31

This report summarizes the achievements and final results of this program. The objective of this program is to develop a general model-based sensor network design methodology and tools to address key issues in the design of an optimal sensor network configuration: the type, location and number of sensors used in a network, for online condition monitoring. In particular, the focus in this work is to develop software tools for optimal sensor placement (OSP) and use these tools to design optimal sensor network configuration for online condition monitoring of gasifier refractory wear and radiant syngas cooler (RSC) fouling. The methodology developedmore » will be applicable to sensing system design for online condition monitoring for broad range of applications. The overall approach consists of (i) defining condition monitoring requirement in terms of OSP and mapping these requirements in mathematical terms for OSP algorithm, (ii) analyzing trade-off of alternate OSP algorithms, down selecting the most relevant ones and developing them for IGCC applications (iii) enhancing the gasifier and RSC models as required by OSP algorithms, (iv) applying the developed OSP algorithm to design the optimal sensor network required for the condition monitoring of an IGCC gasifier refractory and RSC fouling. Two key requirements for OSP for condition monitoring are desired precision for the monitoring variables (e.g. refractory wear) and reliability of the proposed sensor network in the presence of expected sensor failures. The OSP problem is naturally posed within a Kalman filtering approach as an integer programming problem where the key requirements of precision and reliability are imposed as constraints. The optimization is performed over the overall network cost. Based on extensive literature survey two formulations were identified as being relevant to OSP for condition monitoring; one based on LMI formulation and the other being standard INLP formulation. Various algorithms to solve these two formulations were developed and validated. For a given OSP problem the computation efficiency largely depends on the “size” of the problem. Initially a simplified 1-D gasifier model assuming axial and azimuthal symmetry was used to test out various OSP algorithms. Finally these algorithms were used to design the optimal sensor network for condition monitoring of IGCC gasifier refractory wear and RSC fouling. The sensors type and locations obtained as solution to the OSP problem were validated using model based sensing approach. The OSP algorithm has been developed in a modular form and has been packaged as a software tool for OSP design where a designer can explore various OSP design algorithm is a user friendly way. The OSP software tool is implemented in Matlab/Simulink© in-house. The tool also uses few optimization routines that are freely available on World Wide Web. In addition a modular Extended Kalman Filter (EKF) block has also been developed in Matlab/Simulink© which can be utilized for model based sensing of important process variables that are not directly measured through combining the online sensors with model based estimation once the hardware sensor and their locations has been finalized. The OSP algorithm details and the results of applying these algorithms to obtain optimal sensor location for condition monitoring of gasifier refractory wear and RSC fouling profile are summarized in this final report.« less

QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.

PubMed

Jung, Sang-Kyu; Aleman-Meza, Boanerges; Riepe, Celeste; Zhong, Weiwei

2014-01-01

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.

Gastrointestinal Side Effects of the Radioiodine Therapy for the Patients with Differentiated Thyroid Carcinoma Two Days after Prescription.

PubMed

Pashnehsaz, Mehran; Takavar, Abbas; Izadyar, Sina; Zakariaee, Seyed Salman; Mahmoudi, Mahmoud; Paydar, Reza; Geramifar, Parham

2016-09-01

Iodine-131 (I-131) therapy is one of the conventional approaches in the treatment of patients with differentiated thyroid carcinoma (DTC). The radioiodine agents also accumulate in the other organs that cause pain and damage to the patients. Radioiodine therapy is associated with various gastrointestinal (GI) toxicities. In this study, GI side effects of the radioiodine therapy were investigated. GI toxicities of the radioiodine therapy were studied in 137 patients with histologically proven DTC in Jun-Nov 2014. All the patients were treated by radioiodine agents in the research institute of Shariati Hospital, Tehran, Iran. The patients were examined 48 h after prescription (before discharge) and their GI side effects were registered. Correlation of the age, gender, administered dose, administered dose per body weight as the independent factors, and GI side effects were analyzed using the Pearson correlation test with Statistical Package for the Social Sciences (SPSS) version 20. Regression coefficients and linearity of the variable were investigated by MATLAB software. Line fitting was performed using MATLAB curve-fitting toolbox. From the subjects, 38 patients had GI complaints (30.4%). Significant factors influencing GI side effects were dose per body weight and administered doses. There was no significant correlation between age and gender as the independent parameters and GI complaints. The most prevalent GI side effect was nausea that occurs in 26.4% of the patients. From the results, it could be concluded that the GI side effects could be prevented by administering a safe radioiodine dose value less than 5,550 MBq.

Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB(®) graphical user interface.

PubMed

Sridhar, Vishnu B; Tian, Peifang; Dale, Anders M; Devor, Anna; Saisan, Payam A

2014-01-01

We present a database client software-Neurovascular Network Explorer 1.0 (NNE 1.0)-that uses MATLAB(®) based Graphical User Interface (GUI) for interaction with a database of 2-photon single-vessel diameter measurements from our previous publication (Tian et al., 2010). These data are of particular interest for modeling the hemodynamic response. NNE 1.0 is downloaded by the user and then runs either as a MATLAB script or as a standalone program on a Windows platform. The GUI allows browsing the database according to parameters specified by the user, simple manipulation and visualization of the retrieved records (such as averaging and peak-normalization), and export of the results. Further, we provide NNE 1.0 source code. With this source code, the user can database their own experimental results, given the appropriate data structure and naming conventions, and thus share their data in a user-friendly format with other investigators. NNE 1.0 provides an example of seamless and low-cost solution for sharing of experimental data by a regular size neuroscience laboratory and may serve as a general template, facilitating dissemination of biological results and accelerating data-driven modeling approaches.

Vertical bone measurements from cone beam computed tomography images using different software packages.

PubMed

Vasconcelos, Taruska Ventorini; Neves, Frederico Sampaio; Moraes, Lívia Almeida Bueno; Freitas, Deborah Queiroz

2015-01-01

This article aimed at comparing the accuracy of linear measurement tools of different commercial software packages. Eight fully edentulous dry mandibles were selected for this study. Incisor, canine, premolar, first molar and second molar regions were selected. Cone beam computed tomography (CBCT) images were obtained with i-CAT Next Generation. Linear bone measurements were performed by one observer on the cross-sectional images using three different software packages: XoranCat®, OnDemand3D® and KDIS3D®, all able to assess DICOM images. In addition, 25% of the sample was reevaluated for the purpose of reproducibility. The mandibles were sectioned to obtain the gold standard for each region. Intraclass coefficients (ICC) were calculated to examine the agreement between the two periods of evaluation; the one-way analysis of variance performed with the post-hoc Dunnett test was used to compare each of the software-derived measurements with the gold standard. The ICC values were excellent for all software packages. The least difference between the software-derived measurements and the gold standard was obtained with the OnDemand3D and KDIS3D (-0.11 and -0.14 mm, respectively), and the greatest, with the XoranCAT (+0.25 mm). However, there was no statistical significant difference between the measurements obtained with the different software packages and the gold standard (p> 0.05). In conclusion, linear bone measurements were not influenced by the software package used to reconstruct the image from CBCT DICOM data.

A Matlab user interface for the statistically assisted fluid registration algorithm and tensor-based morphometry

NASA Astrophysics Data System (ADS)

Yepes-Calderon, Fernando; Brun, Caroline; Sant, Nishita; Thompson, Paul; Lepore, Natasha

2015-01-01

Tensor-Based Morphometry (TBM) is an increasingly popular method for group analysis of brain MRI data. The main steps in the analysis consist of a nonlinear registration to align each individual scan to a common space, and a subsequent statistical analysis to determine morphometric differences, or difference in fiber structure between groups. Recently, we implemented the Statistically-Assisted Fluid Registration Algorithm or SAFIRA,1 which is designed for tracking morphometric differences among populations. To this end, SAFIRA allows the inclusion of statistical priors extracted from the populations being studied as regularizers in the registration. This flexibility and degree of sophistication limit the tool to expert use, even more so considering that SAFIRA was initially implemented in command line mode. Here, we introduce a new, intuitive, easy to use, Matlab-based graphical user interface for SAFIRA's multivariate TBM. The interface also generates different choices for the TBM statistics, including both the traditional univariate statistics on the Jacobian matrix, and comparison of the full deformation tensors.2 This software will be freely disseminated to the neuroimaging research community.

[Development of a software standardizing optical density with operation settings related to several limitations].

PubMed

Tu, Xiao-Ming; Zhang, Zuo-Heng; Wan, Cheng; Zheng, Yu; Xu, Jin-Mei; Zhang, Yuan-Yuan; Luo, Jian-Ping; Wu, Hai-Wei

2012-12-01

To develop a software that can be used to standardize optical density to normalize the procedures and results of standardization in order to effectively solve several problems generated during standardization of in-direct ELISA results. The software was designed based on the I-STOD method with operation settings to solve the problems that one might encounter during the standardization. Matlab GUI was used as a tool for the development. The software was tested with the results of the detection of sera of persons from schistosomiasis japonica endemic areas. I-STOD V1.0 (WINDOWS XP/WIN 7, 0.5 GB) was successfully developed to standardize optical density. A serial of serum samples from schistosomiasis japonica endemic areas were used to examine the operational effects of I-STOD V1.0 software. The results indicated that the software successfully overcame several problems including reliability of standard curve, applicable scope of samples and determination of dilution for samples outside the scope, so that I-STOD was performed more conveniently and the results of standardization were more consistent. I-STOD V1.0 is a professional software based on I-STOD. It can be easily operated and can effectively standardize the testing results of in-direct ELISA.

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

Beasley, G. P.; Sigman, R. S.

1972-01-01

A multielement data reduction and analysis software package has been developed for use with the Langley differential maneuvering simulator (DMS). This package, which has several independent elements, was developed to support all phases of DMS aircraft simulation studies with a variety of both graphical and tabular information. The overall software package is considered unique because of the number, diversity, and sophistication of the element programs available for use in a single study. The purpose of this paper is to discuss the overall DMS data reduction and analysis package by reviewing the development of the various elements of the software, showing typical results that can be obtained, and discussing how each element can be used.

CSAM Metrology Software Tool

NASA Technical Reports Server (NTRS)

Vu, Duc; Sandor, Michael; Agarwal, Shri

2005-01-01

CSAM Metrology Software Tool (CMeST) is a computer program for analysis of false-color CSAM images of plastic-encapsulated microcircuits. (CSAM signifies C-mode scanning acoustic microscopy.) The colors in the images indicate areas of delamination within the plastic packages. Heretofore, the images have been interpreted by human examiners. Hence, interpretations have not been entirely consistent and objective. CMeST processes the color information in image-data files to detect areas of delamination without incurring inconsistencies of subjective judgement. CMeST can be used to create a database of baseline images of packages acquired at given times for comparison with images of the same packages acquired at later times. Any area within an image can be selected for analysis, which can include examination of different delamination types by location. CMeST can also be used to perform statistical analyses of image data. Results of analyses are available in a spreadsheet format for further processing. The results can be exported to any data-base-processing software.

MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.

PubMed

Muth, Thilo; Kohrs, Fabian; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Reichl, Udo; Martens, Lennart; Renard, Bernhard Y

2018-01-02

Metaproteomics, the mass spectrometry-based analysis of proteins from multispecies samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce the MetaProteomeAnalyzer (MPA) Portable software. In contrast to the original server-based MPA application, this newly developed tool no longer requires computational expertise for installation and is now independent of any relational database system. In addition, MPA Portable now supports state-of-the-art database search engines and a convenient command line interface for high-performance data processing tasks. While search engine results can easily be combined to increase the protein identification yield, an additional two-step workflow is implemented to provide sufficient analysis resolution for further postprocessing steps, such as protein grouping as well as taxonomic and functional annotation. Our new application has been developed with a focus on intuitive usability, adherence to data standards, and adaptation to Web-based workflow platforms. The open source software package can be found at https://github.com/compomics/meta-proteome-analyzer .

Geometry + Technology = Proof

ERIC Educational Resources Information Center

Lyublinskaya, Irina; Funsch, Dan

2012-01-01

Several interactive geometry software packages are available today to secondary school teachers. An example is The Geometer's Sketchpad[R] (GSP), also known as Dynamic Geometry[R] software, developed by Key Curriculum Press. This numeric based technology has been widely adopted in the last twenty years, and a vast amount of creativity has been…

Instructional Support Software System. Final Report.

ERIC Educational Resources Information Center

McDonnell Douglas Astronautics Co. - East, St. Louis, MO.

This report describes the development of the Instructional Support System (ISS), a large-scale, computer-based training system that supports both computer-assisted instruction and computer-managed instruction. Written in the Ada programming language, the ISS software package is designed to be machine independent. It is also grouped into functional…

SIMULATION TOOL KIT FOR INDOOR AIR QUALITY AND INHALATION EXPOSURE (IAQX) VERSION 1.0 USER'S GUIDE

EPA Science Inventory

The User's Guide describes a Microsoft Windows-based indoor air quality (IAQ) simulation software package designed Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short. This software complements and supplements existing IAQ simulation programs and...

Testing Evolutionary Hypotheses in the Classroom with MacClade Software.

ERIC Educational Resources Information Center

Codella, Sylvio G.

2002-01-01

Introduces MacClade which is a Macintosh-based software package that uses the techniques of cladistic analysis to explore evolutionary patterns. Describes a novel and effective exercise that allows undergraduate biology majors to test a hypothesis about behavioral evolution in insects. (Contains 13 references.) (Author/YDS)

Data Reduction and Control Software for Meteor Observing Stations Based on CCD Video Systems

NASA Technical Reports Server (NTRS)

Madiedo, J. M.; Trigo-Rodriguez, J. M.; Lyytinen, E.

2011-01-01

The SPanish Meteor Network (SPMN) is performing a continuous monitoring of meteor activity over Spain and neighbouring countries. The huge amount of data obtained by the 25 video observing stations that this network is currently operating made it necessary to develop new software packages to accomplish some tasks, such as data reduction and remote operation of autonomous systems based on high-sensitivity CCD video devices. The main characteristics of this software are described here.

Design and Implementation of a C++ Software Package to scan for and parse Tsunami Messages issued by the Tsunami Warning Centers for Operational use at the Pacific Tsunami Warning Center

NASA Astrophysics Data System (ADS)

Sardina, V.

2012-12-01

The US Tsunami Warning Centers (TWCs) have traditionally generated their tsunami message products primarily as blocks of text then tagged with headers that identify them on each particular communications' (comms) circuit. Each warning center has a primary area of responsibility (AOR) within which it has an authoritative role regarding parameters such as earthquake location and magnitude. This means that when a major tsunamigenic event occurs the other warning centers need to quickly access the earthquake parameters issued by the authoritative warning center before issuing their message products intended for customers in their own AOR. Thus, within the operational context of the TWCs the scientists on duty have an operational need to access the information contained in the message products issued by other warning centers as quickly as possible. As a solution to this operational problem we designed and implemented a C++ software package that allows scanning for and parsing the entire suite of tsunami message products issued by the Pacific Tsunami Warning Center (PTWC), the West Coast and Alaska Tsunami Warning Center (WCATWC), and the Japan Meteorological Agency (JMA). The scanning and parsing classes composing the resulting C++ software package allow parsing both non-official message products(observatory messages) routinely issued by the TWCs, and all official tsunami message products such as tsunami advisories, watches, and warnings. This software package currently allows scientists on duty at the PTWC to automatically retrieve the parameters contained in tsunami messages issued by WCATWC, JMA, or PTWC itself. Extension of the capabilities of the classes composing the software package would make it possible to generate XML and CAP compliant versions of the TWCs' message products until new messaging software natively adds this capabilities. Customers who receive the TWCs' tsunami message products could also use the package to automatically retrieve information from messages sent via any text-based communications' circuit currently used by the TWCs to disseminate their tsunami message products.

visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.

PubMed

Scales, Matthew; Jäger, Roland; Migliorini, Gabriele; Houlston, Richard S; Henrion, Marc Y R

2014-01-01

We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV). Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).

Western aeronautical test range real-time graphics software package MAGIC

NASA Technical Reports Server (NTRS)

Malone, Jacqueline C.; Moore, Archie L.

1988-01-01

The master graphics interactive console (MAGIC) software package used on the Western Aeronautical Test Range (WATR) of the NASA Ames Research Center is described. MAGIC is a resident real-time research tool available to flight researchers-scientists in the NASA mission control centers of the WATR at the Dryden Flight Research Facility at Edwards, California. The hardware configuration and capabilities of the real-time software package are also discussed.

tweezercalib 2.0: Faster version of MatLab package for precise calibration of optical tweezers

NASA Astrophysics Data System (ADS)

Hansen, Poul Martin; Tolić-Nørrelykke, Iva Marija; Flyvbjerg, Henrik; Berg-Sørensen, Kirstine

2006-03-01

We present a vectorized version of the MatLab (MathWorks Inc.) package tweezercalib for calibration of optical tweezers with precision. The calibration is based on the power spectrum of the Brownian motion of a dielectric bead trapped in the tweezers. Precision is achieved by accounting for a number of factors that affect this power spectrum, as described in vs. 1 of the package [I.M. Tolić-Nørrelykke, K. Berg-Sørensen, H. Flyvbjerg, Matlab program for precision calibration of optical tweezers, Comput. Phys. Comm. 159 (2004) 225-240]. The graphical user interface allows the user to include or leave out each of these factors. Several "health tests" are applied to the experimental data during calibration, and test results are displayed graphically. Thus, the user can easily see whether the data comply with the theory used for their interpretation. Final calibration results are given with statistical errors and covariance matrix. New version program summaryTitle of program: tweezercalib Catalogue identifier: ADTV_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTV_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Reference in CPC to previous version: I.M. Tolić-Nørrelykke, K. Berg-Sørensen, H. Flyvbjerg, Comput. Phys. Comm. 159 (2004) 225 Catalogue identifier of previous version: ADTV Does the new version supersede the original program: Yes Computer for which the program is designed and others on which it has been tested: General computer running MatLab (Mathworks Inc.) Operating systems under with the program has been tested: Windows2000, Windows-XP, Linux Programming language used: MatLab (Mathworks Inc.), standard license Memory required to execute with typical data: Of order four times the size of the data file High speed storage required: none No. of lines in distributed program, including test data, etc.: 135 989 No. of bytes in distributed program, including test data, etc.: 1 527 611 Distribution format: tar. gz Nature of physical problem: Calibrate optical tweezers with precision by fitting theory to experimental power spectrum of position of bead doing Brownian motion in incompressible fluid, possibly near microscope cover slip, while trapped in optical tweezers. Thereby determine spring constant of optical trap and conversion factor for arbitrary-units-to-nanometers for detection system. Method of solution: Elimination of cross-talk between quadrant photo-diode's output channels for positions (optional). Check that distribution of recorded positions agrees with Boltzmann distribution of bead in harmonic trap. Data compression and noise reduction by blocking method applied to power spectrum. Full accounting for hydrodynamic effects: Frequency-dependent drag force and interaction with nearby cover slip (optional). Full accounting for electronic filters (optional), for "virtual filtering" caused by detection system (optional). Full accounting for aliasing caused by finite sampling rate (optional). Standard non-linear least-squares fitting. Statistical support for fit is given, with several plots facilitating inspection of consistency and quality of data and fit. Summary of revisions: A faster fitting routine, adapted from [J. Nocedal, Y.x. Yuan, Combining trust region and line search techniques, Technical Report OTC 98/04, Optimization Technology Center, 1998; W.H. Press, B.P. Flannery, S.A. Teukolsky, W.T. Vetterling, Numerical Recipes. The Art of Scientific Computing, Cambridge University Press, Cambridge, 1986], is applied. It uses fewer function evaluations, and the remaining function evaluations have been vectorized. Calls to routines in Toolboxes not included with a standard MatLab license have been replaced by calls to routines that are included in the present package. Fitting parameters are rescaled to ensure that they are all of roughly the same size (of order 1) while being fitted. Generally, the program package has been updated to comply with MatLab, vs. 7.0, and optimized for speed. Restrictions on the complexity of the problem: Data should be positions of bead doing Brownian motion while held by optical tweezers. For high precision in final results, data should be time series measured over a long time, with sufficiently high experimental sampling rate: The sampling rate should be well above the characteristic frequency of the trap, the so-called corner frequency. Thus, the sampling frequency should typically be larger than 10 kHz. The Fast Fourier Transform used works optimally when the time series contain 2 data points, and long measurement time is obtained with n>12-15. Finally, the optics should be set to ensure a harmonic trapping potential in the range of positions visited by the bead. The fitting procedure checks for harmonic potential. Typical running time: Seconds Unusual features of the program: None References: The theoretical underpinnings for the procedure are found in [K. Berg-Sørensen, H. Flyvbjerg, Power spectrum analysis for optical tweezers, Rev. Sci. Ins. 75 (2004) 594-612].

CheMentor Software System by H. A. Peoples

NASA Astrophysics Data System (ADS)

Reid, Brian P.

1997-09-01

CheMentor Software System H. A. Peoples. Computerized Learning Enhancements: http://www.ecis.com/~clehap; email: clehap@ecis.com; 1996 - 1997. CheMentor is a series of software packages for introductory-level chemistry, which includes Practice Items (I), Stoichiometry (I), Calculating Chemical Formulae, and the CheMentor Toolkit. The first three packages provide practice problems for students and various types of help to solve them; the Toolkit includes "calculators" for determining chemical quantities as well as the Practice Items (I) set of problems. The set of software packages is designed so that each individual product acts as a module of a common CheMentor program. As the name CheMentor implies, the software is designed as a "mentor" for students learning introductory chemistry concepts and problems. The typical use of the software would be by individual students (or perhaps small groups) as an adjunct to lectures. CheMentor is a HyperCard application and the modules are HyperCard stacks. The requirements to run the packages include a Macintosh computer with at least 1 MB of RAM, a hard drive with several MB of available space depending upon the packages selected (10 MB were required for all the packages reviewed here), and the Mac operating system 6.0.5 or later.