Scientific Software: How to Find What You Need and Get What You Pay for.

ERIC Educational Resources Information Center

Gabaldon, Diana J.

1984-01-01

Provides examples of software for the sciences, including: packages for pathology/toxicology laboratories (costing over $15,000), DNA sequencing, and data acquisition/analysis; general-purpose software for scientific uses; and "custom" packages, including a program to maintain a listing of "Escherichia coli" strains and a…

An Overview of Software for Conducting Dimensionality Assessment in Multidimensional Models

ERIC Educational Resources Information Center

Svetina, Dubravka; Levy, Roy

2012-01-01

An overview of popular software packages for conducting dimensionality assessment in multidimensional models is presented. Specifically, five popular software packages are described in terms of their capabilities to conduct dimensionality assessment with respect to the nature of analysis (exploratory or confirmatory), types of data (dichotomous,…

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.

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

Comparison of requirements and capabilities of major multipurpose software packages.

PubMed

Igo, Robert P; Schnell, Audrey H

2012-01-01

The aim of this chapter is to introduce the reader to commonly used software packages and illustrate their input requirements, analysis options, strengths, and limitations. We focus on packages that perform more than one function and include a program for quality control, linkage, and association analyses. Additional inclusion criteria were (1) programs that are free to academic users and (2) currently supported, maintained, and developed. Using those criteria, we chose to review three programs: Statistical Analysis for Genetic Epidemiology (S.A.G.E.), PLINK, and Merlin. We will describe the required input format and analysis options. We will not go into detail about every possible program in the packages, but we will give an overview of the packages requirements and capabilities.

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

PubMed Central

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA. PMID:25541687

Network meta-analysis using R: a review of currently available automated packages.

PubMed

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA)--a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously--has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.

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.

Versatile Software Package For Near Real-Time Analysis of Experimental Data

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Hoadley, Sherwood T.

1998-01-01

This paper provides an overview of a versatile software package developed for time- and frequency-domain analyses of experimental wind-tunnel data. This package, originally developed for analyzing data in the NASA Langley Transonic Dynamics Tunnel (TDT), is applicable for analyzing any time-domain data. A Matlab-based software package, TDT-analyzer, provides a compendium of commonly-required dynamic analysis functions in a user-friendly interactive and batch processing environment. TDT-analyzer has been used extensively to provide on-line near real-time and post-test examination and reduction of measured data acquired during wind tunnel tests of aeroelastically-scaled models of aircraft and rotorcraft as well as a flight test of the NASA High Alpha Research Vehicle (HARV) F-18. The package provides near real-time results in an informative and timely manner far exceeding prior methods of data reduction at the TDT.

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.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

A streamlined Python framework for AT-TPC data analysis

NASA Astrophysics Data System (ADS)

Taylor, J. Z.; Bradt, J.; Bazin, D.; Kuchera, M. P.

2017-09-01

User-friendly data analysis software has been developed for the Active-Target Time Projection Chamber (AT-TPC) experiment at the National Superconducting Cyclotron Laboratory at Michigan State University. The AT-TPC, commissioned in 2014, is a gas-filled detector that acts as both the detector and target for high-efficiency detection of low-intensity, exotic nuclear reactions. The pytpc framework is a Python package for analyzing AT-TPC data. The package was developed for the analysis of 46Ar(p, p) data. The existing software was used to analyze data produced by the 40Ar(p, p) experiment that ran in August, 2015. Usage of the package was documented in an analysis manual both to improve analysis steps and aid in the work of future AT-TPC users. Software features and analysis methods in the pytpc framework will be presented along with the 40Ar results.

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…

Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

PubMed

Gorgolewski, Krzysztof; Burns, Christopher D; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O; Waskom, Michael L; Ghosh, Satrajit S

2011-01-01

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python

PubMed Central

Gorgolewski, Krzysztof; Burns, Christopher D.; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O.; Waskom, Michael L.; Ghosh, Satrajit S.

2011-01-01

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research. PMID:21897815

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.

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

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.

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

Long-term Preservation of Data Analysis Capabilities

NASA Astrophysics Data System (ADS)

Gabriel, C.; Arviset, C.; Ibarra, A.; Pollock, A.

2015-09-01

While the long-term preservation of scientific data obtained by large astrophysics missions is ensured through science archives, the issue of data analysis software preservation has hardly been addressed. Efforts by large data centres have contributed so far to maintain some instrument or mission-specific data reduction packages on top of high-level general purpose data analysis software. However, it is always difficult to keep software alive without support and maintenance once the active phase of a mission is over. This is especially difficult in the budgetary model followed by space agencies. We discuss the importance of extending the lifetime of dedicated data analysis packages and review diverse strategies under development at ESA using new paradigms such as Virtual Machines, Cloud Computing, and Software as a Service for making possible full availability of data analysis and calibration software for decades at minimal cost.

Report: Scientific Software.

ERIC Educational Resources Information Center

Borman, Stuart A.

1985-01-01

Discusses various aspects of scientific software, including evaluation and selection of commercial software products; program exchanges, catalogs, and other information sources; major data analysis packages; statistics and chemometrics software; and artificial intelligence. (JN)

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.

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.

PyPedal, an open source software package for pedigree analysis

USDA-ARS?s Scientific Manuscript database

The open source software package PyPedal (http://pypedal.sourceforge.net/) was first released in 2002, and provided users with a set of simple tools for manipulating pedigrees. Its flexibility has been demonstrated by its used in a number of settings for large and small populations. After substantia...

Design and validation of Segment--freely available software for cardiovascular image analysis.

PubMed

Heiberg, Einar; Sjögren, Jane; Ugander, Martin; Carlsson, Marcus; Engblom, Henrik; Arheden, Håkan

2010-01-11

Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format. Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page http://segment.heiberg.se. Segment is a well-validated comprehensive software package for cardiovascular image analysis. It is freely available for research purposes provided that relevant original research publications related to the software are cited.

Prototyping with Data Dictionaries for Requirements Analysis.

DTIC Science & Technology

1985-03-01

statistical packages and software for screen layout. These items work at a higher level than another category of prototyping tool, program generators... Program generators are software packages which, when given specifications, produce source listings, usually in a high order language such as COBCL...with users and this will not happen if he must stop to develcp a detailed program . [Ref. 241] Hardware as well as software should be considered in

Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

PubMed Central

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

2016-01-01

Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

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

Predictive Utility of Marketed Volumetric Software Tools in Subjects at Risk for Alzheimer's: Do Regions Outside the Hippocampus Matter?

PubMed Central

Tanpitukpongse, Teerath P.; Mazurowski, Maciej A.; Ikhena, John; Petrella, Jeffrey R.

2016-01-01

Background and Purpose To assess prognostic efficacy of individual versus combined regional volumetrics in two commercially-available brain volumetric software packages for predicting conversion of patients with mild cognitive impairment to Alzheimer's disease. Materials and Methods Data was obtained through the Alzheimer's Disease Neuroimaging Initiative. 192 subjects (mean age 74.8 years, 39% female) diagnosed with mild cognitive impairment at baseline were studied. All had T1WI MRI sequences at baseline and 3-year clinical follow-up. Analysis was performed with NeuroQuant® and Neuroreader™. Receiver operating characteristic curves assessing the prognostic efficacy of each software package were generated using a univariable approach employing individual regional brain volumes, as well as two multivariable approaches (multiple regression and random forest), combining multiple volumes. Results On univariable analysis of 11 NeuroQuant® and 11 Neuroreader™ regional volumes, hippocampal volume had the highest area under the curve for both software packages (0.69 NeuroQuant®, 0.68 Neuroreader™), and was not significantly different (p > 0.05) between packages. Multivariable analysis did not increase the area under the curve for either package (0.63 logistic regression, 0.60 random forest NeuroQuant®; 0.65 logistic regression, 0.62 random forest Neuroreader™). Conclusion Of the multiple regional volume measures available in FDA-cleared brain volumetric software packages, hippocampal volume remains the best single predictor of conversion of mild cognitive impairment to Alzheimer's disease at 3-year follow-up. Combining volumetrics did not add additional prognostic efficacy. Therefore, future prognostic studies in MCI, combining such tools with demographic and other biomarker measures, are justified in using hippocampal volume as the only volumetric biomarker. PMID:28057634

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.

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.

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.

Fragman: an R package for fragment analysis.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Salazar, Walter; Zalapa, Juan

2016-04-21

Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® (ABI) either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry (Vaccinium macrocarpon) genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.

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.

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.

MPTinR: analysis of multinomial processing tree models in R.

PubMed

Singmann, Henrik; Kellen, David

2013-06-01

We introduce MPTinR, a software package developed for the analysis of multinomial processing tree (MPT) models. MPT models represent a prominent class of cognitive measurement models for categorical data with applications in a wide variety of fields. MPTinR is the first software for the analysis of MPT models in the statistical programming language R, providing a modeling framework that is more flexible than standalone software packages. MPTinR also introduces important features such as (1) the ability to calculate the Fisher information approximation measure of model complexity for MPT models, (2) the ability to fit models for categorical data outside the MPT model class, such as signal detection models, (3) a function for model selection across a set of nested and nonnested candidate models (using several model selection indices), and (4) multicore fitting. MPTinR is available from the Comprehensive R Archive Network at http://cran.r-project.org/web/packages/MPTinR/ .

Implementation of interconnect simulation tools in spice

NASA Technical Reports Server (NTRS)

Satsangi, H.; Schutt-Aine, J. E.

1993-01-01

Accurate computer simulation of high speed digital computer circuits and communication circuits requires a multimode approach to simulate both the devices and the interconnects between devices. Classical circuit analysis algorithms (lumped parameter) are needed for circuit devices and the network formed by the interconnected devices. The interconnects, however, have to be modeled as transmission lines which incorporate electromagnetic field analysis. An approach to writing a multimode simulator is to take an existing software package which performs either lumped parameter analysis or field analysis and add the missing type of analysis routines to the package. In this work a traditionally lumped parameter simulator, SPICE, is modified so that it will perform lossy transmission line analysis using a different model approach. Modifying SPICE3E2 or any other large software package is not a trivial task. An understanding of the programming conventions used, simulation software, and simulation algorithms is required. This thesis was written to clarify the procedure for installing a device into SPICE3E2. The installation of three devices is documented and the installations of the first two provide a foundation for installation of the lossy line which is the third device. The details of discussions are specific to SPICE, but the concepts will be helpful when performing installations into other circuit analysis packages.

MOSAIC: Software for creating mosaics from collections of images

NASA Technical Reports Server (NTRS)

Varosi, F.; Gezari, D. Y.

1992-01-01

We have developed a powerful, versatile image processing and analysis software package called MOSAIC, designed specifically for the manipulation of digital astronomical image data obtained with (but not limited to) two-dimensional array detectors. The software package is implemented using the Interactive Data Language (IDL), and incorporates new methods for processing, calibration, analysis, and visualization of astronomical image data, stressing effective methods for the creation of mosaic images from collections of individual exposures, while at the same time preserving the photometric integrity of the original data. Since IDL is available on many computers, the MOSAIC software runs on most UNIX and VAX workstations with the X-Windows or Sun View graphics interface.

A User-Friendly Software Package for HIFU Simulation

NASA Astrophysics Data System (ADS)

Soneson, Joshua E.

2009-04-01

A freely-distributed, MATLAB (The Mathworks, Inc., Natick, MA)-based software package for simulating axisymmetric high-intensity focused ultrasound (HIFU) beams and their heating effects is discussed. The package (HIFU_Simulator) consists of a propagation module which solves the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation and a heating module which solves Pennes' bioheat transfer (BHT) equation. The pressure, intensity, heating rate, temperature, and thermal dose fields are computed, plotted, the output is released to the MATLAB workspace for further user analysis or postprocessing.

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

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

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.

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

Salama, A.; Mikhail, M.

Comprehensive software packages have been developed at the Western Research Centre as tools to help coal preparation engineers analyze, evaluate, and control coal cleaning processes. The COal Preparation Software package (COPS) performs three functions: (1) data handling and manipulation, (2) data analysis, including the generation of washability data, performance evaluation and prediction, density and size modeling, evaluation of density and size partition characteristics and attrition curves, and (3) generation of graphics output. The Separation ChARacteristics Estimation software packages (SCARE) are developed to balance raw density or size separation data. The cases of density and size separation data are considered. Themore » generated balanced data can take the balanced or normalized forms. The scaled form is desirable for direct determination of the partition functions (curves). The raw and generated separation data are displayed in tabular and/or graphical forms. The computer softwares described in this paper are valuable tools for coal preparation plant engineers and operators for evaluating process performance, adjusting plant parameters, and balancing raw density or size separation data. These packages have been applied very successfully in many projects carried out by WRC for the Canadian coal preparation industry. The software packages are designed to run on a personal computer (PC).« less

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

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.

Increasing the Number of Replications in Item Response Theory Simulations: Automation through SAS and Disk Operating System

ERIC Educational Resources Information Center

Gagne, Phill; Furlow, Carolyn; Ross, Terris

2009-01-01

In item response theory (IRT) simulation research, it is often necessary to use one software package for data generation and a second software package to conduct the IRT analysis. Because this can substantially slow down the simulation process, it is sometimes offered as a justification for using very few replications. This article provides…

Sampling and sensitivity analyses tools (SaSAT) for computational modelling

PubMed Central

Hoare, Alexander; Regan, David G; Wilson, David P

2008-01-01

SaSAT (Sampling and Sensitivity Analysis Tools) is a user-friendly software package for applying uncertainty and sensitivity analyses to mathematical and computational models of arbitrary complexity and context. The toolbox is built in Matlab®, a numerical mathematical software package, and utilises algorithms contained in the Matlab® Statistics Toolbox. However, Matlab® is not required to use SaSAT as the software package is provided as an executable file with all the necessary supplementary files. The SaSAT package is also designed to work seamlessly with Microsoft Excel but no functionality is forfeited if that software is not available. A comprehensive suite of tools is provided to enable the following tasks to be easily performed: efficient and equitable sampling of parameter space by various methodologies; calculation of correlation coefficients; regression analysis; factor prioritisation; and graphical output of results, including response surfaces, tornado plots, and scatterplots. Use of SaSAT is exemplified by application to a simple epidemic model. To our knowledge, a number of the methods available in SaSAT for performing sensitivity analyses have not previously been used in epidemiological modelling and their usefulness in this context is demonstrated. PMID:18304361

Assessment of left ventricular mechanical dyssynchrony by phase analysis of gated-SPECT myocardial perfusion imaging and tissue Doppler imaging: comparison between QGS and ECTb software packages.

PubMed

Rastgou, Fereydoon; Shojaeifard, Maryam; Amin, Ahmad; Ghaedian, Tahereh; Firoozabadi, Hasan; Malek, Hadi; Yaghoobi, Nahid; Bitarafan-Rajabi, Ahmad; Haghjoo, Majid; Amouzadeh, Hedieh; Barati, Hossein

2014-12-01

Recently, the phase analysis of gated single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) has become feasible via several software packages for the evaluation of left ventricular mechanical dyssynchrony. We compared two quantitative software packages, quantitative gated SPECT (QGS) and Emory cardiac toolbox (ECTb), with tissue Doppler imaging (TDI) as the conventional method for the evaluation of left ventricular mechanical dyssynchrony. Thirty-one patients with severe heart failure (ejection fraction ≤35%) and regular heart rhythm, who referred for gated-SPECT MPI, were enrolled. TDI was performed within 3 days after MPI. Dyssynchrony parameters derived from gated-SPECT MPI were analyzed by QGS and ECTb and were compared with the Yu index and septal-lateral wall delay measured by TDI. QGS and ECTb showed a good correlation for assessment of phase histogram bandwidth (PHB) and phase standard deviation (PSD) (r = 0.664 and r = 0.731, P < .001, respectively). However, the mean value of PHB and PSD by ECTb was significantly higher than that of QGS. No significant correlation was found between ECTb and QGS and the Yu index. Nevertheless, PHB, PSD, and entropy derived from QGS revealed a significant (r = 0.424, r = 0.478, r = 0.543, respectively; P < .02) correlation with septal-lateral wall delay. Despite a good correlation between QGS and ECTb software packages, different normal cut-off values of PSD and PHB should be defined for each software package. There was only a modest correlation between phase analysis of gated-SPECT MPI and TDI data, especially in the population of heart failure patients with both narrow and wide QRS complex.

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.

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

Predictive Utility of Marketed Volumetric Software Tools in Subjects at Risk for Alzheimer Disease: Do Regions Outside the Hippocampus Matter?

PubMed

Tanpitukpongse, T P; Mazurowski, M A; Ikhena, J; Petrella, J R

2017-03-01

Alzheimer disease is a prevalent neurodegenerative disease. Computer assessment of brain atrophy patterns can help predict conversion to Alzheimer disease. Our aim was to assess the prognostic efficacy of individual-versus-combined regional volumetrics in 2 commercially available brain volumetric software packages for predicting conversion of patients with mild cognitive impairment to Alzheimer disease. Data were obtained through the Alzheimer's Disease Neuroimaging Initiative. One hundred ninety-two subjects (mean age, 74.8 years; 39% female) diagnosed with mild cognitive impairment at baseline were studied. All had T1-weighted MR imaging sequences at baseline and 3-year clinical follow-up. Analysis was performed with NeuroQuant and Neuroreader. Receiver operating characteristic curves assessing the prognostic efficacy of each software package were generated by using a univariable approach using individual regional brain volumes and 2 multivariable approaches (multiple regression and random forest), combining multiple volumes. On univariable analysis of 11 NeuroQuant and 11 Neuroreader regional volumes, hippocampal volume had the highest area under the curve for both software packages (0.69, NeuroQuant; 0.68, Neuroreader) and was not significantly different ( P > .05) between packages. Multivariable analysis did not increase the area under the curve for either package (0.63, logistic regression; 0.60, random forest NeuroQuant; 0.65, logistic regression; 0.62, random forest Neuroreader). Of the multiple regional volume measures available in FDA-cleared brain volumetric software packages, hippocampal volume remains the best single predictor of conversion of mild cognitive impairment to Alzheimer disease at 3-year follow-up. Combining volumetrics did not add additional prognostic efficacy. Therefore, future prognostic studies in mild cognitive impairment, combining such tools with demographic and other biomarker measures, are justified in using hippocampal volume as the only volumetric biomarker. © 2017 by American Journal of Neuroradiology.

Reviews.

ERIC Educational Resources Information Center

Science Teacher, 1988

1988-01-01

Reviews four software packages available for IBM PC or Apple II. Includes "Graphical Analysis III"; "Space Max: Space Station Construction Simulation"; "Guesstimation"; and "Genetic Engineering Toolbox." Focuses on each packages' strengths in a high school context. (CW)

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.

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

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

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

Analytical and Methodological Issues in the Use of Qualitative Data Analysis Software: A Description of Three Studies.

ERIC Educational Resources Information Center

Margerum-Leys, Jon; Kupperman, Jeff; Boyle-Heimann, Kristen

This paper presents perspectives on the use of data analysis software in the process of qualitative research. These perspectives were gained in the conduct of three qualitative research studies that differed in theoretical frames, areas of interests, and scope. Their common use of a particular data analysis software package allows the exploration…

Wall adjustment strategy software for use with the NASA Langley 0.3-meter transonic cryogenic tunnel adaptive wall test section

NASA Technical Reports Server (NTRS)

Wolf, Stephen W. D.

1988-01-01

The Wall Adjustment Strategy (WAS) software provides successful on-line control of the 2-D flexible walled test section of the Langley 0.3-m Transonic Cryogenic Tunnel. This software package allows the level of operator intervention to be regulated as necessary for research and production type 2-D testing using and Adaptive Wall Test Section (AWTS). The software is designed to accept modification for future requirements, such as 3-D testing, with a minimum of complexity. The WAS software described is an attempt to provide a user friendly package which could be used to control any flexible walled AWTS. Control system constraints influence the details of data transfer, not the data type. Then this entire software package could be used in different control systems, if suitable interface software is available. A complete overview of the software highlights the data flow paths, the modular architecture of the software and the various operating and analysis modes available. A detailed description of the software modules includes listings of the code. A user's manual is provided to explain task generation, operating environment, user options and what to expect at execution.

Usability study of clinical exome analysis software: top lessons learned and recommendations.

PubMed

Shyr, Casper; Kushniruk, Andre; Wasserman, Wyeth W

2014-10-01

New DNA sequencing technologies have revolutionized the search for genetic disruptions. Targeted sequencing of all protein coding regions of the genome, called exome analysis, is actively used in research-oriented genetics clinics, with the transition to exomes as a standard procedure underway. This transition is challenging; identification of potentially causal mutation(s) amongst ∼10(6) variants requires specialized computation in combination with expert assessment. This study analyzes the usability of user interfaces for clinical exome analysis software. There are two study objectives: (1) To ascertain the key features of successful user interfaces for clinical exome analysis software based on the perspective of expert clinical geneticists, (2) To assess user-system interactions in order to reveal strengths and weaknesses of existing software, inform future design, and accelerate the clinical uptake of exome analysis. Surveys, interviews, and cognitive task analysis were performed for the assessment of two next-generation exome sequence analysis software packages. The subjects included ten clinical geneticists who interacted with the software packages using the "think aloud" method. Subjects' interactions with the software were recorded in their clinical office within an urban research and teaching hospital. All major user interface events (from the user interactions with the packages) were time-stamped and annotated with coding categories to identify usability issues in order to characterize desired features and deficiencies in the user experience. We detected 193 usability issues, the majority of which concern interface layout and navigation, and the resolution of reports. Our study highlights gaps in specific software features typical within exome analysis. The clinicians perform best when the flow of the system is structured into well-defined yet customizable layers for incorporation within the clinical workflow. The results highlight opportunities to dramatically accelerate clinician analysis and interpretation of patient genomic data. We present the first application of usability methods to evaluate software interfaces in the context of exome analysis. Our results highlight how the study of user responses can lead to identification of usability issues and challenges and reveal software reengineering opportunities for improving clinical next-generation sequencing analysis. While the evaluation focused on two distinctive software tools, the results are general and should inform active and future software development for genome analysis software. As large-scale genome analysis becomes increasingly common in healthcare, it is critical that efficient and effective software interfaces are provided to accelerate clinical adoption of the technology. Implications for improved design of such applications are discussed. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

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.

Software Users Manual (SUM): Extended Testability Analysis (ETA) Tool

NASA Technical Reports Server (NTRS)

Maul, William A.; Fulton, Christopher E.

2011-01-01

This software user manual describes the implementation and use the Extended Testability Analysis (ETA) Tool. The ETA Tool is a software program that augments the analysis and reporting capabilities of a commercial-off-the-shelf (COTS) testability analysis software package called the Testability Engineering And Maintenance System (TEAMS) Designer. An initial diagnostic assessment is performed by the TEAMS Designer software using a qualitative, directed-graph model of the system being analyzed. The ETA Tool utilizes system design information captured within the diagnostic model and testability analysis output from the TEAMS Designer software to create a series of six reports for various system engineering needs. The ETA Tool allows the user to perform additional studies on the testability analysis results by determining the detection sensitivity to the loss of certain sensors or tests. The ETA Tool was developed to support design and development of the NASA Ares I Crew Launch Vehicle. The diagnostic analysis provided by the ETA Tool was proven to be valuable system engineering output that provided consistency in the verification of system engineering requirements. This software user manual provides a description of each output report generated by the ETA Tool. The manual also describes the example diagnostic model and supporting documentation - also provided with the ETA Tool software release package - that were used to generate the reports presented in the manual

MNE software for processing MEG and EEG data

PubMed Central

Gramfort, A.; Luessi, M.; Larson, E.; Engemann, D.; Strohmeier, D.; Brodbeck, C.; Parkkonen, L.; Hämäläinen, M.

2013-01-01

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals originating from neural currents in the brain. Using these signals to characterize and locate brain activity is a challenging task, as evidenced by several decades of methodological contributions. MNE, whose name stems from its capability to compute cortically-constrained minimum-norm current estimates from M/EEG data, is a software package that provides comprehensive analysis tools and workflows including preprocessing, source estimation, time–frequency analysis, statistical analysis, and several methods to estimate functional connectivity between distributed brain regions. The present paper gives detailed information about the MNE package and describes typical use cases while also warning about potential caveats in analysis. The MNE package is a collaborative effort of multiple institutes striving to implement and share best methods and to facilitate distribution of analysis pipelines to advance reproducibility of research. Full documentation is available at http://martinos.org/mne. PMID:24161808

Digital PIV (DPIV) Software Analysis System

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A software package was developed to provide a Digital PIV (DPIV) capability for NASA LaRC. The system provides an automated image capture, test correlation, and autocorrelation analysis capability for the Kodak Megaplus 1.4 digital camera system for PIV measurements. The package includes three separate programs that, when used together with the PIV data validation algorithm, constitutes a complete DPIV analysis capability. The programs are run on an IBM PC/AT host computer running either Microsoft Windows 3.1 or Windows 95 using a 'quickwin' format that allows simple user interface and output capabilities to the windows environment.

ConcreteWorks v3 training/user manual (P1) : ConcreteWorks software (P2).

DOT National Transportation Integrated Search

2017-04-01

ConcreteWorks is designed to be a user-friendly software package that can help concrete : professionals optimize concrete mixture proportioning, perform a concrete thermal analysis, and : increase the chloride diffusion service life. The software pac...

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

Ramos, Marcel; Schiffer, Lucas; Re, Angela; Azhar, Rimsha; Basunia, Azfar; Rodriguez, Carmen; Chan, Tiffany; Chapman, Phil; Davis, Sean R; Gomez-Cabrero, David; Culhane, Aedin C; Haibe-Kains, Benjamin; Hansen, Kasper D; Kodali, Hanish; Louis, Marie S; Mer, Arvind S; Riester, Markus; Morgan, Martin; Carey, Vince; Waldron, Levi

2017-11-01

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR . ©2017 American Association for Cancer Research.

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.

Investigation of the Finite Element Software Packages at KSC

NASA Technical Reports Server (NTRS)

Lu, Chu-Ho

1991-01-01

The useful and powerful features of NASTRAN and three real world problems for the testing of the capabilities of different NASTRAN versions are discussed. The test problems involve direct transient analysis, nonlinear analysis, and static analysis. The experiences in using graphics software packages are also discussed. It was found that MSC/XL can be more useful if it can be improved to generate picture files of the analysis results and to extend its capabilities to support finite element codes other than MSC/NASTRAN. It was found that the current version of SDRC/I-DEAS (version VI) may have bugs in the module 'Data Loader'.

High pressure single-crystal micro X-ray diffraction analysis with GSE_ADA/RSV software

NASA Astrophysics Data System (ADS)

Dera, Przemyslaw; Zhuravlev, Kirill; Prakapenka, Vitali; Rivers, Mark L.; Finkelstein, Gregory J.; Grubor-Urosevic, Ognjen; Tschauner, Oliver; Clark, Simon M.; Downs, Robert T.

2013-08-01

GSE_ADA/RSV is a free software package for custom analysis of single-crystal micro X-ray diffraction (SCμXRD) data, developed with particular emphasis on data from samples enclosed in diamond anvil cells and subject to high pressure conditions. The package has been in extensive use at the high pressure beamlines of Advanced Photon Source (APS), Argonne National Laboratory and Advanced Light Source (ALS), Lawrence Berkeley National Laboratory. The software is optimized for processing of wide-rotation images and includes a variety of peak intensity corrections and peak filtering features, which are custom-designed to make processing of high pressure SCμXRD easier and more reliable.

Software package for modeling spin-orbit motion in storage rings

NASA Astrophysics Data System (ADS)

Zyuzin, D. V.

2015-12-01

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 106-109 particles in a beam during 109 turns in an accelerator (about 1012-1015 integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin-orbit dynamics.

Probabilistic Design and Analysis Framework

NASA Technical Reports Server (NTRS)

Strack, William C.; Nagpal, Vinod K.

2010-01-01

PRODAF is a software package designed to aid analysts and designers in conducting probabilistic analysis of components and systems. PRODAF can integrate multiple analysis programs to ease the tedious process of conducting a complex analysis process that requires the use of multiple software packages. The work uses a commercial finite element analysis (FEA) program with modules from NESSUS to conduct a probabilistic analysis of a hypothetical turbine blade, disk, and shaft model. PRODAF applies the response surface method, at the component level, and extrapolates the component-level responses to the system level. Hypothetical components of a gas turbine engine are first deterministically modeled using FEA. Variations in selected geometrical dimensions and loading conditions are analyzed to determine the effects of the stress state within each component. Geometric variations include the cord length and height for the blade, inner radius, outer radius, and thickness, which are varied for the disk. Probabilistic analysis is carried out using developing software packages like System Uncertainty Analysis (SUA) and PRODAF. PRODAF was used with a commercial deterministic FEA program in conjunction with modules from the probabilistic analysis program, NESTEM, to perturb loads and geometries to provide a reliability and sensitivity analysis. PRODAF simplified the handling of data among the various programs involved, and will work with many commercial and opensource deterministic programs, probabilistic programs, or modules.

An Integrated Research Program for the Modeling, Analysis and Control of Aerospace Systems

DTIC Science & Technology

1992-03-03

Fabiano, Jr. - Brown University Mitchell Feigenbaum - Rockefeller University Elena Fernandez - Institudo de Desarrollo Techologico, para la Industria...system. The system runs under DEC Ultrix; we have installed the GKS graphics system and language compilers (FORTRAN and C). The DELIGHT.MIMO software ...which links a sophisticated non-smooth optimization package to some linear system software , is on the system. The package was kindly furnished by

An Integrated Research Program for the Modeling, Analysis and Control of Aerospace Systems

DTIC Science & Technology

1992-03-03

Mitchell Feigenbaum - Rockefeller University Elena Fernandez - Institudo de Desarrollo Techologico, para la Industria Quimica Wilfred M. Greenlee...Ultrix; we have installed the GKS graphics system and language compilers (FORTRAN and C). The DELIGHT.MIMO software , which links a sophisticated non...smooth optimization package to some linear system software , is on the system. The package was kindly furnished by Professor E. Polak, Electrical and

Dynamic Modeling Using MCSim and R (SOT 2016 Biological Modeling Webinar Series)

EPA Science Inventory

MCSim is a stand-alone software package for simulating and analyzing dynamic models, with a focus on Bayesian analysis using Markov Chain Monte Carlo. While it is an extremely powerful package, it is somewhat inflexible, and offers only a limited range of analysis options, with n...

Variations in algorithm implementation among quantitative texture analysis software packages

NASA Astrophysics Data System (ADS)

Foy, Joseph J.; Mitta, Prerana; Nowosatka, Lauren R.; Mendel, Kayla R.; Li, Hui; Giger, Maryellen L.; Al-Hallaq, Hania; Armato, Samuel G.

2018-02-01

Open-source texture analysis software allows for the advancement of radiomics research. Variations in texture features, however, result from discrepancies in algorithm implementation. Anatomically matched regions of interest (ROIs) that captured normal breast parenchyma were placed in the magnetic resonance images (MRI) of 20 patients at two time points. Six first-order features and six gray-level co-occurrence matrix (GLCM) features were calculated for each ROI using four texture analysis packages. Features were extracted using package-specific default GLCM parameters and using GLCM parameters modified to yield the greatest consistency among packages. Relative change in the value of each feature between time points was calculated for each ROI. Distributions of relative feature value differences were compared across packages. Absolute agreement among feature values was quantified by the intra-class correlation coefficient. Among first-order features, significant differences were found for max, range, and mean, and only kurtosis showed poor agreement. All six second-order features showed significant differences using package-specific default GLCM parameters, and five second-order features showed poor agreement; with modified GLCM parameters, no significant differences among second-order features were found, and all second-order features showed poor agreement. While relative texture change discrepancies existed across packages, these differences were not significant when consistent parameters were used.

Validation of a Video Analysis Software Package for Quantifying Movement Velocity in Resistance Exercises.

PubMed

Sañudo, Borja; Rueda, David; Pozo-Cruz, Borja Del; de Hoyo, Moisés; Carrasco, Luis

2016-10-01

Sañudo, B, Rueda, D, del Pozo-Cruz, B, de Hoyo, M, and Carrasco, L. Validation of a video analysis software package for quantifying movement velocity in resistance exercises. J Strength Cond Res 30(10): 2934-2941, 2016-The aim of this study was to establish the validity of a video analysis software package in measuring mean propulsive velocity (MPV) and the maximal velocity during bench press. Twenty-one healthy males (21 ± 1 year) with weight training experience were recruited, and the MPV and the maximal velocity of the concentric phase (Vmax) were compared with a linear position transducer system during a standard bench press exercise. Participants performed a 1 repetition maximum test using the supine bench press exercise. The testing procedures involved the simultaneous assessment of bench press propulsive velocity using 2 kinematic (linear position transducer and semi-automated tracking software) systems. High Pearson's correlation coefficients for MPV and Vmax between both devices (r = 0.473 to 0.993) were observed. The intraclass correlation coefficients for barbell velocity data and the kinematic data obtained from video analysis were high (>0.79). In addition, the low coefficients of variation indicate that measurements had low variability. Finally, Bland-Altman plots with the limits of agreement of the MPV and Vmax with different loads showed a negative trend, which indicated that the video analysis had higher values than the linear transducer. In conclusion, this study has demonstrated that the software used for the video analysis was an easy to use and cost-effective tool with a very high degree of concurrent validity. This software can be used to evaluate changes in velocity of training load in resistance training, which may be important for the prescription and monitoring of training programmes.

Advanced statistical methods for improved data analysis of NASA astrophysics missions

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.

1992-01-01

The investigators under this grant studied ways to improve the statistical analysis of astronomical data. They looked at existing techniques, the development of new techniques, and the production and distribution of specialized software to the astronomical community. Abstracts of nine papers that were produced are included, as well as brief descriptions of four software packages. The articles that are abstracted discuss analytical and Monte Carlo comparisons of six different linear least squares fits, a (second) paper on linear regression in astronomy, two reviews of public domain software for the astronomer, subsample and half-sample methods for estimating sampling distributions, a nonparametric estimation of survival functions under dependent competing risks, censoring in astronomical data due to nondetections, an astronomy survival analysis computer package called ASURV, and improving the statistical methodology of astronomical data analysis.

Applications of decision analysis and related techniques to industrial engineering problems at KSC

NASA Technical Reports Server (NTRS)

Evans, Gerald W.

1995-01-01

This report provides: (1) a discussion of the origination of decision analysis problems (well-structured problems) from ill-structured problems; (2) a review of the various methodologies and software packages for decision analysis and related problem areas; (3) a discussion of how the characteristics of a decision analysis problem affect the choice of modeling methodologies, thus providing a guide as to when to choose a particular methodology; and (4) examples of applications of decision analysis to particular problems encountered by the IE Group at KSC. With respect to the specific applications at KSC, particular emphasis is placed on the use of the Demos software package (Lumina Decision Systems, 1993).

dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing.

PubMed

Gruber, Bernd; Unmack, Peter J; Berry, Oliver F; Georges, Arthur

2018-05-01

Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data-therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well-established format-genlight from the adegenet package-as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub. © 2017 John Wiley & Sons Ltd.

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

Image analysis software versus direct anthropometry for breast measurements.

PubMed

Quieregatto, Paulo Rogério; Hochman, Bernardo; Furtado, Fabianne; Machado, Aline Fernanda Perez; Sabino Neto, Miguel; Ferreira, Lydia Masako

2014-10-01

To compare breast measurements performed using the software packages ImageTool(r), AutoCAD(r) and Adobe Photoshop(r) with direct anthropometric measurements. Points were marked on the breasts and arms of 40 volunteer women aged between 18 and 60 years. When connecting the points, seven linear segments and one angular measurement on each half of the body, and one medial segment common to both body halves were defined. The volunteers were photographed in a standardized manner. Photogrammetric measurements were performed by three independent observers using the three software packages and compared to direct anthropometric measurements made with calipers and a protractor. Measurements obtained with AutoCAD(r) were the most reproducible and those made with ImageTool(r) were the most similar to direct anthropometry, while measurements with Adobe Photoshop(r) showed the largest differences. Except for angular measurements, significant differences were found between measurements of line segments made using the three software packages and those obtained by direct anthropometry. AutoCAD(r) provided the highest precision and intermediate accuracy; ImageTool(r) had the highest accuracy and lowest precision; and Adobe Photoshop(r) showed intermediate precision and the worst accuracy among the three software packages.

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.

A User's Guide to the Meta-Analysis of Research Studies. Meta-Stat: Software To Aid in the Meta-Analysis of Research Findings.

ERIC Educational Resources Information Center

Rudner, Lawrence M.; Glass Gene V.; Evartt, David L.; Emery, Patrick J.

This manual and the accompanying software are intended to provide a step-by-step guide to conducting a meta-analytic study along with references for further reading and free high-quality software, "Meta-Stat.""Meta-Stat" is a comprehensive package designed to help in the meta-analysis of research studies in the social and behavioral sciences.…

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

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.

Aviation Design Software

NASA Technical Reports Server (NTRS)

1997-01-01

DARcorporation developed a General Aviation CAD package through a Small Business Innovation Research contract from Langley Research Center. This affordable, user-friendly preliminary design system for General Aviation aircraft runs on the popular 486 IBM-compatible personal computers. Individuals taking the home-built approach, small manufacturers of General Aviation airplanes, as well as students and others interested in the analysis and design of aircraft are possible users of the package. The software can cut design and development time in half.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.

PubMed

Solernou, Albert; Hanson, Benjamin S; Richardson, Robin A; Welch, Robert; Read, Daniel J; Harlen, Oliver G; Harris, Sarah A

2018-03-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package.

Software engineering the mixed model for genome-wide association studies on large samples.

PubMed

Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

2009-11-01

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

The aquamet Package for R: A Tool for Use with the National Rivers and Streams Assessment

EPA Science Inventory

The use of R software in environmental data analysis has become increasingly common because it is very powerful, versatile and available free of charge, with hundreds of contributed add-on packages available that perform almost every conceivable type of analysis or task. The Envi...

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.

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.

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.

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

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. Kent; Greene, Emily A.; Pence, William

1993-05-01

FTOOLS, a highly modular collection of 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 Research Archive 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 common to high energy astrophysics data sets. 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.

Geospatial approach towards enumerative analysis of suspended sediment concentration for Ganges-Brahmaputra Bay

NASA Astrophysics Data System (ADS)

Pandey, Palak; Kunte, Pravin D.

2016-10-01

This study presents an easy, modular, user-friendly, and flexible software package for processing of Landsat 7 ETM and Landsat 8 OLI-TIRS data for estimating suspended particulate matter concentrations in the coastal waters. This package includes 1) algorithm developed using freely downloadable SCILAB package, 2) ERDAS Models for iterative processing of Landsat images and 3) ArcMAP tool for plotting and map making. Utilizing SCILAB package, a module is written for geometric corrections, radiometric corrections and obtaining normalized water-leaving reflectance by incorporating Landsat 8 OLI-TIRS and Landsat 7 ETM+ data. Using ERDAS models, a sequence of modules are developed for iterative processing of Landsat images and estimating suspended particulate matter concentrations. Processed images are used for preparing suspended sediment concentration maps. The applicability of this software package is demonstrated by estimating and plotting seasonal suspended sediment concentration maps off the Bengal delta. The software is flexible enough to accommodate other remotely sensed data like Ocean Color monitor (OCM) data, Indian Remote Sensing data (IRS), MODIS data etc. by replacing a few parameters in the algorithm, for estimating suspended sediment concentration in coastal waters.

Comparison of two freely available software packages for mass spectrometry imaging data analysis using brains from morphine addicted rats.

PubMed

Bodzon-Kulakowska, Anna; Marszalek-Grabska, Marta; Antolak, Anna; Drabik, Anna; Kotlinska, Jolanta H; Suder, Piotr

Data analysis from mass spectrometry imaging (MSI) imaging experiments is a very complex task. Most of the software packages devoted to this purpose are designed by the mass spectrometer manufacturers and, thus, are not freely available. Laboratories developing their own MS-imaging sources usually do not have access to the commercial software, and they must rely on the freely available programs. The most recognized ones are BioMap, developed by Novartis under Interactive Data Language (IDL), and Datacube, developed by the Dutch Foundation for Fundamental Research of Matter (FOM-Amolf). These two systems were used here for the analysis of images received from rat brain tissues subjected to morphine influence and their capabilities were compared in terms of ease of use and the quality of obtained results.

Real Time Metrology Using Heterodyne Interferometry

NASA Astrophysics Data System (ADS)

Evans, Joseph T..., Jr.

1983-11-01

The Air Force Weapons Laboratory (AFWL) located at Albuquerque, NM has developed a digital heterodyne interferometer capable of real-time, closed loop analysis and control of adaptive optics. The device uses independent phase modulation of two orthogonal polarizations of an argon ion laser to produce a temporally phase modulated interferogram of the test object in a Twyman-Green interferometer. Differential phase detection under the control of a Data General minicomputer helps reconstruct the phase front without noise effects from amplitude modulation in the optical train. The system consists of the interferometer optics, phase detection circuitry, and the minicomputer, allowing for complete software control of the process. The software has been unified into a powerful package that performs automatic data acquisition, OPD reconstruction, and Zernike analysis of the resulting wavefront. The minicomputer has the capability to control external devices so that closed loop analysis and control is possible. New software under development will provide a framework of data acquisition, display, and storage packages which can be integrated with analysis and control packages customized to the user's needs. Preliminary measurements with the system show that it is noise limited by laser beam phase quality and vibration of the optics. Active measures are necessary to reduce the impact of these noise sources.

ggCyto: Next Generation Open-Source Visualization Software for Cytometry.

PubMed

Van, Phu; Jiang, Wenxin; Gottardo, Raphael; Finak, Greg

2018-06-01

Open source software for computational cytometry has gained in popularity over the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have highlighted the importance of efforts to standardize both experimental and computational aspects of cytometry data analysis. The R/BioConductor platform hosts the largest collection of open source cytometry software covering all aspects of data analysis and providing infrastructure to represent and analyze cytometry data with all relevant experimental, gating, and cell population annotations enabling fully reproducible data analysis. Data visualization frameworks to support this infrastructure have lagged behind. ggCyto is a new open-source BioConductor software package for cytometry data visualization built on ggplot2 that enables ggplot-like functionality with the core BioConductor flow cytometry data structures. Amongst its features are the ability to transform data and axes on-the-fly using cytometry-specific transformations, plot faceting by experimental meta-data variables, and partial matching of channel, marker and cell populations names to the contents of the BioConductor cytometry data structures. We demonstrate the salient features of the package using publicly available cytometry data with complete reproducible examples in a supplementary material vignette. https://bioconductor.org/packages/devel/bioc/html/ggcyto.html. gfinak@fredhutch.org. Supplementary data are available at Bioinformatics online and at http://rglab.org/ggcyto/.

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…

Reviews of Instructional Software in Scholarly Journals: A Selected Bibliography.

ERIC Educational Resources Information Center

Bantz, David A.; And Others

This bibliography lists reviews of more than 100 instructional software packages, which are arranged alphabetically by discipline. Information provided for each entry includes the topical emphasis, type of software (i.e., simulation, tutorial, analysis tool, test generator, database, writing tool, drill, plotting tool, videodisc), the journal…

Buying in to bioinformatics: an introduction to commercial sequence analysis software

PubMed Central

2015-01-01

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. PMID:25183247

Buying in to bioinformatics: an introduction to commercial sequence analysis software.

PubMed

Smith, David Roy

2015-07-01

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. © The Author 2014. Published by Oxford University Press.

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

Software Package Completed for Alloy Design at the Atomic Level

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Noebe, Ronald D.; Abel, Phillip B.; Good, Brian S.

2001-01-01

As a result of a multidisciplinary effort involving solid-state physics, quantum mechanics, and materials and surface science, the first version of a software package dedicated to the atomistic analysis of multicomponent systems was recently completed. Based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of alloy and surface energetics, this package includes modules devoted to the analysis of many essential features that characterize any given alloy or surface system, including (1) surface structure analysis, (2) surface segregation, (3) surface alloying, (4) bulk crystalline material properties and atomic defect structures, and (5) thermal processes that allow us to perform phase diagram calculations. All the modules of this Alloy Design Workbench 1.0 (ADW 1.0) are designed to run in PC and workstation environments, and their operation and performance are substantially linked to the needs of the user and the specific application.

PLACE: an open-source python package for laboratory automation, control, and experimentation.

PubMed

Johnson, Jami L; Tom Wörden, Henrik; van Wijk, Kasper

2015-02-01

In modern laboratories, software can drive the full experimental process from data acquisition to storage, processing, and analysis. The automation of laboratory data acquisition is an important consideration for every laboratory. When implementing a laboratory automation scheme, important parameters include its reliability, time to implement, adaptability, and compatibility with software used at other stages of experimentation. In this article, we present an open-source, flexible, and extensible Python package for Laboratory Automation, Control, and Experimentation (PLACE). The package uses modular organization and clear design principles; therefore, it can be easily customized or expanded to meet the needs of diverse laboratories. We discuss the organization of PLACE, data-handling considerations, and then present an example using PLACE for laser-ultrasound experiments. Finally, we demonstrate the seamless transition to post-processing and analysis with Python through the development of an analysis module for data produced by PLACE automation. © 2014 Society for Laboratory Automation and Screening.

FTOOLS: A general package of software to manipulate FITS files

NASA Astrophysics Data System (ADS)

Blackburn, J. K.; Shaw, R. A.; Payne, H. E.; Hayes, J. J. E.; Heasarc

1999-12-01

FTOOLS, a highly modular collection of 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 Research Archive Center) at NASA's Goddard Space Flight Center. The FTOOLS package contains many utility programs which perform modular tasks on any FITS image or table, as well as higher-level analysis programs designed specifically for data from current and past high energy astrophysics missions. The utility programs for FITS tables are especially rich and powerful, and provide functions for 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 FTOOLS programs can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. FTOOLS development began in 1991 and has produced the main set of data analysis software for the current ASCA and RXTE space missions and for other archival sets of X-ray and gamma-ray data. The FTOOLS software package is supported on most UNIX platforms and on Windows machines. The user interface is controlled by standard parameter files that are very similar to those used by IRAF. The package is self documenting through a stand alone help task called fhelp. 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.

Software package for modeling spin–orbit motion in storage rings

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

Zyuzin, D. V., E-mail: d.zyuzin@fz-juelich.de

2015-12-15

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 10{sup 6}–10{sup 9} particles in a beam during 10{supmore » 9} turns in an accelerator (about 10{sup 12}–10{sup 15} integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin–orbit dynamics.« less

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr.

PubMed

Privé, Florian; Aschard, Hugues; Ziyatdinov, Andrey; Blum, Michael G B

2017-03-30

Genome-wide datasets produced for association studies have dramatically increased in size over the past few years, with modern datasets commonly including millions of variants measured in dozens of thousands of individuals. This increase in data size is a major challenge severely slowing down genomic analyses, leading to some software becoming obsolete and researchers having limited access to diverse analysis tools. Here we present two R packages, bigstatsr and bigsnpr, allowing for the analysis of large scale genomic data to be performed within R. To address large data size, the packages use memory-mapping for accessing data matrices stored on disk instead of in RAM. To perform data pre-processing and data analysis, the packages integrate most of the tools that are commonly used, either through transparent system calls to existing software, or through updated or improved implementation of existing methods. In particular, the packages implement fast and accurate computations of principal component analysis and association studies, functions to remove SNPs in linkage disequilibrium and algorithms to learn polygenic risk scores on millions of SNPs. We illustrate applications of the two R packages by analyzing a case-control genomic dataset for celiac disease, performing an association study and computing Polygenic Risk Scores. Finally, we demonstrate the scalability of the R packages by analyzing a simulated genome-wide dataset including 500,000 individuals and 1 million markers on a single desktop computer. https://privefl.github.io/bigstatsr/ & https://privefl.github.io/bigsnpr/. florian.prive@univ-grenoble-alpes.fr & michael.blum@univ-grenoble-alpes.fr. Supplementary materials are available at Bioinformatics online.

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.

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.

PubMed

Gaspar, John M; Hart, Ronald P

2017-11-29

DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements. DMRfinder is a novel computational pipeline that identifies differentially methylated regions efficiently. Following alignment, DMRfinder extracts methylation counts and performs a modified single-linkage clustering of methylation sites into genomic regions. It then compares methylation levels using beta-binomial hierarchical modeling and Wald tests. Among its innovative attributes are the analyses of novel methylation sites and methylation linkage, as well as the simultaneous statistical analysis of multiple sample groups. To demonstrate its efficiency, DMRfinder is benchmarked against other computational approaches using a large published dataset. Contrasting two replicates of the same sample yielded minimal genomic regions with DMRfinder, whereas two alternative software packages reported a substantial number of false positives. Further analyses of biological samples revealed fundamental differences between DMRfinder and another software package, despite the fact that they utilize the same underlying statistical basis. For each step, DMRfinder completed the analysis in a fraction of the time required by other software. Among the computational approaches for identifying differentially methylated regions from high-throughput bisulfite sequencing datasets, DMRfinder is the first that integrates all the post-alignment steps in a single package. Compared to other software, DMRfinder is extremely efficient and unbiased in this process. DMRfinder is free and open-source software, available on GitHub ( github.com/jsh58/DMRfinder ); it is written in Python and R, and is supported on Linux.

Analytical Design Package (ADP2): A computer aided engineering tool for aircraft transparency design

NASA Technical Reports Server (NTRS)

Wuerer, J. E.; Gran, M.; Held, T. W.

1994-01-01

The Analytical Design Package (ADP2) is being developed as a part of the Air Force Frameless Transparency Program (FTP). ADP2 is an integrated design tool consisting of existing analysis codes and Computer Aided Engineering (CAE) software. The objective of the ADP2 is to develop and confirm an integrated design methodology for frameless transparencies, related aircraft interfaces, and their corresponding tooling. The application of this methodology will generate high confidence for achieving a qualified part prior to mold fabrication. ADP2 is a customized integration of analysis codes, CAE software, and material databases. The primary CAE integration tool for the ADP2 is P3/PATRAN, a commercial-off-the-shelf (COTS) software tool. The open architecture of P3/PATRAN allows customized installations with different applications modules for specific site requirements. Integration of material databases allows the engineer to select a material, and those material properties are automatically called into the relevant analysis code. The ADP2 materials database will be composed of four independent schemas: CAE Design, Processing, Testing, and Logistics Support. The design of ADP2 places major emphasis on the seamless integration of CAE and analysis modules with a single intuitive graphical interface. This tool is being designed to serve and be used by an entire project team, i.e., analysts, designers, materials experts, and managers. The final version of the software will be delivered to the Air Force in Jan. 1994. The Analytical Design Package (ADP2) will then be ready for transfer to industry. The package will be capable of a wide range of design and manufacturing applications.

Design Optimization Toolkit: Users' Manual

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

Aguilo Valentin, Miguel Alejandro

The Design Optimization Toolkit (DOTk) is a stand-alone C++ software package intended to solve complex design optimization problems. DOTk software package provides a range of solution methods that are suited for gradient/nongradient-based optimization, large scale constrained optimization, and topology optimization. DOTk was design to have a flexible user interface to allow easy access to DOTk solution methods from external engineering software packages. This inherent flexibility makes DOTk barely intrusive to other engineering software packages. As part of this inherent flexibility, DOTk software package provides an easy-to-use MATLAB interface that enables users to call DOTk solution methods directly from the MATLABmore » command window.« less

XAPiir: A recursive digital filtering package

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

Harris, D.

1990-09-21

XAPiir is a basic recursive digital filtering package, containing both design and implementation subroutines. XAPiir was developed for the experimental array processor (XAP) software package, and is written in FORTRAN. However, it is intended to be incorporated into any general- or special-purpose signal analysis program. It replaces the older package RECFIL, offering several enhancements. RECFIL is used in several large analysis programs developed at LLNL, including the seismic analysis package SAC, several expert systems (NORSEA and NETSEA), and two general purpose signal analysis packages (SIG and VIEW). This report is divided into two sections: the first describes the use ofmore » the subroutine package, and the second, its internal organization. In the first section, the filter design problem is briefly reviewed, along with the definitions of the filter design parameters and their relationship to the subroutine input parameters. In the second section, the internal organization is documented to simplify maintenance and extensions to the package. 5 refs., 9 figs.« less

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

2017-11-01

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for online validation of Monte Carlo event samples through a web interface.

Myocardial blood flow quantification by Rb-82 cardiac PET/CT: A detailed reproducibility study between two semi-automatic analysis programs.

PubMed

Dunet, Vincent; Klein, Ran; Allenbach, Gilles; Renaud, Jennifer; deKemp, Robert A; Prior, John O

2016-06-01

Several analysis software packages for myocardial blood flow (MBF) quantification from cardiac PET studies exist, but they have not been compared using concordance analysis, which can characterize precision and bias separately. Reproducible measurements are needed for quantification to fully develop its clinical potential. Fifty-one patients underwent dynamic Rb-82 PET at rest and during adenosine stress. Data were processed with PMOD and FlowQuant (Lortie model). MBF and myocardial flow reserve (MFR) polar maps were quantified and analyzed using a 17-segment model. Comparisons used Pearson's correlation ρ (measuring precision), Bland and Altman limit-of-agreement and Lin's concordance correlation ρc = ρ·C b (C b measuring systematic bias). Lin's concordance and Pearson's correlation values were very similar, suggesting no systematic bias between software packages with an excellent precision ρ for MBF (ρ = 0.97, ρc = 0.96, C b = 0.99) and good precision for MFR (ρ = 0.83, ρc = 0.76, C b = 0.92). On a per-segment basis, no mean bias was observed on Bland-Altman plots, although PMOD provided slightly higher values than FlowQuant at higher MBF and MFR values (P < .0001). Concordance between software packages was excellent for MBF and MFR, despite higher values by PMOD at higher MBF values. Both software packages can be used interchangeably for quantification in daily practice of Rb-82 cardiac PET.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

PubMed Central

Solernou, Albert

2018-01-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package. PMID:29570700

Analysing the Zenith Tropospheric Delay Estimates in On-line Precise Point Positioning (PPP) Services and PPP Software Packages.

PubMed

Mendez Astudillo, Jorge; Lau, Lawrence; Tang, Yu-Ting; Moore, Terry

2018-02-14

As Global Navigation Satellite System (GNSS) signals travel through the troposphere, a tropospheric delay occurs due to a change in the refractive index of the medium. The Precise Point Positioning (PPP) technique can achieve centimeter/millimeter positioning accuracy with only one GNSS receiver. The Zenith Tropospheric Delay (ZTD) is estimated alongside with the position unknowns in PPP. Estimated ZTD can be very useful for meteorological applications, an example is the estimation of water vapor content in the atmosphere from the estimated ZTD. PPP is implemented with different algorithms and models in online services and software packages. In this study, a performance assessment with analysis of ZTD estimates from three PPP online services and three software packages is presented. The main contribution of this paper is to show the accuracy of ZTD estimation achievable in PPP. The analysis also provides the GNSS users and researchers the insight of the processing algorithm dependence and impact on PPP ZTD estimation. Observation data of eight whole days from a total of nine International GNSS Service (IGS) tracking stations spread in the northern hemisphere, the equatorial region and the southern hemisphere is used in this analysis. The PPP ZTD estimates are compared with the ZTD obtained from the IGS tropospheric product of the same days. The estimates of two of the three online PPP services show good agreement (<1 cm) with the IGS ZTD values at the northern and southern hemisphere stations. The results also show that the online PPP services perform better than the selected PPP software packages at all stations.

Neural Network Prototyping Package Within IRAF

NASA Technical Reports Server (NTRS)

Bazell, David

1997-01-01

The purpose of this contract was to develop a neural network package within the IRAF environment to allow users to easily understand and use different neural network algorithms the analysis of astronomical data. The package was developed for use within IRAF to allow portability to different computing environments and to provide a familiar and easy to use interface with the routines. In addition to developing the software and supporting documentation, we planned to use the system for the analysis of several sample problems to prove its viability and usefulness.

The LARSYS educational package: Instructor's notes. [instructional materials for training people to analyze remotely sensed data

NASA Technical Reports Server (NTRS)

Lindenlaub, J. C.; Davis, S. M.

1974-01-01

Materials are presented for assisting instructors in teaching the LARSYS Educational Package, which is a set of instructional materials to train people to analyze remotely sensed multispectral data. The seven units of the package are described. These units are: quantitative remote sensing, overview of the LARSYS software system, the 2780 remote terminal, demonstration of LARSYS on the 2780 remote terminal, exercises, guide to multispectral data analysis, and a case study using LARSYS for analysis of LANDSAT data.

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

ATTIRE (analytical tools for thermal infrared engineering): A sensor simulation and modeling package

NASA Astrophysics Data System (ADS)

Jaggi, S.

1993-02-01

The Advanced Sensor Development Laboratory (ASDL) at the Stennis Space Center develops, maintains and calibrates remote sensing instruments for the National Aeronautics & Space Administration (NASA). To perform system design trade-offs, analysis, and establish system parameters, ASDL has developed a software package for analytical simulation of sensor systems. This package called 'Analytical Tools for Thermal InfraRed Engineering' - ATTIRE, simulates the various components of a sensor system. The software allows each subsystem of the sensor to be analyzed independently for its performance. These performance parameters are then integrated to obtain system level information such as Signal-to-Noise Ratio (SNR), Noise Equivalent Radiance (NER), Noise Equivalent Temperature Difference (NETD) etc. This paper describes the uses of the package and the physics that were used to derive the performance parameters.

Advances in the REDCAT software package

PubMed Central

2013-01-01

Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development. PMID:24098943

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores.

PubMed

Chikkagoudar, Satish; Wang, Kai; Li, Mingyao

2011-05-26

Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

PubMed Central

2011-01-01

Background Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Findings Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. Conclusions GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/. PMID:21615923

Community-driven computational biology with Debian Linux.

PubMed

Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

2010-12-21

The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

Integrating Statistical Visualization Research into the Political Science Classroom

ERIC Educational Resources Information Center

Draper, Geoffrey M.; Liu, Baodong; Riesenfeld, Richard F.

2011-01-01

The use of computer software to facilitate learning in political science courses is well established. However, the statistical software packages used in many political science courses can be difficult to use and counter-intuitive. We describe the results of a preliminary user study suggesting that visually-oriented analysis software can help…

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.

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

PubMed

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

Computer Lab Tools for Science: An Analysis of Commercially Available Science Interfacing Software for Microcomputers. A Quarterly Report.

ERIC Educational Resources Information Center

Weaver, Dave

Science interfacing packages (also known as microcomputer-based laboratories or probeware) generally consist of a set of programs on disks, a user's manual, and hardware which includes one or more sensory devices. Together with a microcomputer they combine to make a powerful data acquisition and analysis tool. Packages are available for accurately…

Analysis of half diallel mating designs I: a practical analysis procedure for ANOVA approximation.

Treesearch

G.R. Johnson; J.N. King

1998-01-01

Procedures to analyze half-diallel mating designs using the SAS statistical package are presented. The procedure requires two runs of PROC and VARCOMP and results in estimates of additive and non-additive genetic variation. The procedures described can be modified to work on most statistical software packages which can compute variance component estimates. The...

The CASA Software Package

NASA Astrophysics Data System (ADS)

Petry, Dirk

2018-03-01

CASA is the standard science data analysis package for ALMA and VLA but it can also be used for the analysis of data from other observatories. In this talk, I will give an overview of the structure and features of CASA, who develops it, and the present status and plans, and then show typical analysis workflows for ALMA data with special emphasis on the handling of single dish data and its combination with interferometric data.

Use of the MATRIXx Integrated Toolkit on the Microwave Anisotropy Probe Attitude Control System

NASA Technical Reports Server (NTRS)

Ward, David K.; Andrews, Stephen F.; McComas, David C.; ODonnell, James R., Jr.

1999-01-01

Recent advances in analytical software tools allow the analysis, simulation, flight code, and documentation of an algorithm to be generated from a single source, all within one integrated analytical design package. NASA's Microwave Anisotropy Probe project has used one such package, Integrated Systems' MATRIXx suite, in the design of the spacecraft's Attitude Control System. The project's experience with the linear analysis, simulation, code generation, and documentation tools will be presented and compared with more traditional development tools. In particular, the quality of the flight software generated will be examined in detail. Finally, lessons learned on each of the tools will be shared.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.; Olariu, Stephen

1995-01-01

The primary goal of this grant has been the design and implementation of software to be used in the conceptual design of aerospace vehicles particularly focused on the elements of geometric design, graphical user interfaces, and the interaction of the multitude of software typically used in this engineering environment. This has resulted in the development of several analysis packages and design studies. These include two major software systems currently used in the conceptual level design of aerospace vehicles. These tools are SMART, the Solid Modeling Aerospace Research Tool, and EASIE, the Environment for Software Integration and Execution. Additional software tools were designed and implemented to address the needs of the engineer working in the conceptual design environment. SMART provides conceptual designers with a rapid prototyping capability and several engineering analysis capabilities. In addition, SMART has a carefully engineered user interface that makes it easy to learn and use. Finally, a number of specialty characteristics have been built into SMART which allow it to be used efficiently as a front end geometry processor for other analysis packages. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand-alone, analysis codes. Resulting in a streamlining of the exchange of data between programs reducing errors and improving the efficiency. EASIE provides both a methodology and a collection of software tools to ease the task of coordinating engineering design and analysis codes.

ULFEM time series analysis package

USGS Publications Warehouse

Karl, Susan M.; McPhee, Darcy K.; Glen, Jonathan M. G.; Klemperer, Simon L.

2013-01-01

This manual describes how to use the Ultra-Low-Frequency ElectroMagnetic (ULFEM) software package. Casual users can read the quick-start guide and will probably not need any more information than this. For users who may wish to modify the code, we provide further description of the routines.

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.

Analyzing qualitative data with computer software.

PubMed Central

Weitzman, E A

1999-01-01

OBJECTIVE: To provide health services researchers with an overview of the qualitative data analysis process and the role of software within it; to provide a principled approach to choosing among software packages to support qualitative data analysis; to alert researchers to the potential benefits and limitations of such software; and to provide an overview of the developments to be expected in the field in the near future. DATA SOURCES, STUDY DESIGN, METHODS: This article does not include reports of empirical research. CONCLUSIONS: Software for qualitative data analysis can benefit the researcher in terms of speed, consistency, rigor, and access to analytic methods not available by hand. Software, however, is not a replacement for methodological training. PMID:10591282

Evaluation of Solid Rocket Motor Component Data Using a Commercially Available Statistical Software Package

NASA Technical Reports Server (NTRS)

Stefanski, Philip L.

2015-01-01

Commercially available software packages today allow users to quickly perform the routine evaluations of (1) descriptive statistics to numerically and graphically summarize both sample and population data, (2) inferential statistics that draws conclusions about a given population from samples taken of it, (3) probability determinations that can be used to generate estimates of reliability allowables, and finally (4) the setup of designed experiments and analysis of their data to identify significant material and process characteristics for application in both product manufacturing and performance enhancement. This paper presents examples of analysis and experimental design work that has been conducted using Statgraphics®(Registered Trademark) statistical software to obtain useful information with regard to solid rocket motor propellants and internal insulation material. Data were obtained from a number of programs (Shuttle, Constellation, and Space Launch System) and sources that include solid propellant burn rate strands, tensile specimens, sub-scale test motors, full-scale operational motors, rubber insulation specimens, and sub-scale rubber insulation analog samples. Besides facilitating the experimental design process to yield meaningful results, statistical software has demonstrated its ability to quickly perform complex data analyses and yield significant findings that might otherwise have gone unnoticed. One caveat to these successes is that useful results not only derive from the inherent power of the software package, but also from the skill and understanding of the data analyst.

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.

MOFA Software for the COBRA Toolbox

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

Griesemer, Marc; Navid, Ali

MOFA-COBRA is a software code for Matlab that performs Multi-Objective Flux Analysis (MOFA), a solving of linear programming problems. Teh leading software package for conducting different types of analyses using constrain-based models is the COBRA Toolbox for Matlab. MOFA-COBRA is an added tool for COBRA that solves multi-objective problems using a novel algorithm.

EPA and EFSA approaches for Benchmark Dose modeling

EPA Science Inventory

Benchmark dose (BMD) modeling has become the preferred approach in the analysis of toxicological dose-response data for the purpose of deriving human health toxicity values. The software packages most often used are Benchmark Dose Software (BMDS, developed by EPA) and PROAST (de...

ENVIRONMENTAL METHODS TESTING SITE PROJECT: DATA MANAGEMENT PROCEDURES PLAN

EPA Science Inventory

The Environmental Methods Testing Site (EMTS) Data Management Procedures Plan identifies the computer hardware and software resources used in the EMTS project. It identifies the major software packages that are available for use by principal investigators for the analysis of data...

User-driven integrated software lives: ``Paleomag'' paleomagnetics analysis on the Macintosh

NASA Astrophysics Data System (ADS)

Jones, Craig H.

2002-12-01

"PaleoMag," a paleomagnetics analysis package originally developed for the Macintosh operating system in 1988, allows examination of demagnetization of individual samples and analysis of directional data from collections of samples. Prior to recent reinvigorated development of the software for both Macintosh and Windows, it was widely used despite not running properly on machines and operating systems sold after 1995. This somewhat surprising situation demonstrates that there is a continued need for integrated analysis software within the earth sciences, in addition to well-developed scripting and batch-mode software. One distinct advantage of software like PaleoMag is in the ability to combine quality control with analysis within a unique graphical environment. Because such demands are frequent within the earth sciences, means of nurturing the development of similar software should be found.

Mass decomposition of galaxies using DECA software package

NASA Astrophysics Data System (ADS)

Mosenkov, A. V.

2014-01-01

The new DECA software package, which is designed to perform photometric analysis of the images of disk and elliptical galaxies having a regular structure, is presented. DECA is written in Python interpreted language and combines the capabilities of several widely used packages for astronomical data processing such as IRAF, SExtractor, and the GALFIT code used to perform two-dimensional decomposition of galaxy images into several photometric components (bulge+disk). DECA has the advantage that it can be applied to large samples of galaxies with different orientations with respect to the line of sight (including edge-on galaxies) and requires minimum human intervention. Examples of using the package to study a sample of simulated galaxy images and a sample of real objects are shown to demonstrate that DECA can be a reliable tool for the study of the structure of galaxies.

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.

An Innovative Learning Model for Computation in First Year Mathematics

ERIC Educational Resources Information Center

Tonkes, E. J.; Loch, B. I.; Stace, A. W.

2005-01-01

MATLAB is a sophisticated software tool for numerical analysis and visualization. The University of Queensland has adopted Matlab as its official teaching package across large first year mathematics courses. In the past, the package has met severe resistance from students who have not appreciated their computational experience. Several main…

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…

Microcomputer Applications in Local Assessment Systems.

ERIC Educational Resources Information Center

Harnisch, Delwyn L.; And Others

The capabilities and hardware requirements of four microcomputer software packages produced by the Office of Educational Testing, Research and Service at the University of Illinois at Urbana-Champaign are described. These programs are: (1) the Scan-Tron Forms Analysis Package Version 2.0, an interface between an IBM-compatible and a Scan-Tron…

COLDMON -- Cold File Analysis Package

NASA Astrophysics Data System (ADS)

Rawlinson, D. J.

The COLDMON package has been written to allow system managers to identify those items of software that are not used (or used infrequently) on their systems. It consists of a few command procedures and a Fortran program to analyze the results. It makes use of the AUDIT facility and security ACLs in VMS.

Cross-platform validation and analysis environment for particle physics

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

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for onlinemore » validation of Monte Carlo event samples through a web interface.« less

The International Atomic Energy Agency software package for the analysis of scintigraphic renal dynamic studies: a tool for the clinician, teacher, and researcher.

PubMed

Zaknun, John J; Rajabi, Hossein; Piepsz, Amy; Roca, Isabel; Dondi, Maurizio

2011-01-01

Under the auspices of the International Atomic Energy Agency, a new-generation, platform-independent, and x86-compatible software package was developed for the analysis of scintigraphic renal dynamic imaging studies. It provides nuclear medicine professionals cost-free access to the most recent developments in the field. The software package is a step forward towards harmonization and standardization. Embedded functionalities render it a suitable tool for education, research, and for receiving distant expert's opinions. Another objective of this effort is to allow introducing clinically useful parameters of drainage, including normalized residual activity and outflow efficiency. Furthermore, it provides an effective teaching tool for young professionals who are being introduced to dynamic kidney studies by selected teaching case studies. The software facilitates a better understanding through practically approaching different variables and settings and their effect on the numerical results. An effort was made to introduce instruments of quality assurance at the various levels of the program's execution, including visual inspection and automatic detection and correction of patient's motion, automatic placement of regions of interest around the kidneys, cortical regions, and placement of reproducible background region on both primary dynamic and on postmicturition studies. The user can calculate the differential renal function through 2 independent methods, the integral or the Rutland-Patlak approaches. Standardized digital reports, storage and retrieval of regions of interest, and built-in database operations allow the generation and tracing of full image reports and of numerical outputs. The software package is undergoing quality assurance procedures to verify the accuracy and the interuser reproducibility with the final aim of launching the program for use by professionals and teaching institutions worldwide. Copyright © 2011 Elsevier Inc. All rights reserved.

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.

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.

IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java

PubMed Central

Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM’s image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis. PMID:25612319

IQM: an extensible and portable open source application for image and signal analysis in Java.

PubMed

Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM's image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis.

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

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel

PubMed Central

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-01-01

Background Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. Findings The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Conclusion Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software. PMID:19852806

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.

PubMed

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-10-23

Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.

Around and about an application of the GAMLSS package to non-stationary flood frequency analysis

NASA Astrophysics Data System (ADS)

Debele, S. E.; Bogdanowicz, E.; Strupczewski, W. G.

2017-08-01

The non-stationarity of hydrologic processes due to climate change or human activities is challenging for the researchers and practitioners. However, the practical requirements for taking into account non-stationarity as a support in decision-making procedures exceed the up-to-date development of the theory and the of software. Currently, the most popular and freely available software package that allows for non-stationary statistical analysis is the GAMLSS (generalized additive models for location, scale and shape) package. GAMLSS has been used in a variety of fields. There are also several papers recommending GAMLSS in hydrological problems; however, there are still important issues which have not previously been discussed concerning mainly GAMLSS applicability not only for research and academic purposes, but also in a design practice. In this paper, we present a summary of our experiences in the implementation of GAMLSS to non-stationary flood frequency analysis, highlighting its advantages and pointing out weaknesses with regard to methodological and practical topics.

Motofit - integrating neutron reflectometry acquisition, reduction and analysis into one, easy to use, package

NASA Astrophysics Data System (ADS)

Nelson, Andrew

2010-11-01

The efficient use of complex neutron scattering instruments is often hindered by the complex nature of their operating software. This complexity exists at each experimental step: data acquisition, reduction and analysis, with each step being as important as the previous. For example, whilst command line interfaces are powerful at automated acquisition they often reduce accessibility by novice users and sometimes reduce the efficiency for advanced users. One solution to this is the development of a graphical user interface which allows the user to operate the instrument by a simple and intuitive "push button" approach. This approach was taken by the Motofit software package for analysis of multiple contrast reflectometry data. Here we describe the extension of this package to cover the data acquisition and reduction steps for the Platypus time-of-flight neutron reflectometer. Consequently, the complete operation of an instrument is integrated into a single, easy to use, program, leading to efficient instrument usage.

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

PubMed

Tubiana, Luca; Polles, Guido; Orlandini, Enzo; Micheletti, Cristian

2018-06-07

The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .

pyLIMA: An Open-source Package for Microlensing Modeling. I. Presentation of the Software and Analysis of Single-lens Models

NASA Astrophysics Data System (ADS)

Bachelet, E.; Norbury, M.; Bozza, V.; Street, R.

2017-11-01

Microlensing is a unique tool, capable of detecting the “cold” planets between ˜1 and 10 au from their host stars and even unbound “free-floating” planets. This regime has been poorly sampled to date owing to the limitations of alternative planet-finding methods, but a watershed in discoveries is anticipated in the near future thanks to the planned microlensing surveys of WFIRST-AFTA and Euclid's Extended Mission. Of the many challenges inherent in these missions, the modeling of microlensing events will be of primary importance, yet it is often time-consuming, complex, and perceived as a daunting barrier to participation in the field. The large scale of future survey data products will require thorough but efficient modeling software, but, unlike other areas of exoplanet research, microlensing currently lacks a publicly available, well-documented package to conduct this type of analysis. We present version 1.0 of the python Lightcurve Identification and Microlensing Analysis (pyLIMA). This software is written in Python and uses existing packages as much as possible to make it widely accessible. In this paper, we describe the overall architecture of the software and the core modules for modeling single-lens events. To verify the performance of this software, we use it to model both real data sets from events published in the literature and generated test data produced using pyLIMA's simulation module. The results demonstrate that pyLIMA is an efficient tool for microlensing modeling. We will expand pyLIMA to consider more complex phenomena in the following papers.

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)

influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments.

PubMed

Sokol, Serguei; Millard, Pierre; Portais, Jean-Charles

2012-03-01

The problem of stationary metabolic flux analysis based on isotope labelling experiments first appeared in the early 1950s and was basically solved in early 2000s. Several algorithms and software packages are available for this problem. However, the generic stochastic algorithms (simulated annealing or evolution algorithms) currently used in these software require a lot of time to achieve acceptable precision. For deterministic algorithms, a common drawback is the lack of convergence stability for ill-conditioned systems or when started from a random point. In this article, we present a new deterministic algorithm with significantly increased numerical stability and accuracy of flux estimation compared with commonly used algorithms. It requires relatively short CPU time (from several seconds to several minutes with a standard PC architecture) to estimate fluxes in the central carbon metabolism network of Escherichia coli. The software package influx_s implementing this algorithm is distributed under an OpenSource licence at http://metasys.insa-toulouse.fr/software/influx/. Supplementary data are available at Bioinformatics online.

An Aquatic Acoustic Metrics Interface Utility for Underwater Sound Monitoring and Analysis

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

Ren, Huiying; Halvorsen, Michele B.; Deng, Zhiqun

Fishes and other marine mammals suffer a range of potential effects from intense sound sources generated by anthropogenic underwater processes such as pile driving, shipping, sonars, and underwater blasting. Several underwater sound recording devices (USR) were built to monitor the acoustic sound pressure waves generated by those anthropogenic underwater activities, so the relevant processing software becomes indispensable for analyzing the audio files recorded by these USRs. However, existing software packages did not meet performance and flexibility requirements. In this paper, we provide a detailed description of a new software package, named Aquatic Acoustic Metrics Interface (AAMI), which is a Graphicalmore » User Interface (GUI) designed for underwater sound monitoring and analysis. In addition to the general functions, such as loading and editing audio files recorded by USRs, the software can compute a series of acoustic metrics in physical units, monitor the sound's influence on fish hearing according to audiograms from different species of fishes and marine mammals, and batch process the sound files. The detailed applications of the software AAMI will be discussed along with several test case scenarios to illustrate its functionality.« less

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.

SIRU utilization. Volume 2: Software description and program documentation

NASA Technical Reports Server (NTRS)

Oehrle, J.; Whittredge, R.

1973-01-01

A complete description of the additional analysis, development and evaluation provided for the SIRU system as identified in the requirements for the SIRU utilization program is presented. The SIRU configuration is a modular inertial subsystem with hardware and software features that achieve fault tolerant operational capabilities. The SIRU redundant hardware design is formulated about a six gyro and six accelerometer instrument module package. The modules are mounted in this package so that their measurement input axes form a unique symmetrical pattern that corresponds to the array of perpendiculars to the faces of a regular dodecahedron. This six axes array provides redundant independent sensing and the symmetry enables the formulation of an optimal software redundant data processing structure with self-contained fault detection and isolation (FDI) capabilities. Documentation of the additional software and software modifications required to implement the utilization capabilities includes assembly listings and flow charts

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

MIDAS: Software for the detection and analysis of lunar impact flashes

NASA Astrophysics Data System (ADS)

Madiedo, José M.; Ortiz, José L.; Morales, Nicolás; Cabrera-Caño, Jesús

2015-06-01

Since 2009 we are running a project to identify flashes produced by the impact of meteoroids on the surface of the Moon. For this purpose we are employing small telescopes and high-sensitivity CCD video cameras. To automatically identify these events a software package called MIDAS was developed and tested. This package can also perform the photometric analysis of these flashes and estimate the value of the luminous efficiency. Besides, we have implemented in MIDAS a new method to establish which is the likely source of the meteoroids (known meteoroid stream or sporadic background). The main features of this computer program are analyzed here, and some examples of lunar impact events are presented.

Application of Elements of Numerical Methods in the Analysis of Journal Bearings in AC Induction Motors: An Industry Case Study

ERIC Educational Resources Information Center

Ahrens, Fred; Mistry, Rajendra

2005-01-01

In product engineering there often arise design analysis problems for which a commercial software package is either unavailable or cost prohibitive. Further, these calculations often require successive iterations that can be time intensive when performed by hand, thus development of a software application is indicated. This case relates to the…

Description of the GMAO OSSE for Weather Analysis Software Package: Version 3

NASA Technical Reports Server (NTRS)

Koster, Randal D. (Editor); Errico, Ronald M.; Prive, Nikki C.; Carvalho, David; Sienkiewicz, Meta; El Akkraoui, Amal; Guo, Jing; Todling, Ricardo; McCarty, Will; Putman, William M.;

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

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.

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Software Reviews: Programs Worth a Second Look.

ERIC Educational Resources Information Center

Olds, Henry F., Jr.; And Others

1988-01-01

Examines four software packages: (1) "Wordbench"--writing and word processing, grades 9-12 (IBM and Apple); (2) "Muppet Slate"--language arts, grades K-2 (Apple); (3) "Accu-Weather Forecaster"--weather analysis and forecasting, grades 3-12 (modem with IBM or Mac); and (4) "The Ripple That Changed American…

Integrative Lifecourse and Genetic Analysis of Military Working Dogs

DTIC Science & Technology

2012-10-01

Recognition), ICR (Intelligent Character Recognition) and HWR ( Handwriting Recognition). A number of various software packages were evaluated and we have...the third-party software is able to recognize check-boxes and columns and do a reasonable job with handwriting – which is does. This workflow will

Integrative Lifecourse and Genetic Analysis of Military Working Dogs

DTIC Science & Technology

2012-10-01

Intelligent Character Recognition) and HWR ( Handwriting Recognition). A number of various software packages were evaluated and we have settled on a...third-party software is able to recognize check-boxes and columns and do a reasonable job with handwriting – which is does. This workflow will

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.

Putting the 1991 census sample of anonymised records on your Unix workstation.

PubMed

Turton, I; Openshaw, S

1995-03-01

"The authors describe the development of a customised computer software package for easing the analysis of the U.K. 1991 Sample of Anonymised Records. The resulting USAR [Unix Sample of Anonymised Records] package is designed to be portable within the Unix environment. It offers a number of features such as interactive table design, intelligent data interpretation, and fuzzy query. An example of SAR analysis is provided." excerpt

Multiscale analysis of river networks using the R package linbin

USGS Publications Warehouse

Welty, Ethan Z.; Torgersen, Christian E.; Brenkman, Samuel J.; Duda, Jeffrey J.; Armstrong, Jonathan B.

2015-01-01

Analytical tools are needed in riverine science and management to bridge the gap between GIS and statistical packages that were not designed for the directional and dendritic structure of streams. We introduce linbin, an R package developed for the analysis of riverscapes at multiple scales. With this software, riverine data on aquatic habitat and species distribution can be scaled and plotted automatically with respect to their position in the stream network or—in the case of temporal data—their position in time. The linbin package aggregates data into bins of different sizes as specified by the user. We provide case studies illustrating the use of the software for (1) exploring patterns at different scales by aggregating variables at a range of bin sizes, (2) comparing repeat observations by aggregating surveys into bins of common coverage, and (3) tailoring analysis to data with custom bin designs. Furthermore, we demonstrate the utility of linbin for summarizing patterns throughout an entire stream network, and we analyze the diel and seasonal movements of tagged fish past a stationary receiver to illustrate how linbin can be used with temporal data. In short, linbin enables more rapid analysis of complex data sets by fisheries managers and stream ecologists and can reveal underlying spatial and temporal patterns of fish distribution and habitat throughout a riverscape.

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

Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

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

Kee, R.J.; Rupley, F.M.; Miller, J.A.

1989-09-01

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutinemore » Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.« less

Molded underfill (MUF) encapsulation for flip-chip package: A numerical investigation

NASA Astrophysics Data System (ADS)

Azmi, M. A.; Abdullah, M. K.; Abdullah, M. Z.; Ariff, Z. M.; Saad, Abdullah Aziz; Hamid, M. F.; Ismail, M. A.

2017-07-01

This paper presents the numerical simulation of epoxy molding compound (EMC) filling in multi flip-chip packages during encapsulation process. The empty and a group flip chip packages were considered in the mold cavity in order to study the flow profile of the EMC. SOLIDWORKS software was used for three-dimensional modeling and it was incorporated into fluid analysis software namely as ANSYS FLUENT. The volume of fluid (VOF) technique was used for capturing the flow front profiles and Power Law model was applied for its rheology model. The numerical result are compared and discussed with previous experimental and it was shown a good conformity for model validation. The prediction of flow front was observed and analyzed at different filling time. The possibility and visual of void formation in the package is captured and the number of flip-chip is one factor that contributed to the void formation.

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 .

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.

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectropscopy using IFEFFIT

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

Ravel, B.; Newville, M.; UC)

2010-07-20

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demandsmore » of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.« less

MK3TOOLS & NetCDF - storing VLBI data in a machine independent array oriented data format

NASA Astrophysics Data System (ADS)

Hobiger, T.; Koyama, Y.; Kondo, T.

2007-07-01

In the beginning of 2002 the International VLBI Service (IVS) has agreed to introduce a Platform-independent VLBI exchange format (PIVEX) which permits the exchange of observational data and stimulates the research across different analysis groups. Unfortunately PIVEX has never been implemented and many analysis software packages are still depending on prior processing (e.g. ambiguity resolution and computation of ionosphere corrections) done by CALC/SOLVE. Thus MK3TOOLS which handles MK3 databases without CALC/SOLVE being installed has been developed. It uses the NetCDF format to store the data and since interfaces exist for a variety of programming languages (FORTRAN, C/C++, JAVA, Perl, Python) it can be easily incorporated in existing and upcoming analysis software packages.

Structural Analysis Using NX Nastran 9.0

NASA Technical Reports Server (NTRS)

Rolewicz, Benjamin M.

2014-01-01

NX Nastran is a powerful Finite Element Analysis (FEA) software package used to solve linear and non-linear models for structural and thermal systems. The software, which consists of both a solver and user interface, breaks down analysis into four files, each of which are important to the end results of the analysis. The software offers capabilities for a variety of types of analysis, and also contains a respectable modeling program. Over the course of ten weeks, I was trained to effectively implement NX Nastran into structural analysis and refinement for parts of two missions at NASA's Kennedy Space Center, the Restore mission and the Orion mission.

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.

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)

MORTICIA, a statistical analysis software package for determining optical surveillance system effectiveness.

NASA Astrophysics Data System (ADS)

Ramkilowan, A.; Griffith, D. J.

2017-10-01

Surveillance modelling in terms of the standard Detect, Recognise and Identify (DRI) thresholds remains a key requirement for determining the effectiveness of surveillance sensors. With readily available computational resources it has become feasible to perform statistically representative evaluations of the effectiveness of these sensors. A new capability for performing this Monte-Carlo type analysis is demonstrated in the MORTICIA (Monte- Carlo Optical Rendering for Theatre Investigations of Capability under the Influence of the Atmosphere) software package developed at the Council for Scientific and Industrial Research (CSIR). This first generation, python-based open-source integrated software package, currently in the alpha stage of development aims to provide all the functionality required to perform statistical investigations of the effectiveness of optical surveillance systems in specific or generic deployment theatres. This includes modelling of the mathematical and physical processes that govern amongst other components of a surveillance system; a sensor's detector and optical components, a target and its background as well as the intervening atmospheric influences. In this paper we discuss integral aspects of the bespoke framework that are critical to the longevity of all subsequent modelling efforts. Additionally, some preliminary results are presented.

Mousetrap: An integrated, open-source mouse-tracking package.

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

Mouse-tracking - the analysis of mouse movements in computerized experiments - is becoming increasingly popular in the cognitive sciences. Mouse movements are taken as an indicator of commitment to or conflict between choice options during the decision process. Using mouse-tracking, researchers have gained insight into the temporal development of cognitive processes across a growing number of psychological domains. In the current article, we present software that offers easy and convenient means of recording and analyzing mouse movements in computerized laboratory experiments. In particular, we introduce and demonstrate the mousetrap plugin that adds mouse-tracking to OpenSesame, a popular general-purpose graphical experiment builder. By integrating with this existing experimental software, mousetrap allows for the creation of mouse-tracking studies through a graphical interface, without requiring programming skills. Thus, researchers can benefit from the core features of a validated software package and the many extensions available for it (e.g., the integration with auxiliary hardware such as eye-tracking, or the support of interactive experiments). In addition, the recorded data can be imported directly into the statistical programming language R using the mousetrap package, which greatly facilitates analysis. Mousetrap is cross-platform, open-source and available free of charge from https://github.com/pascalkieslich/mousetrap-os .

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/ .

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.

Development problem analysis of correlation leak detector’s software

NASA Astrophysics Data System (ADS)

Faerman, V. A.; Avramchuk, V. S.; Marukyan, V. M.

2018-05-01

In the article, the practical application and the structure of the correlation leak detectors’ software is studied and the task of its designing is analyzed. In the first part of the research paper, the expediency of the facilities development of correlation leak detectors for the following operating efficiency of public utilities exploitation is shown. The analysis of the functional structure of correlation leak detectors is conducted and its program software tasks are defined. In the second part of the research paper some development steps of the software package – requirement forming, program structure definition and software concept creation – are examined in the context of the usage experience of the hardware-software prototype of correlation leak detector.

AMIDE: a free software tool for multimodality medical image analysis.

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Space Shuttle Main Engine Quantitative Risk Assessment: Illustrating Modeling of a Complex System with a New QRA Software Package

NASA Technical Reports Server (NTRS)

Smart, Christian

1998-01-01

During 1997, a team from Hernandez Engineering, MSFC, Rocketdyne, Thiokol, Pratt & Whitney, and USBI completed the first phase of a two year Quantitative Risk Assessment (QRA) of the Space Shuttle. The models for the Shuttle systems were entered and analyzed by a new QRA software package. This system, termed the Quantitative Risk Assessment System(QRAS), was designed by NASA and programmed by the University of Maryland. The software is a groundbreaking PC-based risk assessment package that allows the user to model complex systems in a hierarchical fashion. Features of the software include the ability to easily select quantifications of failure modes, draw Event Sequence Diagrams(ESDs) interactively, perform uncertainty and sensitivity analysis, and document the modeling. This paper illustrates both the approach used in modeling and the particular features of the software package. The software is general and can be used in a QRA of any complex engineered system. The author is the project lead for the modeling of the Space Shuttle Main Engines (SSMEs), and this paper focuses on the modeling completed for the SSMEs during 1997. In particular, the groundrules for the study, the databases used, the way in which ESDs were used to model catastrophic failure of the SSMES, the methods used to quantify the failure rates, and how QRAS was used in the modeling effort are discussed. Groundrules were necessary to limit the scope of such a complex study, especially with regard to a liquid rocket engine such as the SSME, which can be shut down after ignition either on the pad or in flight. The SSME was divided into its constituent components and subsystems. These were ranked on the basis of the possibility of being upgraded and risk of catastrophic failure. Once this was done the Shuttle program Hazard Analysis and Failure Modes and Effects Analysis (FMEA) were used to create a list of potential failure modes to be modeled. The groundrules and other criteria were used to screen out the many failure modes that did not contribute significantly to the catastrophic risk. The Hazard Analysis and FMEA for the SSME were also used to build ESDs that show the chain of events leading from the failure mode occurence to one of the following end states: catastrophic failure, engine shutdown, or siccessful operation( successful with respect to the failure mode under consideration).

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, W. A.; Lepicovsky, J.

1992-01-01

The software for configuring an LV counter processor system has been developed using structured design. The LV system includes up to three counter processors and a rotary encoder. The software for configuring and testing the LV system has been developed, tested, and included in an overall software package for data acquisition, analysis, and reduction. Error handling routines respond to both operator and instrument errors which often arise in the course of measuring complex, high-speed flows. The use of networking capabilities greatly facilitates the software development process by allowing software development and testing from a remote site. In addition, high-speed transfers allow graphics files or commands to provide viewing of the data from a remote site. Further advances in data analysis require corresponding advances in procedures for statistical and time series analysis of nonuniformly sampled data.

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, William A.

1992-01-01

The software for configuring a Laser Velocimeter (LV) counter processor system was developed using structured design. The LV system includes up to three counter processors and a rotary encoder. The software for configuring and testing the LV system was developed, tested, and included in an overall software package for data acquisition, analysis, and reduction. Error handling routines respond to both operator and instrument errors which often arise in the course of measuring complex, high-speed flows. The use of networking capabilities greatly facilitates the software development process by allowing software development and testing from a remote site. In addition, high-speed transfers allow graphics files or commands to provide viewing of the data from a remote site. Further advances in data analysis require corresponding advances in procedures for statistical and time series analysis of nonuniformly sampled data.

IMCS reflight certification requirements and design specifications

NASA Technical Reports Server (NTRS)

1984-01-01

The requirements for reflight certification are established. Software requirements encompass the software programs that are resident in the PCC, DEP, PDSS, EC, or any related GSE. A design approach for the reflight software packages is recommended. These designs will be of sufficient detail to permit the implementation of reflight software. The PDSS/IMC Reflight Certification system provides the tools and mechanisms for the user to perform the reflight certification test procedures, test data capture, test data display, and test data analysis. The system as defined will be structured to permit maximum automation of reflight certification procedures and test data analysis.

C%2B%2B tensor toolbox user manual.

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

Plantenga, Todd D.; Kolda, Tamara Gibson

2012-04-01

The C++ Tensor Toolbox is a software package for computing tensor decompositions. It is based on the Matlab Tensor Toolbox, and is particularly optimized for sparse data sets. This user manual briefly overviews tensor decomposition mathematics, software capabilities, and installation of the package. Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors in C++. The Toolbox compiles into libraries and is intended for use with custom applications written by users.

Federal Emergency Management Information System (FEMIS) system administration guide. Version 1.2

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

Burford, M.J.; Burnett, R.A.; Curtis, L.M.

The Federal Emergency Management Information System (FEMIS) is an emergency management planning and analysis tool that is being developed under the direction of the US Army Chemical biological Defense Command. The FEMIS System Administration Guide defines FEMIS hardware and software requirements and gives instructions for installing the FEMIS system package. System administrators, database administrators, and general users can use this guide to install, configure, and maintain the FEMIS client software package. This document provides a description of the FEMIS environment; distribution media; data, communications, and electronic mail servers; user workstations; and system management.

Finite element for rotor/stator interactive forces in general engine dynamic simulation. Part 1: Development of bearing damper element

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1980-01-01

A general purpose squeeze-film damper interactive force element was developed, coded into a software package (module) and debugged. This software package was applied to nonliner dynamic analyses of some simple rotor systems. Results for pressure distributions show that the long bearing (end sealed) is a stronger bearing as compared to the short bearing as expected. Results of the nonlinear dynamic analysis, using a four degree of freedom simulation model, showed that the orbit of the rotating shaft increases nonlinearity to fill the bearing clearance as the unbalanced weight increases.

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.

Implementation of building information modeling in Malaysian construction industry

NASA Astrophysics Data System (ADS)

Memon, Aftab Hameed; Rahman, Ismail Abdul; Harman, Nur Melly Edora

2014-10-01

This study has assessed the implementation level of Building Information Modeling (BIM) in the construction industry of Malaysia. It also investigated several computer software packages facilitating BIM and challenges affecting its implementation. Data collection for this study was carried out using questionnaire survey among the construction practitioners. 95 completed forms of questionnaire received against 150 distributed questionnaire sets from consultant, contractor and client organizations were analyzed statistically. Analysis findings indicated that the level of implementation of BIM in the construction industry of Malaysia is very low. Average index method employed to assess the effectiveness of various software packages of BIM highlighted that Bentley construction, AutoCAD and ArchiCAD are three most popular and effective software packages. Major challenges to BIM implementation are it requires enhanced collaboration, add work to a designer, interoperability and needs enhanced collaboration. For improving the level of implementing BIM in Malaysian industry, it is recommended that a flexible training program of BIM for all practitioners must be created.

Hybrid PV/diesel solar power system design using multi-level factor analysis optimization

NASA Astrophysics Data System (ADS)

Drake, Joshua P.

Solar power systems represent a large area of interest across a spectrum of organizations at a global level. It was determined that a clear understanding of current state of the art software and design methods, as well as optimization methods, could be used to improve the design methodology. Solar power design literature was researched for an in depth understanding of solar power system design methods and algorithms. Multiple software packages for the design and optimization of solar power systems were analyzed for a critical understanding of their design workflow. In addition, several methods of optimization were studied, including brute force, Pareto analysis, Monte Carlo, linear and nonlinear programming, and multi-way factor analysis. Factor analysis was selected as the most efficient optimization method for engineering design as it applied to solar power system design. The solar power design algorithms, software work flow analysis, and factor analysis optimization were combined to develop a solar power system design optimization software package called FireDrake. This software was used for the design of multiple solar power systems in conjunction with an energy audit case study performed in seven Tibetan refugee camps located in Mainpat, India. A report of solar system designs for the camps, as well as a proposed schedule for future installations was generated. It was determined that there were several improvements that could be made to the state of the art in modern solar power system design, though the complexity of current applications is significant.

Software technology testbed softpanel prototype

NASA Technical Reports Server (NTRS)

1991-01-01

The following subject areas are covered: analysis of using Ada for the development of real-time control systems for the Space Station; analysis of the functionality of the Application Generator; analysis of the User Support Environment criteria; analysis of the SSE tools and procedures which are to be used for the development of ground/flight software for the Space Station; analysis if the CBATS tutorial (an Ada tutorial package); analysis of Interleaf; analysis of the Integration, Test and Verification process of the Space Station; analysis of the DMS on-orbit flight architecture; analysis of the simulation architecture.

Orbiter Flying Qualities (OFQ) Workstation user's guide

NASA Technical Reports Server (NTRS)

Myers, Thomas T.; Parseghian, Zareh; Hogue, Jeffrey R.

1988-01-01

This project was devoted to the development of a software package, called the Orbiter Flying Qualities (OFQ) Workstation, for working with the OFQ Archives which are specially selected sets of space shuttle entry flight data relevant to flight control and flying qualities. The basic approach to creation of the workstation software was to federate and extend commercial software products to create a low cost package that operates on personal computers. Provision was made to link the workstation to large computers, but the OFQ Archive files were also converted to personal computer diskettes and can be stored on workstation hard disk drives. The primary element of the workstation developed in the project is the Interactive Data Handler (IDH) which allows the user to select data subsets from the archives and pass them to specialized analysis programs. The IDH was developed as an application in a relational database management system product. The specialized analysis programs linked to the workstation include a spreadsheet program, FREDA for spectral analysis, MFP for frequency domain system identification, and NIPIP for pilot-vehicle system parameter identification. The workstation also includes capability for ensemble analysis over groups of missions.

An Interactive Tool for Discrete Phase Analysis in Two-Phase Flows

NASA Technical Reports Server (NTRS)

Dejong, Frederik J.; Thoren, Stephen J.

1993-01-01

Under a NASA MSFC SBIR Phase 1 effort an interactive software package has been developed for the analysis of discrete (particulate) phase dynamics in two-phase flows in which the discrete phase does not significantly affect the continuous phase. This package contains a Graphical User Interface (based on the X Window system and the Motif tool kit) coupled to a particle tracing program, which allows the user to interactively set up and run a case for which a continuous phase grid and flow field are available. The software has been applied to a solid rocket motor problem, to demonstrate its ease of use and its suitability for problems of engineering interest, and has been delivered to NASA Marshall Space Flight Center.

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.

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

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.

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.

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

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.

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.

Can I Trust This Software Package? An Exercise in Validation of Computational Results

ERIC Educational Resources Information Center

Shacham, Mordechai; Brauner, Neima; Ashurst, W. Robert; Cutlip, Michael B.

2008-01-01

Mathematical software packages such as Polymath, MATLAB, and Mathcad are currently widely used for engineering problem solving. Applications of several of these packages to typical chemical engineering problems have been demonstrated by Cutlip, et al. The main characteristic of these packages is that they provide a "problem-solving environment…

Information Technology.

ERIC Educational Resources Information Center

Marcum, Deanna; Boss, Richard

1983-01-01

Relates office automation to its application in libraries, discussing computer software packages for microcomputers performing tasks involved in word processing, accounting, statistical analysis, electronic filing cabinets, and electronic mail systems. (EJS)

Computerised curve deconvolution of TL/OSL curves using a popular spreadsheet program.

PubMed

Afouxenidis, D; Polymeris, G S; Tsirliganis, N C; Kitis, G

2012-05-01

This paper exploits the possibility of using commercial software for thermoluminescence and optically stimulated luminescence curve deconvolution analysis. The widely used software package Microsoft Excel, with the Solver utility has been used to perform deconvolution analysis to both experimental and reference glow curves resulted from the GLOw Curve ANalysis INtercomparison project. The simple interface of this programme combined with the powerful Solver utility, allows the analysis of complex stimulated luminescence curves into their components and the evaluation of the associated luminescence parameters.

NASGRO(registered trademark): Fracture Mechanics and Fatigue Crack Growth Analysis Software

NASA Technical Reports Server (NTRS)

Forman, Royce; Shivakumar, V.; Mettu, Sambi; Beek, Joachim; Williams, Leonard; Yeh, Feng; McClung, Craig; Cardinal, Joe

2004-01-01

This viewgraph presentation describes NASGRO, which is a fracture mechanics and fatigue crack growth analysis software package that is used to reduce risk of fracture in Space Shuttles. The contents include: 1) Consequences of Fracture; 2) NASA Fracture Control Requirements; 3) NASGRO Reduces Risk; 4) NASGRO Use Inside NASA; 5) NASGRO Components: Crack Growth Module; 6) NASGRO Components:Material Property Module; 7) Typical NASGRO analysis: Crack growth or component life calculation; and 8) NASGRO Sample Application: Orbiter feedline flowliner crack analysis.

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

PubMed

Robinson, Mark D; McCarthy, Davis J; Smyth, Gordon K

2010-01-01

It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).

Proposing a Mathematical Software Tool in Physics Secondary Education

ERIC Educational Resources Information Center

Baltzis, Konstantinos B.

2009-01-01

MathCad® is a very popular software tool for mathematical and statistical analysis in science and engineering. Its low cost, ease of use, extensive function library, and worksheet-like user interface distinguish it among other commercial packages. Its features are also well suited to educational process. The use of natural mathematical notation…

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…

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…

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.

Optomechanical design software for segmented mirrors

NASA Astrophysics Data System (ADS)

Marrero, Juan

2016-08-01

The software package presented in this paper, still under development, was born to help analyzing the influence of the many parameters involved in the design of a large segmented mirror telescope. In summary, it is a set of tools which were added to a common framework as they were needed. Great emphasis has been made on the graphical presentation, as scientific visualization nowadays cannot be conceived without the use of a helpful 3d environment, showing the analyzed system as close to reality as possible. Use of third party software packages is limited to ANSYS, which should be available in the system only if the FEM results are needed. Among the various functionalities of the software, the next ones are worth mentioning here: automatic 3d model construction of a segmented mirror from a set of parameters, geometric ray tracing, automatic 3d model construction of a telescope structure around the defined mirrors from a set of parameters, segmented mirror human access assessment, analysis of integration tolerances, assessment of segments collision, structural deformation under gravity and thermal variation, mirror support system analysis including warping harness mechanisms, etc.

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.

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, William A.

1991-01-01

During 1991, the software developed allowed an operator to configure and checkout the TSI, Inc. laser velocimeter (LV) system prior to a run. This setup procedure established the operating conditions for the TSI MI-990 multichannel interface and the RMR-1989 rotating machinery resolver. In addition to initializing the instruments, the software package provides a means of specifying LV calibration constants, controlling the sampling process, and identifying the test parameters.

Image Processing Software

NASA Technical Reports Server (NTRS)

1990-01-01

The Ames digital image velocimetry technology has been incorporated in a commercially available image processing software package that allows motion measurement of images on a PC alone. The software, manufactured by Werner Frei Associates, is IMAGELAB FFT. IMAGELAB FFT is a general purpose image processing system with a variety of other applications, among them image enhancement of fingerprints and use by banks and law enforcement agencies for analysis of videos run during robberies.

Control Systems

NASA Technical Reports Server (NTRS)

1984-01-01

Boeing Commercial Airplane Company's Flight Control Department engineers relied on Langley developed software package known as ORACLS to develop an advanced control synthesis package for both continuous and discrete control system. Package was used by Boeing for computerized analysis of new system designs. Resulting applications include a multiple input/output control system for the terrain-following navigation equipment of the Air Forces B-1 Bomber, and another for controlling in flight changes of wing camber on an experimental airplane. ORACLS is one of 1,300 computer programs available from COSMIC.

Software Models Impact Stresses

NASA Technical Reports Server (NTRS)

Hanshaw, Timothy C.; Roy, Dipankar; Toyooka, Mark

1991-01-01

Generalized Impact Stress Software designed to assist engineers in predicting stresses caused by variety of impacts. Program straightforward, simple to implement on personal computers, "user friendly", and handles variety of boundary conditions applied to struck body being analyzed. Applications include mathematical modeling of motions and transient stresses of spacecraft, analysis of slamming of piston, of fast valve shutoffs, and play of rotating bearing assembly. Provides fast and inexpensive analytical tool for analysis of stresses and reduces dependency on expensive impact tests. Written in FORTRAN 77. Requires use of commercial software package PLOT88.

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...

BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.

PubMed

Angelini, Claudia; Cutillo, Luisa; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna

2008-10-06

Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5-6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website: http://www.na.iac.cnr.it/bats.

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…

[Development of analysis software package for the two kinds of Japanese fluoro-d-glucose-positron emission tomography guideline].

PubMed

Matsumoto, Keiichi; Endo, Keigo

2013-06-01

Two kinds of Japanese guidelines for the data acquisition protocol of oncology fluoro-D-glucose-positron emission tomography (FDG-PET)/computed tomography (CT) scans were created by the joint task force of the Japanese Society of Nuclear Medicine Technology (JSNMT) and the Japanese Society of Nuclear Medicine (JSNM), and published in Kakuigaku-Gijutsu 27(5): 425-456, 2007 and 29(2): 195-235, 2009. These guidelines aim to standardize PET image quality among facilities and different PET/CT scanner models. The objective of this study was to develop a personal computer-based performance measurement and image quality processor for the two kinds of Japanese guidelines for oncology (18)F-FDG PET/CT scans. We call this software package the "PET quality control tool" (PETquact). Microsoft Corporation's Windows(™) is used as the operating system for PETquact, which requires 1070×720 image resolution and includes 12 different applications. The accuracy was examined for numerous applications of PETquact. For example, in the sensitivity application, the system sensitivity measurement results were equivalent when comparing two PET sinograms obtained from the PETquact and the report. PETquact is suited for analysis of the two kinds of Japanese guideline, and it shows excellent spec to performance measurements and image quality analysis. PETquact can be used at any facility if the software package is installed on a laptop computer.

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

Comparative exploration of multidimensional flow cytometry software: a model approach evaluating T cell polyfunctional behavior.

PubMed

Spear, Timothy T; Nishimura, Michael I; Simms, Patricia E

2017-08-01

Advancement in flow cytometry reagents and instrumentation has allowed for simultaneous analysis of large numbers of lineage/functional immune cell markers. Highly complex datasets generated by polychromatic flow cytometry require proper analytical software to answer investigators' questions. A problem among many investigators and flow cytometry Shared Resource Laboratories (SRLs), including our own, is a lack of access to a flow cytometry-knowledgeable bioinformatics team, making it difficult to learn and choose appropriate analysis tool(s). Here, we comparatively assess various multidimensional flow cytometry software packages for their ability to answer a specific biologic question and provide graphical representation output suitable for publication, as well as their ease of use and cost. We assessed polyfunctional potential of TCR-transduced T cells, serving as a model evaluation, using multidimensional flow cytometry to analyze 6 intracellular cytokines and degranulation on a per-cell basis. Analysis of 7 parameters resulted in 128 possible combinations of positivity/negativity, far too complex for basic flow cytometry software to analyze fully. Various software packages were used, analysis methods used in each described, and representative output displayed. Of the tools investigated, automated classification of cellular expression by nonlinear stochastic embedding (ACCENSE) and coupled analysis in Pestle/simplified presentation of incredibly complex evaluations (SPICE) provided the most user-friendly manipulations and readable output, evaluating effects of altered antigen-specific stimulation on T cell polyfunctionality. This detailed approach may serve as a model for other investigators/SRLs in selecting the most appropriate software to analyze complex flow cytometry datasets. Further development and awareness of available tools will help guide proper data analysis to answer difficult biologic questions arising from incredibly complex datasets. © Society for Leukocyte Biology.

KMWin--a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis.

PubMed

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups.

KMWin – A Convenient Tool for Graphical Presentation of Results from Kaplan-Meier Survival Time Analysis

PubMed Central

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

Background Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. Results On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. Conclusions We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups. PMID:22723912

Powerlaw: a Python package for analysis of heavy-tailed distributions.

PubMed

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

Power laws are theoretically interesting probability distributions that are also frequently used to describe empirical data. In recent years, effective statistical methods for fitting power laws have been developed, but appropriate use of these techniques requires significant programming and statistical insight. In order to greatly decrease the barriers to using good statistical methods for fitting power law distributions, we developed the powerlaw Python package. This software package provides easy commands for basic fitting and statistical analysis of distributions. Notably, it also seeks to support a variety of user needs by being exhaustive in the options available to the user. The source code is publicly available and easily extensible.

ddpcr: an R package and web application for analysis of droplet digital PCR data.

PubMed

Attali, Dean; Bidshahri, Roza; Haynes, Charles; Bryan, Jennifer

2016-01-01

Droplet digital polymerase chain reaction (ddPCR) is a novel platform for exact quantification of DNA which holds great promise in clinical diagnostics. It is increasingly popular due to its digital nature, which provides more accurate quantification and higher sensitivity than traditional real-time PCR. However, clinical adoption has been slowed in part by the lack of software tools available for analyzing ddPCR data. Here, we present ddpcr - a new R package for ddPCR visualization and analysis. In addition, ddpcr includes a web application (powered by the Shiny R package) that allows users to analyze ddPCR data using an interactive graphical interface.

LFSTAT - Low-Flow Analysis in R

NASA Astrophysics Data System (ADS)

Koffler, Daniel; Laaha, Gregor

2013-04-01

The calculation of characteristic stream flow during dry conditions is a basic requirement for many problems in hydrology, ecohydrology and water resources management. As opposed to floods, a number of different indices are used to characterise low flows and streamflow droughts. Although these indices and methods of calculation have been well documented in the WMO Manual on Low-flow Estimation and Prediction [1], a comprehensive software was missing which enables a fast and standardized calculation of low flow statistics. We present the new software package lfstat to fill in this obvious gap. Our software package is based on the statistical open source software R, and expands it to analyse daily stream flow data records focusing on low-flows. As command-line based programs are not everyone's preference, we also offer a plug-in for the R-Commander, an easy to use graphical user interface (GUI) provided for R which is based on tcl/tk. The functionality of lfstat includes estimation methods for low-flow indices, extreme value statistics, deficit characteristics, and additional graphical methods to control the computation of complex indices and to illustrate the data. Beside the basic low flow indices, the baseflow index and recession constants can be computed. For extreme value statistics, state-of-the-art methods for L-moment based local and regional frequency analysis (RFA) are available. The tools for deficit characteristics include various pooling and threshold selection methods to support the calculation of drought duration and deficit indices. The most common graphics for low flow analysis are available, and the plots can be modified according to the user preferences. Graphics include hydrographs for different periods, flexible streamflow deficit plots, baseflow visualisation, recession diagnostic, flow duration curves as well as double mass curves, and many more. From a technical point of view, the package uses a S3-class called lfobj (low-flow objects). This objects are usual R-data-frames including date, flow, hydrological year and possibly baseflow information. Once these objects are created, analysis can be performed by mouse-click and a script can be saved to make the analysis easily reproducible. At the moment we are offering implementation of all major methods proposed in the WMO manual on Low-flow Estimation and Predictions [1]. Future plans include a dynamic low flow report in odt-file format using odf-weave which allows automatic updates if data or analysis change. We hope to offer a tool to ease and structure the analysis of stream flow data focusing on low-flows and to make analysis transparent and communicable. The package can also be used in teaching students the first steps in low-flow hydrology. The software packages can be installed from CRAN (latest stable) and R-Forge: http://r-forge.r-project.org (development version). References: [1] Gustard, Alan; Demuth, Siegfried, (eds.) Manual on Low-flow Estimation and Prediction. Geneva, Switzerland, World Meteorological Organization, (Operational Hydrology Report No. 50, WMO-No. 1029).

Contrast Analysis: A Tutorial

ERIC Educational Resources Information Center

Haans, Antal

2018-01-01

Contrast analysis is a relatively simple but effective statistical method for testing theoretical predictions about differences between group means against the empirical data. Despite its advantages, contrast analysis is hardly used to date, perhaps because it is not implemented in a convenient manner in many statistical software packages. This…

GenomeGraphs: integrated genomic data visualization with R.

PubMed

Durinck, Steffen; Bullard, James; Spellman, Paul T; Dudoit, Sandrine

2009-01-06

Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

obitools: a unix-inspired software package for DNA metabarcoding.

PubMed

Boyer, Frédéric; Mercier, Céline; Bonin, Aurélie; Le Bras, Yvan; Taberlet, Pierre; Coissac, Eric

2016-01-01

DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org. © 2015 John Wiley & Sons Ltd.

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.

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.

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

Playing with Plug-ins

ERIC Educational Resources Information Center

Thompson, Douglas E.

2013-01-01

In today's complex music software packages, many features can remain unexplored and unused. Software plug-ins--available in most every music software package, yet easily overlooked in the software's basic operations--are one such feature. In this article, I introduce readers to plug-ins and offer tips for purchasing plug-ins I have…

PsychoPy--Psychophysics software in Python.

PubMed

Peirce, Jonathan W

2007-05-15

The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits.

PsychoPy—Psychophysics software in Python

PubMed Central

Peirce, Jonathan W.

2007-01-01

The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits. PMID:17254636

INSPECT: A graphical user interface software package for IDARC-2D

NASA Astrophysics Data System (ADS)

AlHamaydeh, Mohammad; Najib, Mohamad; Alawnah, Sameer

Modern day Performance-Based Earthquake Engineering (PBEE) pivots about nonlinear analysis and its feasibility. IDARC-2D is a widely used and accepted software for nonlinear analysis; it possesses many attractive features and capabilities. However, it is operated from the command prompt in the DOS/Unix systems and requires elaborate text-based input files creation by the user. To complement and facilitate the use of IDARC-2D, a pre-processing GUI software package (INSPECT) is introduced herein. INSPECT is created in the C# environment and utilizes the .NET libraries and SQLite database. Extensive testing and verification demonstrated successful and high-fidelity re-creation of several existing IDARC-2D input files. Its design and built-in features aim at expediting, simplifying and assisting in the modeling process. Moreover, this practical aid enhances the reliability of the results and improves accuracy by reducing and/or eliminating many potential and common input mistakes. Such benefits would be appreciated by novice and veteran IDARC-2D users alike.

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

Program Aids Design Of Fluid-Circulating Systems

NASA Technical Reports Server (NTRS)

Bacskay, Allen; Dalee, Robert

1992-01-01

Computer Aided Systems Engineering and Analysis (CASE/A) program is interactive software tool for trade study and analysis, designed to increase productivity during all phases of systems engineering. Graphics-based command-driven software package provides user-friendly computing environment in which engineer analyzes performance and interface characteristics of ECLS/ATC system. Useful during all phases of spacecraft-design program, from initial conceptual design trade studies to actual flight, including pre-flight prediction and in-flight analysis of anomalies. Written in FORTRAN 77.

User’s Manual for the Modular Analysis-Package Libraries ANAPAC and TRANL

DTIC Science & Technology

1977-09-01

number) Computer software Fourier transforms Computer software library Interpolation software Digitized data...disregarded to give the user a simplified plot. (b) The last digit of ISPACE determines the type of line to be drawn, provided KODE is not...negative. If the last digit of ISPACE is 0 a solid line is drawn 1 a dashed line is drawn - - - 2 a dotted line is drawn .... 3 a dash-dot line is

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies.

PubMed

Uebe, Steffen; Pasutto, Francesca; Krumbiegel, Mandy; Schanze, Denny; Ekici, Arif B; Reis, André

2010-09-21

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

Introduction to Software Packages. [Final Report.

ERIC Educational Resources Information Center

Frankel, Sheila, Ed.; And Others

This document provides an introduction to applications computer software packages that support functional managers in government and encourages the use of such packages as an alternative to in-house development. A review of current application areas includes budget/project management, financial management/accounting, payroll, personnel,…

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.

NASA Applications for Computational Electromagnetic Analysis

NASA Technical Reports Server (NTRS)

Lewis, Catherine C.; Trout, Dawn H.; Krome, Mark E.; Perry, Thomas A.

2011-01-01

Computational Electromagnetic Software is used by NASA to analyze the compatibility of systems too large or too complex for testing. Recent advances in software packages and computer capabilities have made it possible to determine the effects of a transmitter inside a launch vehicle fairing, better analyze the environment threats, and perform on-orbit replacements with assured electromagnetic compatibility.

Introducing Dynamic Mathematics Software to Secondary School Teachers: The Case of GeoGebra

ERIC Educational Resources Information Center

Hohenwarter, Judith; Hohenwarter, Markus; Lavicza, Zsolt

2009-01-01

This paper describes a study aimed to identify most common impediments related to the introduction of an open-source mathematical software package GeoGebra. We report on the analysis of data collected during a three-week professional development programme organised for middle and high school teachers in Florida. The study identified challenges…

Evaluation of open source data mining software packages

Treesearch

Bonnie Ruefenacht; Greg Liknes; Andrew J. Lister; Haans Fisk; Dan Wendt

2009-01-01

Since 2001, the USDA Forest Service (USFS) has used classification and regression-tree technology to map USFS Forest Inventory and Analysis (FIA) biomass, forest type, forest type groups, and National Forest vegetation. This prior work used Cubist/See5 software for the analyses. The objective of this project, sponsored by the Remote Sensing Steering Committee (RSSC),...

Generic Space Science Visualization in 2D/3D using SDDAS

NASA Astrophysics Data System (ADS)

Mukherjee, J.; Murphy, Z. B.; Gonzalez, C. A.; Muller, M.; Ybarra, S.

2017-12-01

The Southwest Data Display and Analysis System (SDDAS) is a flexible multi-mission / multi-instrument software system intended to support space physics data analysis, and has been in active development for over 20 years. For the Magnetospheric Multi-Scale (MMS), Juno, Cluster, and Mars Express missions, we have modified these generic tools for visualizing data in two and three dimensions. The SDDAS software is open source and makes use of various other open source packages, including VTK and Qwt. The software offers interactive plotting as well as a Python and Lua module to modify the data before plotting. In theory, by writing a Lua or Python module to read the data, any data could be used. Currently, the software can natively read data in IDFS, CEF, CDF, FITS, SEG-Y, ASCII, and XLS formats. We have integrated the software with other Python packages such as SPICE and SpacePy. Included with the visualization software is a database application and other utilities for managing data that can retrieve data from the Cluster Active Archive and Space Physics Data Facility at Goddard, as well as other local archives. Line plots, spectrograms, geographic, volume plots, strip charts, etc. are just some of the types of plots one can generate with SDDAS. Furthermore, due to the design, output is not limited to strictly visualization as SDDAS can also be used to generate stand-alone IDL or Python visualization code.. Lastly, SDDAS has been successfully used as a backend for several web based analysis systems as well.

A CAD approach to magnetic bearing design

NASA Technical Reports Server (NTRS)

Jeyaseelan, M.; Anand, D. K.; Kirk, J. A.

1988-01-01

A design methodology has been developed at the Magnetic Bearing Research Laboratory for designing magnetic bearings using a CAD approach. This is used in the algorithm of an interactive design software package. The package is a design tool developed to enable the designer to simulate the entire process of design and analysis of the system. Its capabilities include interactive input/modification of geometry, finding any possible saturation at critical sections of the system, and the design and analysis of a control system that stabilizes and maintains magnetic suspension.

The feasibility of implementing the data analysis and reporting techniques (DART) package in Virginia.

DOT National Transportation Integrated Search

1980-01-01

This project was undertaken for the Virginia Department of Transportation Safety to assess the feasibility of implementing the Data Analysis and Reporting Techniques (DART) computer software system in Virginia. Following a review of available literat...

Software and the Scientist: Coding and Citation Practices in Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, Lorraine; Fish, Allison; Soito, Laura; Smith, MacKenzie; Kellogg, Louise H.

2017-11-01

In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long- and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.

'Isotopo' a database application for facile analysis and management of mass isotopomer data.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eylert, Eva; Eisenreich, Wolfgang; Dandekar, Thomas

2014-01-01

The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application 'Isotopo'. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of (13)C-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. The 'Isotopo' software is available at the following web link (section Download): http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. The package contains three additional files: software executable setup (installer), one data set file (discussed in this article) and one excel file (which can be used to convert data from excel to '.iso' format). The 'Isotopo' software is compatible only with the Microsoft Windows operating system. http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. © The Author(s) 2014. Published by Oxford University Press.

Comparative quantification of dietary supplemented neural creatine concentrations with (1)H-MRS peak fitting and basis spectrum methods.

PubMed

Turner, Clare E; Russell, Bruce R; Gant, Nicholas

2015-11-01

Magnetic resonance spectroscopy (MRS) is an analytical procedure that can be used to non-invasively measure the concentration of a range of neural metabolites. Creatine is an important neurometabolite with dietary supplementation offering therapeutic potential for neurological disorders with dysfunctional energetic processes. Neural creatine concentrations can be probed using proton MRS and quantified using a range of software packages based on different analytical methods. This experiment examines the differences in quantification performance of two commonly used analysis packages following a creatine supplementation strategy with potential therapeutic application. Human participants followed a seven day dietary supplementation regime in a placebo-controlled, cross-over design interspersed with a five week wash-out period. Spectroscopy data were acquired the day immediately following supplementation and analyzed with two commonly-used software packages which employ vastly different quantification methods. Results demonstrate that neural creatine concentration was augmented following creatine supplementation when analyzed using the peak fitting method of quantification (105.9%±10.1). In contrast, no change in neural creatine levels were detected with supplementation when analysis was conducted using the basis spectrum method of quantification (102.6%±8.6). Results suggest that software packages that employ the peak fitting procedure for spectral quantification are possibly more sensitive to subtle changes in neural creatine concentrations. The relative simplicity of the spectroscopy sequence and the data analysis procedure suggest that peak fitting procedures may be the most effective means of metabolite quantification when detection of subtle alterations in neural metabolites is necessary. The straightforward technique can be used on a clinical magnetic resonance imaging system. Copyright © 2015 Elsevier Inc. All rights reserved.

Preliminary Dynamic Feasibility and Analysis of a Spherical, Wind-Driven (Tumbleweed), Martian Rover

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

The process and findings are presented from a preliminary feasibility study examining the dynamics characteristics of a spherical wind-driven (or Tumbleweed) rover, which is intended for exploration of the Martian surface. The results of an initial feasibility study involving several worst-case mobility situations that a Tumbleweed rover might encounter on the surface of Mars are discussed. Additional topics include the evaluation of several commercially available analysis software packages that were examined as possible platforms for the development of a Monte Carlo Tumbleweed mission simulation tool. This evaluation lead to the development of the Mars Tumbleweed Monte Carlo Simulator (or Tumbleweed Simulator) using the Vortex physics software package from CM-Labs, Inc. Discussions regarding the development and evaluation of the Tumbleweed Simulator, as well as the results of a preliminary analysis using the tool are also presented. Finally, a brief conclusions section is presented.

Laboratory Connections: Review of Two Commercial Interfacing Packages.

ERIC Educational Resources Information Center

Powers, Michael H.

1989-01-01

Evaluates two Apple II interfacing packages designed to measure pH: (1) "Experiments in Chemistry" by HRM Software and (2) "Voltage Plotter III" by Vernier Software. Provides characteristics and screen dumps of each package. Reports both systems are suitable for high school or beginning college laboratories. (MVL)

MicroSIFT Courseware Evaluations [Set 15 (362-388) and Set 16 (389-441), with an Index Listing the Contents of Each Set (Sets 1-16) and a Cumulative Subject Index (Sets 1-16)].

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

This document consists of 80 microcomputer software package evaluations prepared by the MicroSIFT (Microcomputer Software and Information for Teachers) Clearinghouse at the Northwest Regional Education Laboratory. Set 15 consists of 27 packages; set 16 consists of 53 packages. Each software review lists producer, time and place of evaluation,…

PIV/HPIV Film Analysis Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A PIV/HPIV film analysis software system was developed that calculates the 2-dimensional spatial autocorrelations of subregions of Particle Image Velocimetry (PIV) or Holographic Particle Image Velocimetry (HPIV) film recordings. The software controls three hardware subsystems including (1) a Kodak Megaplus 1.4 camera and EPIX 4MEG framegrabber subsystem, (2) an IEEE/Unidex 11 precision motion control subsystem, and (3) an Alacron I860 array processor subsystem. The software runs on an IBM PC/AT host computer running either the Microsoft Windows 3.1 or Windows 95 operating system. It is capable of processing five PIV or HPIV displacement vectors per second, and is completely automated with the exception of user input to a configuration file prior to analysis execution for update of various system parameters.

PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.

PubMed

Hanke, Michael; Halchenko, Yaroslav O; Sederberg, Per B; Hanson, Stephen José; Haxby, James V; Pollmann, Stefan

2009-01-01

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data

PubMed Central

Hanke, Michael; Halchenko, Yaroslav O.; Sederberg, Per B.; Hanson, Stephen José; Haxby, James V.; Pollmann, Stefan

2009-01-01

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine-learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability. PMID:19184561

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

A Comparison of Authoring Software for Developing Mathematics Self-Learning Software Packages.

ERIC Educational Resources Information Center

Suen, Che-yin; Pok, Yang-ming

Four years ago, the authors started to develop a self-paced mathematics learning software called NPMaths by using an authoring package called Tencore. However, NPMaths had some weak points. A development team was hence formed to develop similar software called Mathematics On Line. This time the team used another development language called…

Development and validation of MIX: comprehensive free software for meta-analysis of causal research data.

PubMed

Bax, Leon; Yu, Ly-Mee; Ikeda, Noriaki; Tsuruta, Harukazu; Moons, Karel G M

2006-10-13

Meta-analysis has become a well-known method for synthesis of quantitative data from previously conducted research in applied health sciences. So far, meta-analysis has been particularly useful in evaluating and comparing therapies and in assessing causes of disease. Consequently, the number of software packages that can perform meta-analysis has increased over the years. Unfortunately, it can take a substantial amount of time to get acquainted with some of these programs and most contain little or no interactive educational material. We set out to create and validate an easy-to-use and comprehensive meta-analysis package that would be simple enough programming-wise to remain available as a free download. We specifically aimed at students and researchers who are new to meta-analysis, with important parts of the development oriented towards creating internal interactive tutoring tools and designing features that would facilitate usage of the software as a companion to existing books on meta-analysis. We took an unconventional approach and created a program that uses Excel as a calculation and programming platform. The main programming language was Visual Basic, as implemented in Visual Basic 6 and Visual Basic for Applications in Excel 2000 and higher. The development took approximately two years and resulted in the 'MIX' program, which can be downloaded from the program's website free of charge. Next, we set out to validate the MIX output with two major software packages as reference standards, namely STATA (metan, metabias, and metatrim) and Comprehensive Meta-Analysis Version 2. Eight meta-analyses that had been published in major journals were used as data sources. All numerical and graphical results from analyses with MIX were identical to their counterparts in STATA and CMA. The MIX program distinguishes itself from most other programs by the extensive graphical output, the click-and-go (Excel) interface, and the educational features. The MIX program is a valid tool for performing meta-analysis and may be particularly useful in educational environments. It can be downloaded free of charge via http://www.mix-for-meta-analysis.info or http://sourceforge.net/projects/meta-analysis.

Application of mixsep software package: Performance verification of male-mixed DNA analysis

PubMed Central

HU, NA; CONG, BIN; GAO, TAO; CHEN, YU; SHEN, JUNYI; LI, SHUJIN; MA, CHUNLING

2015-01-01

An experimental model of male-mixed DNA (n=297) was constructed according to the mixed DNA construction principle. This comprised the use of the Applied Biosystems (ABI) 7500 quantitative polymerase chain reaction system, with scientific validation of mixture proportion (Mx; root-mean-square error ≤0.02). Statistical analysis was performed on locus separation accuracy using mixsep, a DNA mixture separation R-package, and the analytical performance of mixsep was assessed by examining the data distribution pattern of different mixed gradients, short tandem repeat (STR) loci and mixed DNA types. The results showed that locus separation accuracy had a negative linear correlation with the mixed gradient (R2=−0.7121). With increasing mixed gradient imbalance, locus separation accuracy first increased and then decreased, with the highest value detected at a gradient of 1:3 (≥90%). The mixed gradient, which is the theoretical Mx, was one of the primary factors that influenced the success of mixed DNA analysis. Among the 16 STR loci detected by Identifiler®, the separation accuracy was relatively high (>88%) for loci D5S818, D8S1179 and FGA, whereas the median separation accuracy value was lowest for the D7S820 locus. STR loci with relatively large numbers of allelic drop-out (ADO; >15) were all located in the yellow and red channels, including loci D18S51, D19S433, FGA, TPOX and vWA. These five loci featured low allele peak heights, which was consistent with the low sensitivity of the ABI 3130xl Genetic Analyzer to yellow and red fluorescence. The locus separation accuracy of the mixsep package was substantially different with and without the inclusion of ADO loci; inclusion of ADO significantly reduced the analytical performance of the mixsep package, which was consistent with the lack of an ADO functional module in this software. The present study demonstrated that the mixsep software had a number of advantages and was recommended for analysis of mixed DNA. This software was easy to operate and produced understandable results with a degree of controllability. PMID:25936428

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.

Introducing a New Software for Geodetic Analysis

NASA Astrophysics Data System (ADS)

Hjelle, Geir Arne; Dähnn, Michael; Fausk, Ingrid; Kirkvik, Ann-Silje; Mysen, Eirik

2017-04-01

At the Norwegian Mapping Authority, we are currently developing Where, a new software for geodetic analysis. Where is built on our experiences with the Geosat software, and will be able to analyse and combine data from VLBI, SLR, GNSS and DORIS. The software is mainly written in Python which has proved very fruitful. The code is quick to write and the architecture is easily extendable and maintainable, while at the same time taking advantage of well-tested code like the SOFA and IERS libraries. This presentation will show some of the current capabilities of Where, including benchmarks against other software packages, and outline our plans for further progress. In addition we will report on some investigations we have done experimenting with alternative weighting strategies for VLBI.

Technology Assessment Software Package: Final Report.

ERIC Educational Resources Information Center

Hutinger, Patricia L.

This final report describes the Technology Assessment Software Package (TASP) Project, which produced developmentally appropriate technology assessment software for children from 18 months through 8 years of age who have moderate to severe disabilities that interfere with their interaction with people, objects, tasks, and events in their…

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)

Software for Managing Personal Files.

ERIC Educational Resources Information Center

Lundeen, Gerald

1989-01-01

Discusses the special characteristics of personal file management software and compares four microcomputer software packages: Notebook II with Bibliography and Convert, Pro-Cite with Biblio-Links, askSam, and Reference Manager. Each package is evaluated in terms of the user interface, file maintenance, retrieval capabilities, output, and…

An R package for the design, analysis and operation of reservoir systems

NASA Astrophysics Data System (ADS)

Turner, Sean; Ng, Jia Yi; Galelli, Stefano

2016-04-01

We present a new R package - named "reservoir" - which has been designed for rapid and easy routing of runoff through storage. The package comprises well-established tools for capacity design (e.g., the sequent peak algorithm), performance analysis (storage-yield-reliability and reliability-resilience-vulnerability analysis) and release policy optimization (Stochastic Dynamic Programming). Operating rules can be optimized for water supply, flood control and amenity objectives, as well as for maximum hydropower production. Storage-depth-area relationships are in-built, allowing users to incorporate evaporation from the reservoir surface. We demonstrate the capabilities of the software for global studies using thousands of reservoirs from the Global Reservoir and Dam (GRanD) database fed by historical monthly inflow time series from a 0.5 degree gridded global runoff dataset. The package is freely available through the Comprehensive R Archive Network (CRAN).

Unidata: 30 Years of FOSS for the Geosciences

NASA Astrophysics Data System (ADS)

Davis, E.; Ramamurthy, M. K.; Young, J. W.; Fisher, W. I.; Rew, R. K.

2015-12-01

Unidata's core mission is to serve academic research and education communities by facilitating access and use of real-time weather data. To this end, Unidata develops, distributes, and supports several Free and Open Source Software (FOSS) packages. These packages are largely focused on data management, access, analysis and visualization. This presentation will discuss the lessons Unidata has gathered over thirty years of FOSS development, support, and community building. These lessons include what it takes to be a successful FOSS organization, how to adapt to changing "best practices" and the emergence of new FOSS tools and services, and techniques for dealing with software end-of-life. We will also discuss our approach when supporting a varied user community spanning end users and software developers. Strong user support has been an important key to Unidata's successful community building.

Development of automation software for neutron activation analysis process in Malaysian nuclear agency

NASA Astrophysics Data System (ADS)

Yussup, N.; Rahman, N. A. A.; Ibrahim, M. M.; Mokhtar, M.; Salim, N. A. A.; Soh@Shaari, S. C.; Azman, A.

2017-01-01

Neutron Activation Analysis (NAA) process has been established in Malaysian Nuclear Agency (Nuclear Malaysia) since 1980s. Most of the procedures established especially from sample registration to sample analysis are performed manually. These manual procedures carried out by the NAA laboratory personnel are time consuming and inefficient. Hence, a software to support the system automation is developed to provide an effective method to replace redundant manual data entries and produce faster sample analysis and calculation process. This paper describes the design and development of automation software for NAA process which consists of three sub-programs. The sub-programs are sample registration, hardware control and data acquisition; and sample analysis. The data flow and connection between the sub-programs will be explained. The software is developed by using National Instrument LabView development package.

Influence of standardization on the precision (reproducibility) of dental cast analysis with virtual 3-dimensional models.

PubMed

Hayashi, Kazuo; Chung, Onejune; Park, Seojung; Lee, Seung-Pyo; Sachdeva, Rohit C L; Mizoguchi, Itaru

2015-03-01

Virtual 3-dimensional (3D) models obtained by scanning of physical casts have become an alternative to conventional dental cast analysis in orthodontic treatment. If the precision (reproducibility) of virtual 3D model analysis can be further improved, digital orthodontics could be even more widely accepted. The purpose of this study was to clarify the influence of "standardization" of the target points for dental cast analysis using virtual 3D models. Physical plaster models were also measured to obtain additional information. Five sets of dental casts were used. The dental casts were scanned with R700 (3Shape, Copenhagen, Denmark) and REXCAN DS2 3D (Solutionix, Seoul, Korea) scanners. In this study, 3 system and software packages were used: SureSmile (OraMetrix, Richardson, Tex), Rapidform (Inus, Seoul, Korea), and I-DEAS (SDRC, Milford, Conn). Without standardization, the maximum differences were observed between the SureSmile software and the Rapidform software (0.39 mm ± 0.07). With standardization, the maximum differences were observed between the SureSmile software and measurements with a digital caliper (0.099 mm ± 0.01), and this difference was significantly greater (P <0.05) than the 2 other mean difference values. Furthermore, the results of this study showed that the mean differences "WITH" standardization were significantly lower than those "WITHOUT" standardization for all systems, software packages, or methods. The results showed that elimination of the influence of usability or habituation is important for improving the reproducibility of dental cast analysis. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

1986 Petroleum Software Directory. [800 mini, micro and mainframe computer software packages

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

Not Available

1985-01-01

Pennwell's 1986 Petroleum Software Directory is a complete listing of software created specifically for the petroleum industry. Details are provided on over 800 mini, micro and mainframe computer software packages from more than 250 different companies. An accountant can locate programs to automate bookkeeping functions in large oil and gas production firms. A pipeline engineer will find programs designed to calculate line flow and wellbore pressure drop.

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.

UFMulti: A new parallel processing software system for HEP

NASA Astrophysics Data System (ADS)

Avery, Paul; White, Andrew

1989-12-01

UFMulti is a multiprocessing software package designed for general purpose high energy physics applications, including physics and detector simulation, data reduction and DST physics analysis. The system is particularly well suited for installations where several workstation or computers are connected through a local area network (LAN). The initial configuration of the software is currently running on VAX/VMS machines with a planned extension to ULTRIX, using the new RISC CPUs from Digital, in the near future.

Automation system for neutron activation analysis at the reactor IBR-2, Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia.

PubMed

Pavlov, Sergey S; Dmitriev, Andrey Yu; Frontasyeva, Marina V

The present status of development of software packages and equipment designed for automation of NAA at the reactor IBR-2 of FLNP, JINR, Dubna, RF, is described. The NAA database, construction of sample changers and software for automation of spectra measurement and calculation of concentrations are presented. Automation of QC procedures is integrated in the software developed. Details of the design are shown.

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.

Data Processing System (DPS) software with experimental design, statistical analysis and data mining developed for use in entomological research.

PubMed

Tang, Qi-Yi; Zhang, Chuan-Xi

2013-04-01

A comprehensive but simple-to-use software package called DPS (Data Processing System) has been developed to execute a range of standard numerical analyses and operations used in experimental design, statistics and data mining. This program runs on standard Windows computers. Many of the functions are specific to entomological and other biological research and are not found in standard statistical software. This paper presents applications of DPS to experimental design, statistical analysis and data mining in entomology. © 2012 The Authors Insect Science © 2012 Institute of Zoology, Chinese Academy of Sciences.

OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

NASA Astrophysics Data System (ADS)

Grohmann, C. H.; Campanha, G. A.

2010-12-01

Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of each dataset (poles, great circles etc). The GUI shows the opened files in a tree structure, similar to “layers” of many illustration software, where the vertical order of the files in the tree reflects the drawing order of the selected elements. At this stage, the software performs plotting operations of poles to planes, lineations, great circles, density contours and rose diagrams. A set of statistics is calculated for each file and its eigenvalues and eigenvectors are used to suggest if the data is clustered about a mean value or distributed along a girdle. Modified Flinn, Triangular and histograms plots are also available. Next step of development will focus on tools as merging and rotation of datasets, possibility to save 'projects' and paleostress analysis. In its current state, OpenStereo requires Python, wxPython, Numpy and Matplotlib installed in the system. We recommend installing PythonXY or the Enthought Python Distribution on MS-Windows and MacOS machines, since all dependencies are provided. Most Linux distributions provide an easy way to install all dependencies through software repositories. OpenStereo is released under the GNU General Public License. Programmers willing to contribute are encouraged to contact the authors directly. FAPESP Grant #09/17675-5

An Ada Linear-Algebra Software Package Modeled After HAL/S

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Lawson, Charles L.

1990-01-01

New avionics software written more easily. Software package extends Ada programming language to include linear-algebra capabilities similar to those of HAL/S programming language. Designed for such avionics applications as Space Station flight software. In addition to built-in functions of HAL/S, package incorporates quaternion functions used in Space Shuttle and Galileo projects and routines from LINPAK solving systems of equations involving general square matrices. Contains two generic programs: one for floating-point computations and one for integer computations. Written on IBM/AT personal computer running under PC DOS, v.3.1.

On Fitting Generalized Linear Mixed-effects Models for Binary Responses using Different Statistical Packages

PubMed Central

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W.; Xia, Yinglin; Tu, Xin M.

2011-01-01

Summary The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. PMID:21671252

Advanced gamma ray balloon experiment ground checkout and data analysis

NASA Technical Reports Server (NTRS)

Blackstone, M.

1976-01-01

A software programming package to be used in the ground checkout and handling of data from the advanced gamma ray balloon experiment is described. The Operator's Manual permits someone unfamiliar with the inner workings of the software system (called LEO) to operate on the experimental data as it comes from the Pulse Code Modulation interface, converting it to a form for later analysis, and monitoring the program of an experiment. A Programmer's Manual is included.

Introducing a New Software for Geodetic Analysis

NASA Astrophysics Data System (ADS)

Hjelle, G. A.; Dähnn, M.; Fausk, I.; Kirkvik, A. S.; Mysen, E.

2016-12-01

At the Norwegian Mapping Authority, we are currently developing Where, a newsoftware for geodetic analysis. Where is built on our experiences with theGeosat software, and will be able to analyse and combine data from VLBI, SLR,GNSS and DORIS. The software is mainly written in Python which has proved veryfruitful. The code is quick to write and the architecture is easily extendableand maintainable. The Python community provides a rich eco-system of tools fordoing data-analysis, including effective data storage and powerfulvisualization. Python interfaces well with other languages so that we can easilyreuse existing, well-tested code like the SOFA and IERS libraries. This presentation will show some of the current capabilities of Where,including benchmarks against other software packages. In addition we will reporton some simple investigations we have done using the software, and outline ourplans for further progress.

NDAS Hardware Translation Layer Development

NASA Technical Reports Server (NTRS)

Nazaretian, Ryan N.; Holladay, Wendy T.

2011-01-01

The NASA Data Acquisition System (NDAS) project is aimed to replace all DAS software for NASA s Rocket Testing Facilities. There must be a software-hardware translation layer so the software can properly talk to the hardware. Since the hardware from each test stand varies, drivers for each stand have to be made. These drivers will act more like plugins for the software. If the software is being used in E3, then the software should point to the E3 driver package. If the software is being used at B2, then the software should point to the B2 driver package. The driver packages should also be filled with hardware drivers that are universal to the DAS system. For example, since A1, A2, and B2 all use the Preston 8300AU signal conditioners, then the driver for those three stands should be the same and updated collectively.

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…

Event visualization in ATLAS

NASA Astrophysics Data System (ADS)

Bianchi, R. M.; Boudreau, J.; Konstantinidis, N.; Martyniuk, A. C.; Moyse, E.; Thomas, J.; Waugh, B. M.; Yallup, D. P.; ATLAS Collaboration

2017-10-01

At the beginning, HEP experiments made use of photographical images both to record and store experimental data and to illustrate their findings. Then the experiments evolved and needed to find ways to visualize their data. With the availability of computer graphics, software packages to display event data and the detector geometry started to be developed. Here, an overview of the usage of event display tools in HEP is presented. Then the case of the ATLAS experiment is considered in more detail and two widely used event display packages are presented, Atlantis and VP1, focusing on the software technologies they employ, as well as their strengths, differences and their usage in the experiment: from physics analysis to detector development, and from online monitoring to outreach and communication. Towards the end, the other ATLAS visualization tools will be briefly presented as well. Future development plans and improvements in the ATLAS event display packages will also be discussed.

Onboard utilization of ground control points for image correction. Volume 3: Ground control point simulation software design

NASA Technical Reports Server (NTRS)

1981-01-01

The software developed to simulate the ground control point navigation system is described. The Ground Control Point Simulation Program (GCPSIM) is designed as an analysis tool to predict the performance of the navigation system. The system consists of two star trackers, a global positioning system receiver, a gyro package, and a landmark tracker.

A Paradigm Shift in Nuclear Spectrum Analysis

NASA Astrophysics Data System (ADS)

Westmeier, Wolfram; Siemon, Klaus

2012-08-01

An overview of the latest developments in quantitative spectrometry software is presented. New strategies and algorithms introduced are characterized by buzzwords “Physics, no numerology”, “Fuzzy logic” and “Repeated analyses”. With the implementation of these new ideas one arrives at software capabilities that were unreachable before and which are now realized in the GAMMA-W, SODIGAM and ALPS packages.

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…

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

Data from fitting Gaussian process models to various data sets using eight Gaussian process software packages.

PubMed

Erickson, Collin B; Ankenman, Bruce E; Sanchez, Susan M

2018-06-01

This data article provides the summary data from tests comparing various Gaussian process software packages. Each spreadsheet represents a single function or type of function using a particular input sample size. In each spreadsheet, a row gives the results for a particular replication using a single package. Within each spreadsheet there are the results from eight Gaussian process model-fitting packages on five replicates of the surface. There is also one spreadsheet comparing the results from two packages performing stochastic kriging. These data enable comparisons between the packages to determine which package will give users the best results.

Development and validation of MIX: comprehensive free software for meta-analysis of causal research data

PubMed Central

Bax, Leon; Yu, Ly-Mee; Ikeda, Noriaki; Tsuruta, Harukazu; Moons, Karel GM

2006-01-01

Background Meta-analysis has become a well-known method for synthesis of quantitative data from previously conducted research in applied health sciences. So far, meta-analysis has been particularly useful in evaluating and comparing therapies and in assessing causes of disease. Consequently, the number of software packages that can perform meta-analysis has increased over the years. Unfortunately, it can take a substantial amount of time to get acquainted with some of these programs and most contain little or no interactive educational material. We set out to create and validate an easy-to-use and comprehensive meta-analysis package that would be simple enough programming-wise to remain available as a free download. We specifically aimed at students and researchers who are new to meta-analysis, with important parts of the development oriented towards creating internal interactive tutoring tools and designing features that would facilitate usage of the software as a companion to existing books on meta-analysis. Results We took an unconventional approach and created a program that uses Excel as a calculation and programming platform. The main programming language was Visual Basic, as implemented in Visual Basic 6 and Visual Basic for Applications in Excel 2000 and higher. The development took approximately two years and resulted in the 'MIX' program, which can be downloaded from the program's website free of charge. Next, we set out to validate the MIX output with two major software packages as reference standards, namely STATA (metan, metabias, and metatrim) and Comprehensive Meta-Analysis Version 2. Eight meta-analyses that had been published in major journals were used as data sources. All numerical and graphical results from analyses with MIX were identical to their counterparts in STATA and CMA. The MIX program distinguishes itself from most other programs by the extensive graphical output, the click-and-go (Excel) interface, and the educational features. Conclusion The MIX program is a valid tool for performing meta-analysis and may be particularly useful in educational environments. It can be downloaded free of charge via or . PMID:17038197

Domain analysis for the reuse of software development experiences

NASA Technical Reports Server (NTRS)

Basili, V. R.; Briand, L. C.; Thomas, W. M.

1994-01-01

We need to be able to learn from past experiences so we can improve our software processes and products. The Experience Factory is an organizational structure designed to support and encourage the effective reuse of software experiences. This structure consists of two organizations which separates project development concerns from organizational concerns of experience packaging and learning. The experience factory provides the processes and support for analyzing, packaging, and improving the organization's stored experience. The project organization is structured to reuse this stored experience in its development efforts. However, a number of questions arise: What past experiences are relevant? Can they all be used (reused) on our current project? How do we take advantage of what has been learned in other parts of the organization? How do we take advantage of experience in the world-at-large? Can someone else's best practices be used in our organization with confidence? This paper describes approaches to help answer these questions. We propose both quantitative and qualitative approaches for effectively reusing software development experiences.

Decision Analysis Using Spreadsheets.

ERIC Educational Resources Information Center

Sounderpandian, Jayavel

1989-01-01

Discussion of decision analysis and its importance in a business curriculum focuses on the use of spreadsheets instead of commercial software packages for computer assisted instruction. A hypothetical example is given of a company drilling for oil, and suggestions are provided for classroom exercises using spreadsheets. (seven references) (LRW)

Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) User's Guide

NASA Technical Reports Server (NTRS)

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

2014-01-01

The Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) software package is an open source, MATLABSimulink toolbox (plug in) that can be used by industry professionals and academics for the development of thermodynamic and controls simulations.

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…

A Characteristics Approach to the Evaluation of Economics Software Packages.

ERIC Educational Resources Information Center

Lumsden, Keith; Scott, Alex

1988-01-01

Utilizes Bloom's Taxonomy to identify elements of teacher and student interest. Depicts the way in which these interests are developed into characteristics for use in analytically evaluating software. Illustrates the use of this evaluating technique by appraising the much used software package "Running the British Economy." (KO)

Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

Mondrian is state-of-the-art statistical data visualization software featuring modern interactive visualization techniques for a wide range of data types. This article reviews the capabilities, functionality, and interactive properties of this software package. Key features of Mondrian are illustrated with data from the Programme for International…

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

PubMed

Yip, Shun H; Sham, Pak Chung; Wang, Junwen

2018-02-21

Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.

Advanced complex trait analysis.

PubMed

Gray, A; Stewart, I; Tenesa, A

2012-12-01

The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279,435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min. The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta. a.gray@ed.ac.uk Supplementary data are available at Bioinformatics online.

Cognitive Foundry v. 3.0 (OSS)

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

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

2009-11-18

The Cognitive Foundry is a unified collection of tools designed for research and applications that use cognitive modeling, machine learning, or pattern recognition. The software library contains design patterns, interface definitions, and default implementations of reusable software components and algorithms designed to support a wide variety of research and development needs. The library contains three main software packages: the Common package that contains basic utilities and linear algebraic methods, the Cognitive Framework package that contains tools to assist in implementing and analyzing theories of cognition, and the Machine Learning package that provides general algorithms and methods for populating Cognitive Frameworkmore » components from domain-relevant data.« less

Software package for performing experiments about the convolutionally encoded Voyager 1 link

NASA Technical Reports Server (NTRS)

Cheng, U.

1989-01-01

A software package enabling engineers to conduct experiments to determine the actual performance of long constraint-length convolutional codes over the Voyager 1 communication link directly from the Jet Propulsion Laboratory (JPL) has been developed. Using this software, engineers are able to enter test data from the Laboratory in Pasadena, California. The software encodes the data and then sends the encoded data to a personal computer (PC) at the Goldstone Deep Space Complex (GDSC) over telephone lines. The encoded data are sent to the transmitter by the PC at GDSC. The received data, after being echoed back by Voyager 1, are first sent to the PC at GDSC, and then are sent back to the PC at the Laboratory over telephone lines for decoding and further analysis. All of these operations are fully integrated and are completely automatic. Engineers can control the entire software system from the Laboratory. The software encoder and the hardware decoder interface were developed for other applications, and have been modified appropriately for integration into the system so that their existence is transparent to the users. This software provides: (1) data entry facilities, (2) communication protocol for telephone links, (3) data displaying facilities, (4) integration with the software encoder and the hardware decoder, and (5) control functions.

Mining Bug Databases for Unidentified Software Vulnerabilities

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

Dumidu Wijayasekara; Milos Manic; Jason Wright

2012-06-01

Identifying software vulnerabilities is becoming more important as critical and sensitive systems increasingly rely on complex software systems. It has been suggested in previous work that some bugs are only identified as vulnerabilities long after the bug has been made public. These vulnerabilities are known as hidden impact vulnerabilities. This paper discusses the feasibility and necessity to mine common publicly available bug databases for vulnerabilities that are yet to be identified. We present bug database analysis of two well known and frequently used software packages, namely Linux kernel and MySQL. It is shown that for both Linux and MySQL, amore » significant portion of vulnerabilities that were discovered for the time period from January 2006 to April 2011 were hidden impact vulnerabilities. It is also shown that the percentage of hidden impact vulnerabilities has increased in the last two years, for both software packages. We then propose an improved hidden impact vulnerability identification methodology based on text mining bug databases, and conclude by discussing a few potential problems faced by such a classifier.« less

MicroSIFT Courseware Evaluations. [Set 11 (223-259), Set 12 (260-293), and a Special Set of 99 LIBRA Reviews of Junior High School Science Software, Including Subject and Title Indexes Covering Sets 1-12 and Special Set L].

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

This document consists of 170 microcomputer software package evaluations prepared by the MicroSIFT (Microcomputer Software and Information for Teachers) Clearinghouse at the Northwest Regional Education Laboratory. Set 11 consists of 37 packages. Set 12 consists of 34 packages. A special unnumbered set, entitled LIBRA Reviews, treats 99 packages…

DRUGDOG 3.0: U.S. Navy Random Urinalysis Software Package

DTIC Science & Technology

1994-03-15

NAVAL PO11GRADUATE SCHOOL Monterey, California AD-A281 748 THESIS LJuEoTE DRUGDOG 3.0: U. S . NAVY RANDOM URINALYSIS SOFTWARE PACKAGE by (% Dale E...ONLY (Leave blank) 2. REPORT DATE 3. REPORT TYPE AND DATES COVERED 15 MAR 94 Master’s Thesis 4. TITLE AND SUBTITLE DRUGDOG 3.0: U. S . NAVY RANDOM 5...FUNDING NUMBERS URINALYSIS SOFTWARE PACKAGE 6. AUTHOR( S ) Dale E. Wilson 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) 8. PERFORMING Naval

The R package 'Luminescence': a history of unexpected complexity and concepts to deal with it

NASA Astrophysics Data System (ADS)

Kreutzer, Sebastian; Burow, Christoph; Dietze, Michael; Fuchs, Margret C.; Friedrich, Johannes; Fischer, Manfred; Schmidt, Christoph

2017-04-01

Overcoming limitations in the so far used standard software, developing an efficient solution of low weight for a very specific task or creating graphs of high quality: the reasons that may had initially lead a scientist to work with R are manifold. And as long as developed solutions, e.g., R scripts, are needed for personal use only, code can remain unstructured and a documentation is not compulsory. However, this changes with the first friendly request for help after the code has been reused by others. In contrast to single scripts, written without intention to ever get published, for R packages the CRAN policy demands a more structured and elaborated approach including a minimum of documentation. Nevertheless, growing projects with thousands of lines of code that need to be maintained can become overwhelming, in particular as researchers are not by definition experts on managing software projects. The R package 'Luminescence' (Kreutzer et al., 2017), a collection of tools dealing with the analysis of luminescence data in a geoscientific, geochronological context, started as one single R script, but quickly evolved into a comprehensive solution connected with various other R packages. We present (1) a very brief development history of the package 'Luminescence', before we (2) sketch technical challenges encountered over time and solutions that have been found to deal with it by using various open source tools. Our presentation is considered as a collection of concepts and approaches to set up R projects in geosciences. References. Kreutzer, S., Dietze, M., Burow, C., Fuchs, M. C., Schmidt, C., Fischer, M., Friedrich, J., 2017. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.6.4. https://CRAN.R-project.org/package=Luminescence

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

PubMed

Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

2012-06-08

Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

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.

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.

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.

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.

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.

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.

Stackfile Database

NASA Technical Reports Server (NTRS)

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

Structural Analysis and Design Software

NASA Technical Reports Server (NTRS)

1997-01-01

Collier Research and Development Corporation received a one-of-a-kind computer code for designing exotic hypersonic aircraft called ST-SIZE in the first ever Langley Research Center software copyright license agreement. Collier transformed the NASA computer code into a commercial software package called HyperSizer, which integrates with other Finite Element Modeling and Finite Analysis private-sector structural analysis program. ST-SIZE was chiefly conceived as a means to improve and speed the structural design of a future aerospace plane for Langley Hypersonic Vehicles Office. Including the NASA computer code into HyperSizer has enabled the company to also apply the software to applications other than aerospace, including improved design and construction for offices, marine structures, cargo containers, commercial and military aircraft, rail cars, and a host of everyday consumer products.

Comparison Campaign of VLBI Data Analysis Software - First Results

NASA Technical Reports Server (NTRS)

Plank, Lucia; Bohm, Johannes; Schuh, Harald

2010-01-01

During the development of the Vienna VLBI Software VieVS at the Institute of Geodesy and Geophysics at Vienna University of Technology, a special comparison setup was developed with the goal of easily finding links between deviations of results achieved with different software packages and certain parameters of the observation. The object of comparison is the computed time delay, a value calculated for each observation including all relevant models and corrections that need to be applied in geodetic VLBI analysis. Besides investigating the effects of the various models on the total delay, results of comparisons between VieVS and Occam 6.1 are shown. Using the same methods, a Comparison Campaign of VLBI data analysis software called DeDeCC is about to be launched within the IVS soon.

QFASAR: Quantitative fatty acid signature analysis with R

USGS Publications Warehouse

Bromaghin, Jeffrey F.

2017-01-01

Knowledge of predator diets provides essential insights into their ecology, yet diet estimation is challenging and remains an active area of research.Quantitative fatty acid signature analysis (QFASA) is a popular method of estimating diet composition that continues to be investigated and extended. However, software to implement QFASA has only recently become publicly available.I summarize a new R package, qfasar, for diet estimation using QFASA methods. The package also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research. Several procedures in the package have not previously been published.qfasar makes traditional and recently published QFASA diet estimation methods accessible to ecologists for the first time. Use of the package is illustrated with signature data from Chukchi Sea polar bears and potential prey species.

What's New in GSAS-II

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

Toby, Brian H.; Von Dreele, Robert B.

The General Structure and Analysis Software II (GSAS-II) package is an all-new crystallographic analysis package written to replace and extend the capabilities of the universal and widely used GSAS and EXPGUI packages. GSAS-II was described in a 2013 article, but considerable work has been completed since then. This paper describes the advances, which include: rigid body fitting and structure solution modules; improved treatment for parametric refinements and equation of state fitting; and small-angle scattering data reduction and analysis. GSAS-II offers versatile and extensible modules for import and export of data and results. Capabilities are provided for users to select anymore » version of the code. Code documentation has reached 150 pages and 17 web-tutorials are offered. © 2014 International Centre for Diffraction Data.« less

On fitting generalized linear mixed-effects models for binary responses using different statistical packages.

PubMed

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W; Xia, Yinglin; Zhu, Liang; Tu, Xin M

2011-09-10

The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. Copyright © 2011 John Wiley & Sons, Ltd.

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

PubMed

Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N

2013-12-01

Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

NASA Astrophysics Data System (ADS)

Pascal, Bruce D.; Willis, Scooter; Lauer, Janelle L.; Landgraf, Rachelle R.; West, Graham M.; Marciano, David; Novick, Scott; Goswami, Devrishi; Chalmers, Michael J.; Griffin, Patrick R.

2012-09-01

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu.

OAO-C Copernicus Operations Report

NASA Technical Reports Server (NTRS)

1981-01-01

An analysis of the operation of OAO 3, Copernicus, the orbiting astronomical observatory, is given with particular emphasis upon the Princeton Experiment Package. Malfunctions and their impact are discussed, as are orbital observations and operations. Software is described.

Automated analysis of biological oscillator models using mode decomposition.

PubMed

Konopka, Tomasz

2011-04-01

Oscillating signals produced by biological systems have shapes, described by their Fourier spectra, that can potentially reveal the mechanisms that generate them. Extracting this information from measured signals is interesting for the validation of theoretical models, discovery and classification of interaction types, and for optimal experiment design. An automated workflow is described for the analysis of oscillating signals. A software package is developed to match signal shapes to hundreds of a priori viable model structures defined by a class of first-order differential equations. The package computes parameter values for each model by exploiting the mode decomposition of oscillating signals and formulating the matching problem in terms of systems of simultaneous polynomial equations. On the basis of the computed parameter values, the software returns a list of models consistent with the data. In validation tests with synthetic datasets, it not only shortlists those model structures used to generate the data but also shows that excellent fits can sometimes be achieved with alternative equations. The listing of all consistent equations is indicative of how further invalidation might be achieved with additional information. When applied to data from a microarray experiment on mice, the procedure finds several candidate model structures to describe interactions related to the circadian rhythm. This shows that experimental data on oscillators is indeed rich in information about gene regulation mechanisms. The software package is available at http://babylone.ulb.ac.be/autoosc/.

Bayesian Hierarchical Random Effects Models in Forensic Science.

PubMed

Aitken, Colin G G

2018-01-01

Statistical modeling of the evaluation of evidence with the use of the likelihood ratio has a long history. It dates from the Dreyfus case at the end of the nineteenth century through the work at Bletchley Park in the Second World War to the present day. The development received a significant boost in 1977 with a seminal work by Dennis Lindley which introduced a Bayesian hierarchical random effects model for the evaluation of evidence with an example of refractive index measurements on fragments of glass. Many models have been developed since then. The methods have now been sufficiently well-developed and have become so widespread that it is timely to try and provide a software package to assist in their implementation. With that in mind, a project (SAILR: Software for the Analysis and Implementation of Likelihood Ratios) was funded by the European Network of Forensic Science Institutes through their Monopoly programme to develop a software package for use by forensic scientists world-wide that would assist in the statistical analysis and implementation of the approach based on likelihood ratios. It is the purpose of this document to provide a short review of a small part of this history. The review also provides a background, or landscape, for the development of some of the models within the SAILR package and references to SAILR as made as appropriate.

General-Purpose Ada Software Packages

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.

1991-01-01

Collection of subprograms brings to Ada many features from other programming languages. All generic packages designed to be easily instantiated for types declared in user's facility. Most packages have widespread applicability, although some oriented for avionics applications. All designed to facilitate writing new software in Ada. Written on IBM/AT personal computer running under PC DOS, v.3.1.

Advance Directives and Do Not Resuscitate Orders

MedlinePlus

... a form. Call a lawyer. Use a computer software package for legal documents. Advance directives and living ... you write by yourself or with a computer software package should follow your state laws. You may ...

Nested Cohort - R software package

Cancer.gov

NestedCohort is an R software package for fitting Kaplan-Meier and Cox Models to estimate standardized survival and attributable risks for studies where covariates of interest are observed on only a sample of the cohort.

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

Software packager user's guide

NASA Technical Reports Server (NTRS)

Callahan, John R.

1995-01-01

Software integration is a growing area of concern for many programmers and software managers because the need to build new programs quickly from existing components is greater than ever. This includes building versions of software products for multiple hardware platforms and operating systems, building programs from components written in different languages, and building systems from components that must execute on different machines in a distributed network. The goal of software integration is to make building new programs from existing components more seamless -- programmers should pay minimal attention to the underlying configuration issues involved. Libraries of reusable components and classes are important tools but only partial solutions to software development problems. Even though software components may have compatible interfaces, there may be other reasons, such as differences between execution environments, why they cannot be integrated. Often, components must be adapted or reimplemented to fit into another application because of implementation differences -- they are implemented in different programming languages, dependent on different operating system resources, or must execute on different physical machines. The software packager is a tool that allows programmers to deal with interfaces between software components and ignore complex integration details. The packager takes modular descriptions of the structure of a software system written in the package specification language and produces an integration program in the form of a makefile. If complex integration tools are needed to integrate a set of components, such as remote procedure call stubs, their use is implied by the packager automatically and stub generation tools are invoked in the corresponding makefile. The programmer deals only with the components themselves and not the details of how to build the system on any given platform.

A Survey of Popular R Packages for Cluster Analysis

ERIC Educational Resources Information Center

Flynt, Abby; Dean, Nema

2016-01-01

Cluster analysis is a set of statistical methods for discovering new group/class structure when exploring data sets. This article reviews the following popular libraries/commands in the R software language for applying different types of cluster analysis: from the stats library, the kmeans, and hclust functions; the mclust library; the poLCA…

eXtended CASA Line Analysis Software Suite (XCLASS)

NASA Astrophysics Data System (ADS)

Möller, T.; Endres, C.; Schilke, P.

2017-02-01

The eXtended CASA Line Analysis Software Suite (XCLASS) is a toolbox for the Common Astronomy Software Applications package (CASA) containing new functions for modeling interferometric and single dish data. Among the tools is the myXCLASS program which calculates synthetic spectra by solving the radiative transfer equation for an isothermal object in one dimension, whereas the finite source size and dust attenuation are considered as well. Molecular data required by the myXCLASS program are taken from an embedded SQLite3 database containing entries from the Cologne Database for Molecular Spectroscopy (CDMS) and JPL using the Virtual Atomic and Molecular Data Center (VAMDC) portal. Additionally, the toolbox provides an interface for the model optimizer package Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX), which helps to find the best description of observational data using myXCLASS (or another external model program), that is, finding the parameter set that most closely reproduces the data. http://www.astro.uni-koeln.de/projects/schilke/myXCLASSInterface A copy of the code is available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/598/A7

A high-level 3D visualization API for Java and ImageJ.

PubMed

Schmid, Benjamin; Schindelin, Johannes; Cardona, Albert; Longair, Mark; Heisenberg, Martin

2010-05-21

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.

MicroSIFT Courseware Evaluations (169-198). Set 9. Including Subject and Title Indexes Covering Sets 1-9.

ERIC Educational Resources Information Center

Weaver, Dave, Ed.

This document consists of 30 microcomputer software package evaluations prepared for the MicroSIFT (Microcomputer Software and Information for Teachers) Clearinghouse at the Northwest Regional Educational Laboratory (NWREL). The concise, single-sheet resume describing and evaluating each software package includes source, cost, ability level,…

Annotated Bibliography of Computer Software for Teaching Early Reading and Spelling. Project RIMES 2000.

ERIC Educational Resources Information Center

Rhein, Deborah; Alibrandi, Mary; Lyons, Mary; Sammons, Janice; Doyle, Luther

This bibliography, developed by Project RIMES (Reading Instructional Methods of Efficacy with Students) lists 80 software packages for teaching early reading and spelling to students at risk for reading and spelling failure. The software packages are presented alphabetically by title. Entries usually include a grade level indicator, a brief…

PINT, a New Pulsar Timing Software

NASA Astrophysics Data System (ADS)

Luo, Jing; Jenet, Fredrick A.; Ransom, Scott M.; Demorest, Paul; Van Haasteren, Rutger; Archibald, Anne

2015-01-01

We are presenting a new pulsar timing software PINT. The current pulsar timing group are heavily depending on Tempo/Tempo2, a package for analysis pulsar data. However, for a high accuracy pulsar timing related project, such as pulsar timing for gravitational waves, an alternative software is needed for the purpose of examing the results. We are developing a Tempo independent software with a different structure. Different modules is designed to be more isolated and easier to be expanded. Instead of C, we are using Python as our programming language for the advantage of flexibility and powerful docstring. Here, we are presenting the detailed design and the first result of the software.

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PubMed

Gonçalves, Emanuel; Mirlach, Franz; Saez-Rodriguez, Julio

2013-01-01

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface's utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface's homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store ( http://apps.cytoscape.org/apps/cyrface).

Software Library for Bruker TopSpin NMR Data Files

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

A software library for parsing and manipulating frequency-domain data files that have been processed using the Bruker TopSpin NMR software package. In the context of NMR, the term "processed" indicates that the end-user of the Bruker TopSpin NMR software package has (a) Fourier transformed the raw, time-domain data (the Free Induction Decay) into the frequency-domain and (b) has extracted the list of NMR peaks.

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.

RevEcoR: an R package for the reverse ecology analysis of microbiomes.

PubMed

Cao, Yang; Wang, Yuanyuan; Zheng, Xiaofei; Li, Fei; Bo, Xiaochen

2016-07-29

All species live in complex ecosystems. The structure and complexity of a microbial community reflects not only diversity and function, but also the environment in which it occurs. However, traditional ecological methods can only be applied on a small scale and for relatively well-understood biological systems. Recently, a graph-theory-based algorithm called the reverse ecology approach has been developed that can analyze the metabolic networks of all the species in a microbial community, and predict the metabolic interface between species and their environment. Here, we present RevEcoR, an R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities. This software allows users to obtain large-scale ecological insights into species' ecology directly from high-throughput metagenomic data. The software has great potential for facilitating the study of microbiomes. RevEcoR is open source software for the study of microbial community ecology. The RevEcoR R package is freely available under the GNU General Public License v. 2.0 at http://cran.r-project.org/web/packages/RevEcoR/ with the vignette and typical usage examples, and the interactive Shiny web application is available at http://yiluheihei.shinyapps.io/shiny-RevEcoR , or can be installed locally with the source code accessed from https://github.com/yiluheihei/shiny-RevEcoR .

An Algorithm and R Program for Fitting and Simulation of Pharmacokinetic and Pharmacodynamic Data.

PubMed

Li, Jijie; Yan, Kewei; Hou, Lisha; Du, Xudong; Zhu, Ping; Zheng, Li; Zhu, Cairong

2017-06-01

Pharmacokinetic/pharmacodynamic link models are widely used in dose-finding studies. By applying such models, the results of initial pharmacokinetic/pharmacodynamic studies can be used to predict the potential therapeutic dose range. This knowledge can improve the design of later comparative large-scale clinical trials by reducing the number of participants and saving time and resources. However, the modeling process can be challenging, time consuming, and costly, even when using cutting-edge, powerful pharmacological software. Here, we provide a freely available R program for expediently analyzing pharmacokinetic/pharmacodynamic data, including data importation, parameter estimation, simulation, and model diagnostics. First, we explain the theory related to the establishment of the pharmacokinetic/pharmacodynamic link model. Subsequently, we present the algorithms used for parameter estimation and potential therapeutic dose computation. The implementation of the R program is illustrated by a clinical example. The software package is then validated by comparing the model parameters and the goodness-of-fit statistics generated by our R package with those generated by the widely used pharmacological software WinNonlin. The pharmacokinetic and pharmacodynamic parameters as well as the potential recommended therapeutic dose can be acquired with the R package. The validation process shows that the parameters estimated using our package are satisfactory. The R program developed and presented here provides pharmacokinetic researchers with a simple and easy-to-access tool for pharmacokinetic/pharmacodynamic analysis on personal computers.

A Microsoft-Excel-based tool for running and critically appraising network meta-analyses--an overview and application of NetMetaXL.

PubMed

Brown, Stephen; Hutton, Brian; Clifford, Tammy; Coyle, Doug; Grima, Daniel; Wells, George; Cameron, Chris

2014-09-29

The use of network meta-analysis has increased dramatically in recent years. WinBUGS, a freely available Bayesian software package, has been the most widely used software package to conduct network meta-analyses. However, the learning curve for WinBUGS can be daunting, especially for new users. Furthermore, critical appraisal of network meta-analyses conducted in WinBUGS can be challenging given its limited data manipulation capabilities and the fact that generation of graphical output from network meta-analyses often relies on different software packages than the analyses themselves. We developed a freely available Microsoft-Excel-based tool called NetMetaXL, programmed in Visual Basic for Applications, which provides an interface for conducting a Bayesian network meta-analysis using WinBUGS from within Microsoft Excel. . This tool allows the user to easily prepare and enter data, set model assumptions, and run the network meta-analysis, with results being automatically displayed in an Excel spreadsheet. It also contains macros that use NetMetaXL's interface to generate evidence network diagrams, forest plots, league tables of pairwise comparisons, probability plots (rankograms), and inconsistency plots within Microsoft Excel. All figures generated are publication quality, thereby increasing the efficiency of knowledge transfer and manuscript preparation. We demonstrate the application of NetMetaXL using data from a network meta-analysis published previously which compares combined resynchronization and implantable defibrillator therapy in left ventricular dysfunction. We replicate results from the previous publication while demonstrating result summaries generated by the software. Use of the freely available NetMetaXL successfully demonstrated its ability to make running network meta-analyses more accessible to novice WinBUGS users by allowing analyses to be conducted entirely within Microsoft Excel. NetMetaXL also allows for more efficient and transparent critical appraisal of network meta-analyses, enhanced standardization of reporting, and integration with health economic evaluations which are frequently Excel-based.

A Microsoft-Excel-based tool for running and critically appraising network meta-analyses—an overview and application of NetMetaXL

PubMed Central

2014-01-01

Background The use of network meta-analysis has increased dramatically in recent years. WinBUGS, a freely available Bayesian software package, has been the most widely used software package to conduct network meta-analyses. However, the learning curve for WinBUGS can be daunting, especially for new users. Furthermore, critical appraisal of network meta-analyses conducted in WinBUGS can be challenging given its limited data manipulation capabilities and the fact that generation of graphical output from network meta-analyses often relies on different software packages than the analyses themselves. Methods We developed a freely available Microsoft-Excel-based tool called NetMetaXL, programmed in Visual Basic for Applications, which provides an interface for conducting a Bayesian network meta-analysis using WinBUGS from within Microsoft Excel. . This tool allows the user to easily prepare and enter data, set model assumptions, and run the network meta-analysis, with results being automatically displayed in an Excel spreadsheet. It also contains macros that use NetMetaXL’s interface to generate evidence network diagrams, forest plots, league tables of pairwise comparisons, probability plots (rankograms), and inconsistency plots within Microsoft Excel. All figures generated are publication quality, thereby increasing the efficiency of knowledge transfer and manuscript preparation. Results We demonstrate the application of NetMetaXL using data from a network meta-analysis published previously which compares combined resynchronization and implantable defibrillator therapy in left ventricular dysfunction. We replicate results from the previous publication while demonstrating result summaries generated by the software. Conclusions Use of the freely available NetMetaXL successfully demonstrated its ability to make running network meta-analyses more accessible to novice WinBUGS users by allowing analyses to be conducted entirely within Microsoft Excel. NetMetaXL also allows for more efficient and transparent critical appraisal of network meta-analyses, enhanced standardization of reporting, and integration with health economic evaluations which are frequently Excel-based. PMID:25267416

Software Review. Macintosh Laboratory Automation: Three Software Packages.

ERIC Educational Resources Information Center

Jezl, Barbara Ann

1990-01-01

Reviewed are "LABTECH NOTEBOOK,""LabVIEW," and "Parameter Manager pmPLUS/pmTALK." Each package is described including functions, uses, hardware, and costs. Advantages and disadvantages of this type of laboratory approach are discussed. (CW)

pyLIMA : an open source microlensing software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne

2017-01-01

Planetary microlensing is a unique tool to detect cold planets around low-mass stars which is approaching a watershed in discoveries as near-future missions incorporate dedicated surveys. NASA and ESA have decided to complement WFIRST-AFTA and Euclid with microlensing programs to enrich our statistics about this planetary population. Of the nany challenges in- herent in these missions, the data analysis is of primary importance, yet is often perceived as time consuming, complex and daunting barrier to participation in the field. We present the first open source modeling software to conduct a microlensing analysis. This software is written in Python and use as much as possible existing packages.

GPS Software Packages Deliver Positioning Solutions

NASA Technical Reports Server (NTRS)

2010-01-01

"To determine a spacecraft s position, the Jet Propulsion Laboratory (JPL) developed an innovative software program called the GPS (global positioning system)-Inferred Positioning System and Orbit Analysis Simulation Software, abbreviated as GIPSY-OASIS, and also developed Real-Time GIPSY (RTG) for certain time-critical applications. First featured in Spinoff 1999, JPL has released hundreds of licenses for GIPSY and RTG, including to Longmont, Colorado-based DigitalGlobe. Using the technology, DigitalGlobe produces satellite imagery with highly precise latitude and longitude coordinates and then supplies it for uses within defense and intelligence, civil agencies, mapping and analysis, environmental monitoring, oil and gas exploration, infrastructure management, Internet portals, and navigation technology."

Dynamic simulation of train derailments

DOT National Transportation Integrated Search

2006-11-05

This paper describes a planar rigid-body model to examine the gross motions of rail cars in a train derailment. The model is implemented using a commercial software package called ADAMS (Automatic Dynamic Analysis of Mechanical Systems). The results ...

Lessons Learned from Autonomous Sciencecraft Experiment

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Sherwood, Rob; Tran, Daniel; Cichy, Benjamin; Rabideau, Gregg; Castano, Rebecca; Davies, Ashley; Mandl, Dan; Frye, Stuart; Trout, Bruce;

The Equivalence of Three Statistical Packages for Performing Hierarchical Cluster Analysis

ERIC Educational Resources Information Center

Blashfield, Roger

1977-01-01

Three different software programs which contain hierarchical agglomerative cluster analysis procedures were shown to generate different solutions on the same data set using apparently the same options. The basis for the differences in the solutions was the formulae used to calculate Euclidean distance. (Author/JKS)

Cellular Consequences of Telomere Shortening in Histologically Normal Breast Tissues

DTIC Science & Technology

2013-09-01

using the open source, JAVA -based image analysis software package ImageJ (http://rsb.info.nih.gov/ij/) and a custom designed plugin (“Telometer...Tabulated data were stored in a MySQL (http://www.mysql.com) database and viewed through Microsoft Access (Microsoft Corp.). Statistical Analysis For

Direct Method Transcription for a Human-Class Translunar Injection Trajectory Optimization

NASA Technical Reports Server (NTRS)

Witzberger, Kevin E.; Zeiler, Tom

2012-01-01

This paper presents a new trajectory optimization software package developed in the framework of a low-to-high fidelity 3 degrees-of-freedom (DOF)/6-DOF vehicle simulation program named Mission Analysis Simulation Tool in Fortran (MASTIF) and its application to a translunar trajectory optimization problem. The functionality of the developed optimization package is implemented as a new "mode" in generalized settings to make it applicable for a general trajectory optimization problem. In doing so, a direct optimization method using collocation is employed for solving the problem. Trajectory optimization problems in MASTIF are transcribed to a constrained nonlinear programming (NLP) problem and solved with SNOPT, a commercially available NLP solver. A detailed description of the optimization software developed is provided as well as the transcription specifics for the translunar injection (TLI) problem. The analysis includes a 3-DOF trajectory TLI optimization and a 3-DOF vehicle TLI simulation using closed-loop guidance.

User manual of the CATSS system (version 1.0) communication analysis tool for space station

NASA Technical Reports Server (NTRS)

Tsang, C. S.; Su, Y. T.; Lindsey, W. C.

1983-01-01

The Communication Analysis Tool for the Space Station (CATSS) is a FORTRAN language software package capable of predicting the communications links performance for the Space Station (SS) communication and tracking (C & T) system. An interactive software package was currently developed to run on the DEC/VAX computers. The CATSS models and evaluates the various C & T links of the SS, which includes the modulation schemes such as Binary-Phase-Shift-Keying (BPSK), BPSK with Direct Sequence Spread Spectrum (PN/BPSK), and M-ary Frequency-Shift-Keying with Frequency Hopping (FH/MFSK). Optical Space Communication link is also included. CATSS is a C & T system engineering tool used to predict and analyze the system performance for different link environment. Identification of system weaknesses is achieved through evaluation of performance with varying system parameters. System tradeoff for different values of system parameters are made based on the performance prediction.

The SeaDAS Processing and Analysis System: SeaWiFS, MODIS, and Beyond

NASA Astrophysics Data System (ADS)

MacDonald, M. D.; Ruebens, M.; Wang, L.; Franz, B. A.

2005-12-01

The SeaWiFS Data Analysis System (SeaDAS) is a comprehensive software package for the processing, display, and analysis of ocean data from a variety of satellite sensors. Continuous development and user support by programmers and scientists for more than a decade has helped to make SeaDAS the most widely used software package in the world for ocean color applications, with a growing base of users from the land and sea surface temperature community. Full processing support for past (CZCS, OCTS, MOS) and present (SeaWiFS, MODIS) sensors, and anticipated support for future missions such as NPP/VIIRS, enables end users to reproduce the standard ocean archive product suite distributed by NASA's Ocean Biology Processing Group (OBPG), as well as a variety of evaluation and intermediate ocean, land, and atmospheric products. Availability of the processing algorithm source codes and a software build environment also provide users with the tools to implement custom algorithms. Recent SeaDAS enhancements include synchronization of MODIS processing with the latest code and calibration updates from the MODIS Calibration Support Team (MCST), support for all levels of MODIS processing including Direct Broadcast, a port to the Macintosh OS X operating system, release of the display/analysis-only SeaDAS-Lite, and an extremely active web-based user support forum.

The Implication of Using NVivo Software in Qualitative Data Analysis: Evidence-Based Reflections.

PubMed

Zamawe, F C

2015-03-01

For a long time, electronic data analysis has been associated with quantitative methods. However, Computer Assisted Qualitative Data Analysis Software (CAQDAS) are increasingly being developed. Although the CAQDAS has been there for decades, very few qualitative health researchers report using it. This may be due to the difficulties that one has to go through to master the software and the misconceptions that are associated with using CAQDAS. While the issue of mastering CAQDAS has received ample attention, little has been done to address the misconceptions associated with CAQDAS. In this paper, the author reflects on his experience of interacting with one of the popular CAQDAS (NVivo) in order to provide evidence-based implications of using the software. The key message is that unlike statistical software, the main function of CAQDAS is not to analyse data but rather to aid the analysis process, which the researcher must always remain in control of. In other words, researchers must equally know that no software can analyse qualitative data. CAQDAS are basically data management packages, which support the researcher during analysis.

Integrated Baseline System (IBS). Version 1.03, System Management Guide

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

Williams, J.R.; Bailey, S.; Bower, J.C.

This IBS System Management Guide explains how to install or upgrade the Integrated Baseline System (IBS) software package. The IBS is an emergency management planning and analysis tool that was developed under the direction of the Federal Emergency Management Agency (FEMA). This guide includes detailed instructions for installing the IBS software package on a Digital Equipment Corporation (DEC) VAX computer from the IBS distribution tapes. The installation instructions include procedures for both first-time installations and upgrades to existing IBS installations. To ensure that the system manager has the background necessary for successful installation of the IBS package, this guide alsomore » includes information on IBS computer requirements, software organization, and the generation of IBS distribution tapes. When special utility programs are used during IBS installation and setups, this guide refers you to the IBS Utilities Guide for specific instructions. This guide also refers you to the IBS Data Management Guide for detailed descriptions of some IBS data files and structures. Any special requirements for installation are not documented here but should be included in a set of installation notes that come with the distribution tapes.« less

NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

PubMed Central

Rothman, Jason S.; Silver, R. Angus

2018-01-01

Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such as online analysis. To address this, we developed NeuroMatic, an open-source software toolkit that performs data acquisition (episodic, continuous and triggered recordings), data analysis (spike rasters, spontaneous event detection, curve fitting, stationarity) and simulations (stochastic synaptic transmission, synaptic short-term plasticity, integrate-and-fire and Hodgkin-Huxley-like single-compartment models). The merging of a wide range of tools into a single package facilitates a more integrated style of research, from the development of online analysis functions during data acquisition, to the simulation of synaptic conductance trains during dynamic-clamp experiments. Moreover, NeuroMatic has the advantage of working within Igor Pro, a platform-independent environment that includes an extensive library of built-in functions, a history window for reviewing the user's workflow and the ability to produce publication-quality graphics. Since its original release, NeuroMatic has been used in a wide range of scientific studies and its user base has grown considerably. NeuroMatic version 3.0 can be found at http://www.neuromatic.thinkrandom.com and https://github.com/SilverLabUCL/NeuroMatic. PMID:29670519

modlAMP: Python for antimicrobial peptides.

PubMed

Müller, Alex T; Gabernet, Gisela; Hiss, Jan A; Schneider, Gisbert

2017-09-01

We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification and visual representation of peptide data. modlAMP offers functions for molecular descriptor calculation and the retrieval of amino acid sequences from public or local sequence databases, and provides instant access to precompiled datasets for machine learning. The package also contains methods for the analysis and representation of circular dichroism spectra. The modlAMP Python package is available under the BSD license from URL http://doi.org/10.5905/ethz-1007-72 or via pip from the Python Package Index (PyPI). gisbert.schneider@pharma.ethz.ch. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Data Analysis for the LISA Pathfinder Mission

NASA Technical Reports Server (NTRS)

Thorpe, James Ira

2009-01-01

The LTP (LISA Technology Package) is the core part of the Laser Interferometer Space Antenna (LISA) Pathfinder mission. The main goal of the mission is to study the sources of any disturbances that perturb the motion of the freely-falling test masses from their geodesic trajectories as well as 10 test various technologies needed for LISA. The LTP experiment is designed as a sequence of experimental runs in which the performance of the instrument is studied and characterized under different operating conditions. In order to best optimize subsequent experimental runs, each run must be promptly analysed to ensure that the following ones make best use of the available knowledge of the instrument ' In order to do this, all analyses must be designed and tested in advance of the mission and have sufficient built-in flexibility to account for unexpected results or behaviour. To support this activity, a robust and flexible data analysis software package is also required. This poster presents two of the main components that make up the data analysis effort: the data analysis software and the mock-data challenges used to validate analysis procedures and experiment designs.

Comparison of estimates of left ventricular ejection fraction obtained from gated blood pool imaging, different software packages and cameras.

PubMed

Steyn, Rachelle; Boniaszczuk, John; Geldenhuys, Theodore

2014-01-01

To determine how two software packages, supplied by Siemens and Hermes, for processing gated blood pool (GBP) studies should be used in our department and whether the use of different cameras for the acquisition of raw data influences the results. The study had two components. For the first component, 200 studies were acquired on a General Electric (GE) camera and processed three times by three operators using the Siemens and Hermes software packages. For the second part, 200 studies were acquired on two different cameras (GE and Siemens). The matched pairs of raw data were processed by one operator using the Siemens and Hermes software packages. The Siemens method consistently gave estimates that were 4.3% higher than the Hermes method (p < 0.001). The differences were not associated with any particular level of left ventricular ejection fraction (LVEF). There was no difference in the estimates of LVEF obtained by the three operators (p = 0.1794). The reproducibility of estimates was good. In 95% of patients, using the Siemens method, the SD of the three estimates of LVEF by operator 1 was ≤ 1.7, operator 2 was ≤ 2.1 and operator 3 was ≤ 1.3. The corresponding values for the Hermes method were ≤ 2.5, ≤ 2.0 and ≤ 2.1. There was no difference in the results of matched pairs of data acquired on different cameras (p = 0.4933) CONCLUSION: Software packages for processing GBP studies are not interchangeable. The report should include the name and version of the software package used. Wherever possible, the same package should be used for serial studies. If this is not possible, the report should include the limits of agreement of the different packages. Data acquisition on different cameras did not influence the results.

ELAS: A powerful, general purpose image processing package

NASA Technical Reports Server (NTRS)

Walters, David; Rickman, Douglas

1991-01-01

ELAS is a software package which has been utilized as an image processing tool for more than a decade. It has been the source of several commercial packages. Now available on UNIX workstations it is a very powerful, flexible set of software. Applications at Stennis Space Center have included a very wide range of areas including medicine, forestry, geology, ecological modeling, and sonar imagery. It remains one of the most powerful image processing packages available, either commercially or in the public domain.

Analyzing longitudinal data with the linear mixed models procedure in SPSS.

PubMed

West, Brady T

2009-09-01

Many applied researchers analyzing longitudinal data share a common misconception: that specialized statistical software is necessary to fit hierarchical linear models (also known as linear mixed models [LMMs], or multilevel models) to longitudinal data sets. Although several specialized statistical software programs of high quality are available that allow researchers to fit these models to longitudinal data sets (e.g., HLM), rapid advances in general purpose statistical software packages have recently enabled analysts to fit these same models when using preferred packages that also enable other more common analyses. One of these general purpose statistical packages is SPSS, which includes a very flexible and powerful procedure for fitting LMMs to longitudinal data sets with continuous outcomes. This article aims to present readers with a practical discussion of how to analyze longitudinal data using the LMMs procedure in the SPSS statistical software package.

Digital 3D Microstructure Analysis of Concrete using X-Ray Micro Computed Tomography SkyScan 1173: A Preliminary Study

NASA Astrophysics Data System (ADS)

Latief, F. D. E.; Mohammad, I. H.; Rarasati, A. D.

2017-11-01

Digital imaging of a concrete sample using high resolution tomographic imaging by means of X-Ray Micro Computed Tomography (μ-CT) has been conducted to assess the characteristic of the sample’s structure. A standard procedure of image acquisition, reconstruction, image processing of the method using a particular scanning device i.e., the Bruker SkyScan 1173 High Energy Micro-CT are elaborated. A qualitative and a quantitative analysis were briefly performed on the sample to deliver some basic ideas of the capability of the system and the bundled software package. Calculation of total VOI volume, object volume, percent of object volume, total VOI surface, object surface, object surface/volume ratio, object surface density, structure thickness, structure separation, total porosity were conducted and analysed. This paper should serve as a brief description of how the device can produce the preferred image quality as well as the ability of the bundled software packages to help in performing qualitative and quantitative analysis.

Comparison of software packages for detecting differential expression in RNA-seq studies

PubMed Central

Seyednasrollah, Fatemeh; Laiho, Asta

2015-01-01

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task. Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice. PMID:24300110

Comparison of software packages for detecting differential expression in RNA-seq studies.

PubMed

Seyednasrollah, Fatemeh; Laiho, Asta; Elo, Laura L

2015-01-01

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task. Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice. © The Author 2013. Published by Oxford University Press.

R classes and methods for SNP array data.

PubMed

Scharpf, Robert B; Ruczinski, Ingo

2010-01-01

The Bioconductor project is an "open source and open development software project for the analysis and comprehension of genomic data" (1), primarily based on the R programming language. Infrastructure packages, such as Biobase, are maintained by Bioconductor core developers and serve several key roles to the broader community of Bioconductor software developers and users. In particular, Biobase introduces an S4 class, the eSet, for high-dimensional assay data. Encapsulating the assay data as well as meta-data on the samples, features, and experiment in the eSet class definition ensures propagation of the relevant sample and feature meta-data throughout an analysis. Extending the eSet class promotes code reuse through inheritance as well as interoperability with other R packages and is less error-prone. Recently proposed class definitions for high-throughput SNP arrays extend the eSet class. This chapter highlights the advantages of adopting and extending Biobase class definitions through a working example of one implementation of classes for the analysis of high-throughput SNP arrays.

GWAMA: software for genome-wide association meta-analysis.

PubMed

Mägi, Reedik; Morris, Andrew P

2010-05-28

Despite the recent success of genome-wide association studies in identifying novel loci contributing effects to complex human traits, such as type 2 diabetes and obesity, much of the genetic component of variation in these phenotypes remains unexplained. One way to improving power to detect further novel loci is through meta-analysis of studies from the same population, increasing the sample size over any individual study. Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies. We have developed flexible, open-source software for the meta-analysis of genome-wide association studies. The software incorporates a variety of error trapping facilities, and provides a range of meta-analysis summary statistics. The software is distributed with scripts that allow simple formatting of files containing the results of each association study and generate graphical summaries of genome-wide meta-analysis results. The GWAMA (Genome-Wide Association Meta-Analysis) software has been developed to perform meta-analysis of summary statistics generated from genome-wide association studies of dichotomous phenotypes or quantitative traits. Software with source files, documentation and example data files are freely available online at http://www.well.ox.ac.uk/GWAMA.

lumpR 2.0.0: an R package facilitating landscape discretisation for hillslope-based hydrological models

NASA Astrophysics Data System (ADS)

Pilz, Tobias; Francke, Till; Bronstert, Axel

2017-08-01

The characteristics of a landscape pose essential factors for hydrological processes. Therefore, an adequate representation of the landscape of a catchment in hydrological models is vital. However, many of such models exist differing, amongst others, in spatial concept and discretisation. The latter constitutes an essential pre-processing step, for which many different algorithms along with numerous software implementations exist. In that context, existing solutions are often model specific, commercial, or depend on commercial back-end software, and allow only a limited or no workflow automation at all. Consequently, a new package for the scientific software and scripting environment R, called lumpR, was developed. lumpR employs an algorithm for hillslope-based landscape discretisation directed to large-scale application via a hierarchical multi-scale approach. The package addresses existing limitations as it is free and open source, easily extendible to other hydrological models, and the workflow can be fully automated. Moreover, it is user-friendly as the direct coupling to a GIS allows for immediate visual inspection and manual adjustment. Sufficient control is furthermore retained via parameter specification and the option to include expert knowledge. Conversely, completely automatic operation also allows for extensive analysis of aspects related to landscape discretisation. In a case study, the application of the package is presented. A sensitivity analysis of the most important discretisation parameters demonstrates its efficient workflow automation. Considering multiple streamflow metrics, the employed model proved reasonably robust to the discretisation parameters. However, parameters determining the sizes of subbasins and hillslopes proved to be more important than the others, including the number of representative hillslopes, the number of attributes employed for the lumping algorithm, and the number of sub-discretisations of the representative hillslopes.

The connectome mapper: an open-source processing pipeline to map connectomes with MRI.

PubMed

Daducci, Alessandro; Gerhard, Stephan; Griffa, Alessandra; Lemkaddem, Alia; Cammoun, Leila; Gigandet, Xavier; Meuli, Reto; Hagmann, Patric; Thiran, Jean-Philippe

2012-01-01

Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.

SMARTSware for SMARTS users to facilitate data reduction and data analysis

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

2005-01-01

The software package SMARTSware is made by one of the instrument scientist on the engineering neutron diffractometer SMARTS at the Lujan Center, a national user facility at Los Alamos Neutron Scattering Center (LANSCE). The purpose of the software is to facilitate the data analysis of powder diffraction data recorded at the Lujan Center, and hence the target audience is users performing experiments at the one of the powder diffractometers (SMARTS, HIPPO, HIPD and NPDF) at the Lujan Center. The beam time at the Lujan Center is allocated by peer review of internally and extenally submitted proposals, and therefore many ofmore » the users who are granted beam time are from the international science community. Generally, the users are only at the Lujan Center for a short period of time while they are performing the experiments, and often they leave with several data sets that have not been analyzed. The distribution of the SMARTSware software package will minimize their efforts when analyzing the data once they are back at their institution. Description of software: There are two main parts of the software; a part used to generate instrument parameter files from a set of calibration runs (Smartslparm, SmartsBin, SmartsFitDif and SmartsFitspec); and a part that facilitates the batch refinement of multiple diffraction patterns (SmartsRunRep, SmartsABC, SmartsSPF and SmartsExtract). The former part may only be peripheral to most users, but is a critical part of the instrument scientists' efforts in calibrating their instruments. The latter part is highly applicable to the users as they often need to analyze or re-analyze large sets of data. The programs within the SMARTSware package heavily rely on GSAS for the Rietveld and single peak refinements of diffraction data. GSAS (General Structure Analysis System) is a public available software also originating from LANL. Subroutines and libraries from the NeXus project (a world wide trust to standardize diffraction data formats) and National Center for Supercomputing Applications (NCSA) at the University of Illinois (the Hierarchical Data Format Software Library and Utilities) are used in the programs. All these subroutines and libraries are publicly available through the GNU Public License and/or Freeware. The package also contains sample input and output text files and a manual (LA-UR 04-6581). The executables and sample files will be available for down load at http://public.lanl.gov/clausen/SMARTSware.html and ftp://lansce.lanl.gov/clausen/SMARTSware/SMARTSware.zip, but the source codes will only be made available by written request to clausen@lanl.gov.« less

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

PubMed Central

2014-01-01

Background The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. Results The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. Conclusions The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. Software availability The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests. PMID:24564732

Automatic sample changer control software for automation of neutron activation analysis process in Malaysian Nuclear Agency

NASA Astrophysics Data System (ADS)

Yussup, N.; Ibrahim, M. M.; Rahman, N. A. A.; Mokhtar, M.; Salim, N. A. A.; Soh@Shaari, S. C.; Azman, A.; Lombigit, L.; Azman, A.; Omar, S. A.

2018-01-01

Most of the procedures in neutron activation analysis (NAA) process that has been established in Malaysian Nuclear Agency (Nuclear Malaysia) since 1980s were performed manually. These manual procedures carried out by the NAA laboratory personnel are time consuming and inefficient especially for sample counting and measurement process. The sample needs to be changed and the measurement software needs to be setup for every one hour counting time. Both of these procedures are performed manually for every sample. Hence, an automatic sample changer system (ASC) that consists of hardware and software is developed to automate sample counting process for up to 30 samples consecutively. This paper describes the ASC control software for NAA process which is designed and developed to control the ASC hardware and call GammaVision software for sample measurement. The software is developed by using National Instrument LabVIEW development package.

Hera - The HEASARC's New Data Analysis Service

NASA Technical Reports Server (NTRS)

Pence, William

2006-01-01

Hera is the new computer service provided by the HEASARC at the NASA Goddard Space Flight Center that enables qualified student and professional astronomical researchers to immediately begin analyzing scientific data from high-energy astrophysics missions. All the necessary resources needed to do the data analysis are freely provided by Hera, including: * the latest version of the hundreds of scientific analysis programs in the HEASARC's HEASOFT package, as well as most of the programs in the Chandra CIAO package and the XMM-Newton SAS package. * high speed access to the terabytes of data in the HEASARC's high energy astrophysics Browse data archive. * a cluster of fast Linw workstations to run the software * ample local disk space to temporarily store the data and results. Some of the many features and different modes of using Hera are illustrated in this poster presentation.

Office Computer Software: A Comprehensive Review of Software Programs.

ERIC Educational Resources Information Center

Secretary, 1992

1992-01-01

Describes types of software including system software, application software, spreadsheets, accounting software, graphics packages, desktop publishing software, database, desktop and personal information management software, project and records management software, groupware, and shareware. (JOW)

PAMLX: a graphical user interface for PAML.

PubMed

Xu, Bo; Yang, Ziheng

2013-12-01

This note announces pamlX, a graphical user interface/front end for the paml (for Phylogenetic Analysis by Maximum Likelihood) program package (Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556; Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591). pamlX is written in C++ using the Qt library and communicates with paml programs through files. It can be used to create, edit, and print control files for paml programs and to launch paml runs. The interface is available for free download at http://abacus.gene.ucl.ac.uk/software/paml.html.

Subband/Transform MATLAB Functions For Processing Images

NASA Technical Reports Server (NTRS)

Glover, D.

1995-01-01

SUBTRANS software is package of routines implementing image-data-processing functions for use with MATLAB*(TM) software. Provides capability to transform image data with block transforms and to produce spatial-frequency subbands of transformed data. Functions cascaded to provide further decomposition into more subbands. Also used in image-data-compression systems. For example, transforms used to prepare data for lossy compression. Written for use in MATLAB mathematical-analysis environment.

Scalable computing for evolutionary genomics.

PubMed

Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

2012-01-01

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project, BioNode encourages creating free and open source VM images, for multiple targets, through one central project. BioNode can be deployed on Windows, OSX, Linux, and in the Cloud. Next to the downloadable BioNode images, we provide tutorials online, which empower bioinformaticians to install and run BioNode in different environments, as well as information for future initiatives, on creating and building such images.

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.

Application of the AMBUR R package for spatio-temporal analysis of shoreline change: Jekyll Island, Georgia, USA

NASA Astrophysics Data System (ADS)

Jackson, Chester W.; Alexander, Clark R.; Bush, David M.

2012-04-01

The AMBUR (Analyzing Moving Boundaries Using R) package for the R software environment provides a collection of functions for assisting with analyzing and visualizing historical shoreline change. The package allows import and export of geospatial data in ESRI shapefile format, which is compatible with most commercial and open-source GIS software. The "baseline and transect" method is the primary technique used to quantify distances and rates of shoreline movement, and to detect classification changes across time. Along with the traditional "perpendicular" transect method, two new transect methods, "near" and "filtered," assist with quantifying changes along curved shorelines that are problematic for perpendicular transect methods. Output from the analyses includes data tables, graphics, and geospatial data, which are useful in rapidly assessing trends and potential errors in the dataset. A forecasting function also allows the user to estimate the future location of the shoreline and store the results in a shapefile. Other utilities and tools provided in the package assist with preparing and manipulating geospatial data, error checking, and generating supporting graphics and shapefiles. The package can be customized to perform additional statistical, graphical, and geospatial functions, and, it is capable of analyzing the movement of any boundary (e.g., shorelines, glacier terminus, fire edge, and marine and terrestrial ecozones).

Tree Classification Software

NASA Technical Reports Server (NTRS)

Buntine, Wray

1993-01-01

This paper introduces the IND Tree Package to prospective users. IND does supervised learning using classification trees. This learning task is a basic tool used in the development of diagnosis, monitoring and expert systems. The IND Tree Package was developed as part of a NASA project to semi-automate the development of data analysis and modelling algorithms using artificial intelligence techniques. The IND Tree Package integrates features from CART and C4 with newer Bayesian and minimum encoding methods for growing classification trees and graphs. The IND Tree Package also provides an experimental control suite on top. The newer features give improved probability estimates often required in diagnostic and screening tasks. The package comes with a manual, Unix 'man' entries, and a guide to tree methods and research. The IND Tree Package is implemented in C under Unix and was beta-tested at university and commercial research laboratories in the United States.

Application of a neural network to simulate analysis in an optimization process

NASA Technical Reports Server (NTRS)

Rogers, James L.; Lamarsh, William J., II

1992-01-01

A new experimental software package called NETS/PROSSS aimed at reducing the computing time required to solve a complex design problem is described. The software combines a neural network for simulating the analysis program with an optimization program. The neural network is applied to approximate results of a finite element analysis program to quickly obtain a near-optimal solution. Results of the NETS/PROSSS optimization process can also be used as an initial design in a normal optimization process and make it possible to converge to an optimum solution with significantly fewer iterations.

User Documentation for Multiple Software Releases

NASA Technical Reports Server (NTRS)

Humphrey, R.

1982-01-01

In proposed solution to problems of frequent software releases and updates, documentation would be divided into smaller packages, each of which contains data relating to only one of several software components. Changes would not affect entire document. Concept would improve dissemination of information regarding changes and would improve quality of data supporting packages. Would help to insure both timeliness and more thorough scrutiny of changes.

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.

PubMed

Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

2013-04-22

For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations.

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

PubMed

Bieri, Michael; d'Auvergne, Edward J; Gooley, Paul R

2011-06-01

Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

Utility of coupling nonlinear optimization methods with numerical modeling software

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

Murphy, M.J.

1996-08-05

Results of using GLO (Global Local Optimizer), a general purpose nonlinear optimization software package for investigating multi-parameter problems in science and engineering is discussed. The package consists of the modular optimization control system (GLO), a graphical user interface (GLO-GUI), a pre-processor (GLO-PUT), a post-processor (GLO-GET), and nonlinear optimization software modules, GLOBAL & LOCAL. GLO is designed for controlling and easy coupling to any scientific software application. GLO runs the optimization module and scientific software application in an iterative loop. At each iteration, the optimization module defines new values for the set of parameters being optimized. GLO-PUT inserts the new parametermore » values into the input file of the scientific application. GLO runs the application with the new parameter values. GLO-GET determines the value of the objective function by extracting the results of the analysis and comparing to the desired result. GLO continues to run the scientific application over and over until it finds the ``best`` set of parameters by minimizing (or maximizing) the objective function. An example problem showing the optimization of material model is presented (Taylor cylinder impact test).« less

Software Comparison for Renewable Energy Deployment in a Distribution Network

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

Gao, David Wenzhong; Muljadi, Eduard; Tian, Tian

The main objective of this report is to evaluate different software options for performing robust distributed generation (DG) power system modeling. The features and capabilities of four simulation tools, OpenDSS, GridLAB-D, CYMDIST, and PowerWorld Simulator, are compared to analyze their effectiveness in analyzing distribution networks with DG. OpenDSS and GridLAB-D, two open source software, have the capability to simulate networks with fluctuating data values. These packages allow the running of a simulation each time instant by iterating only the main script file. CYMDIST, a commercial software, allows for time-series simulation to study variations on network controls. PowerWorld Simulator, another commercialmore » tool, has a batch mode simulation function through the 'Time Step Simulation' tool, which obtains solutions for a list of specified time points. PowerWorld Simulator is intended for analysis of transmission-level systems, while the other three are designed for distribution systems. CYMDIST and PowerWorld Simulator feature easy-to-use graphical user interfaces (GUIs). OpenDSS and GridLAB-D, on the other hand, are based on command-line programs, which increase the time necessary to become familiar with the software packages.« less

Information systems analysis approach in hospitals: a national survey.

PubMed

Wong, B K; Sellaro, C L; Monaco, J A

1995-03-01

A survey of 216 hospitals reveals that some hospitals do not conduct cost-benefit analyses or analyze possible adverse effects in feasibility studies. In determining and analyzing system requirements, external factors that initiate the transaction are not examined, and computer-aided software engineering (CASE) tools are seldom used. Some hospitals do not investigate the advantages and disadvantages of using in-house-developed software versus purchased software packages in the evaluation of alternatives. The survey finds that, overall, most hospitals follow the traditional systems development life cycle (SDLC) approach in analyzing information systems.

Substructured multibody molecular dynamics.

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

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

AnthropMMD: An R package with a graphical user interface for the mean measure of divergence.

PubMed

Santos, Frédéric

2018-01-01

The mean measure of divergence is a dissimilarity measure between groups of individuals described by dichotomous variables. It is well suited to datasets with many missing values, and it is generally used to compute distance matrices and represent phenograms. Although often used in biological anthropology and archaeozoology, this method suffers from a lack of implementation in common statistical software. A package for the R statistical software, AnthropMMD, is presented here. Offering a dynamic graphical user interface, it is the first one dedicated to Smith's mean measure of divergence. The package also provides facilities for graphical representations and the crucial step of trait selection, so that the entire analysis can be performed through the graphical user interface. Its use is demonstrated using an artificial dataset, and the impact of trait selection is discussed. Finally, AnthropMMD is compared to three other free tools available for calculating the mean measure of divergence, and is proven to be consistent with them. © 2017 Wiley Periodicals, Inc.

Performance evaluation of the RITG148+ set of TomoTherapy quality assurance tools using RTQA2 radiochromic film.

PubMed

Lobb, Eric C

2016-07-08

Version 6.3 of the RITG148+ software package offers eight automated analysis routines for quality assurance of the TomoTherapy platform. A performance evaluation of each routine was performed in order to compare RITG148+ results with traditionally accepted analysis techniques and verify that simulated changes in machine parameters are correctly identified by the software. Reference films were exposed according to AAPM TG-148 methodology for each routine and the RITG148+ results were compared with either alternative software analysis techniques or manual analysis techniques in order to assess baseline agreement. Changes in machine performance were simulated through translational and rotational adjustments to subsequently irradiated films, and these films were analyzed to verify that the applied changes were accurately detected by each of the RITG148+ routines. For the Hounsfield unit routine, an assessment of the "Frame Averaging" functionality and the effects of phantom roll on the routine results are presented. All RITG148+ routines reported acceptable baseline results consistent with alternative analysis techniques, with 9 of the 11 baseline test results showing agreement of 0.1mm/0.1° or better. Simulated changes were correctly identified by the RITG148+ routines within approximately 0.2 mm/0.2° with the exception of the Field Centervs. Jaw Setting routine, which was found to have limited accuracy in cases where field centers were not aligned for all jaw settings due to inaccurate autorotation of the film during analysis. The performance of the RITG148+ software package was found to be acceptable for introduction into our clinical environment as an automated alternative to traditional analysis techniques for routine TomoTherapy quality assurance testing.

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2013 CFR

2013-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2014 CFR

2014-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2012 CFR

2012-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

Environmental databases and other computerized information tools

NASA Technical Reports Server (NTRS)

Clark-Ingram, Marceia

1995-01-01

Increasing environmental legislation has brought about the development of many new environmental databases and software application packages to aid in the quest for environmental compliance. These databases and software packages are useful tools and applicable to a wide range of environmental areas from atmospheric modeling to materials replacement technology. The great abundance of such products and services can be very overwhelming when trying to identify the tools which best meet specific needs. This paper will discuss the types of environmental databases and software packages available. This discussion will also encompass the affected environmental areas of concern, product capabilities, and hardware requirements for product utilization.

User guide to Exploration and Graphics for RivEr Trends (EGRET) and dataRetrieval: R packages for hydrologic data

USGS Publications Warehouse

Hirsch, Robert M.; De Cicco, Laura A.

2015-01-01

Evaluating long-term changes in river conditions (water quality and discharge) is an important use of hydrologic data. To carry out such evaluations, the hydrologist needs tools to facilitate several key steps in the process: acquiring the data records from a variety of sources, structuring it in ways that facilitate the analysis, processing the data with routines that extract information about changes that may be happening, and displaying findings with graphical techniques. A pair of tightly linked R packages, called dataRetrieval and EGRET (Exploration and Graphics for RivEr Trends), have been developed for carrying out each of these steps in an integrated manner. They are designed to easily accept data from three sources: U.S. Geological Survey hydrologic data, U.S. Environmental Protection Agency (EPA) STORET data, and user-supplied flat files. The dataRetrieval package not only serves as a “front end” to the EGRET package, it can also be used to easily download many types of hydrologic data and organize it in ways that facilitate many other hydrologic applications. The EGRET package has components oriented towards the description of long-term changes in streamflow statistics (high flow, average flow, and low flow) as well as changes in water quality. For the water-quality analysis, it uses Weighted Regressions on Time, Discharge and Season (WRTDS) to describe long-term trends in both concentration and flux. EGRET also creates a wide range of graphical presentations of the water-quality data and of the WRTDS results. This report serves as a user guide to these two R packages, providing detailed guidance on installation and use of the software, documentation of the analysis methods used, as well as guidance on some of the kinds of questions and approaches that the software can facilitate.

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)

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

Analysis of XMM-Newton Data from Extended Sources and the Diffuse X-Ray Background

NASA Technical Reports Server (NTRS)

Snowden, Steven

2011-01-01

Reduction of X-ray data from extended objects and the diffuse background is a complicated process that requires attention to the details of the instrumental response as well as an understanding of the multiple background components. We present methods and software that we have developed to reduce data from XMM-Newton EPIC imaging observations for both the MOS and PN instruments. The software has now been included in the Science Analysis System (SAS) package available through the XMM-Newton Science Operations Center (SOC).

Problems in Analyzing Time Series with Gaps and Their Solution with the WinABD Software Package

NASA Astrophysics Data System (ADS)

Desherevskii, A. V.; Zhuravlev, V. I.; Nikolsky, A. N.; Sidorin, A. Ya.

2017-12-01

Technologies for the analysis of time series with gaps are considered. Some algorithms of signal extraction (purification) and evaluation of its characteristics, such as rhythmic components, are discussed for series with gaps. Examples are given for the analysis of data obtained during long-term observations at the Garm geophysical test site and in other regions. The technical solutions used in the WinABD software are considered to most efficiently arrange the operation of relevant algorithms in the presence of observational defects.

A Meta-Analysis of Referential Communication Studies: A Computer Readable Literature Review.

ERIC Educational Resources Information Center

Dickson, W. Patrick; Moskoff, Mary

A computer-assisted analysis of studies on referential communication (giving directions/explanations) located 66 reports involving 80 experiments, 114 referential tasks, and over 6,200 individuals. The studies were entered into a statistical software package system (SPSS) and analyzed for characteristics of the subjects and experimental designs,…

Modular Open-Source Software for Item Factor Analysis

ERIC Educational Resources Information Center

Pritikin, Joshua N.; Hunter, Micheal D.; Boker, Steven M.

2015-01-01

This article introduces an item factor analysis (IFA) module for "OpenMx," a free, open-source, and modular statistical modeling package that runs within the R programming environment on GNU/Linux, Mac OS X, and Microsoft Windows. The IFA module offers a novel model specification language that is well suited to programmatic generation…

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

PubMed

Chen, Yunshun; Lun, Aaron T L; Smyth, Gordon K

2016-01-01

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.

Linear Discriminant Analysis on a Spreadsheet.

ERIC Educational Resources Information Center

Busbey, Arthur Bresnahan III

1989-01-01

Described is a software package, "Trapeze," within which a routine called LinDis can be used. Discussed are teaching methods, the linear discriminant model and equations, the LinDis worksheet, and an example. The set up for this routine is included. (CW)

GIS-Based System of Hydrologic and Hydraulic Applications for Highway Engineering

DOT National Transportation Integrated Search

1999-10-01

In this research project, a GIS has been developed to assist in the design of highway drainage facilities by utilizing hydrologic spatial data to calculate the input parameters for standard hydrologic software packages. This GIS reduces the analysis ...

A survey of tools for the analysis of quantitative PCR (qPCR) data.

PubMed

Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

2014-09-01

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

User’s guide for MapMark4—An R package for the probability calculations in three-part mineral resource assessments

USGS Publications Warehouse

Ellefsen, Karl J.

2017-06-27

MapMark4 is a software package that implements the probability calculations in three-part mineral resource assessments. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of this user’s guide are bundled together in R’s unit of shareable code, which is called a “package.” This user’s guide includes step-by-step instructions showing how the functions are used to carry out the probability calculations. The calculations are demonstrated using test data, which are included in the package.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.

1992-01-01

The goal was the design and implementation of software to be used in the conceptual design of aerospace vehicles. Several packages and design studies were completed, including two software tools currently used in the conceptual level design of aerospace vehicles. These tools are the Solid Modeling Aerospace Research Tool (SMART) and the Environment for Software Integration and Execution (EASIE). SMART provides conceptual designers with a rapid prototyping capability and additionally provides initial mass property analysis. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand alone analysis codes that result in the streamlining of the exchange of data between programs, reducing errors and improving efficiency.

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...-compatible format. All databases must be supported with adequate documentation on data attributes, SQL...

Scout 2008 Version 1.0 User Guide

EPA Science Inventory

The Scout 2008 version 1.0 software package provides a wide variety of classical and robust statistical methods that are not typically available in other commercial software packages. A major part of Scout deals with classical, robust, and resistant univariate and multivariate ou...

’Pushing a Big Rock Up a Steep Hill’: Acquisition Lessons Learned from DoD Applications Storefront

DTIC Science & Technology

2014-04-30

software patches, web applications, widgets, and mobile application packages. The envisioned application store will deliver software from a central...automated delivery of software patches, web applications, widgets, and mobile application packages. The envisioned application store will deliver... mobile technologies, hoping to enhance warfighter situational awareness and access to information. Unfortunately, the Defense Acquisition System has not

MicroSIFT Courseware Evaluation. [Set 13 (294-319), Set 14 (320-361), with Hardware (HRD) and Subject (SBJ) Indexes to Both Sets.

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

This document consists of 68 microcomputer software package evaluations prepared by MicroSIFT (Microcomputer Software and Information for Teachers) Clearinghouse at the Northwest Regional Education Laboratory. There are 26 packages in set 13 and 42 in set 14. Each software review lists producer, time and place of evaluation, cost, ability level,…

Enhancing the Portability of GBT Data

NASA Astrophysics Data System (ADS)

Cowan, A. W.; Radziwill, N.; Fleming, D.; Sessoms, E.

2003-12-01

The Green Bank Telescope currently produces its raw data as a suite of FITS files, which are then consolidated and pre-processed before being packaged into a Measurement Set (the data structure understood by AIPS++). The separation of data adds to the complexity of data analysis, and we would like to reduce the artificial complexity involved in reading the data. Also, in order to support a broader cross-section of observers' backgrounds and interests, we would like to begin supporting data reduction packages in addition to AIPS++. Therefore, GBT data must be readily accessible to IDL, CLASS, and other data reduction packages, as well as any software that observers write themselves. In pursuit of this goal, we are currently developing a unified FITS data product that contains the entirety of the data and can be readily assimilated into multiple software packages. During the summer of 2003, prototyping exercises were initiated based on the SDFITS convention, which have led to an alpha-test period now in progress. This poster discusses the process of generating the unified FITS data product and details the current status of the project. Thanks to the National Science Foundation REU program for their financial support.

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

PubMed Central

Lun, Aaron T.L.; Smyth, Gordon K.

2016-01-01

Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target protein in the genome. An important scientific application is to identify changes in protein binding between different treatment conditions, i.e. to detect differential binding. This can reveal potential mechanisms through which changes in binding may contribute to the treatment effect. The csaw package provides a framework for the de novo detection of differentially bound genomic regions. It uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical software to test for significant differences in each window. Finally, it clusters windows into regions for output and controls the false discovery rate properly over all detected regions. The csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied to both transcription factor and histone mark datasets, and, more generally, to any type of sequencing data measuring genomic coverage. csaw performs favorably against existing methods for de novo DB analyses on both simulated and real data. csaw is implemented as a R software package and is freely available from the open-source Bioconductor project. PMID:26578583

PIV Data Validation Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A PIV data validation and post-processing software package was developed to provide semi-automated data validation and data reduction capabilities for Particle Image Velocimetry data sets. The software provides three primary capabilities including (1) removal of spurious vector data, (2) filtering, smoothing, and interpolating of PIV data, and (3) calculations of out-of-plane vorticity, ensemble statistics, and turbulence statistics information. The software runs on an IBM PC/AT host computer working either under Microsoft Windows 3.1 or Windows 95 operating systems.

Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

PubMed

Thomas, Philipp; Matuschek, Hannes; Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

PubMed Central

Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA’s performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license. PMID:22723865

VSO For Dummies

NASA Astrophysics Data System (ADS)

Schwartz, Richard A.; Zarro, D.; Csillaghy, A.; Dennis, B.; Tolbert, A. K.; Etesi, L.

2009-05-01

We report on our activities to integrate VSO search and retrieval capabilities into standard data access, display, and analysis tools. In addition to its standard Web-based search form, the VSO provides an Interactive Data Language (IDL) client (vso_search) that is available through the Solar Software (SSW) package. We have incorporated this client into an IDL-widget interface program (show_synop) that allows for more simplified searching and downloading of VSO datasets directly into a user's IDL data analysis environment. In particular, we have provided the capability to read VSO datasets into a general purpose IDL package (plotman) that can display different datatypes (lightcurves, images, and spectra) and perform basic data operations such as zooming, image overlays, solar rotation, etc. Currently, the show_synop tool supports access to ground-based and space-based (SOHO, STEREO, and Hinode) observations, and has the capability to include new datasets as they become available. A user encounters two major hurdles when using the VSO: (1) Instrument-specific software (such as level-0 file readers and data-prepping procedures) may not be available in the user's local SSW distribution. (2) Recent calibration files (such as flat-fields) are not automatically distributed with the analysis software. To address these issues, we have developed a dedicated server (prepserver) that incorporates all the latest instrument-specific software libraries and calibration files. The prepserver uses an IDL-Java bridge to read and implement data processing requests from a client and return a processed data file that can be readily displayed with the show_synop/plotman package. The advantage of the prepserver is that the user is only required to install the general branch (gen) of the SSW tree, and is freed from the more onerous task of installing instrument-specific libraries and calibration files. We will demonstrate how the prepserver can be used to read, process, and overlay SOHO/EIT, TRACE, SECCHI/EUVI, and RHESSI images.

Easily extensible unix software for spectral analysis, display, modification, and synthesis of musical sounds

NASA Astrophysics Data System (ADS)

Beauchamp, James W.

2002-11-01

Software has been developed which enables users to perform time-varying spectral analysis of individual musical tones or successions of them and to perform further processing of the data. The package, called sndan, is freely available in source code, uses EPS graphics for display, and is written in ansi c for ease of code modification and extension. Two analyzers, a fixed-filter-bank phase vocoder (''pvan'') and a frequency-tracking analyzer (''mqan'') constitute the analysis front end of the package. While pvan's output consists of continuous amplitudes and frequencies of harmonics, mqan produces disjoint ''tracks.'' However, another program extracts a fundamental frequency and separates harmonics from the tracks, resulting in a continuous harmonic output. ''monan'' is a program used to display harmonic data in a variety of formats, perform various spectral modifications, and perform additive resynthesis of the harmonic partials, including possible pitch-shifting and time-scaling. Sounds can also be synthesized according to a musical score using a companion synthesis language, Music 4C. Several other programs in the sndan suite can be used for specialized tasks, such as signal display and editing. Applications of the software include producing specialized sounds for music compositions or psychoacoustic experiments or as a basis for developing new synthesis algorithms.

Electromagnetic Field Effects in Semiconductor Crystal Growth

NASA Technical Reports Server (NTRS)

Dulikravich, George S.

1996-01-01

This proposed two-year research project was to involve development of an analytical model, a numerical algorithm for its integration, and a software for the analysis of a solidification process under the influence of electric and magnetic fields in microgravity. Due to the complexity of the analytical model that was developed and its boundary conditions, only a preliminary version of the numerical algorithm was developed while the development of the software package was not completed.

LFSTAT - An R-Package for Low-Flow Analysis

NASA Astrophysics Data System (ADS)

Koffler, D.; Laaha, G.

2012-04-01

When analysing daily streamflow data focusing on low flow and drought, the state of the art is well documented in the Manual on Low-Flow Estimation and Prediction [1] published by the WMO. While it is clear what has to be done, it is not so clear how to preform the analysis and make the calculation as reproducible as possible. Our software solution expands the high preforming statistical open source software package R to analyse daily stream flow data focusing on low-flows. As command-line based programs are not everyone's preference, we also offer a plug-in for the R-Commander, an easy to use graphical user interface (GUI) to analyse data in R. Functionality includes estimation of the most important low-flow indices. Beside standardly used flow indices also BFI and Recession constants can be computed. The main applications of L-moment based Extreme value analysis and regional frequency analysis (RFA) are available. Calculation of streamflow deficits is another important feature. The most common graphics are prepared and can easily be modified according to the users preferences. Graphics include hydrographs for different periods, flexible streamflow deficit plots, baseflow visualisation, flow duration curves as well as double mass curves just to name a few. The package uses a S3-class called lfobj (low-flow objects). Once this objects are created, analysis can be preformed by mouse-click, and a script can be saved to make the analysis easy reproducible. At the moment we are offering implementation of all major methods proposed in the WMO manual on Low-flow Estimation and Predictions. Future plans include e.g. report export in odt-file using odf-weave. We hope to offer a tool to ease and structure the analysis of stream flow data focusing on low-flows and to make analysis transparent and communicable. The package is designed for hydrological research and water management practice, but can also be used in teaching students the first steps in low-flow hydrology.

When to Renew Software Licences at HPC Centres? A Mathematical Analysis

NASA Astrophysics Data System (ADS)

Baolai, Ge; MacIsaac, Allan B.

2010-11-01

In this paper we study a common problem faced by many high performance computing (HPC) centres: When and how to renew commercial software licences. Software vendors often sell perpetual licences along with forward update and support contracts at an additional, annual cost. Every year or so, software support personnel and the budget units of HPC centres are required to make the decision of whether or not to renew such support, and usually such decisions are made intuitively. The total cost for a continuing support contract can, however, be costly. One might therefore want a rational answer to the question of whether the option for a renewal should be exercised and when. In an attempt to study this problem within a market framework, we present the mathematical problem derived for the day to day operation of a hypothetical HPC centre that charges for the use of software packages. In the mathematical model, we assume that the uncertainty comes from the demand, number of users using the packages, as well as the price. Further we assume the availability of up to date software versions may also affect the demand. We develop a renewal strategy that aims to maximize the expected profit from the use the software under consideration. The derived problem involves a decision tree, which constitutes a numerical procedure that can be processed in parallel.

User's guide to noise data acquisition and analysis programs for HP9845: Nicolet analyzers

NASA Technical Reports Server (NTRS)

Mcgary, M. C.

1982-01-01

A software interface package was written for use with a desktop computer and two models of single channel Fast Fourier analyzers. This software features a portable measurement and analysis system with several options. Two types of interface hardware can alternately be used in conjunction with the software. Either an IEEE-488 Bus interface or a 16-bit parallel system may be used. Two types of storage medium, either tape cartridge or floppy disc can be used with the software. Five types of data may be stored, plotted, and/or printed. The data types include time histories, narrow band power spectra, and narrow band, one-third octave band, or octave band sound pressure level. The data acquisition programming includes a front panel remote control option for the FFT analyzers. Data analysis options include choice of line type and pen color for plotting.

Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

NASA Astrophysics Data System (ADS)

Fisher, Ward

2014-05-01

Planning software compatibility across forthcoming generations of computing platforms is a problem commonly encountered in software engineering and development. While this problem can affect any class of software, data analysis and visualization programs are particularly vulnerable. This is due in part to their inherent dependency on specialized hardware and computing environments. A number of strategies and tools have been designed to aid software engineers with this task. While generally embraced by developers at 'traditional' software companies, these methodologies are often dismissed by the scientific software community as unwieldy, inefficient and unnecessary. As a result, many important and storied scientific software packages can struggle to adapt to a new computing environment; for example, one in which much work is carried out on sub-laptop devices (such as tablets and smartphones). Rewriting these packages for a new platform often requires significant investment in terms of development time and developer expertise. In many cases, porting older software to modern devices is neither practical nor possible. As a result, replacement software must be developed from scratch, wasting resources better spent on other projects. Enabled largely by the rapid rise and adoption of cloud computing platforms, 'Application Streaming' technologies allow legacy visualization and analysis software to be operated wholly from a client device (be it laptop, tablet or smartphone) while retaining full functionality and interactivity. It mitigates much of the developer effort required by other more traditional methods while simultaneously reducing the time it takes to bring the software to a new platform. This work will provide an overview of Application Streaming and how it compares against other technologies which allow scientific visualization software to be executed from a remote computer. We will discuss the functionality and limitations of existing application streaming frameworks and how a developer might prepare their software for application streaming. We will also examine the secondary benefits realized by moving legacy software to the cloud. Finally, we will examine the process by which a legacy Java application, the Integrated Data Viewer (IDV), is to be adapted for tablet computing via Application Streaming.

Improvement of calculation method for electrical parameters of short network of ore-thermal furnaces

NASA Astrophysics Data System (ADS)

Aliferov, A. I.; Bikeev, R. A.; Goreva, L. P.

2017-10-01

The paper describes a new calculation method for active and inductive resistance of split interleaved current leads packages in ore-thermal electric furnaces. The method is developed on basis of regression analysis of dependencies of active and inductive resistances of the packages on their geometrical parameters, mutual disposition and interleaving pattern. These multi-parametric calculations have been performed with ANSYS software. The proposed method allows solving split current lead electrical parameters minimization and balancing problems for ore-thermal furnaces.

Athena X-IFU event reconstruction software: SIRENA

NASA Astrophysics Data System (ADS)

Ceballos, Maria Teresa; Cobo, Beatriz; Peille, Philippe; Wilms, Joern; Brand, Thorsten; Dauser, Thomas; Bandler, Simon; Smith, Stephen

2015-09-01

This contribution describes the status and technical details of the SIRENA package, the software currently in development to perform the on board event energy reconstruction for the Athena calorimeter X-IFU. This on board processing will be done in the X-IFU DRE unit and it will consist in an initial triggering of event pulses followed by an analysis (with the SIRENA package) to determine the energy content of such events.The current algorithm used by SIRENA is the optimal filtering technique (also used by ASTRO-H processor) although some other algorithms are also being tested.Here we present these studies and some preliminary results about the energy resolution of the instrument based on simulations done with the SIXTE simulator (http://www.sternwarte.uni-erlangen.de/research/sixte/) in which SIRENA is integrated.

Extreme Ultraviolet Imaging Telescope (EIT)

NASA Technical Reports Server (NTRS)

Lemen, J. R.; Freeland, S. L.

1997-01-01

Efforts concentrated on development and implementation of the SolarSoft (SSW) data analysis system. From an EIT analysis perspective, this system was designed to facilitate efficient reuse and conversion of software developed for Yohkoh/SXT and to take advantage of a large existing body of software developed by the SDAC, Yohkoh, and SOHO instrument teams. Another strong motivation for this system was to provide an EIT analysis environment which permits coordinated analysis of EIT data in conjunction with data from important supporting instruments, including Yohkoh/SXT and the other SOHO coronal instruments; CDS, SUMER, and LASCO. In addition, the SSW system will support coordinated EIT/TRACE analysis (by design) when TRACE data is available; TRACE launch is currently planned for March 1998. Working with Jeff Newmark, the Chianti software package (K.P. Dere et al) and UV /EUV data base was fully integrated into the SSW system to facilitate EIT temperature and emission analysis.

EXP-PAC: providing comparative analysis and storage of next generation gene expression data.

PubMed

Church, Philip C; Goscinski, Andrzej; Lefèvre, Christophe

2012-07-01

Microarrays and more recently RNA sequencing has led to an increase in available gene expression data. How to manage and store this data is becoming a key issue. In response we have developed EXP-PAC, a web based software package for storage, management and analysis of gene expression and sequence data. Unique to this package is SQL based querying of gene expression data sets, distributed normalization of raw gene expression data and analysis of gene expression data across experiments and species. This package has been populated with lactation data in the international milk genomic consortium web portal (http://milkgenomics.org/). Source code is also available which can be hosted on a Windows, Linux or Mac APACHE server connected to a private or public network (http://mamsap.it.deakin.edu.au/~pcc/Release/EXP_PAC.html). Copyright © 2012 Elsevier Inc. All rights reserved.

AN ADA LINEAR ALGEBRA PACKAGE MODELED AFTER HAL/S

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

This package extends the Ada programming language to include linear algebra capabilities similar to those of the HAL/S programming language. The package is designed for avionics applications such as Space Station flight software. In addition to the HAL/S built-in functions, the package incorporates the quaternion functions used in the Shuttle and Galileo projects, and routines from LINPAK that solve systems of equations involving general square matrices. Language conventions in this package follow those of HAL/S to the maximum extent practical and minimize the effort required for writing new avionics software and translating existent software into Ada. Valid numeric types in this package include scalar, vector, matrix, and quaternion declarations. (Quaternions are fourcomponent vectors used in representing motion between two coordinate frames). Single precision and double precision floating point arithmetic is available in addition to the standard double precision integer manipulation. Infix operators are used instead of function calls to define dot products, cross products, quaternion products, and mixed scalar-vector, scalar-matrix, and vector-matrix products. The package contains two generic programs: one for floating point, and one for integer. The actual component type is passed as a formal parameter to the generic linear algebra package. The procedures for solving systems of linear equations defined by general matrices include GEFA, GECO, GESL, and GIDI. The HAL/S functions include ABVAL, UNIT, TRACE, DET, INVERSE, TRANSPOSE, GET, PUT, FETCH, PLACE, and IDENTITY. This package is written in Ada (Version 1.2) for batch execution and is machine independent. The linear algebra software depends on nothing outside the Ada language except for a call to a square root function for floating point scalars (such as SQRT in the DEC VAX MATHLIB library). This program was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

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.

Integrated optomechanical analysis and testing software development at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2013-09-01

Advanced analytical software capabilities are being developed to advance the design of prototypical hardware in the Engineering Division at MIT Lincoln Laboratory. The current effort is focused on the integration of analysis tools tailored to the work flow, organizational structure, and current technology demands. These tools are being designed to provide superior insight into the interdisciplinary behavior of optical systems and enable rapid assessment and execution of design trades to optimize the design of optomechanical systems. The custom software architecture is designed to exploit and enhance the functionality of existing industry standard commercial software, provide a framework for centralizing internally developed tools, and deliver greater efficiency, productivity, and accuracy through standardization, automation, and integration. Specific efforts have included the development of a feature-rich software package for Structural-Thermal-Optical Performance (STOP) modeling, advanced Line Of Sight (LOS) jitter simulations, and improved integration of dynamic testing and structural modeling.

Experience with case tools in the design of process-oriented software

NASA Astrophysics Data System (ADS)

Novakov, Ognian; Sicard, Claude-Henri

1994-12-01

In Accelerator systems such as the CERN PS complex, process equipment has a life time which may exceed the typical life cycle of its related software. Taking into account the variety of such equipment, it is important to keep the analysis and design of the software in a system-independent form. This paper discusses the experience gathered in using commercial CASE tools for analysis, design and reverse engineering of different process-oriented software modules, with a principal emphasis on maintaining the initial analysis in a standardized form. Such tools have been in existence for several years, but this paper shows that they are not fully adapted to our needs. In particular, the paper stresses the problems of integrating such a tool into an existing data-base-dependent development chain, the lack of real-time simulation tools and of Object-Oriented concepts in existing commercial packages. Finally, the paper gives a broader view of software engineering needs in our particular context.

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.

Spotlight-8 Image Analysis Software

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2006-01-01

Spotlight is a cross-platform GUI-based software package designed to perform image analysis on sequences of images generated by combustion and fluid physics experiments run in a microgravity environment. Spotlight can perform analysis on a single image in an interactive mode or perform analysis on a sequence of images in an automated fashion. Image processing operations can be employed to enhance the image before various statistics and measurement operations are performed. An arbitrarily large number of objects can be analyzed simultaneously with independent areas of interest. Spotlight saves results in a text file that can be imported into other programs for graphing or further analysis. Spotlight can be run on Microsoft Windows, Linux, and Apple OS X platforms.

Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

NASA Astrophysics Data System (ADS)

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2014-01-01

In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

Development of a ROV Deployed Video Analysis Tool for Rapid Measurement of Submerged Oil/Gas Leaks

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

Savas, Omer

Expanded deep sea drilling around the globe makes it necessary to have readily available tools to quickly and accurately measure discharge rates from accidental submerged oil/gas leak jets for the first responders to deploy adequate resources for containment. We have developed and tested a field deployable video analysis software package which is able to provide in the field sufficiently accurate flow rate estimates for initial responders in accidental oil discharges in submarine operations. The essence of our approach is based on tracking coherent features at the interface in the near field of immiscible turbulent jets. The software package, UCB_Plume, ismore » ready to be used by the first responders for field implementation. We have tested the tool on submerged water and oil jets which are made visible using fluorescent dyes. We have been able to estimate the discharge rate within 20% accuracy. A high end WINDOWS laptop computer is suggested as the operating platform and a USB connected high speed, high resolution monochrome camera as the imaging device are sufficient for acquiring flow images under continuous unidirectional illumination and running the software in the field. Results are obtained over a matter of minutes.« less

Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

PubMed

Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

2014-01-01

In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

Reviewing and Viewing.

ERIC Educational Resources Information Center

Clements, Douglas H., Ed.; And Others

1988-01-01

Presents reviews of three software packages. Includes "Cube Builder: A 3-D Geometry Tool," which allows students to build three-dimensional shapes; "Number Master," a multipurpose practice program for whole number computation; and "Safari Search: Problem Solving and Inference," which focuses on decision making in mathematical analysis. (PK)

System Operations Studies : Feeder System Model. User's Manual.

DOT National Transportation Integrated Search

1982-11-01

The Feeder System Model (FSM) is one of the analytic models included in the System Operations Studies (SOS) software package developed for urban transit systems analysis. The objective of the model is to assign a proportion of the zone-to-zone travel...

Effects of MicroCAD on Learning Fundamental Engineering Graphical Concepts: A Qualitative Study.

ERIC Educational Resources Information Center

Leach, James A.; Gull, Randall L.

1990-01-01

Students' reactions and performances were examined when taught engineering geometry concepts using a standard microcomputer-aided drafting software package. Two sample groups were compared based on their computer experience. Included are the methodology, data analysis, and conclusions. (KR)

Analysis, annotation, and profiling of the oat seed transcriptome

USDA-ARS?s Scientific Manuscript database

Novel high-throughput next generation sequencing (NGS) technologies are providing opportunities to explore genomes and transcriptomes in a cost-effective manner. To construct a gene expression atlas of developing oat (Avena sativa) seeds, two software packages specifically designed for RNA-seq (Trin...

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data

PubMed Central

Vernick, Kenneth D.

2017-01-01

Metavisitor is a software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets. The package is composed of a set of modular bioinformatic tools and workflows that are implemented in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. Metavisitor works with DNA, RNA or small RNA sequencing data over a range of read lengths and can use a combination of de novo and guided approaches to assemble genomes from sequencing reads. We show that the software has the potential for quick diagnosis as well as discovery of viruses from a vast array of organisms. Importantly, we provide here executable Metavisitor use cases, which increase the accessibility and transparency of the software, ultimately enabling biologists or clinicians to focus on biological or medical questions. PMID:28045932

High resolution ultrasonic spectroscopy system for nondestructive evaluation

NASA Technical Reports Server (NTRS)

Chen, C. H.

1991-01-01

With increased demand for high resolution ultrasonic evaluation, computer based systems or work stations become essential. The ultrasonic spectroscopy method of nondestructive evaluation (NDE) was used to develop a high resolution ultrasonic inspection system supported by modern signal processing, pattern recognition, and neural network technologies. The basic system which was completed consists of a 386/20 MHz PC (IBM AT compatible), a pulser/receiver, a digital oscilloscope with serial and parallel communications to the computer, an immersion tank with motor control of X-Y axis movement, and the supporting software package, IUNDE, for interactive ultrasonic evaluation. Although the hardware components are commercially available, the software development is entirely original. By integrating signal processing, pattern recognition, maximum entropy spectral analysis, and artificial neural network functions into the system, many NDE tasks can be performed. The high resolution graphics capability provides visualization of complex NDE problems. The phase 3 efforts involve intensive marketing of the software package and collaborative work with industrial sectors.

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.

Evaluating Dense 3d Reconstruction Software Packages for Oblique Monitoring of Crop Canopy Surface

NASA Astrophysics Data System (ADS)

Brocks, S.; Bareth, G.

2016-06-01

Crop Surface Models (CSMs) are 2.5D raster surfaces representing absolute plant canopy height. Using multiple CMSs generated from data acquired at multiple time steps, a crop surface monitoring is enabled. This makes it possible to monitor crop growth over time and can be used for monitoring in-field crop growth variability which is useful in the context of high-throughput phenotyping. This study aims to evaluate several software packages for dense 3D reconstruction from multiple overlapping RGB images on field and plot-scale. A summer barley field experiment located at the Campus Klein-Altendorf of University of Bonn was observed by acquiring stereo images from an oblique angle using consumer-grade smart cameras. Two such cameras were mounted at an elevation of 10 m and acquired images for a period of two months during the growing period of 2014. The field experiment consisted of nine barley cultivars that were cultivated in multiple repetitions and nitrogen treatments. Manual plant height measurements were carried out at four dates during the observation period. The software packages Agisoft PhotoScan, VisualSfM with CMVS/PMVS2 and SURE are investigated. The point clouds are georeferenced through a set of ground control points. Where adequate results are reached, a statistical analysis is performed.

A PC-based computer package for automatic detection and location of earthquakes: Application to a seismic network in eastern sicity (Italy)

NASA Astrophysics Data System (ADS)

Patanè, Domenico; Ferrari, Ferruccio; Giampiccolo, Elisabetta; Gresta, Stefano

Few automated data acquisition and processing systems operate on mainframes, some run on UNIX-based workstations and others on personal computers, equipped with either DOS/WINDOWS or UNIX-derived operating systems. Several large and complex software packages for automatic and interactive analysis of seismic data have been developed in recent years (mainly for UNIX-based systems). Some of these programs use a variety of artificial intelligence techniques. The first operational version of a new software package, named PC-Seism, for analyzing seismic data from a local network is presented in Patanè et al. (1999). This package, composed of three separate modules, provides an example of a new generation of visual object-oriented programs for interactive and automatic seismic data-processing running on a personal computer. In this work, we mainly discuss the automatic procedures implemented in the ASDP (Automatic Seismic Data-Processing) module and real time application to data acquired by a seismic network running in eastern Sicily. This software uses a multi-algorithm approach and a new procedure MSA (multi-station-analysis) for signal detection, phase grouping and event identification and location. It is designed for an efficient and accurate processing of local earthquake records provided by single-site and array stations. Results from ASDP processing of two different data sets recorded at Mt. Etna volcano by a regional network are analyzed to evaluate its performance. By comparing the ASDP pickings with those revised manually, the detection and subsequently the location capabilities of this software are assessed. The first data set is composed of 330 local earthquakes recorded in the Mt. Etna erea during 1997 by the telemetry analog seismic network. The second data set comprises about 970 automatic locations of more than 2600 local events recorded at Mt. Etna during the last eruption (July 2001) at the present network. For the former data set, a comparison of the automatic results with the manual picks indicates that the ASDP module can accurately pick 80% of the P-waves and 65% of S-waves. The on-line application on the latter data set shows that automatic locations are affected by larger errors, due to the preliminary setting of the configuration parameters in the program. However, both automatic ASDP and manual hypocenter locations are comparable within the estimated error bounds. New improvements of the PC-Seism software for on-line analysis are also discussed.

Orbit determination for ISRO satellite missions

NASA Astrophysics Data System (ADS)

Rao, Ch. Sreehari; Sinha, S. K.

Indian Space Research Organisation (ISRO) has been successful in using the in-house developed orbit determination and prediction software for satellite missions of Bhaskara, Rohini and APPLE. Considering the requirements of satellite missions, software packages are developed, tested and their accuracies are assessed. Orbit determination packages developed are SOIP, for low earth orbits of Bhaskara and Rohini missions, ORIGIN and ODPM, for orbits related to all phases of geo-stationary missions and SEGNIP, for drift and geo-stationary orbits. Software is tested and qualified using tracking data of SIGNE-3, D5-B, OTS, SYMPHONIE satellites with the help of software available with CNES, ESA and DFVLR. The results match well with those available from these agencies. These packages have supported orbit determination successfully throughout the mission life for all ISRO satellite missions. Member-Secretary

Electronic and software subsystems for an autonomous roving vehicle. M.S. Thesis

NASA Technical Reports Server (NTRS)

Doig, G. A.

1980-01-01

The complete electronics packaging which controls the Mars roving vehicle is described in order to provide a broad overview of the systems that are part of that package. Some software debugging tools are also discussed. Particular emphasis is given to those systems that are controlled by the microprocessor. These include the laser mast, the telemetry system, the command link prime interface board, and the prime software.

The Shock and Vibration Digest. Volume 17, Number 4

DTIC Science & Technology

1985-04-01

software packages for engineering signed to be easy to use from the outset, computations which were specifically writ- and this design philosophy is largely...re- ten for use on microcomputers. Software sponsible for their increasing popularity; packages related to shock and vibration are this same design...philosophy appears to have available for both experimental and for been carried over to the design of today’s analytical applications. Typical software

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

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

Grama, Ananth

2013-12-18

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less

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…

Teaching Science and Mathematics Subjects Using the Excel Spreadsheet Package

ERIC Educational Resources Information Center

Ibrahim, Dogan

2009-01-01

The teaching of scientific subjects usually require laboratories where students can put the theory they have learned into practice. Traditionally, electronic programmable calculators, dedicated software, or expensive software simulation packages, such as MATLAB have been used to simulate scientific experiments. Recently, spreadsheet programs have…

Description of the IV + V System Software Package.

ERIC Educational Resources Information Center

Microcomputers for Information Management: An International Journal for Library and Information Services, 1984

1984-01-01

Describes the IV + V System, a software package designed by the Institut fur Maschinelle Dokumentation for the United Nations General Information Programme and UNISIST to support automation of local information and documentation services. Principle program features and functions outlined include input/output, databank, text image, output, and…

User’s guide for GcClust—An R package for clustering of regional geochemical data

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

GcClust is a software package developed by the U.S. Geological Survey for statistical clustering of regional geochemical data, and similar data such as regional mineralogical data. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of the user’s guide are bundled together in R’s unit of sharable code, which is called a “package.” The user’s guide includes step-by-step instructions showing how the functions are used to cluster data and to evaluate the clustering results. These functions are demonstrated in this report using test data, which are included in the package.

MAP - a mapping and analysis program for harvest planning

Treesearch

Robert N. Eli; Chris B. LeDoux; Penn A. Peters

1984-01-01

The Northeastern Forest Experiment Station and the Department of Civil Engineering at West Virginia University are cooperating in the development of a Mapping and Analysis Program, to be named MAP. The goal of this computer software package is to significantly improve the planning and harvest efficiency of small to moderately sized harvest units located in mountainous...

Aaron's Solution, Instructor's Problem: Teaching Surface Analysis Using GIS

ERIC Educational Resources Information Center

Koch, Tom; Denike, Ken

2007-01-01

Teaching GIS is relatively simple, a matter of helping students develop familiarity with the software. Mapping as an aid to thinking is harder to instruct. This article presents a laboratory and lecture package developed to teach the utility of mapping in a course on spatial data analysis. Following a historical review of the use of surface…

Quantitative and Descriptive Comparison of Four Acoustic Analysis Systems: Vowel Measurements

ERIC Educational Resources Information Center

Burris, Carlyn; Vorperian, Houri K.; Fourakis, Marios; Kent, Ray D.; Bolt, Daniel M.

2014-01-01

Purpose: This study examines accuracy and comparability of 4 trademarked acoustic analysis software packages (AASPs): Praat, WaveSurfer, TF32, and CSL by using synthesized and natural vowels. Features of AASPs are also described. Method: Synthesized and natural vowels were analyzed using each of the AASP's default settings to secure 9…

Increasing the trustworthiness of research results: the role of computers in qualitative text analysis

Treesearch

Lynne M. Westphal

2000-01-01

By using computer packages designed for qualitative data analysis a researcher can increase trustworthiness (i.e., validity and reliability) of conclusions drawn from qualitative research results. This paper examines trustworthiness issues and therole of computer software (QSR's NUD*IST) in the context of a current research project investigating the social...

Multifit / Polydefix : a framework for the analysis of polycrystal deformation using X-rays

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

Merkel, Sébastien; Hilairet, Nadège

2015-06-27

Multifit/Polydefixis an open source IDL software package for the efficient processing of diffraction data obtained in deformation apparatuses at synchrotron beamlines.Multifitallows users to decompose two-dimensional diffraction images into azimuthal slices, fit peak positions, shapes and intensities, and propagate the results to other azimuths and images.Polydefixis for analysis of deformation experiments. Starting from output files created inMultifitor other packages, it will extract elastic lattice strains, evaluate sample pressure and differential stress, and prepare input files for further texture analysis. TheMultifit/Polydefixpackage is designed to make the tedious data analysis of synchrotron-based plasticity, rheology or other time-dependent experiments very straightforward and accessible tomore » a wider community.« less