EQS Goes R: Simulations for SEM Using the Package REQS

ERIC Educational Resources Information Center

Mair, Patrick; Wu, Eric; Bentler, Peter M.

2010-01-01

The REQS package is an interface between the R environment of statistical computing and the EQS software for structural equation modeling. The package consists of 3 main functions that read EQS script files and import the results into R, call EQS script files from R, and run EQS script files from R and import the results after EQS computations.…

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.

RAPTR-SV: a hybrid method for the detection of structural variants

USDA-ARS?s Scientific Manuscript database

Motivation: Identification of Structural Variants (SV) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation. Results: Simulations using RAPTR-SV and another software package that uses a similar algorithm for SV detection...

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.

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.

45 CFR Appendix C to Part 1355 - Electronic Data Transmission Format

Code of Federal Regulations, 2010 CFR

2010-10-01

... mainframe-to-mainframe data exchange system using the Sterling Software data transfer package called “SUPERTRACS.” This package will allow data exchange between most computer platforms (both mini and mainframe... 45 Public Welfare 4 2010-10-01 2010-10-01 false Electronic Data Transmission Format C Appendix C...

45 CFR Appendix C to Part 1355 - Electronic Data Transmission Format

Code of Federal Regulations, 2011 CFR

2011-10-01

... mainframe-to-mainframe data exchange system using the Sterling Software data transfer package called “SUPERTRACS.” This package will allow data exchange between most computer platforms (both mini and mainframe... 45 Public Welfare 4 2011-10-01 2011-10-01 false Electronic Data Transmission Format C Appendix C...

smwrGraphs—An R package for graphing hydrologic data, version 1.1.2

USGS Publications Warehouse

Lorenz, David L.; Diekoff, Aliesha L.

2017-01-31

This report describes an R package called smwrGraphs, which consists of a collection of graphing functions for hydrologic data within R, a programming language and software environment for statistical computing. The functions in the package have been developed by the U.S. Geological Survey to create high-quality graphs for publication or presentation of hydrologic data that meet U.S. Geological Survey graphics guidelines.

Quick Prototyping of Educational Software: An Object-Oriented Approach.

ERIC Educational Resources Information Center

Wong, Simon C-H

1994-01-01

Introduces and demonstrates a quick-prototyping model for educational software development that can be used by teachers developing their own courseware using an object-oriented programming system. Development of a courseware package called "The Match-Maker" is explained as an example that uses HyperCard for quick prototyping. (Contains…

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.

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.

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.

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

Program SPACECAP: software for estimating animal density using spatially explicit capture-recapture models

USGS Publications Warehouse

Gopalaswamy, Arjun M.; Royle, J. Andrew; Hines, James E.; Singh, Pallavi; Jathanna, Devcharan; Kumar, N. Samba; Karanth, K. Ullas

2012-01-01

1. The advent of spatially explicit capture-recapture models is changing the way ecologists analyse capture-recapture data. However, the advantages offered by these new models are not fully exploited because they can be difficult to implement. 2. To address this need, we developed a user-friendly software package, created within the R programming environment, called SPACECAP. This package implements Bayesian spatially explicit hierarchical models to analyse spatial capture-recapture data. 3. Given that a large number of field biologists prefer software with graphical user interfaces for analysing their data, SPACECAP is particularly useful as a tool to increase the adoption of Bayesian spatially explicit capture-recapture methods in practice.

Remote control of astronomical instruments via the Internet

NASA Astrophysics Data System (ADS)

Ashley, M. C. B.; Brooks, P. W.; Lloyd, J. P.

1996-01-01

A software package called ERIC is described that provides a framework for allowing scientific instruments to be remotely controlled via the Internet. The package has been used to control four diverse astronomical instruments, and is now being made freely available to the community. For a description of ERIC's capabilities, and how to obtain a copy, see the conclusion to this paper.

KiT: a MATLAB package for kinetochore tracking.

PubMed

Armond, Jonathan W; Vladimirou, Elina; McAinsh, Andrew D; Burroughs, Nigel J

2016-06-15

During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present 'KiT' (Kinetochore Tracking)-an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization. KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development. Supplementary data are available at Bioinformatics online. jonathan.armond@warwick.ac.uk. © The Author 2016. Published by Oxford University Press.

Reviews.

ERIC Educational Resources Information Center

Science Teacher, 1989

1989-01-01

Reviews a software planetarium package called "Sky Travel." Includes two audiovisuals: "Conquest of Space" and "Windows on Science: Earth Science"; and four books: "Small Energy Sources: Choices that Work,""Stonehenge Complete,""Uneasy Careers and Intimate Lives: Women in Science…

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

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 .

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 ...

Enhanced Electric Power Transmission by Hybrid Compensation Technique

NASA Astrophysics Data System (ADS)

Palanichamy, C.; Kiu, G. Q.

2015-04-01

In today's competitive environment, new power system engineers are likely to contribute immediately to the task, without years of seasoning via on-the-job training, mentoring, and rotation assignments. At the same time it is becoming obligatory to train power system engineering graduates for an increasingly quality-minded corporate environment. In order to achieve this, there is a need to make available better-quality tools for educating and training power system engineering students and in-service system engineers too. As a result of the swift advances in computer hardware and software, many windows-based computer software packages were developed for the purpose of educating and training. In line with those packages, a simulation package called Hybrid Series-Shunt Compensators (HSSC) has been developed and presented in this paper for educational purposes.

A Multi­Discipline Approach to Digitizing Historic Seismograms

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

Bartlett, Andrew

2016-04-07

Retriever Technology has developed and has made available free of charge a seismogram digitization software package called SKATE (Seismogram Kit for Automatic Trace Extraction). We have developed an extensive set of algorithms that process seismogram image files, provide editing tools, and output time series data. The software is available online and free of charge at seismo.redfish.com. To demonstrate the speed and cost effectiveness of the software, we have processed over 30,000 images.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-04-01

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

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.

Specificity of software cooperating with an optoelectronic sensor in the pulse oximeter system

NASA Astrophysics Data System (ADS)

Cysewska-Sobusiak, Anna; Wiczynski, Grzegorz; Jedwabny, Tomasz

1995-06-01

Specificity of a software package composed of two parts which control an optoelectronic sensor of the computer-aided system made to realize the noninvasive measurements of the arterial blood oxygen saturation as well as some parameters of the peripheral pulse waveform, has been described. Principles of the transmission variant of the one and only noninvasive measurement method, so-called pulse oximetry, has been utilized. The software co-ordinates the suitable cooperation of an IBM PC compatible microcomputer with the sensor and one specialized card. This novel card is a key part of the whole measuring system which some application fields are extended in comparison to pulse oximeters commonly attainable. The user-friendly MS Windows graphical environment which creates the system to be multitask and non-preemptive, has been used to design the specific part of the programming presented here. With this environment, sophisticated tasks of the software package can be performed without excessive complication.

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)

tscvh R Package: Computational of the two samples test on microarray-sequencing data

NASA Astrophysics Data System (ADS)

Fajriyah, Rohmatul; Rosadi, Dedi

2017-12-01

We present a new R package, a tscvh (two samples cross-variance homogeneity), as we called it. This package is a software of the cross-variance statistical test which has been proposed and introduced by Fajriyah ([3] and [4]), based on the cross-variance concept. The test can be used as an alternative test for the significance difference between two means when sample size is small, the situation which is usually appeared in the bioinformatics research. Based on its statistical distribution, the p-value can be also provided. The package is built under a homogeneity of variance between samples.

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.

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.

The graphics and data acquisition software package

NASA Technical Reports Server (NTRS)

Crosier, W. G.

1981-01-01

A software package was developed for use with micro and minicomputers, particularly the LSI-11/DPD-11 series. The package has a number of Fortran-callable subroutines which perform a variety of frequently needed tasks for biomedical applications. All routines are well documented, flexible, easy to use and modify, and require minimal programmer knowledge of peripheral hardware. The package is also economical of memory and CPU time. A single subroutine call can perform any one of the following functions: (1) plot an array of integer values from sampled A/D data, (2) plot an array of Y values versus an array of X values; (3) draw horizontal and/or vertical grid lines of selectable type; (4) annotate grid lines with user units; (5) get coordinates of user controlled crosshairs from the terminal for interactive graphics; (6) sample any analog channel with program selectable gain; (7) wait a specified time interval, and (8) perform random access I/O of one or more blocks of a sequential disk file. Several miscellaneous functions are also provided.

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.

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.

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.

Dealing Your Own Hands with Hypercard.

ERIC Educational Resources Information Center

Larsen, Mark D.

1988-01-01

Extensively reviews Hypercard, a multifaceted software package for the Macintosh. HyperCard uses a language called "hypertext" which was patterned after everyday language and designed to allow flexibility in the linking and manipulation of text, graphics, and sounds. Describes one use for Hypercard in an advanced course on Latin American…

Scenario-Based Spoken Interaction with Virtual Agents

ERIC Educational Resources Information Center

Morton, Hazel; Jack, Mervyn A.

2005-01-01

This paper describes a CALL approach which integrates software for speaker independent continuous speech recognition with embodied virtual agents and virtual worlds to create an immersive environment in which learners can converse in the target language in contextualised scenarios. The result is a self-access learning package: SPELL (Spoken…

Economic Risk Analysis of Agricultural Tillage Systems Using the SMART Stochastic Efficiency Software Package

USDA-ARS?s Scientific Manuscript database

Recently, a variant of stochastic dominance called stochastic efficiency with respect to a function (SERF) has been developed and applied. Unlike traditional stochastic dominance approaches, SERF uses the concept of certainty equivalents (CEs) to rank a set of risk-efficient alternatives instead of...

College Students' Misconceptions about Evolutionary Trees

ERIC Educational Resources Information Center

Meir, Eli; Perry, Judy; Herron, Jon C.; Kingsolver, Joel

2007-01-01

Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and…

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.

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.

Algorithms and software for solving finite element equations on serial and parallel architectures

NASA Technical Reports Server (NTRS)

George, Alan

1989-01-01

Over the past 15 years numerous new techniques have been developed for solving systems of equations and eigenvalue problems arising in finite element computations. A package called SPARSPAK has been developed by the author and his co-workers which exploits these new methods. The broad objective of this research project is to incorporate some of this software in the Computational Structural Mechanics (CSM) testbed, and to extend the techniques for use on multiprocessor architectures.

Flight Software Development for the CHEOPS Instrument with the CORDET Framework

NASA Astrophysics Data System (ADS)

Cechticky, V.; Ottensamer, R.; Pasetti, A.

2015-09-01

CHEOPS is an ESA S-class mission dedicated to the precise measurement of radii of already known exoplanets using ultra-high precision photometry. The instrument flight software controlling the instrument and handling the science data is developed by the University of Vienna using the CORDET Framework offered by P&P Software GmbH. The CORDET Framework provides a generic software infrastructure for PUS-based applications. This paper describes how the framework is used for the CHEOPS application software to provide a consistent solution for to the communication and control services, event handling and FDIR procedures. This approach is innovative in four respects: (a) it is a true third-party reuse; (b) re-use is done at specification, validation and code level; (c) the re-usable assets and their qualification data package are entirely open-source; (d) re-use is based on call-back with the application developer providing functions which are called by the reusable architecture. File names missing from here on out (I tried to mimic the files names from before.)

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.

DCL System Using Deep Learning Approaches for Land-based or Ship-based Real-Time Recognition and Localization of Marine Mammals

DTIC Science & Technology

2012-09-30

platform (HPC) was developed, called the HPC-Acoustic Data Accelerator, or HPC-ADA for short. The HPC-ADA was designed based on fielded systems [1-4...software (Detection cLassificaiton for MAchine learning - High Peformance Computing). The software package was designed to utilize parallel and...Sedna [7] and is designed using a parallel architecture2, allowing existing algorithms to distribute to the various processing nodes with minimal changes

PAD_AUDIT -- PAD Auditing Package

NASA Astrophysics Data System (ADS)

Clayton, C. A.

The PAD (Packet Assembler Disassembler) utility is the part of the VAX/VMS Coloured Book Software (CBS) which allows a user to log onto remote computers from a local VAX. Unfortunately, logging into a computer via either the Packet SwitchStream (PSS) or the International Packet SwitchStream (IPSS) costs real money. Some users either do not appreciate this or do not care and have been known to clock up rather large quarterly bills. This software package allows a system manager to determine who has used PAD to call where and (most importantly) how much it has cost. The system manager can then take appropriate action - either charging the individuals, warning them to use the facility with more care or even denying access to a greedy user to one or more sites.

cyvcf2: fast, flexible variant analysis with Python.

PubMed

Pedersen, Brent S; Quinlan, Aaron R

2017-06-15

Variant call format (VCF) files document the genetic variation observed after DNA sequencing, alignment and variant calling of a sample cohort. Given the complexity of the VCF format as well as the diverse variant annotations and genotype metadata, there is a need for fast, flexible methods enabling intuitive analysis of the variant data within VCF and BCF files. We introduce cyvcf2 , a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. bpederse@gmail.com or aaronquinlan@gmail.com. cyvcf2 is available from https://github.com/brentp/cyvcf2 under the MIT license and from common python package managers. Detailed documentation is available at http://brentp.github.io/cyvcf2/. © The Author 2017. Published by Oxford University Press.

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 .

The AST3 controlling and operating software suite for automatic sky survey

NASA Astrophysics Data System (ADS)

Hu, Yi; Shang, Zhaohui; Ma, Bin; Hu, Keliang

2016-07-01

We have developed a specialized software package, called ast3suite, to achieve the remote control and automatic sky survey for AST3 (Antarctic Survey Telescope) from scratch. It includes several daemon servers and many basic commands. Each program does only one single task, and they work together to make AST3 a robotic telescope. A survey script calls basic commands to carry out automatic sky survey. Ast3suite was carefully tested in Mohe, China in 2013 and has been used at Dome, Antarctica in 2015 and 2016 with the real hardware for practical sky survey. Both test results and practical using showed that ast3suite had worked very well without any manual auxiliary as we expected.

VENVAL : a plywood mill cost accounting program

Treesearch

Henry Spelter

1991-01-01

This report documents a package of computer programs called VENVAL. These programs prepare plywood mill data for a linear programming (LP) model that, in turn, calculates the optimum mix of products to make, given a set of technologies and market prices. (The software to solve a linear program is not provided and must be obtained separately.) Linear programming finds...

A New Image Processing and GIS Package

NASA Technical Reports Server (NTRS)

Rickman, D.; Luvall, J. C.; Cheng, T.

1998-01-01

The image processing and GIS package ELAS was developed during the 1980's by NASA. It proved to be a popular, influential and powerful in the manipulation of digital imagery. Before the advent of PC's it was used by hundreds of institutions, mostly schools. It is the unquestioned, direct progenitor or two commercial GIS remote sensing packages, ERDAS and MapX and influenced others, such as PCI. Its power was demonstrated by its use for work far beyond its original purpose, having worked several different types of medical imagery, photomicrographs of rock, images of turtle flippers and numerous other esoteric imagery. Although development largely stopped in the early 1990's the package still offers as much or more power and flexibility than any other roughly comparable package, public or commercial. It is a huge body or code, representing more than a decade of work by full time, professional programmers. The current versions all have several deficiencies compared to current software standards and usage, notably its strictly command line interface. In order to support their research needs the authors are in the process of fundamentally changing ELAS, and in the process greatly increasing its power, utility, and ease of use. The new software is called ELAS II. This paper discusses the design of ELAS II.

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."

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

Electron tunneling in proteins program.

PubMed

Hagras, Muhammad A; Stuchebrukhov, Alexei A

2016-06-05

We developed a unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi-empirical quantum mechanical calculation, and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins. ETP program is developed as a cross-platform client-server program in which all the different calculations are conducted at the server side while only the client terminal displays the resulting calculation outputs in the different supported representations. ETP program is integrated with a set of well-known computational software packages including Gaussian, BALLVIEW, Dowser, pKip, and APBS. In addition, ETP program supports various visualization methods for the tunneling calculation results that assist in a more comprehensive understanding of the tunneling process. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594

Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

Introducing Python tools for magnetotellurics: MTpy

NASA Astrophysics Data System (ADS)

Krieger, L.; Peacock, J.; Inverarity, K.; Thiel, S.; Robertson, K.

2013-12-01

Within the framework of geophysical exploration techniques, the magnetotelluric method (MT) is relatively immature: It is still not as widely spread as other geophysical methods like seismology, and its processing schemes and data formats are not thoroughly standardized. As a result, the file handling and processing software within the academic community is mainly based on a loose collection of codes, which are sometimes highly adapted to the respective local specifications. Although tools for the estimation of the frequency dependent MT transfer function, as well as inversion and modelling codes, are available, the standards and software for handling MT data are generally not unified throughout the community. To overcome problems that arise from missing standards, and to simplify the general handling of MT data, we have developed the software package "MTpy", which allows the handling, processing, and imaging of magnetotelluric data sets. It is written in Python and the code is open-source. The setup of this package follows the modular approach of successful software packages like GMT or Obspy. It contains sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides pure Python classes and functions, MTpy provides wrappers and convenience scripts to call external software, e.g. modelling and inversion codes. Even though still under development, MTpy already contains ca. 250 functions that work on raw and preprocessed data. However, as our aim is not to produce a static collection of software, we rather introduce MTpy as a flexible framework, which will be dynamically extended in the future. It then has the potential to help standardise processing procedures and at same time be a versatile supplement for existing algorithms. We introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing utilising MTpy on an example data set collected over a geothermal exploration site in South Australia. Workflow of MT data processing. Within the structural diagram, the MTpy sub-packages are shown in red (time series data processing), green (handling of EDI files and impedance tensor data), yellow (connection to modelling/inversion algorithms), black (impedance tensor interpretation, e.g. by Phase Tensor calculations), and blue (generation of visual representations, e.g pseudo sections or resistivity models).

Component Technology for High-Performance Scientific Simulation Software

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

Epperly, T; Kohn, S; Kumfert, G

2000-11-09

We are developing scientific software component technology to manage the complexity of modem, parallel simulation software and increase the interoperability and re-use of scientific software packages. In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques. We have created a scientific IDL that focuses on the unique interface description needs of scientific codes, such as complex numbers, dense multidimensional arrays, complicated data types, and parallelism. Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for thinking about themore » design of modem object-oriented scientific software libraries. Finally, we also describe a web-based component repository called Alexandria that facilitates the distribution, documentation, and re-use of scientific components and libraries.« less

Modeling Antimicrobial Activity of Clorox(R) Using an Agar-Diffusion Test: A New Twist On an Old Experiment.

ERIC Educational Resources Information Center

Mitchell, James K.; Carter, William E.

2000-01-01

Describes using a computer statistical software package called Minitab to model the sensitivity of several microbes to the disinfectant NaOCl (Clorox') using the Kirby-Bauer technique. Each group of students collects data from one microbe, conducts regression analyses, then chooses the best-fit model based on the highest r-values obtained.…

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.

Proposed software system for atomic-structure calculation

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

Fischer, C.F.

1981-07-01

Atomic structure calculations are understood well enough that, at a routine level, an atomic structure software package can be developed. At the Atomic Physics Conference in Riga, 1978 L.V. Chernysheva and M.Y. Amusia of Leningrad University, presented a paper on Software for Atomic Calculations. Their system, called ATOM is based on the Hartree-Fock approximation and correlation is included within the framework of RPAE. Energy level calculations, transition probabilities, photo-ionization cross-sections, electron scattering cross-sections are some of the physical properties that can be evaluated by their system. The MCHF method, together with CI techniques and the Breit-Pauli approximation also provides amore » sound theoretical basis for atomic structure calculations.« less

Single-crystal diffraction at the Extreme Conditions beamline P02.2: procedure for collecting and analyzing high-pressure single-crystal data.

PubMed

Rothkirch, André; Gatta, G Diego; Meyer, Mathias; Merkel, Sébastien; Merlini, Marco; Liermann, Hanns Peter

2013-09-01

Fast detectors employed at third-generation synchrotrons have reduced collection times significantly and require the optimization of commercial as well as customized software packages for data reduction and analysis. In this paper a procedure to collect, process and analyze single-crystal data sets collected at high pressure at the Extreme Conditions beamline (P02.2) at PETRA III, DESY, is presented. A new data image format called `Esperanto' is introduced that is supported by the commercial software package CrysAlis(Pro) (Agilent Technologies UK Ltd). The new format acts as a vehicle to transform the most common area-detector data formats via a translator software. Such a conversion tool has been developed and converts tiff data collected on a Perkin Elmer detector, as well as data collected on a MAR345/555, to be imported into the CrysAlis(Pro) software. In order to demonstrate the validity of the new approach, a complete structure refinement of boron-mullite (Al5BO9) collected at a pressure of 19.4 (2) GPa is presented. Details pertaining to the data collections and refinements of B-mullite are presented.

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

HUBER, J.H.

An Enraf Densitometer is installed on tank 241-AY-102. The Densitometer will frequently be tasked to obtain and log density profiles. The activity can be effected a number of ways. Enraf Incorporated provides a software package called ''Logger18'' to its customers for the purpose of in-shop testing of their gauges. Logger18 is capable of accepting an input file which can direct the gauge to obtain a density profile for a given tank level and bottom limit. Logger18 is a complex, DOS based program which will require trained technicians and/or tank farm entries to obtain the data. ALARA considerations have prompted themore » development of a more user-friendly, computer-based interface to the Enraf densitometers. This document records the plan by which this new Enraf data acquisition software will be developed, reviewed, verified, and released. This plan applies to the development and implementation of a one-time-use software program, which will be called ''Enraf Control Panel.'' The software will be primarily used for remote operation of Enraf Densitometers for the purpose of obtaining and logging tank product density profiles.« less

Health Physics Positions Data Base: Revision 1

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

Kerr, G.D.; Borges, T.; Stafford, R.S.

1994-02-01

The Health Physics Positions (HPPOS) Data Base of the Nuclear Regulatory Commission (NRC) is a collection of NRC staff positions on a wide range of topics involving radiation protection (health physics). It consists of 328 documents in the form of letters, memoranda, and excerpts from technical reports. The HPPOS Data Base was developed by the NRC Headquarters and Regional Offices to help ensure uniformity in inspections, enforcement, and licensing actions. Staff members of the Oak Ridge National Laboratory (ORNL) have assisted the NRC staff in summarizing the documents during the preparation of this NUREG report. These summaries are also beingmore » made available as a {open_quotes}stand alone{close_quotes} software package for IBM and IBM-compatible personal computers. The software package for this report is called HPPOS Version 2.0. A variety of indexing schemes were used to increase the usefulness of the NUREG report and its associated software. The software package and the summaries in the report are written in the context of the {open_quotes}new{close_quotes} 10 CFR Part 20 ({section}{section}20.1001--20.2401). The purpose of this NUREG report is to allow interested individuals to familiarize themselves with the contents of the HPPOS Data Base and with the basis of many NRC decisions and regulations. The HPPOS summaries and original documents are intended to serve as a source of information for radiation protection programs at nuclear research and power reactors, nuclear medicine, and other industries that either process or use nuclear materials.« less

Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.

PubMed

Ostrovnaya, Irina; Seshan, Venkatraman E; Olshen, Adam B; Begg, Colin B

2011-06-15

If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called 'Clonality'. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results. Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.

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.

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.

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.

Universal programming interface with concurrent access

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

Alferov, Oleg

2004-10-07

There exist a number of devices with a positioning nature of operation, such as mechanical linear stages, temperature controllers, or filterwheels with discrete state, and most of them have different programming interfaces. The Universal Positioner software suggests the way to handle all of them is with a single approach, whereby a particular hardware driver is created from the template and by translating the actual commands used by the hardware to and from the universal programming interface. The software contains the universal API module itself, the demo simulation of hardware, and the front-end programs to help developers write their own softwaremore » drivers along with example drivers for actual hardware controllers. The software allows user application programs to call devices simultaneously without race conditions (multitasking and concurrent access). The template suggested in this package permits developers to integrate various devices easily into their applications using the same API. The drivers can be stacked; i.e., they can call each other via the same interface.« less

Conversion and Retrievability of Hard Copy and Digital Documents on Optical Disks

DTIC Science & Technology

1992-03-01

53 B. CURRENT THESIS PREPARATION TOOLS . ....... 54 1. Thesis Preparation using G-Thesis ..... 55 2. Thesis Preparation using Framemaker ...School mainframe. • Computer Science department students can use a software package called Framemaker , available on Sun work stations in their...by most thesis typists and students. For this reason, the discussion of thesis preparation tools will be limited to; G-thesis, Framemaker and

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.

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.

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.

A Direct Algorithm Maple Package of One-Dimensional Optimal System for Group Invariant Solutions

NASA Astrophysics Data System (ADS)

Zhang, Lin; Han, Zhong; Chen, Yong

2018-01-01

To construct the one-dimensional optimal system of finite dimensional Lie algebra automatically, we develop a new Maple package One Optimal System. Meanwhile, we propose a new method to calculate the adjoint transformation matrix and find all the invariants of Lie algebra in spite of Killing form checking possible constraints of each classification. Besides, a new conception called invariance set is raised. Moreover, this Maple package is proved to be more efficiency and precise than before by applying it to some classic examples. Supported by the Global Change Research Program of China under Grant No. 2015CB95390, National Natural Science Foundation of China under Grant Nos. 11675054 and 11435005, and Shanghai Collaborative Innovation Center of Trustworthy Software for Internet of Things under Grant No. ZF1213

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.

A low-cost PC-based telemetry data-reduction system

NASA Astrophysics Data System (ADS)

Simms, D. A.; Butterfield, C. P.

1990-04-01

The Solar Energy Research Institute's (SERI) Wind Research Branch is using Pulse Code Modulation (PCM) telemetry data-acquisition systems to study horizontal-axis wind turbines. PCM telemetry systems are used in test installations that require accurate multiple-channel measurements taken from a variety of different locations. SERI has found them ideal for use in tests requiring concurrent acquisition of data-reduction system to facilitate quick, in-the-field multiple-channel data analysis. Called the PC-PCM System, it consists of two basic components. First, AT-compatible hardware boards are used for decoding and combining PCM data streams. Up to four hardware boards can be installed in a single PC, which provides the capability to combine data from four PCM streams directly to PC disk or memory. Each stream can have up to 62 data channels. Second, a software package written for the DOS operating system was developed to simplify data-acquisition control and management. The software provides a quick, easy-to-use interface between the PC and PCM data streams. Called the Quick-Look Data Management Program, it is a comprehensive menu-driven package used to organize, acquire, process, and display information from incoming PCM data streams. This paper describes both hardware and software aspects of the SERI PC-PCM system, concentrating on features that make it useful in an experiment test environment to quickly examine and verify incoming data. Also discussed are problems and techniques associated with PC-based telemetry data acquisition, processing, and real-time display.

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

Radiative transfer through terrestrial atmosphere and ocean: Software package SCIATRAN

NASA Astrophysics Data System (ADS)

Rozanov, V. V.; Rozanov, A. V.; Kokhanovsky, A. A.; Burrows, J. P.

2014-01-01

SCIATRAN is a comprehensive software package for the modeling of radiative transfer processes in the terrestrial atmosphere and ocean in the spectral range from the ultraviolet to the thermal infrared (0.18 - 40 μm) including multiple scattering processes, polarization, thermal emission and ocean-atmosphere coupling. The software is capable of modeling spectral and angular distributions of the intensity or the Stokes vector of the transmitted, scattered, reflected, and emitted radiation assuming either a plane-parallel or a spherical atmosphere. Simulations are done either in the scalar or in the vector mode (i.e. accounting for the polarization) for observations by space-, air-, ship- and balloon-borne, ground-based, and underwater instruments in various viewing geometries (nadir, off-nadir, limb, occultation, zenith-sky, off-axis). All significant radiative transfer processes are accounted for. These are, e.g. the Rayleigh scattering, scattering by aerosol and cloud particles, absorption by gaseous components, and bidirectional reflection by an underlying surface including Fresnel reflection from a flat or roughened ocean surface. The software package contains several radiative transfer solvers including finite difference and discrete-ordinate techniques, an extensive database, and a specific module for solving inverse problems. In contrast to many other radiative transfer codes, SCIATRAN incorporates an efficient approach to calculate the so-called Jacobians, i.e. derivatives of the intensity with respect to various atmospheric and surface parameters. In this paper we discuss numerical methods used in SCIATRAN to solve the scalar and vector radiative transfer equation, describe databases of atmospheric, oceanic, and surface parameters incorporated in SCIATRAN, and demonstrate how to solve some selected radiative transfer problems using the SCIATRAN package. During the last decades, a lot of studies have been published demonstrating that SCIATRAN is a valuable tool for a wide range of remote sensing applications. Here, we present some selected comparisons of SCIATRAN simulations to published benchmark results, independent radiative transfer models, and various measurements from satellite, ground-based, and ship instruments. Methods for solving inverse problems related to remote sensing of the Earth's atmosphere using the SCIATRAN software are outside the scope of this study and will be discussed in a follow-up paper. The SCIATRAN software package along with a detailed User's Guide is freely available for non-commercial use via the webpage of the Institute of Environmental Physics (IUP), University of Bremen: http://www.iup.physik.uni-bremen.de/sciatran.

[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.

Virtual surgery for patients with nasal obstruction: Use of computational fluid dynamics (MeComLand®, Digbody® & Noseland®) to document objective flow parameters and optimise surgical results.

PubMed

Burgos, Manuel A; Sevilla García, Maria Agustina; Sanmiguel Rojas, Enrique; Del Pino, Carlos; Fernández Velez, Carlos; Piqueras, Francisco; Esteban Ortega, Francisco

Computational fluid dynamics (CFD) is a mathematical tool to analyse airflow. We present a novel CFD software package to improve results following nasal surgery for obstruction. A group of engineers in collaboration with otolaryngologists have developed a very intuitive CFD software package called MeComLand®, which uses the patient's cross-sectional (tomographic) images, thus showing in detail results originated by CFD such as airflow distributions, velocity profiles, pressure, or wall shear stress. NOSELAND® helps medical evaluation with dynamic reports by using a 3D endoscopic view. Using this CFD-based software a patient underwent virtual surgery (septoplasty, turbinoplasty, spreader grafts, lateral crural J-flap and combinations) to choose the best improvement in nasal flow. To present a novel software package to improve nasal surgery results. To apply the software on CT slices from a patient affected by septal deviation. To evaluate several surgical procedures (septoplasty, turbinectomy, spreader-grafts, J-flap and combination among them) to find the best alternative with less morbidity. The combination of all the procedures does not provide the best nasal flow improvement. Septoplasty plus turbinoplasty obtained the best results. Turbinoplasty alone rendered almost similar results to septoplasty in our simulation. CFD provides useful complementary information to cover diagnosis, prognosis, and follow-up of nasal pathologies based on quantitative magnitudes linked to fluid flow. MeComLand®, DigBody® and NoseLand® represent a non-invasive, low-cost alternative for the functional study of patients with nasal obstruction. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Otorrinolaringología y Cirugía de Cabeza y Cuello. All rights reserved.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Selection of software for mechanical engineering undergraduates

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

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

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

Multivariate Statistical Analysis Software Technologies for Astrophysical Research Involving Large Data Bases

NASA Technical Reports Server (NTRS)

Djorgovski, S. G.

1994-01-01

We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complex database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects of the SKICAT system, and of some of the scientific results achieved to date. We also developed a user-friendly package for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications and has produced real, published results.

Error Prevention Aid

NASA Technical Reports Server (NTRS)

1987-01-01

In a complex computer environment there is ample opportunity for error, a mistake by a programmer, or a software-induced undesirable side effect. In insurance, errors can cost a company heavily, so protection against inadvertent change is a must for the efficient firm. The data processing center at Transport Life Insurance Company has taken a step to guard against accidental changes by adopting a software package called EQNINT (Equations Interpreter Program). EQNINT cross checks the basic formulas in a program against the formulas that make up the major production system. EQNINT assures that formulas are coded correctly and helps catch errors before they affect the customer service or its profitability.

LongISLND: in silico sequencing of lengthy and noisy datatypes

PubMed Central

Lau, Bayo; Mohiyuddin, Marghoob; Mu, John C.; Fang, Li Tai; Bani Asadi, Narges; Dallett, Carolina; Lam, Hugo Y. K.

2016-01-01

Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. Availability and Implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd Contact: hugo.lam@roche.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27667791

Innovative Techniques Simplify Vibration Analysis

NASA Technical Reports Server (NTRS)

2010-01-01

In the early years of development, Marshall Space Flight Center engineers encountered challenges related to components in the space shuttle main engine. To assess the problems, they evaluated the effects of vibration and oscillation. To enhance the method of vibration signal analysis, Marshall awarded Small Business Innovation Research (SBIR) contracts to AI Signal Research, Inc. (ASRI), in Huntsville, Alabama. ASRI developed a software package called PC-SIGNAL that NASA now employs on a daily basis, and in 2009, the PKP-Module won Marshall s Software of the Year award. The technology is also used in many industries: aircraft and helicopter, rocket engine manufacturing, transportation, and nuclear power."

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

PubMed

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

2017-08-01

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

GAPIT: genome association and prediction integrated tool.

PubMed

Lipka, Alexander E; Tian, Feng; Wang, Qishan; Peiffer, Jason; Li, Meng; Bradbury, Peter J; Gore, Michael A; Buckler, Edward S; Zhang, Zhiwu

2012-09-15

Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results. http://www.maizegenetics.net/GAPIT. zhiwu.zhang@cornell.edu Supplementary data are available at Bioinformatics online.

Design and development of conformal antenna composite structure

NASA Astrophysics Data System (ADS)

Xie, Zonghong; Zhao, Wei; Zhang, Peng; Li, Xiang

2017-09-01

In the manufacturing process of the common smart skin antenna, the adhesive covered on the radiating elements of the antenna led to severe deviation of the resonant frequency, which degraded the electromagnetic performance of the antenna. In this paper, a new component called package cover was adopted to prevent the adhesive from covering on the radiating elements of the microstrip antenna array. The package cover and the microstrip antenna array were bonded together as packaged antenna which was then embedded into the composite sandwich structure to develop a new structure called conformal antenna composite structure (CACS). The geometric parameters of the microstrip antenna array and the CACS were optimized by the commercial software CST microwave studio. According to the optimal results, the microstrip antenna array and the CACS were manufactured and tested. The experimental and numerical results of electromagnetic performance showed that the resonant frequency of the CACS was close to that of the microstrip antenna array (with error less than 1%) and the CACS had a higher gain (about 2 dB) than the microstrip antenna array. The package system would increase the electromagnetic radiating energy at the design frequency nearly 66%. The numerical model generated by CST microwave studio in this study could successfully predict the electromagnetic performance of the microstrip antenna array and the CACS with relatively good accuracy. The mechanical analysis results showed that the CACS had better flexural property than the composite sandwich structure without the embedment of packaged antenna. The comparison of the electromagnetic performance for the CACS and the MECSSA showed that the package system was useful and effective.

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 .

An overview of NSPCG: A nonsymmetric preconditioned conjugate gradient package

NASA Astrophysics Data System (ADS)

Oppe, Thomas C.; Joubert, Wayne D.; Kincaid, David R.

1989-05-01

The most recent research-oriented software package developed as part of the ITPACK Project is called "NSPCG" since it contains many nonsymmetric preconditioned conjugate gradient procedures. It is designed to solve large sparse systems of linear algebraic equations by a variety of different iterative methods. One of the main purposes for the development of the package is to provide a common modular structure for research on iterative methods for nonsymmetric matrices. Another purpose for the development of the package is to investigate the suitability of several iterative methods for vector computers. Since the vectorizability of an iterative method depends greatly on the matrix structure, NSPCG allows great flexibility in the operator representation. The coefficient matrix can be passed in one of several different matrix data storage schemes. These sparse data formats allow matrices with a wide range of structures from highly structured ones such as those with all nonzeros along a relatively small number of diagonals to completely unstructured sparse matrices. Alternatively, the package allows the user to call the accelerators directly with user-supplied routines for performing certain matrix operations. In this case, one can use the data format from an application program and not be required to copy the matrix into one of the package formats. This is particularly advantageous when memory space is limited. Some of the basic preconditioners that are available are point methods such as Jacobi, Incomplete LU Decomposition and Symmetric Successive Overrelaxation as well as block and multicolor preconditioners. The user can select from a large collection of accelerators such as Conjugate Gradient (CG), Chebyshev (SI, for semi-iterative), Generalized Minimal Residual (GMRES), Biconjugate Gradient Squared (BCGS) and many others. The package is modular so that almost any accelerator can be used with almost any preconditioner.

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

NASA Astrophysics Data System (ADS)

Lourderaj, Upakarasamy; Sun, Rui; Kohale, Swapnil C.; Barnes, George L.; de Jong, Wibe A.; Windus, Theresa L.; Hase, William L.

2014-03-01

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

A finite-element study of a piezoelectric/poroelastic sound package concept

NASA Astrophysics Data System (ADS)

Batifol, C.; Zielinski, T. G.; Ichchou, M. N.; Galland, M.-A.

2007-02-01

This paper presents a complete finite-element description of a hybrid passive/active sound package concept for acoustic insulation. The sandwich created includes a poroelastic core and piezoelectric patches to ensure high panel performance over the medium/high and low frequencies, respectively. All layers are modelled thanks to a Comsol environmentComsol is the new name of the finite element software previously called Femlab.. The piezoelectric/elastic and poroelastic/elastic coupling are fully considered. The study highlights the reliability of the model by comparing results with those obtained from the Ansys finite-element software and with analytical developments. The chosen shape functions and mesh convergence rate for each layer are discussed in terms of dynamic behaviour. Several layer configurations are then tested, with the aim of designing the panel and its hybrid functionality in an optimal manner. The differences in frequency responses are discussed from a physical perspective. Lastly, an initial experimental test shows the concept to be promising.

Information Operations Team Training & Information Operations Training Aid, Information Warfare Effectiveness (IWE) Program, Delivery Order 8

DTIC Science & Technology

2010-03-01

submenus and toolbar with icon buttons 4. The IFOTA shall conform to Defense Information Infrastructure Common Operating Environment ( DII COE) and...him my business card , but it might come in the package we request via AFRL). PSYOP Instructor IWST is now called IWT (??) SME MD MD Instructor...Engineering and Software Engineering CTA Cognitive Task Analysis DII COE Defense Information Infrastructure Common Operating Environment EJB Enterprise Java

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

NASA Technical Reports Server (NTRS)

1981-01-01

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

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

PubMed

Hansen, Peter; Hecht, Jochen; Ibn-Salem, Jonas; Menkuec, Benjamin S; Roskosch, Sebastian; Truss, Matthias; Robinson, Peter N

2016-11-04

ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/ .

A Predictive Safety Management System Software Package Based on the Continuous Hazard Tracking and Failure Prediction Methodology

NASA Technical Reports Server (NTRS)

Quintana, Rolando

2003-01-01

The goal of this research was to integrate a previously validated and reliable safety model, called Continuous Hazard Tracking and Failure Prediction Methodology (CHTFPM), into a software application. This led to the development of a safety management information system (PSMIS). This means that the theory or principles of the CHTFPM were incorporated in a software package; hence, the PSMIS is referred to as CHTFPM management information system (CHTFPM MIS). The purpose of the PSMIS is to reduce the time and manpower required to perform predictive studies as well as to facilitate the handling of enormous quantities of information in this type of studies. The CHTFPM theory encompasses the philosophy of looking at the concept of safety engineering from a new perspective: from a proactive, than a reactive, viewpoint. That is, corrective measures are taken before a problem instead of after it happened. That is why the CHTFPM is a predictive safety because it foresees or anticipates accidents, system failures and unacceptable risks; therefore, corrective action can be taken in order to prevent all these unwanted issues. Consequently, safety and reliability of systems or processes can be further improved by taking proactive and timely corrective actions.

Mississippi Company Using NASA Software Program to Provide Unique Imaging Service: DATASTAR Success Story

NASA Technical Reports Server (NTRS)

2001-01-01

DATASTAR, Inc., of Picayune, Miss., has taken NASA's award-winning Earth Resources Laboratory Applications (ELAS) software program and evolved it to the point that the company is now providing a unique, spatial imagery service over the Internet. ELAS was developed in the early 80's to process satellite and airborne sensor imagery data of the Earth's surface into readable and useable information. While there are several software packages on the market that allow the manipulation of spatial data into useable products, this is usually a laborious task. The new program, called the DATASTAR Image Processing Exploitation, or DIPX, Delivery Service, is a subscription service available over the Internet that takes the work out of the equation and provides normalized geo-spatial data in the form of decision products.

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.

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.

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

PubMed

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

2017-12-21

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

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

Part II: preparing and assessing first-year radiology resident on-call readiness technical implementation.

PubMed

Yam, Chun-Shan; Kruskal, Jonathan; Pedrosa, Ivan; Kressel, Herbert

2006-06-01

The effectiveness of using a Digital Imaging and Communications in Medicine (DICOM)-based interactive examination system in evaluating the readiness of first year radiology residents before taking overnight call in the emergency department (ED) was reported in part I of this article. This report describes technical aspects for the design and implementation of this system. The examination system consists of two modules: Data Collection and Image Viewing. The Data Collection module was a personal computer (PC)-based DICOM storage server based on a free public domain software package, the Mallinckrodt Central Test Node. The Image Viewing module was a Java-based DICOM viewer created using another freeware package: zDicom ActiveX component. The examination takes place once a year at the end of the first 6-month rotation. Cases selected for the examination were actual clinical cases according to the American Society of Emergency Radiology core curriculum. In the 3-hour timed examination, each resident was required to read the cases and provide clinical findings and recommendations. Upper-level residents also participated in the examination to serve as a control. Answers were scored by two staff radiologists. We have been using this examination system successfully in our institution since 2003 to evaluate the readiness of the first-year residents before they take overnight call in the ED. This report describes a step-by-step procedure for implementing this system into a PC-based platform. This DICOM viewing software is available as freeware to other academic radiology institutions. The total cost for implementing this system is approximately 2000 US dollars.

Calculation of the relative metastabilities of proteins using the CHNOSZ software package

PubMed Central

Dick, Jeffrey M

2008-01-01

Background Proteins of various compositions are required by organisms inhabiting different environments. The energetic demands for protein formation are a function of the compositions of proteins as well as geochemical variables including temperature, pressure, oxygen fugacity and pH. The purpose of this study was to explore the dependence of metastable equilibrium states of protein systems on changes in the geochemical variables. Results A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules. Conclusion Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations. PMID:18834534

Design of Amphoteric Refraction Models Using WAVICA and RAYICA

NASA Technical Reports Server (NTRS)

Su, Richard

2004-01-01

The phenomenon of refraction of light is due to refractive index mismatches in two different media. However, to achieve this effect, a finite reflection loss is inevitable. A recent finding presented a unique type of interface, ferroelastic materials, that enables refraction without any reflection for either an electron or a light beam. This property is called total refraction. The same type of interface that yields total refraction can also yield amphoteric refraction, where the index of refraction can be either positive or negative depending on the incident angle. This interface could potentially be used to steer light without reflections which could have major applications in high power optics. My goal this summer is to first familiarize myself with the Mathematica software, especially the Wavica and Rayica packages. I will then model the amphoteric refraction by either modifying the Wavica and Rayica packages or using the built-in functions in these packages.

Method to simulate and analyse induced stresses for laser crystal packaging technologies.

PubMed

Ribes-Pleguezuelo, Pol; Zhang, Site; Beckert, Erik; Eberhardt, Ramona; Wyrowski, Frank; Tünnermann, Andreas

2017-03-20

A method to simulate induced stresses for a laser crystal packaging technique and the consequent study of birefringent effects inside the laser cavities has been developed. The method has been implemented by thermo-mechanical simulations implemented with ANSYS 17.0. ANSYS results were later imported in VirtualLab Fusion software where input/output beams in terms of wavelengths and polarization were analysed. The study has been built in the context of a low-stress soldering technique implemented for glass or crystal optics packaging's called the solderjet bumping technique. The outcome of the analysis showed almost no difference between the input and output laser beams for the laser cavity constructed with an yttrium aluminum garnet active laser crystal, a second harmonic generator beta-barium borate, and the output laser mirror made of fused silica assembled by the low-stress solderjet bumping technique.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

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.

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

PubMed

Ou, Jianhong; Liu, Haibo; Yu, Jun; Kelliher, Michelle A; Castilla, Lucio H; Lawson, Nathan D; Zhu, Lihua Julie

2018-03-01

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

PubMed

Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank T

2015-06-01

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

PubMed

Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank Thomas

2015-09-04

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

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.

[MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

PubMed

Liu, Ren-Hu; Meng, Jin-Ling

2003-05-01

MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

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.

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.

LongISLND: in silico sequencing of lengthy and noisy datatypes.

PubMed

Lau, Bayo; Mohiyuddin, Marghoob; Mu, John C; Fang, Li Tai; Bani Asadi, Narges; Dallett, Carolina; Lam, Hugo Y K

2016-12-15

LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd CONTACT: hugo.lam@roche.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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.

MTpy: A Python toolbox for magnetotellurics

NASA Astrophysics Data System (ADS)

Krieger, Lars; Peacock, Jared R.

2014-11-01

We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

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

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.

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

Multivariate statistical analysis software technologies for astrophysical research involving large data bases

NASA Technical Reports Server (NTRS)

Djorgovski, S. George

1994-01-01

We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complete database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful, and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications, and has produced real, published results.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

3DRT-MPASS

NASA Technical Reports Server (NTRS)

Lickly, Ben

2005-01-01

Data from all current JPL missions are stored in files called SPICE kernels. At present, animators who want to use data from these kernels have to either read through the kernels looking for the desired data, or write programs themselves to retrieve information about all the needed objects for their animations. In this project, methods of automating the process of importing the data from the SPICE kernels were researched. In particular, tools were developed for creating basic scenes in Maya, a 3D computer graphics software package, from SPICE kernels.

Image Processing

NASA Technical Reports Server (NTRS)

1987-01-01

A new spinoff product was derived from Geospectra Corporation's expertise in processing LANDSAT data in a software package. Called ATOM (for Automatic Topographic Mapping), it's capable of digitally extracting elevation information from stereo photos taken by spaceborne cameras. ATOM offers a new dimension of realism in applications involving terrain simulations, producing extremely precise maps of an area's elevations at a lower cost than traditional methods. ATOM has a number of applications involving defense training simulations and offers utility in architecture, urban planning, forestry, petroleum and mineral exploration.

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

NASA Ames Participates in Two Major Bay Area Events (Reporter Package)NASA Ames Research Center participated in two important outreach events: Maker Faire and a gathering of hardware and software industry professionals called the Solid Conference. The conference was an opportunity for the Intelligent Robotics Group from NASA Ames to publicly unveil their latest version of the free flying robot used on the International Space Station. NASA also participated at the Bay Area Maker Faire, a gathering of more than 120,000 innovators, enthusiasts, crafters, hobbyists and tinkerers to share what they have invented and made.

NASA Image and Video Library

2014-05-28

NASA Ames Research Center participated in two important outreach events: Maker Faire and a gathering of hardware and software industry professionals called the Solid Conference. The conference was an opportunity for the Intelligent Robotics Group from NASA Ames to publicly unveil their latest version of the free flying robot used on the International Space Station. NASA also participated at the Bay Area Maker Faire, a gathering of more than 120,000 innovators, enthusiasts, crafters, hobbyists and tinkerers to share what they have invented and made.

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.

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…

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.

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…

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.

nu-TRLan User Guide Version 1.0: A High-Performance Software Package for Large-Scale Harmitian Eigenvalue Problems

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

Yamazaki, Ichitaro; Wu, Kesheng; Simon, Horst

2008-10-27

The original software package TRLan, [TRLan User Guide], page 24, implements the thick restart Lanczos method, [Wu and Simon 2001], page 24, for computing eigenvalues {lambda} and their corresponding eigenvectors v of a symmetric matrix A: Av = {lambda}v. Its effectiveness in computing the exterior eigenvalues of a large matrix has been demonstrated, [LBNL-42982], page 24. However, its performance strongly depends on the user-specified dimension of a projection subspace. If the dimension is too small, TRLan suffers from slow convergence. If it is too large, the computational and memory costs become expensive. Therefore, to balance the solution convergence and costs,more » users must select an appropriate subspace dimension for each eigenvalue problem at hand. To free users from this difficult task, nu-TRLan, [LNBL-1059E], page 23, adjusts the subspace dimension at every restart such that optimal performance in solving the eigenvalue problem is automatically obtained. This document provides a user guide to the nu-TRLan software package. The original TRLan software package was implemented in Fortran 90 to solve symmetric eigenvalue problems using static projection subspace dimensions. nu-TRLan was developed in C and extended to solve Hermitian eigenvalue problems. It can be invoked using either a static or an adaptive subspace dimension. In order to simplify its use for TRLan users, nu-TRLan has interfaces and features similar to those of TRLan: (1) Solver parameters are stored in a single data structure called trl-info, Chapter 4 [trl-info structure], page 7. (2) Most of the numerical computations are performed by BLAS, [BLAS], page 23, and LAPACK, [LAPACK], page 23, subroutines, which allow nu-TRLan to achieve optimized performance across a wide range of platforms. (3) To solve eigenvalue problems on distributed memory systems, the message passing interface (MPI), [MPI forum], page 23, is used. The rest of this document is organized as follows. In Chapter 2 [Installation], page 2, we provide an installation guide of the nu-TRLan software package. In Chapter 3 [Example], page 3, we present a simple nu-TRLan example program. In Chapter 4 [trl-info structure], page 7, and Chapter 5 [trlan subroutine], page 14, we describe the solver parameters and interfaces in detail. In Chapter 6 [Solver parameters], page 21, we discuss the selection of the user-specified parameters. In Chapter 7 [Contact information], page 22, we give the acknowledgements and contact information of the authors. In Chapter 8 [References], page 23, we list reference to related works.« less

Features of free software packages in flow cytometry: a comparison between four non-commercial software sources.

PubMed

Sahraneshin Samani, Fazel; Moore, Jodene K; Khosravani, Pardis; Ebrahimi, Marzieh

2014-08-01

Flow cytometers designed to analyze large particles are enabling new applications in biology. Data analysis is a critical component of the process FCM. In this article we compare features of four free software packages including WinMDI, Cyflogic, Flowing software, and Cytobank.

Development of a Nevada Statewide Database for Safety Analyst Software

DOT National Transportation Integrated Search

2017-02-02

Safety Analyst is a software package developed by the Federal Highway Administration (FHWA) and twenty-seven participating state and local agencies including the Nevada Department of Transportation (NDOT). The software package implemented many of the...

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…

OCEAN-PC and a distributed network for ocean data

NASA Technical Reports Server (NTRS)

Mclain, Douglas R.

1992-01-01

The Intergovernmental Oceanographic Commission (IOC) wishes to develop an integrated software package for oceanographic data entry and access in developing countries. The software, called 'OCEAN-PC', would run on low cost PC microcomputers and would encourage and standardize: (1) entry of local ocean observations; (2) quality control of the local data; (3) merging local data with historical data; (4) improved display and analysis of the merged data; and (5) international data exchange. OCEAN-PC will link existing MS-DOS oceanographic programs and data sets with table-driven format conversions. Since many ocean data sets are now being distributed on optical discs (Compact Discs - Read Only Memory, CD-ROM, Mass et al. 1987), OCEAN-PC will emphasize access to CD-ROMs.

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.

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.

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

Beasley, G. P.; Sigman, R. S.

1972-01-01

A multielement data reduction and analysis software package has been developed for use with the Langley differential maneuvering simulator (DMS). This package, which has several independent elements, was developed to support all phases of DMS aircraft simulation studies with a variety of both graphical and tabular information. The overall software package is considered unique because of the number, diversity, and sophistication of the element programs available for use in a single study. The purpose of this paper is to discuss the overall DMS data reduction and analysis package by reviewing the development of the various elements of the software, showing typical results that can be obtained, and discussing how each element can be used.

Software Architecture for a Virtual Environment for Nano Scale Assembly (VENSA).

PubMed

Lee, Yong-Gu; Lyons, Kevin W; Feng, Shaw C

2004-01-01

A Virtual Environment (VE) uses multiple computer-generated media to let a user experience situations that are temporally and spatially prohibiting. The information flow between the user and the VE is bidirectional and the user can influence the environment. The software development of a VE requires orchestrating multiple peripherals and computers in a synchronized way in real time. Although a multitude of useful software components for VEs exists, many of these are packaged within a complex framework and can not be used separately. In this paper, an architecture is presented which is designed to let multiple frameworks work together while being shielded from the application program. This architecture, which is called the Virtual Environment for Nano Scale Assembly (VENSA), has been constructed for interfacing with an optical tweezers instrument for nanotechnology development. However, this approach can be generalized for most virtual environments. Through the use of VENSA, the programmer can rely on existing solutions and concentrate more on the application software design.

Software Architecture for a Virtual Environment for Nano Scale Assembly (VENSA)

PubMed Central

Lee, Yong-Gu; Lyons, Kevin W.; Feng, Shaw C.

2004-01-01

A Virtual Environment (VE) uses multiple computer-generated media to let a user experience situations that are temporally and spatially prohibiting. The information flow between the user and the VE is bidirectional and the user can influence the environment. The software development of a VE requires orchestrating multiple peripherals and computers in a synchronized way in real time. Although a multitude of useful software components for VEs exists, many of these are packaged within a complex framework and can not be used separately. In this paper, an architecture is presented which is designed to let multiple frameworks work together while being shielded from the application program. This architecture, which is called the Virtual Environment for Nano Scale Assembly (VENSA), has been constructed for interfacing with an optical tweezers instrument for nanotechnology development. However, this approach can be generalized for most virtual environments. Through the use of VENSA, the programmer can rely on existing solutions and concentrate more on the application software design. PMID:27366610

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.

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.

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE PAGES

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-10-25

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

IBS: an illustrator for the presentation and visualization of biological sequences.

PubMed

Liu, Wenzhong; Xie, Yubin; Ma, Jiyong; Luo, Xiaotong; Nie, Peng; Zuo, Zhixiang; Lahrmann, Urs; Zhao, Qi; Zheng, Yueyuan; Zhao, Yong; Xue, Yu; Ren, Jian

2015-10-15

Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy.

PubMed

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-01-01

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic , using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic .

IBS: an illustrator for the presentation and visualization of biological sequences

PubMed Central

Liu, Wenzhong; Xie, Yubin; Ma, Jiyong; Luo, Xiaotong; Nie, Peng; Zuo, Zhixiang; Lahrmann, Urs; Zhao, Qi; Zheng, Yueyuan; Zhao, Yong; Xue, Yu; Ren, Jian

2015-01-01

Summary: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26069263

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

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

Pryor, Alan; Ophus, Colin; Miao, Jianwei

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

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…

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

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

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.

A comparison of InVivoStat with other statistical software packages for analysis of data generated from animal experiments.

PubMed

Clark, Robin A; Shoaib, Mohammed; Hewitt, Katherine N; Stanford, S Clare; Bate, Simon T

2012-08-01

InVivoStat is a free-to-use statistical software package for analysis of data generated from animal experiments. The package is designed specifically for researchers in the behavioural sciences, where exploiting the experimental design is crucial for reliable statistical analyses. This paper compares the analysis of three experiments conducted using InVivoStat with other widely used statistical packages: SPSS (V19), PRISM (V5), UniStat (V5.6) and Statistica (V9). We show that InVivoStat provides results that are similar to those from the other packages and, in some cases, are more advanced. This investigation provides evidence of further validation of InVivoStat and should strengthen users' confidence in this new software package.

HCI∧2 framework: a software framework for multimodal human-computer interaction systems.

PubMed

Shen, Jie; Pantic, Maja

2013-12-01

This paper presents a novel software framework for the development and research in the area of multimodal human-computer interface (MHCI) systems. The proposed software framework, which is called the HCI∧2 Framework, is built upon publish/subscribe (P/S) architecture. It implements a shared-memory-based data transport protocol for message delivery and a TCP-based system management protocol. The latter ensures that the integrity of system structure is maintained at runtime. With the inclusion of bridging modules, the HCI∧2 Framework is interoperable with other software frameworks including Psyclone and ActiveMQ. In addition to the core communication middleware, we also present the integrated development environment (IDE) of the HCI∧2 Framework. It provides a complete graphical environment to support every step in a typical MHCI system development process, including module development, debugging, packaging, and management, as well as the whole system management and testing. The quantitative evaluation indicates that our framework outperforms other similar tools in terms of average message latency and maximum data throughput under a typical single PC scenario. To demonstrate HCI∧2 Framework's capabilities in integrating heterogeneous modules, we present several example modules working with a variety of hardware and software. We also present an example of a full system developed using the proposed HCI∧2 Framework, which is called the CamGame system and represents a computer game based on hand-held marker(s) and low-cost camera(s).

CHEMKIN-III: A FORTRAN chemical kinetics package for the analysis of gas-phase chemical and plasma kinetics

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

Kee, R.J.; Rupley, F.M.; Meeks, E.

1996-05-01

This document is the user`s manual for the third-generation CHEMKIN package. CHEMKIN is a software package whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides a 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 a 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 Subroutine Library.more » This library is a collection of about 100 highly modular FORTRAN subroutines that may be called to return information on equations of state, thermodynamic properties, and chemical production rates. CHEMKIN-III includes capabilities for treating multi-fluid plasma systems, that are not in thermal equilibrium. These new capabilities allow researchers to describe chemistry systems that are characterized by more than one temperature, in which reactions may depend on temperatures associated with different species; i.e. reactions may be driven by collisions with electrons, ions, or charge-neutral species. These new features have been implemented in such a way as to require little or no changes to CHEMKIN implementation for systems in thermal equilibrium, where all species share the same gas temperature. CHEMKIN-III now has the capability to handle weakly ionized plasma chemistry, especially for application related to advanced semiconductor processing.« less

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,…

Software Development for the Hobby-Eberly Telescope's Segment Alignment Maintenance System using LABView

NASA Technical Reports Server (NTRS)

Hall, Drew P.; Ly, William; Howard, Richard T.; Weir, John; Rakoczy, John; Roe, Fred (Technical Monitor)

2002-01-01

The software development for an upgrade to the Hobby-Eberly Telescope (HET) was done in LABView. In order to improve the performance of the HET at the McDonald Observatory, a closed-loop system had to be implemented to keep the mirror segments aligned during periods of observation. The control system, called the Segment Alignment Maintenance System (SAMs), utilized inductive sensors to measure the relative motions of the mirror segments. Software was developed in LABView to tie the sensors, operator interface, and mirror-control motors together. Developing the software in LABView allowed the system to be flexible, understandable, and able to be modified by the end users. Since LABView is built using block diagrams, the software naturally followed the designed control system's block and flow diagrams, and individual software blocks could be easily verified. LABView's many built-in display routines allowed easy visualization of diagnostic and health-monitoring data during testing. Also, since LABView is a multi-platform software package, different programmers could develop the code remotely on various types of machines. LABView s ease of use facilitated rapid prototyping and field testing. There were some unanticipated difficulties in the software development, but the use of LABView as the software "language" for the development of SAMs contributed to the overall success of the project.

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

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

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

2012-01-15

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

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.

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.

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…

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

PubMed

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

2002-11-01

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

Development of a Spacecraft Materials Selector Expert System

NASA Technical Reports Server (NTRS)

Pippin, G.; Kauffman, W. (Technical Monitor)

2002-01-01

This report contains a description of the knowledge base tool and examples of its use. A downloadable version of the Spacecraft Materials Selector (SMS) knowledge base is available through the NASA Space Environments and Effects Program. The "Spacecraft Materials Selector" knowledge base is part of an electronic expert system. The expert system consists of an inference engine that contains the "decision-making" code and the knowledge base that contains the selected body of information. The inference engine is a software package previously developed at Boeing, called the Boeing Expert System Tool (BEST) kit.

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.

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

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.

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

NASA Astrophysics Data System (ADS)

Luc̆ić, Vladan

1995-11-01

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

A 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

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

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…

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.

PubMed

Puritz, Jonathan B; Hollenbeck, Christopher M; Gold, John R

2014-01-01

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

PubMed Central

Hollenbeck, Christopher M.; Gold, John R.

2014-01-01

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com. PMID:24949246

A knowledge based application of the extended aircraft interrogation and display system

NASA Technical Reports Server (NTRS)

Glover, Richard D.; Larson, Richard R.

1991-01-01

A family of multiple-processor ground support test equipment was used to test digital flight-control systems on high-performance research aircraft. A unit recently built for the F-18 high alpha research vehicle project is the latest model in a series called the extended aircraft interrogation and display system. The primary feature emphasized monitors the aircraft MIL-STD-1553B data buses and provides real-time engineering units displays of flight-control parameters. A customized software package was developed to provide real-time data interpretation based on rules embodied in a highly structured knowledge database. The configuration of this extended aircraft interrogation and display system is briefly described, and the evolution of the rule based package and its application to failure modes and effects testing on the F-18 high alpha research vehicle is discussed.

Machine-learning in astronomy

NASA Astrophysics Data System (ADS)

Hobson, Michael; Graff, Philip; Feroz, Farhan; Lasenby, Anthony

2014-05-01

Machine-learning methods may be used to perform many tasks required in the analysis of astronomical data, including: data description and interpretation, pattern recognition, prediction, classification, compression, inference and many more. An intuitive and well-established approach to machine learning is the use of artificial neural networks (NNs), which consist of a group of interconnected nodes, each of which processes information that it receives and then passes this product on to other nodes via weighted connections. In particular, I discuss the first public release of the generic neural network training algorithm, called SkyNet, and demonstrate its application to astronomical problems focusing on its use in the BAMBI package for accelerated Bayesian inference in cosmology, and the identification of gamma-ray bursters. The SkyNet and BAMBI packages, which are fully parallelised using MPI, are available at http://www.mrao.cam.ac.uk/software/.

NanoStringNormCNV: pre-processing of NanoString CNV data.

PubMed

Sendorek, Dorota H; Lalonde, Emilie; Yao, Cindy Q; Sabelnykova, Veronica Y; Bristow, Robert G; Boutros, Paul C

2018-03-15

The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses. To demonstrate its utility, we apply it to a new dataset of 96 genes profiled on 41 prostate tumour and 24 matched normal samples. NanoStringNormCNV is implemented in R and is freely available at http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv. paul.boutros@oicr.on.ca. Supplementary data are available at Bioinformatics online.

System and Method for Providing a Climate Data Analytic Services Application Programming Interface Distribution Package

NASA Technical Reports Server (NTRS)

Tamkin, Glenn S. (Inventor); Duffy, Daniel Q. (Inventor); Schnase, John L. (Inventor)

2016-01-01

A system, method and computer-readable storage devices for providing a climate data analytic services application programming interface distribution package. The example system can provide various components. The system provides a climate data analytic services application programming interface library that enables software applications running on a client device to invoke the capabilities of a climate data analytic service. The system provides a command-line interface that provides a means of interacting with a climate data analytic service by issuing commands directly to the system's server interface. The system provides sample programs that call on the capabilities of the application programming interface library and can be used as templates for the construction of new client applications. The system can also provide test utilities, build utilities, service integration utilities, and documentation.

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.

System for NIS Forecasting Based on Ensembles Analysis

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

2014-01-02

BMA-NIS is a package/library designed to be called by a script (e.g. Perl or Python). The software itself is written in the language of R. The software assists electric power delivery systems in planning resource availability and demand, based on historical data and current data variables. Net Interchange Schedule (NIS) is the algebraic sum of all energy scheduled to flow into or out of a balancing area during any interval. Accurate forecasts for NIS are important so that the Area Control Error (ACE) stays within an acceptable limit. To date, there are many approaches for forecasting NIS but all nonemore » of these are based on single models that can be sensitive to time of day and day of week effects.« less

Geometric registration of remotely sensed data with SAMIR

NASA Astrophysics Data System (ADS)

Gianinetto, Marco; Barazzetti, Luigi; Dini, Luigi; Fusiello, Andrea; Toldo, Roberto

2015-06-01

The commercial market offers several software packages for the registration of remotely sensed data through standard one-to-one image matching. Although very rapid and simple, this strategy does not take into consideration all the interconnections among the images of a multi-temporal data set. This paper presents a new scientific software, called Satellite Automatic Multi-Image Registration (SAMIR), able to extend the traditional registration approach towards multi-image global processing. Tests carried out with high-resolution optical (IKONOS) and high-resolution radar (COSMO-SkyMed) data showed that SAMIR can improve the registration phase with a more rigorous and robust workflow without initial approximations, user's interaction or limitation in spatial/spectral data size. The validation highlighted a sub-pixel accuracy in image co-registration for the considered imaging technologies, including optical and radar imagery.

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)

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…

Learn by Yourself: The Self-Learning Tools for Qualitative Analysis Software Packages

ERIC Educational Resources Information Center

Freitas, Fábio; Ribeiro, Jaime; Brandão, Catarina; Reis, Luís Paulo; de Souza, Francislê Neri; Costa, António Pedro

2017-01-01

Computer Assisted Qualitative Data Analysis Software (CAQDAS) are tools that help researchers to develop qualitative research projects. These software packages help the users with tasks such as transcription analysis, coding and text interpretation, writing and annotation, content search and analysis, recursive abstraction, grounded theory…

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…

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,…

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

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

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

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.

The New Web-Based Hera Data Processing System at the HEASARC

NASA Technical Reports Server (NTRS)

Pence, W.

2011-01-01

The HEASARC at NASA/GSFC has provide an on-line astronomical data processing system called Hera for several years. Hera provides a complete data processing environment, including installed software packages, local data storage, and the CPU resources needed to process the user's data. The original design of Hera, however, has 2 requirements that has limited it's usefulness for some users, namely, that 1) the user must download and install a small helper program on their own computer before using Hera, and 2) Hera requires that several computer ports/sockets be allowed to communicate through any local firewalls on the users machine. Both of these restrictions can be problematic for some users, therefore we are now migrating Hera into a purely Web based environment which only requires a standard Web browser. The first release of Web Hera is now publicly available at http://heasarc.gsfc.nasa.gov/webheara/. It currently provides a standard graphical interface for running hundreds of different data processing programs that are available in the HEASARC's ftools software package. Over the next year we to add more features to Web Hera, including an interactive command line interface, and more display and line capabilities.

Accelerating the Original Profile Kernel.

PubMed

Hamp, Tobias; Goldberg, Tatyana; Rost, Burkhard

2013-01-01

One of the most accurate multi-class protein classification systems continues to be the profile-based SVM kernel introduced by the Leslie group. Unfortunately, its CPU requirements render it too slow for practical applications of large-scale classification tasks. Here, we introduce several software improvements that enable significant acceleration. Using various non-redundant data sets, we demonstrate that our new implementation reaches a maximal speed-up as high as 14-fold for calculating the same kernel matrix. Some predictions are over 200 times faster and render the kernel as possibly the top contender in a low ratio of speed/performance. Additionally, we explain how to parallelize various computations and provide an integrative program that reduces creating a production-quality classifier to a single program call. The new implementation is available as a Debian package under a free academic license and does not depend on commercial software. For non-Debian based distributions, the source package ships with a traditional Makefile-based installer. Download and installation instructions can be found at https://rostlab.org/owiki/index.php/Fast_Profile_Kernel. Bugs and other issues may be reported at https://rostlab.org/bugzilla3/enter_bug.cgi?product=fastprofkernel.

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.

Global review of open access risk assessment software packages valid for global or continental scale analysis

NASA Astrophysics Data System (ADS)

Daniell, James; Simpson, Alanna; Gunasekara, Rashmin; Baca, Abigail; Schaefer, Andreas; Ishizawa, Oscar; Murnane, Rick; Tijssen, Annegien; Deparday, Vivien; Forni, Marc; Himmelfarb, Anne; Leder, Jan

2015-04-01

Over the past few decades, a plethora of open access software packages for the calculation of earthquake, volcanic, tsunami, storm surge, wind and flood have been produced globally. As part of the World Bank GFDRR Review released at the Understanding Risk 2014 Conference, over 80 such open access risk assessment software packages were examined. Commercial software was not considered in the evaluation. A preliminary analysis was used to determine whether the 80 models were currently supported and if they were open access. This process was used to select a subset of 31 models that include 8 earthquake models, 4 cyclone models, 11 flood models, and 8 storm surge/tsunami models for more detailed analysis. By using multi-criteria analysis (MCDA) and simple descriptions of the software uses, the review allows users to select a few relevant software packages for their own testing and development. The detailed analysis evaluated the models on the basis of over 100 criteria and provides a synopsis of available open access natural hazard risk modelling tools. In addition, volcano software packages have since been added making the compendium of risk software tools in excess of 100. There has been a huge increase in the quality and availability of open access/source software over the past few years. For example, private entities such as Deltares now have an open source policy regarding some flood models (NGHS). In addition, leaders in developing risk models in the public sector, such as Geoscience Australia (EQRM, TCRM, TsuDAT, AnuGA) or CAPRA (ERN-Flood, Hurricane, CRISIS2007 etc.), are launching and/or helping many other initiatives. As we achieve greater interoperability between modelling tools, we will also achieve a future wherein different open source and open access modelling tools will be increasingly connected and adapted towards unified multi-risk model platforms and highly customised solutions. It was seen that many software tools could be improved by enabling user-defined exposure and vulnerability. Without this function, many tools can only be used regionally and not at global or continental scale. It is becoming increasingly easy to use multiple packages for a single region and/or hazard to characterize the uncertainty in the risk, or use as checks for the sensitivities in the analysis. There is a potential for valuable synergy between existing software. A number of open source software packages could be combined to generate a multi-risk model with multiple views of a hazard. This extensive review has simply attempted to provide a platform for dialogue between all open source and open access software packages and to hopefully inspire collaboration between developers, given the great work done by all open access and open source developers.

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.

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.

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

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…

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.

Highly-optimized TWSM software package for seismic diffraction modeling adapted for GPU-cluster

NASA Astrophysics Data System (ADS)

Zyatkov, Nikolay; Ayzenberg, Alena; Aizenberg, Arkady

2015-04-01

Oil producing companies concern to increase resolution capability of seismic data for complex oil-and-gas bearing deposits connected with salt domes, basalt traps, reefs, lenses, etc. Known methods of seismic wave theory define shape of hydrocarbon accumulation with nonsufficient resolution, since they do not account for multiple diffractions explicitly. We elaborate alternative seismic wave theory in terms of operators of propagation in layers and reflection-transmission at curved interfaces. Approximation of this theory is realized in the seismic frequency range as the Tip-Wave Superposition Method (TWSM). TWSM based on the operator theory allows to evaluate of wavefield in bounded domains/layers with geometrical shadow zones (in nature it can be: salt domes, basalt traps, reefs, lenses, etc.) accounting for so-called cascade diffraction. Cascade diffraction includes edge waves from sharp edges, creeping waves near concave parts of interfaces, waves of the whispering galleries near convex parts of interfaces, etc. The basic algorithm of TWSM package is based on multiplication of large-size matrices (make hundreds of terabytes in size). We use advanced information technologies for effective realization of numerical procedures of the TWSM. In particular, we actively use NVIDIA CUDA technology and GPU accelerators allowing to significantly improve the performance of the TWSM software package, that is important in using it for direct and inverse problems. The accuracy, stability and efficiency of the algorithm are justified by numerical examples with curved interfaces. TWSM package and its separate components can be used in different modeling tasks such as planning of acquisition systems, physical interpretation of laboratory modeling, modeling of individual waves of different types and in some inverse tasks such as imaging in case of laterally inhomogeneous overburden, AVO inversion.

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

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.

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)

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Design and implementation of a Windows NT network to support CNC activities

NASA Technical Reports Server (NTRS)

Shearrow, C. A.

1996-01-01

The Manufacturing, Materials, & Processes Technology Division is undergoing dramatic changes to bring it's manufacturing practices current with today's technological revolution. The Division is developing Computer Automated Design and Computer Automated Manufacturing (CAD/CAM) abilities. The development of resource tracking is underway in the form of an accounting software package called Infisy. These two efforts will bring the division into the 1980's in relationship to manufacturing processes. Computer Integrated Manufacturing (CIM) is the final phase of change to be implemented. This document is a qualitative study and application of a CIM application capable of finishing the changes necessary to bring the manufacturing practices into the 1990's. The documentation provided in this qualitative research effort includes discovery of the current status of manufacturing in the Manufacturing, Materials, & Processes Technology Division including the software, hardware, network and mode of operation. The proposed direction of research included a network design, computers to be used, software to be used, machine to computer connections, estimate a timeline for implementation, and a cost estimate. Recommendation for the division's improvement include action to be taken, software to utilize, and computer configurations.

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.

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.

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.

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

OPTICON: Pro-Matlab software for large order controlled structure design

NASA Technical Reports Server (NTRS)

Peterson, Lee D.

1989-01-01

A software package for large order controlled structure design is described and demonstrated. The primary program, called OPTICAN, uses both Pro-Matlab M-file routines and selected compiled FORTRAN routines linked into the Pro-Matlab structure. The program accepts structural model information in the form of state-space matrices and performs three basic design functions on the model: (1) open loop analyses; (2) closed loop reduced order controller synthesis; and (3) closed loop stability and performance assessment. The current controller synthesis methods which were implemented in this software are based on the Generalized Linear Quadratic Gaussian theory of Bernstein. In particular, a reduced order Optimal Projection synthesis algorithm based on a homotopy solution method was successfully applied to an experimental truss structure using a 58-state dynamic model. These results are presented and discussed. Current plans to expand the practical size of the design model to several hundred states and the intention to interface Pro-Matlab to a supercomputing environment are discussed.

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

PubMed

Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

2017-12-14

Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

Microscopy image segmentation tool: Robust image data analysis

NASA Astrophysics Data System (ADS)

Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

2014-03-01

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

Design and implementation of Ada programs to facilitate automated testing

NASA Technical Reports Server (NTRS)

Dean, Jack; Fox, Barry; Oropeza, Michael

1991-01-01

An automated method utilized to test the software components of COMPASS, an interactive computer aided scheduling system, is presented. Each package of this system introduces a private type, and works to construct instances of that type, along with read and write routines for that type. Generic procedures that can generate test drivers for these functions are given and show how the test drivers can read from a test data file the functions to call, the arguments for those functions, what the anticipated result should be, and whether an exception should be raised for the function given the arguments.

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)

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.

HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline.

PubMed

Khomtchouk, Bohdan B; Van Booven, Derek J; Wahlestedt, Claes

2014-01-01

The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expression levels, such as those measured with RNAseq and microarray experiments, to provide qualitative large-scale views of the transcriptonomic landscape. Creating high-quality heatmaps is a computationally intensive task, often requiring considerable programming experience, particularly for customizing features to a specific dataset at hand. Software to create publication-quality heatmaps is developed with the R programming language, C++ programming language, and OpenGL application programming interface (API) to create industry-grade high performance graphics. We create a graphical user interface (GUI) software package called HeatmapGenerator for Windows OS and Mac OS X as an intuitive, user-friendly alternative to researchers with minimal prior coding experience to allow them to create publication-quality heatmaps using R graphics without sacrificing their desired level of customization. The simplicity of HeatmapGenerator is that it only requires the user to upload a preformatted input file and download the publicly available R software language, among a few other operating system-specific requirements. Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge. We provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R. The software is available for Microsoft Windows and Apple Mac OS X. HeatmapGenerator is released under the GNU General Public License and publicly available at: http://sourceforge.net/projects/heatmapgenerator/. The Mac OS X direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_MAC_OSX.tar.gz/download. The Windows OS direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_WINDOWS.zip/download.

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.

Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data

NASA Astrophysics Data System (ADS)

Gerber, Florian; Mösinger, Kaspar; Furrer, Reinhard

2017-07-01

Software packages for spatial data often implement a hybrid approach of interpreted and compiled programming languages. The compiled parts are usually written in C, C++, or Fortran, and are efficient in terms of computational speed and memory usage. Conversely, the interpreted part serves as a convenient user-interface and calls the compiled code for computationally demanding operations. The price paid for the user friendliness of the interpreted component is-besides performance-the limited access to low level and optimized code. An example of such a restriction is the 64-bit vector support of the widely used statistical language R. On the R side, users do not need to change existing code and may not even notice the extension. On the other hand, interfacing 64-bit compiled code efficiently is challenging. Since many R packages for spatial data could benefit from 64-bit vectors, we investigate strategies to efficiently pass 64-bit vectors to compiled languages. More precisely, we show how to simply extend existing R packages using the foreign function interface to seamlessly support 64-bit vectors. This extension is shown with the sparse matrix algebra R package spam. The new capabilities are illustrated with an example of GIMMS NDVI3g data featuring a parametric modeling approach for a non-stationary covariance matrix.

HyDe: a Python Package for Genome-Scale Hybridization Detection.

PubMed

Blischak, Paul D; Chifman, Julia; Wolfe, Andrea D; Kubatko, Laura S

2018-03-19

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this paper we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python, and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).

An Open-source Meteorological Operational System and its Installation in Portuguese- speaking Countries

NASA Astrophysics Data System (ADS)

Almeida, W. G.; Ferreira, A. L.; Mendes, M. V.; Ribeiro, A.; Yoksas, T.

2007-05-01

CPTEC, a division of Brazil’s INPE, has been using several open-source software packages for a variety of tasks in its Data Division. Among these tools are ones traditionally used in research and educational communities such as GrADs (Grid Analysis and Display System from the Center for Ocean-Land-Atmosphere Studies (COLA)), the Local Data Manager (LDM) and GEMPAK (from Unidata), andl operational tools such the Automatic File Distributor (AFD) that are popular among National Meteorological Services. In addition, some tools developed locally at CPTEC are also being made available as open-source packages. One package is being used to manage the data from Automatic Weather Stations that INPE operates. This system uses only open- source tools such as MySQL database, PERL scripts and Java programs for web access, and Unidata’s Internet Data Distribution (IDD) system and AFD for data delivery. All of these packages are get bundled into a low-cost and easy to install and package called the Meteorological Data Operational System. Recently, in a cooperation with the SICLIMAD project, this system has been modified for use by Portuguese- speaking countries in Africa to manage data from many Automatic Weather Stations that are being installed in these countries under SICLIMAD sponsorship. In this presentation we describe the tools included-in and and architecture-of the Meteorological Data Operational System.

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.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

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

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

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

2011-01-25

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

User's Manual and Final Report for Hot-SMAC GUI Development

NASA Technical Reports Server (NTRS)

Yarrington, Phil

2001-01-01

A new software package called Higher Order Theory-Structural/Micro Analysis Code (HOT-SMAC) has been developed as an effective alternative to the finite element approach for Functionally Graded Material (FGM) modeling. HOT-SMAC is a self-contained package including pre- and post-processing through an intuitive graphical user interface, along with the well-established Higher Order Theory for Functionally Graded Materials (HOTFGM) thermomechanical analysis engine. This document represents a Getting Started/User's Manual for HOT-SMAC and a final report for its development. First, the features of the software are presented in a simple step-by-step example where a HOT-SMAC model representing a functionally graded material is created, mechanical and thermal boundary conditions are applied, the model is analyzed and results are reviewed. In a second step-by-step example, a HOT-SMAC model of an actively cooled metallic channel with ceramic thermal barrier coating is built and analyzed. HOT-SMAC results from this model are compared to recently published results (NASA/TM-2001-210702) for two grid densities. Finally, a prototype integration of HOTSMAC with the commercially available HyperSizer(R) structural analysis and sizing software is presented. In this integration, local strain results from HyperSizer's structural analysis are fed to a detailed HOT-SMAC model of the flange-to-facesheet bond region of a stiffened panel. HOT-SMAC is then used to determine the peak shear and peel (normal) stresses between the facesheet and bonded flange of the panel and determine the "free edge" effects.

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.

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

Motmot, an open-source toolkit for realtime video acquisition and analysis.

PubMed

Straw, Andrew D; Dickinson, Michael H

2009-07-22

Video cameras sense passively from a distance, offer a rich information stream, and provide intuitively meaningful raw data. Camera-based imaging has thus proven critical for many advances in neuroscience and biology, with applications ranging from cellular imaging of fluorescent dyes to tracking of whole-animal behavior at ecologically relevant spatial scales. Here we present 'Motmot': an open-source software suite for acquiring, displaying, saving, and analyzing digital video in real-time. At the highest level, Motmot is written in the Python computer language. The large amounts of data produced by digital cameras are handled by low-level, optimized functions, usually written in C. This high-level/low-level partitioning and use of select external libraries allow Motmot, with only modest complexity, to perform well as a core technology for many high-performance imaging tasks. In its current form, Motmot allows for: (1) image acquisition from a variety of camera interfaces (package motmot.cam_iface), (2) the display of these images with minimal latency and computer resources using wxPython and OpenGL (package motmot.wxglvideo), (3) saving images with no compression in a single-pass, low-CPU-use format (package motmot.FlyMovieFormat), (4) a pluggable framework for custom analysis of images in realtime and (5) firmware for an inexpensive USB device to synchronize image acquisition across multiple cameras, with analog input, or with other hardware devices (package motmot.fview_ext_trig). These capabilities are brought together in a graphical user interface, called 'FView', allowing an end user to easily view and save digital video without writing any code. One plugin for FView, 'FlyTrax', which tracks the movement of fruit flies in real-time, is included with Motmot, and is described to illustrate the capabilities of FView. Motmot enables realtime image processing and display using the Python computer language. In addition to the provided complete applications, the architecture allows the user to write relatively simple plugins, which can accomplish a variety of computer vision tasks and be integrated within larger software systems. The software is available at http://code.astraw.com/projects/motmot.

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.

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

NASA Technical Reports Server (NTRS)

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

2014-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2014-01-01

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

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...

INTERFACING SAS TO ORACLE IN THE UNIX ENVIRONMENT

EPA Science Inventory

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

AN ADA NAMELIST PACKAGE

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

The Ada Namelist Package, developed for the Ada programming language, enables a calling program to read and write FORTRAN-style namelist files. A namelist file consists of any number of assignment statements in any order. Features of the Ada Namelist Package are: the handling of any combination of user-defined types; the ability to read vectors, matrices, and slices of vectors and matrices; the handling of mismatches between variables in the namelist file and those in the programmed list of namelist variables; and the ability to avoid searching the entire input file for each variable. The principle user benefits of this software are the following: the ability to write namelist-readable files, the ability to detect most file errors in the initialization phase, a package organization that reduces the number of instantiated units to a few packages rather than to many subprograms, a reduced number of restrictions, and an increased execution speed. The Ada Namelist reads data from an input file into variables declared within a user program. It then writes data from the user program to an output file, printer, or display. The input file contains a sequence of assignment statements in arbitrary order. The output is in namelist-readable form. There is a one-to-one correspondence between namelist I/O statements executed in the user program and variables read or written. Nevertheless, in the input file, mismatches are allowed between assignment statements in the file and the namelist read procedure statements in the user program. The Ada Namelist Package itself is non-generic. However, it has a group of nested generic packages following the nongeneric opening portion. The opening portion declares a variety of useraccessible constants, variables and subprograms. The subprograms are procedures for initializing namelists for reading, reading and writing strings. The subprograms are also functions for analyzing the content of the current dataset and diagnosing errors. Two nested generic packages follow the opening portion. The first generic package contains procedures that read and write objects of scalar type. The second contains subprograms that read and write one and two-dimensional arrays whose components are of scalar type and whose indices are of either of the two discrete types (integer or enumeration). Subprograms in the second package also read and write vector and matrix slices. The Ada Namelist ASCII text files are available on a 360k 5.25" floppy disk written on an IBM PC/AT running under the PC DOS operating system. The largest subprogram in the package requires 150k of memory. The package was developed using VAX Ada v. 1.5 under DEC VMS v. 4.5. It should be portable to any validated Ada compiler. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

’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,…

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.

Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer.

PubMed

Covarrubias-Pazaran, Giovanny

2016-01-01

Most traits of agronomic importance are quantitative in nature, and genetic markers have been used for decades to dissect such traits. Recently, genomic selection has earned attention as next generation sequencing technologies became feasible for major and minor crops. Mixed models have become a key tool for fitting genomic selection models, but most current genomic selection software can only include a single variance component other than the error, making hybrid prediction using additive, dominance and epistatic effects unfeasible for species displaying heterotic effects. Moreover, Likelihood-based software for fitting mixed models with multiple random effects that allows the user to specify the variance-covariance structure of random effects has not been fully exploited. A new open-source R package called sommer is presented to facilitate the use of mixed models for genomic selection and hybrid prediction purposes using more than one variance component and allowing specification of covariance structures. The use of sommer for genomic prediction is demonstrated through several examples using maize and wheat genotypic and phenotypic data. At its core, the program contains three algorithms for estimating variance components: Average information (AI), Expectation-Maximization (EM) and Efficient Mixed Model Association (EMMA). Kernels for calculating the additive, dominance and epistatic relationship matrices are included, along with other useful functions for genomic analysis. Results from sommer were comparable to other software, but the analysis was faster than Bayesian counterparts in the magnitude of hours to days. In addition, ability to deal with missing data, combined with greater flexibility and speed than other REML-based software was achieved by putting together some of the most efficient algorithms to fit models in a gentle environment such as R.

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

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

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

PubMed Central

Browning, Brian L.; Yu, Zhaoxia

2009-01-01

We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype-calling methods, using genotype data from the Illumina 550K and Affymetrix 500K arrays. We show that our method has higher genotype-call accuracy and yields fewer uncalled genotypes than competing methods. We perform single-marker analysis of data from the Wellcome Trust Case Control Consortium bipolar disorder and type 2 diabetes studies. For bipolar disorder, the genotype calls in the original study yield 25 markers with apparent false-positive association with bipolar disorder at a p < 10−7 significance level, whereas genotype calls made with our method yield no associated markers at this significance threshold. Conversely, for markers with replicated association with type 2 diabetes, there is good concordance between genotype calls used in the original study and calls made by our method. Results from single-marker and haplotypic analysis of our method's genotype calls for the bipolar disorder study indicate that our method is highly effective at eliminating genotyping artifacts that cause false-positive associations in genome-wide association studies. Our new genotype-calling methods are implemented in the BEAGLE and BEAGLECALL software packages. PMID:19931040

Long term stability and individual distinctiveness in captive orca vocalizations

NASA Astrophysics Data System (ADS)

Noonan, Michael; Suchak, Malini

2005-04-01

With focus on the question of signature calling in killer whales, recordings from five captive orcas (of Icelandic origin) held at Marineland of Canada were compared. For the present analysis, samples of three different call syllables were selected from recordings made five years apart and from instances in which the identity of the calling whale was unambiguous due to temporary isolation, concomitant bubbling, and/or head nodding. The Raven software package was used to ascertain the frequency range, frequency (max), duration, and timing of maximum and minimum power within each sample. For two of the three call syllables, statistically significant differences were found among the five whales for call length and for the timing of maximums and minimums (p<0.01-0.001). This similarly proved true for nearly all pairwise comparisons between whales, including mother-offspring dyads. By contrast, for three of four whales for which we had sufficient samples, no significant differences were found on any measure between samples taken from the same whales five years apart. These findings therefore support the notion that the voices of individual orcas are distinct from one another in ways that are stable over the course of multiple years.

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).

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.

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.

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

SURFACE CHEMKIN-III: A Fortran package for analyzing heterogeneous chemical kinetics at a solid-surface - gas-phase interface

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

Coltrin, M.E.; Kee, R.J.; Rupley, F.M.

1996-05-01

This document is the user`s manual for the SURFACE CHEMKIN-III package. Together with CHEMKIN-III, this software facilitates the formation, solution, and interpretation of problems involving elementary heterogeneous and gas-phase chemical kinetics in the presence of a solid surface. The package consists of two major software components: an Interpreter and a Surface Subroutine Library. The Interpreter is a program that reads a symbolic description of a user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Surface Subroutine Library, which is a collection of about seventy modular Fortran subroutines that may bemore » called from a user`s application code to return information on chemical production rates and thermodynamic properties. This version of SURFACE CHEMKIN-III includes many modifications to allow treatment of multi-fluid plasma systems, for example modeling the reactions of highly energetic ionic species with a surface. Optional rate expressions allow reaction rates to depend upon ion energy rather than a single thermodynamic temperature. In addition, subroutines treat temperature as an array, allowing an application code to define a different temperature for each species. This version of SURFACE CHEMKIN-III allows use of real (non-integer) stoichiometric coefficients; the reaction order with respect to species concentrations can also be specified independent of the reaction`s stoichiometric coefficients. Several different reaction mechanisms can be specified in the Interpreter input file through the new construct of multiple materials.« less

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

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…

Evaluation of 3-D graphics software: A case study

NASA Technical Reports Server (NTRS)

Lores, M. E.; Chasen, S. H.; Garner, J. M.

1984-01-01

An efficient 3-D geometry graphics software package which is suitable for advanced design studies was developed. The advanced design system is called GRADE--Graphics for Advanced Design. Efficiency and ease of use are gained by sacrificing flexibility in surface representation. The immediate options were either to continue development of GRADE or to acquire a commercially available system which would replace or complement GRADE. Test cases which would reveal the ability of each system to satisfy the requirements were developed. A scoring method which adequately captured the relative capabilities of the three systems was presented. While more complex multi-attribute decision methods could be used, the selected method provides all the needed information without being so complex that it is difficult to understand. If the value factors are modestly perturbed, system Z is a clear winner based on its overall capabilities. System Z is superior in two vital areas: surfacing and ease of interface with application programs.

Microcomputer based software for biodynamic simulation

NASA Technical Reports Server (NTRS)

Rangarajan, N.; Shams, T.

1993-01-01

This paper presents a description of a microcomputer based software package, called DYNAMAN, which has been developed to allow an analyst to simulate the dynamics of a system consisting of a number of mass segments linked by joints. One primary application is in predicting the motion of a human occupant in a vehicle under the influence of a variety of external forces, specially those generated during a crash event. Extensive use of a graphical user interface has been made to aid the user in setting up the input data for the simulation and in viewing the results from the simulation. Among its many applications, it has been successfully used in the prototype design of a moving seat that aids in occupant protection during a crash, by aircraft designers in evaluating occupant injury in airplane crashes, and by users in accident reconstruction for reconstructing the motion of the occupant and correlating the impacts with observed injuries.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)

PubMed Central

2013-01-01

Background The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. Results We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Conclusions Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools. PMID:24209455

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

PubMed

Sturgill, David; Malone, John H; Sun, Xia; Smith, Harold E; Rabinow, Leonard; Samson, Marie-Laure; Oliver, Brian

2013-11-09

The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools.

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.

Evolution of a modular software network

PubMed Central

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

2011-01-01

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

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.

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...

A Simple Interactive Software Package for Plotting, Animating, and Calculating

ERIC Educational Resources Information Center

Engelhardt, Larry

2012-01-01

We introduce a new open source (free) software package that provides a simple, highly interactive interface for carrying out certain mathematical tasks that are commonly encountered in physics. These tasks include plotting and animating functions, solving systems of coupled algebraic equations, and basic calculus (differentiating and integrating…

A Software Development Approach for Computer Assisted Language Learning

ERIC Educational Resources Information Center

Cushion, Steve

2005-01-01

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

Analysis of Variance: What Is Your Statistical Software Actually Doing?

ERIC Educational Resources Information Center

Li, Jian; Lomax, Richard G.

2011-01-01

Users assume statistical software packages produce accurate results. In this article, the authors systematically examined Statistical Package for the Social Sciences (SPSS) and Statistical Analysis System (SAS) for 3 analysis of variance (ANOVA) designs, mixed-effects ANOVA, fixed-effects analysis of covariance (ANCOVA), and nested ANOVA. For each…

A Multi-User Microcomputer System for Small Libraries.

ERIC Educational Resources Information Center

Leggate, Peter

1988-01-01

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

Microcomputer Software Programs for Vocational Education.

ERIC Educational Resources Information Center

Rodenstein, Judith, Ed.; Lambert, Roger, Ed.

Over 200 microcomputer software packages applicable to vocational education are listed. Most of the programs are available for the Apple, TRS-80, and Commodore microcomputers. The packages have been reviewed, but have not been formally evaluated. Titles of the programs with names and addresses of the distributors are provided. Telephone numbers…

Software, Copyright, and Site-License Agreements: Publishers' Perspective of Library Practice.

ERIC Educational Resources Information Center

Happer, Stephanie K.

Thirty-one academic publishers of stand-alone software and book/disk packages were surveyed to determine whether publishers have addressed the copyright issues inherent in circulating these packages within the library environment. Twenty-two questionnaires were returned, providing a 71% return rate. There were 18 usable questionnaires. Publishers…

Computerised data reduction.

PubMed

Datson, D J; Carter, N G

1988-10-01

The use of personal computers in accountancy and business generally has been stimulated by the availability of flexible software packages. We describe the implementation of a commercial software package designed for interfacing with laboratory instruments and highlight the ease with which it can be implemented, without the need for specialist computer programming staff.

wbstats

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

Piburn, Jesse

2016-04-22

Availability of accessing the World Bank Data API through the R language was limited to one existing package, which is limited in its ability. The software provides access to all of the features in World Bank API in one software package for the R language and provides functions for searching and downloading data from the World Bank API.

Propensity Score Analysis in R: A Software Review

ERIC Educational Resources Information Center

Keller, Bryan; Tipton, Elizabeth

2016-01-01

In this article, we review four software packages for implementing propensity score analysis in R: "Matching, MatchIt, PSAgraphics," and "twang." After briefly discussing essential elements for propensity score analysis, we apply each package to a data set from the Early Childhood Longitudinal Study in order to estimate the…

A comparison of acoustic montoring methods for common anurans of the northeastern United States

USGS Publications Warehouse

Brauer, Corinne; Donovan, Therese; Mickey, Ruth M.; Katz, Jonathan; Mitchell, Brian R.

2016-01-01

Many anuran monitoring programs now include autonomous recording units (ARUs). These devices collect audio data for extended periods of time with little maintenance and at sites where traditional call surveys might be difficult. Additionally, computer software programs have grown increasingly accurate at automatically identifying the calls of species. However, increased automation may cause increased error. We collected 435 min of audio data with 2 types of ARUs at 10 wetland sites in Vermont and New York, USA, from 1 May to 1 July 2010. For each minute, we determined presence or absence of 4 anuran species (Hyla versicolor, Pseudacris crucifer, Anaxyrus americanus, and Lithobates clamitans) using 1) traditional human identification versus 2) computer-mediated identification with software package, Song Scope® (Wildlife Acoustics, Concord, MA). Detections were compared with a data set consisting of verified calls in order to quantify false positive, false negative, true positive, and true negative rates. Multinomial logistic regression analysis revealed a strong (P < 0.001) 3-way interaction between the ARU recorder type, identification method, and focal species, as well as a trend in the main effect of rain (P = 0.059). Overall, human surveyors had the lowest total error rate (<2%) compared with 18–31% total errors with automated methods. Total error rates varied by species, ranging from 4% for A. americanus to 26% for L. clamitans. The presence of rain may reduce false negative rates. For survey minutes where anurans were known to be calling, the odds of a false negative were increased when fewer individuals of the same species were calling.

Existing Fortran interfaces to Trilinos in preparation for exascale ForTrilinos development

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

Evans, Katherine J.; Young, Mitchell T.; Collins, Benjamin S.

This report summarizes the current state of Fortran interfaces to the Trilinos library within several key applications of the Exascale Computing Program (ECP), with the aim of informing developers about strategies to develop ForTrilinos, an exascale-ready, Fortran interface software package within Trilinos. The two software projects assessed within are the DOE Office of Science's Accelerated Climate Model for Energy (ACME) atmosphere component, CAM, and the DOE Office of Nuclear Energy's core-simulator portion of VERA, a nuclear reactor simulation code. Trilinos is an object-oriented, C++ based software project, and spans a collection of algorithms and other enabling technologies such as uncertaintymore » quantification and mesh generation. To date, Trilinos has enabled these codes to achieve large-scale simulation results, however the simulation needs of CAM and VERA-CS will approach exascale over the next five years. A Fortran interface to Trilinos that enables efficient use of programming models and more advanced algorithms is necessary. Where appropriate, the needs of the CAM and VERA-CS software to achieve their simulation goals are called out specifically. With this report, a design document and execution plan for ForTrilinos development can proceed.« less

The maturing of the quality improvement paradigm in the SEL

NASA Technical Reports Server (NTRS)

Basili, Victor R.

1993-01-01

The Software Engineering Laboratory uses a paradigm for improving the software process and product, called the quality improvement paradigm. This paradigm has evolved over the past 18 years, along with our software development processes and product. Since 1976, when we first began the SEL, we have learned a great deal about improving the software process and product, making a great many mistakes along the way. Quality improvement paradigm, as it is currently defined, can be broken up into six steps: characterize the current project and its environment with respect to the appropriate models and metrics; set the quantifiable goals for successful project performance and improvement; choose the appropriate process model and supporting methods and tools for this project; execute the processes, construct the products, and collect, validate, and analyze the data to provide real-time feedback for corrective action; analyze the data to evaluate the current practices, determine problems, record findings, and make recommendations for future project improvements; and package the experience gained in the form of updated and refined models and other forms of structured knowledge gained from this and prior projects and save it in an experience base to be reused on future projects.

Advanced fingerprint verification software

NASA Astrophysics Data System (ADS)

Baradarani, A.; Taylor, J. R. B.; Severin, F.; Maev, R. Gr.

2016-05-01

We have developed a fingerprint software package that can be used in a wide range of applications from law enforcement to public and private security systems, and to personal devices such as laptops, vehicles, and door- locks. The software and processing units are a unique implementation of new and sophisticated algorithms that compete with the current best systems in the world. Development of the software package has been in line with the third generation of our ultrasonic fingerprinting machine1. Solid and robust performance is achieved in the presence of misplaced and low quality fingerprints.

Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: the Collaborative Chemistry Database Tool (CCDBT).

PubMed

Chen, Mingyang; Stott, Amanda C; Li, Shenggang; Dixon, David A

2012-04-01

A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the metadata. Computational chemistry data in various formats from different computing sources, software packages, and users can be parsed into uniform metadata for storage in a MySQL database. Parsing is performed by a parsing pyramid, including parsers written for different levels of data types and sets created by the parser loader after loading parser engines and configurations. Copyright © 2011 Elsevier Inc. All rights reserved.

PRISM software—Processing and review interface for strong-motion data

USGS Publications Warehouse

Jones, Jeanne M.; Kalkan, Erol; Stephens, Christopher D.; Ng, Peter

2017-11-28

Rapidly available and accurate ground-motion acceleration time series (seismic recordings) and derived data products are essential to quickly providing scientific and engineering analysis and advice after an earthquake. To meet this need, the U.S. Geological Survey National Strong Motion Project has developed a software package called PRISM (Processing and Review Interface for Strong-Motion data). PRISM automatically processes strong-motion acceleration records, producing compatible acceleration, velocity, and displacement time series; acceleration, velocity, and displacement response spectra; Fourier amplitude spectra; and standard earthquake-intensity measures. PRISM is intended to be used by strong-motion seismic networks, as well as by earthquake engineers and seismologists.

Earth Global Reference Atmospheric Model 2007 (Earth-GRAM07)

NASA Technical Reports Server (NTRS)

Leslie, Fred W.; Justus, C. G.

2008-01-01

GRAM is a Fortran software package that can run on a variety of platforms including PC's. GRAM provides values of atmospheric quantities such as temperature, pressure, density, winds, constituents, etc. GRAM99 covers all global locations, all months, and heights from the surface to approx. 1000 km). Dispersions (perturbations) of these parameters are also provided and are spatially and temporally correlated. GRAM can be run in a stand-alone mode or called as a subroutine from a trajectory program. GRAM07 is diagnostic, not prognostic (i.e., it describes the atmosphere, but it does not forecast). The source code is distributed free-of-charge to eligible recipients.

Precise control and animation creation over the DMD for projection-based applications

NASA Astrophysics Data System (ADS)

Koudsi, Badia

2014-03-01

Digital micromirror devices (DMDs) are used in a variety of display and projection applications to produce high resolution images, both static and animated. A common obstacle to working with DMDs in research and development applications is the steep learning curve required to obtain proficiency in programming the boards that control the behavior of the DMDs. This can discourage developers who wish to use DMDs in new or novel research and development applications which might benefit from their light-control properties. A new software package called Light Animator has been developed that provides a user friendly and more intuitive interface for controlling the DMD. The software allows users to address the micromirror array by the drawing and animation of objects in a style similar to that of commercial drawing programs. Sequences and animation are controlled by dividing the sequence into frames which the user can draw individually or the software can fill in for the user. Examples and descriptions of the software operation are described and operational performance measures are provided. Potential applications include 3D volumetric displays, a 3D scanner when combining the DMD with a CCD camera, and most any 2D application for which DMDs are currently used. The software's capabilities allow scientists to develop applications more easily and effectively.

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)

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

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

Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui

2016-11-02

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmannmore » Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.« less

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

WannierTools: An open-source software package for novel topological materials

NASA Astrophysics Data System (ADS)

Wu, QuanSheng; Zhang, ShengNan; Song, Hai-Feng; Troyer, Matthias; Soluyanov, Alexey A.

2018-03-01

We present an open-source software package WannierTools, a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 (Mostofi et al., 2008). It can help to classify the topological phase of a given material by calculating the Wilson loop, and can get the surface state spectrum, which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone (BZ).

Use of symbolic computation in robotics education

NASA Technical Reports Server (NTRS)

Vira, Naren; Tunstel, Edward

1992-01-01

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

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.

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.

The jmzQuantML programming interface and validator for the mzQuantML data standard.

PubMed

Qi, Da; Krishna, Ritesh; Jones, Andrew R

2014-03-01

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages

PubMed Central

Nunez-Iglesias, Juan; Kennedy, Ryan; Plaza, Stephen M.; Chakraborty, Anirban; Katz, William T.

2014-01-01

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them. PMID:24772079

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.

Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.unity Algorithm.

PubMed

Mahieu, Nathaniel G; Spalding, Jonathan L; Gelman, Susan J; Patti, Gary J

2016-09-20

Analysis of a single analyte by mass spectrometry can result in the detection of more than 100 degenerate peaks. These degenerate peaks complicate spectral interpretation and are challenging to annotate. In mass spectrometry-based metabolomics, this degeneracy leads to inflated false discovery rates, data sets containing an order of magnitude more features than analytes, and an inefficient use of resources during data analysis. Although software has been introduced to annotate spectral degeneracy, current approaches are unable to represent several important classes of peak relationships. These include heterodimers and higher complex adducts, distal fragments, relationships between peaks in different polarities, and complex adducts between features and background peaks. Here we outline sources of peak degeneracy in mass spectra that are not annotated by current approaches and introduce a software package called mz.unity to detect these relationships in accurate mass data. Using mz.unity, we find that data sets contain many more complex relationships than we anticipated. Examples include the adduct of glutamate and nicotinamide adenine dinucleotide (NAD), fragments of NAD detected in the same or opposite polarities, and the adduct of glutamate and a background peak. Further, the complex relationships we identify show that several assumptions commonly made when interpreting mass spectral degeneracy do not hold in general. These contributions provide new tools and insight to aid in the annotation of complex spectral relationships and provide a foundation for improved data set identification. Mz.unity is an R package and is freely available at https://github.com/nathaniel-mahieu/mz.unity as well as our laboratory Web site http://pattilab.wustl.edu/software/ .

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.

Reference datasets for bioequivalence trials in a two-group parallel design.

PubMed

Fuglsang, Anders; Schütz, Helmut; Labes, Detlew

2015-03-01

In order to help companies qualify and validate the software used to evaluate bioequivalence trials with two parallel treatment groups, this work aims to define datasets with known results. This paper puts a total 11 datasets into the public domain along with proposed consensus obtained via evaluations from six different software packages (R, SAS, WinNonlin, OpenOffice Calc, Kinetica, EquivTest). Insofar as possible, datasets were evaluated with and without the assumption of equal variances for the construction of a 90% confidence interval. Not all software packages provide functionality for the assumption of unequal variances (EquivTest, Kinetica), and not all packages can handle datasets with more than 1000 subjects per group (WinNonlin). Where results could be obtained across all packages, one showed questionable results when datasets contained unequal group sizes (Kinetica). A proposal is made for the results that should be used as validation targets.

"FluSpec": A Simulated Experiment in Fluorescence Spectroscopy

ERIC Educational Resources Information Center

Bigger, Stephen W.; Bigger, Andrew S.; Ghiggino, Kenneth P.

2014-01-01

The "FluSpec" educational software package is a fully contained tutorial on the technique of fluorescence spectroscopy as well as a simulator on which experiments can be performed. The procedure for each of the experiments is also contained within the package along with example analyses of results that are obtained using the software.

Comparative Analyses of MIRT Models and Software (BMIRT and flexMIRT)

ERIC Educational Resources Information Center

Yavuz, Guler; Hambleton, Ronald K.

2017-01-01

Application of MIRT modeling procedures is dependent on the quality of parameter estimates provided by the estimation software and techniques used. This study investigated model parameter recovery of two popular MIRT packages, BMIRT and flexMIRT, under some common measurement conditions. These packages were specifically selected to investigate the…

Macintosh Computer Classroom and Laboratory Security: Preventing Unwanted Changes to the System.

ERIC Educational Resources Information Center

Senn, Gary J.; Smyth, Thomas J. C.

Because of the graphical interface and "openness" of the operating system, Macintosh computers are susceptible to undesirable changes by the user. This presentation discusses the advantages and disadvantages of software packages that offer protection for the Macintosh system. The two basic forms of software security packages include a…

Virginia Transit Performance Evaluation Package (VATPEP).

DOT National Transportation Integrated Search

1987-01-01

The Virginia Transit Performance Evaluation Package (VATPEP), a computer software package, is documented. This is the computerized version of the methodology used by the Virginia Department of Transportation to evaluate the performance of public tran...

Cooperative Work and Sustainable Scientific Software Practices in R

NASA Astrophysics Data System (ADS)

Weber, N.

2013-12-01

Most scientific software projects are dependent on the work of many diverse people, institutions and organizations. Incentivizing these actors to cooperatively develop software that is both reliable, and sustainable is complicated by the fact that the reward structures of these various actors greatly differ: research scientists want results from a software or model run in order to publish papers, produce new data, or test a hypothesis; software engineers and research centers want compilable, well documented code that is refactorable, reusable and reproducible in future research scenarios. While much research has been done on incentives and motivations for participating in open source software projects or cyberinfrastrcture development, little work has been done on what motivates or incentivizes developers to maintain scientific software projects beyond their original application. This poster will present early results of research into the incentives and motivation for cooperative scientific software development. In particular, this work focuses on motivations for the maintenance and repair of libraries on the software platform R. Our work here uses a sample of R packages that were created by research centers, or are specific to earth, environmental and climate science applications. We first mined 'check' logs from the Comprehensive R Archive Network (CRAN) to determine the amount of time a package has existed, the number of versions it has gone through over this time, the number of releases, and finally the contact information for each official package 'maintainer'. We then sent a survey to each official maintainer, asking them questions about what role they played in developing the original package, and what their motivations were for sustaining the project over time. We will present early results from this mining and our survey of R maintainers.

Laser velocimeter data acquisition system for the Langley 14- by 22-foot subsonic tunnel. Software reference guide version 3.3

NASA Technical Reports Server (NTRS)

Jumper, Judith K.

1994-01-01

The Laser Velocimeter Data Acquisition System (LVDAS) in the Langley 14- by 22-Foot Tunnel is controlled by a comprehensive software package. The software package was designed to control the data acquisition process during wind tunnel tests which employ a laser velocimeter measurement system. This report provides detailed explanations on how to configure and operate the LVDAS system to acquire laser velocimeter and static wind tunnel data.

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.

Space-Shuttle Emulator Software

NASA Technical Reports Server (NTRS)

Arnold, Scott; Askew, Bill; Barry, Matthew R.; Leigh, Agnes; Mermelstein, Scott; Owens, James; Payne, Dan; Pemble, Jim; Sollinger, John; Thompson, Hiram;

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

PubMed

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

2016-08-01

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

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

Comparison of Perfusion CT Software to Predict the Final Infarct Volume After Thrombectomy.

PubMed

Austein, Friederike; Riedel, Christian; Kerby, Tina; Meyne, Johannes; Binder, Andreas; Lindner, Thomas; Huhndorf, Monika; Wodarg, Fritz; Jansen, Olav

2016-09-01

Computed tomographic perfusion represents an interesting physiological imaging modality to select patients for reperfusion therapy in acute ischemic stroke. The purpose of our study was to determine the accuracy of different commercial perfusion CT software packages (Philips (A), Siemens (B), and RAPID (C)) to predict the final infarct volume (FIV) after mechanical thrombectomy. Single-institutional computed tomographic perfusion data from 147 mechanically recanalized acute ischemic stroke patients were postprocessed. Ischemic core and FIV were compared about thrombolysis in cerebral infarction (TICI) score and time interval to reperfusion. FIV was measured at follow-up imaging between days 1 and 8 after stroke. In 118 successfully recanalized patients (TICI 2b/3), a moderately to strongly positive correlation was observed between ischemic core and FIV. The highest accuracy and best correlation are shown in early and fully recanalized patients (Pearson r for A=0.42, B=0.64, and C=0.83; P<0.001). Bland-Altman plots and boxplots demonstrate smaller ranges in package C than in A and B. Significant differences were found between the packages about over- and underestimation of the ischemic core. Package A, compared with B and C, estimated more than twice as many patients with a malignant stroke profile (P<0.001). Package C best predicted hypoperfusion volume in nonsuccessfully recanalized patients. Our study demonstrates best accuracy and approximation between the results of a fully automated software (RAPID) and FIV, especially in early and fully recanalized patients. Furthermore, this software package overestimated the FIV to a significantly lower degree and estimated a malignant mismatch profile less often than other software. © 2016 American Heart Association, Inc.

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

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.

The Leicester AATSR Global Analyser (LAGA) - Giving Young Students the Opportunity to Examine Space Observations of Global Climate-Related Processes

NASA Astrophysics Data System (ADS)

Llewellyn-Jones, David; Good, Simon; Corlett, Gary

A pc-based analysis package has been developed, for the dual purposes of, firstly, providing ‘quick-look' capability to research workers inspecting long time-series of global satellite datasets of Sea-surface Temperature (SST); and, secondly, providing an introduction for students, either undergraduates, or advanced high-school students to the characteristics of commonly used analysis techniques for large geophysical data-sets from satellites. Students can also gain insight into the behaviour of some basic climate-related large-scale or global processes. The package gives students immediate access to up to 16 years of continuous global SST data, mainly from the Advanced Along-Track Scanning Radiometer, currently flying on ESA's Envisat satellite. The data are available and are presented in the form of monthly averages and spatial averaged to half-degree or one-sixth degree longitude-latitude grids. There are simple button-operated facilities for defining and calculating box-averages; producing time-series of such averages; defining and displaying transects and their evolution over time; and the examination anomalous behaviour by displaying the difference between observed values and values derived from climatological means. By using these facilities a student rapidly gains familiarity with such processes as annual variability, the El Nĩo effect, as well as major current systems n such as the Gulf Stream and other climatically important phenomena. In fact, the student is given immediate insights into the basic methods of examining geophysical data in a research context, without needing to acquire special analysis skills are go trough lengthy data retrieval and preparation procedures which are more generally required, as precursors to serious investigation, in the research laboratory. This software package, called the Leicester AAATSR Global Analyser (LAGA), is written in a well-known and widely used analysis language and the package can be run by using software that is readily available free-of-charge.

Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1, Introducing a Python Edition

NASA Astrophysics Data System (ADS)

Barron, Eric G.; Kaplan, G. H.; Bangert, J.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

2011-01-01

The Naval Observatory Vector Astrometry Software (NOVAS) is a source-code library that provides common astrometric quantities and transformations. NOVAS calculations are accurate at the sub-milliarcsecond level. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and, currently, mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to harness the object-oriented nature of the Python language, and will implement the ability to handle large quantities of objects or observers using the array functionality in NumPy (a third-party scientific package for Python). NOVAS 3.1 also adds a module to transform GCRS vectors to the ITRS; the ITRS to GCRS transformation was already provided in NOVAS 3.0. The module that corrects an ITRS vector for polar motion has been modified to undo that correction upon demand. In the C edition, the ephemeris-access functions have been revised for use on 64-bit systems and for improved performance in general. NOVAS, including documentation, is available from the USNO website (http://www.usno.navy.mil/USNO/astronomical-applications/software-products/novas).

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

USGS Publications Warehouse

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

2006-01-01

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

CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data.

PubMed

Zheng, Guangyong; Xu, Yaochen; Zhang, Xiujun; Liu, Zhi-Ping; Wang, Zhuo; Chen, Luonan; Zhu, Xin-Guang

2016-12-23

A gene regulatory network (GRN) represents interactions of genes inside a cell or tissue, in which vertexes and edges stand for genes and their regulatory interactions respectively. Reconstruction of gene regulatory networks, in particular, genome-scale networks, is essential for comparative exploration of different species and mechanistic investigation of biological processes. Currently, most of network inference methods are computationally intensive, which are usually effective for small-scale tasks (e.g., networks with a few hundred genes), but are difficult to construct GRNs at genome-scale. Here, we present a software package for gene regulatory network reconstruction at a genomic level, in which gene interaction is measured by the conditional mutual information measurement using a parallel computing framework (so the package is named CMIP). The package is a greatly improved implementation of our previous PCA-CMI algorithm. In CMIP, we provide not only an automatic threshold determination method but also an effective parallel computing framework for network inference. Performance tests on benchmark datasets show that the accuracy of CMIP is comparable to most current network inference methods. Moreover, running tests on synthetic datasets demonstrate that CMIP can handle large datasets especially genome-wide datasets within an acceptable time period. In addition, successful application on a real genomic dataset confirms its practical applicability of the package. This new software package provides a powerful tool for genomic network reconstruction to biological community. The software can be accessed at http://www.picb.ac.cn/CMIP/ .

Surface CHEMKIN (Version 4. 0): A Fortran package for analyzing heterogeneous chemical kinetics at a solid-surface---gas-phase interface

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

Coltrin, M.E.; Kee, R.J.; Rupley, F.M.

1991-07-01

Heterogeneous reaction at the interface between a solid surface and adjacent gas is central to many chemical processes. Our purpose for developing the software package SURFACE CHEMKIN was motivated by our need to understand the complex surface chemistry in chemical vapor deposition systems involving silicon, silicon nitride, and gallium arsenide. However, we have developed the approach and implemented the software in a general setting. Thus, we expect it will find use in such diverse applications as chemical vapor deposition, chemical etching, combustion of solids, and catalytic processes, and for a wide range of chemical systems. We believe that it providesmore » a powerful capability to help model, understand, and optimize important industrial and research chemical processes. The SURFACE CHEMKIN software is designed to work in conjunction with the CHEMKIN-2 software, which handles the chemical kinetics in the gas phase. It may also be used in conjunction with the Transport Property Package, which provides information about molecular diffusion. Thus, these three packages provide a foundation on which a user can build applications software to analyze gas-phase and heterogeneous chemistry in flowing systems. These packages should not be considered programs'' in the ordinary sense. That is, they are not designed to accept input, solve a particular problem, and report the answer. Instead, they are software tools intended to help a user work efficiently with large systems of chemical reactions and develop Fortran representations of systems of equations that define a particular problem. It is up the user to solve the problem and interpret the answer. 11 refs., 15 figs., 5 tabs.« less

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.

Flight simulation software at NASA Dryden Flight Research Center

NASA Technical Reports Server (NTRS)

Norlin, Ken A.

1995-01-01

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

The Ettention software package.

PubMed

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

2016-02-01

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

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

PubMed

Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

2017-06-05

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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.

Detection And Mapping (DAM) package. Volume 4A: Software System Manual, part 1

NASA Technical Reports Server (NTRS)

Schlosser, E. H.

1980-01-01

The package is an integrated set of manual procedures, computer programs, and graphic devices designed for efficient production of precisely registered and formatted maps from digital LANDSAT multispectral scanner (MSS) data. The software can be readily implemented on any Univac 1100 series computer with standard peripheral equipment. This version of the software includes predefined spectral limits for use in classifying and mapping surface water for LANDSAT-1, LANDSAT-2, and LANDSAT-3. Tape formats supported include X, AM, and PM.

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

ERIC Educational Resources Information Center

McConkie, George W.; And Others

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

Sigma 2 Graphic Display Software Program Description

NASA Technical Reports Server (NTRS)

Johnson, B. T.

1973-01-01

A general purpose, user oriented graphic support package was implemented. A comprehensive description of the two software components comprising this package is given: Display Librarian and Display Controller. These programs have been implemented in FORTRAN on the XDS Sigma 2 Computer Facility. This facility consists of an XDS Sigma 2 general purpose computer coupled to a Computek Display Terminal.

Textbook Software versus Professional Software: Which Is Better for Instructional Purposes?

ERIC Educational Resources Information Center

Snell, Meggan; Yatsenko, Olga

2002-01-01

Compares textbook software with professional packages such as Peachtree for teaching accounting, in terms of cost, availability, ease of teaching and learning, and applicability. Makes suggestions for choosing accounting software. (SK)

StreamThermal: A software package for calculating thermal metrics from stream temperature data

USGS Publications Warehouse

Tsang, Yin-Phan; Infante, Dana M.; Stewart, Jana S.; Wang, Lizhu; Tingly, Ralph; Thornbrugh, Darren; Cooper, Arthur; Wesley, Daniel

2016-01-01

Improving quality and better availability of continuous stream temperature data allows natural resource managers, particularly in fisheries, to understand associations between different characteristics of stream thermal regimes and stream fishes. However, there is no convenient tool to efficiently characterize multiple metrics reflecting stream thermal regimes with the increasing amount of data. This article describes a software program packaged as a library in R to facilitate this process. With this freely-available package, users will be able to quickly summarize metrics that describe five categories of stream thermal regimes: magnitude, variability, frequency, timing, and rate of change. The installation and usage instruction of this package, the definition of calculated thermal metrics, as well as the output format from the package are described, along with an application showing the utility for multiple metrics. We believe this package can be widely utilized by interested stakeholders and greatly assist more studies in fisheries.

A New Paradigm to Analyze Data Completeness of Patient Data.

PubMed

Nasir, Ayan; Gurupur, Varadraj; Liu, Xinliang

2016-08-03

There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data.

A New Paradigm to Analyze Data Completeness of Patient Data

PubMed Central

Nasir, Ayan; Liu, Xinliang

2016-01-01

Summary Background There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Objectives Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. Methods The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. Results The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. Conclusion DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data. PMID:27484918

RxGen General Optical Model Prescription Generator

NASA Technical Reports Server (NTRS)

Sigrist, Norbert

2012-01-01

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

Multiphysics Application Coupling Toolkit

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

Campbell, Michael T.

2013-12-02

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems;more » with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.« less

FLIMX: A Software Package to Determine and Analyze the Fluorescence Lifetime in Time-Resolved Fluorescence Data from the Human Eye.

PubMed

Klemm, Matthias; Schweitzer, Dietrich; Peters, Sven; Sauer, Lydia; Hammer, Martin; Haueisen, Jens

2015-01-01

Fluorescence lifetime imaging ophthalmoscopy (FLIO) is a new technique for measuring the in vivo autofluorescence intensity decays generated by endogenous fluorophores in the ocular fundus. Here, we present a software package called FLIM eXplorer (FLIMX) for analyzing FLIO data. Specifically, we introduce a new adaptive binning approach as an optimal tradeoff between the spatial resolution and the number of photons required per pixel. We also expand existing decay models (multi-exponential, stretched exponential, spectral global analysis, incomplete decay) to account for the layered structure of the eye and present a method to correct for the influence of the crystalline lens fluorescence on the retina fluorescence. Subsequently, the Holm-Bonferroni method is applied to FLIO measurements to allow for group comparisons between patients and controls on the basis of fluorescence lifetime parameters. The performance of the new approaches was evaluated in five experiments. Specifically, we evaluated static and adaptive binning in a diabetes mellitus patient, we compared the different decay models in a healthy volunteer and performed a group comparison between diabetes patients and controls. An overview of the visualization capabilities and a comparison of static and adaptive binning is shown for a patient with macular hole. FLIMX's applicability to fluorescence lifetime imaging microscopy is shown in the ganglion cell layer of a porcine retina sample, obtained by a laser scanning microscope using two-photon excitation.

Modifications of the U.S. Geological Survey modular, finite-difference, ground-water flow model to read and write geographic information system files

USGS Publications Warehouse

Orzol, Leonard L.; McGrath, Timothy S.

1992-01-01

This report documents modifications to the U.S. Geological Survey modular, three-dimensional, finite-difference, ground-water flow model, commonly called MODFLOW, so that it can read and write files used by a geographic information system (GIS). The modified model program is called MODFLOWARC. Simulation programs such as MODFLOW generally require large amounts of input data and produce large amounts of output data. Viewing data graphically, generating head contours, and creating or editing model data arrays such as hydraulic conductivity are examples of tasks that currently are performed either by the use of independent software packages or by tedious manual editing, manipulating, and transferring data. Programs such as GIS programs are commonly used to facilitate preparation of the model input data and analyze model output data; however, auxiliary programs are frequently required to translate data between programs. Data translations are required when different programs use different data formats. Thus, the user might use GIS techniques to create model input data, run a translation program to convert input data into a format compatible with the ground-water flow model, run the model, run a translation program to convert the model output into the correct format for GIS, and use GIS to display and analyze this output. MODFLOWARC, avoids the two translation steps and transfers data directly to and from the ground-water-flow model. This report documents the design and use of MODFLOWARC and includes instructions for data input/output of the Basic, Block-centered flow, River, Recharge, Well, Drain, Evapotranspiration, General-head boundary, and Streamflow-routing packages. The modification to MODFLOW and the Streamflow-Routing package was minimized. Flow charts and computer-program code describe the modifications to the original computer codes for each of these packages. Appendix A contains a discussion on the operation of MODFLOWARC using a sample problem.

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.

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.

A distributed version of the NASA Engine Performance Program

NASA Technical Reports Server (NTRS)

Cours, Jeffrey T.; Curlett, Brian P.

1993-01-01

Distributed NEPP, a version of the NASA Engine Performance Program, uses the original NEPP code but executes it in a distributed computer environment. Multiple workstations connected by a network increase the program's speed and, more importantly, the complexity of the cases it can handle in a reasonable time. Distributed NEPP uses the public domain software package, called Parallel Virtual Machine, allowing it to execute on clusters of machines containing many different architectures. It includes the capability to link with other computers, allowing them to process NEPP jobs in parallel. This paper discusses the design issues and granularity considerations that entered into programming Distributed NEPP and presents the results of timing runs.

Monte Carlo based statistical power analysis for mediation models: methods and software.

PubMed

Zhang, Zhiyong

2014-12-01

The existing literature on statistical power analysis for mediation models often assumes data normality and is based on a less powerful Sobel test instead of the more powerful bootstrap test. This study proposes to estimate statistical power to detect mediation effects on the basis of the bootstrap method through Monte Carlo simulation. Nonnormal data with excessive skewness and kurtosis are allowed in the proposed method. A free R package called bmem is developed to conduct the power analysis discussed in this study. Four examples, including a simple mediation model, a multiple-mediator model with a latent mediator, a multiple-group mediation model, and a longitudinal mediation model, are provided to illustrate the proposed method.

Automated data collection in single particle electron microscopy

PubMed Central

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

Defense AT and L. Volume 42, Number 1

DTIC Science & Technology

2013-02-01

Agnish The U.S. Army late last year began equipping brigade combat teams with its first package of radios, satellite systems, software applications...Army’s first package of radios, satellite systems, software applications, smartphone-like devices, and other network components that provide integrated... satellite communications, intelligence, mission command applications, and the integration of C4ISR equip- ment onto various vehicle platforms. This

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…

Software for Teaching about AIDS & Sex: A Critical Review of Products. A MicroSIFT Report.

ERIC Educational Resources Information Center

Weaver, Dave

This document contains critical reviews of 10 microcomputer software packages and two interactive videodisc products designed for use in teaching about Acquired Immune Deficiency Syndrome (AIDS) and sex at the secondary school level and above. Each package was reviewed by one or two secondary school health teachers and by a staff member from the…

User's manual for the VAX-Gerber link software package. Revision 1. 0

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

Isobe, G.W.

1985-10-01

This manual provides a user the information necessary to run the VAX-Gerber link software package. It is expected that the user already knows how to login to the VAX, and is familiar with the Gerber Photo Plotter. It is also highly desirable that the user be familiar with the full screen editor on the VAX, EDT.

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

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.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

Modular modeling system for building distributed hydrologic models with a user-friendly software package

NASA Astrophysics Data System (ADS)

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

2015-12-01

A software package developed to facilitate building distributed hydrologic models in a modular modeling system is presented. The software package provides a user-friendly graphical user interface that eases its practical use in water resources-related research and practice. The modular modeling system organizes the options available to users when assembling models according to the stages of hydrological cycle, such as potential evapotranspiration, soil moisture accounting, and snow/glacier melting processes. The software is intended to be a comprehensive tool that simplifies the task of developing, calibrating, validating, and using hydrologic models through the inclusion of intelligent automation to minimize user effort, and reduce opportunities for error. Processes so far automated include the definition of system boundaries (i.e., watershed delineation), climate and geographical input generation, and parameter calibration. Built-in post-processing toolkits greatly improve the functionality of the software as a decision support tool for water resources system management and planning. Example post-processing toolkits enable streamflow simulation at ungauged sites with predefined model parameters, and perform climate change risk assessment by means of the decision scaling approach. The software is validated through application to watersheds representing a variety of hydrologic regimes.

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

The Ocean Observatories Initiative: Data Acquisition Functions and Its Built-In Automated Python Modules

NASA Astrophysics Data System (ADS)

Smith, M. J.; Vardaro, M.; Crowley, M. F.; Glenn, S. M.; Schofield, O.; Belabbassi, L.; Garzio, L. M.; Knuth, F.; Fram, J. P.; Kerfoot, J.

2016-02-01

The Ocean Observatories Initiative (OOI), funded by the National Science Foundation, provides users with access to long-term datasets from a variety of oceanographic sensors. The Endurance Array in the Pacific Ocean consists of two separate lines off the coasts of Oregon and Washington. The Oregon line consists of 7 moorings, two cabled benthic experiment packages and 6 underwater gliders. The Washington line comprises 6 moorings and 6 gliders. Each mooring is outfitted with a variety of instrument packages. The raw data from these instruments are sent to shore via satellite communication and in some cases, via fiber optic cable. Raw data is then sent to the cyberinfrastructure (CI) group at Rutgers where it is aggregated, parsed into thousands of different data streams, and integrated into a software package called uFrame. The OOI CI delivers the data to the general public via a web interface that outputs data into commonly used scientific data file formats such as JSON, netCDF, and CSV. The Rutgers data management team has developed a series of command-line Python tools that streamline data acquisition in order to facilitate the QA/QC review process. The first step in the process is querying the uFrame database for a list of all available platforms. From this list, a user can choose a specific platform and automatically download all available datasets from the specified platform. The downloaded dataset is plotted using a generalized Python netcdf plotting routine that utilizes a data visualization toolbox called matplotlib. This routine loads each netCDF file separately and outputs plots by each available parameter. These Python tools have been uploaded to a Github repository that is openly available to help facilitate OOI data access and visualization.

Psyplot: Visualizing rectangular and triangular Climate Model Data with Python

NASA Astrophysics Data System (ADS)

Sommer, Philipp

2016-04-01

The development and use of climate models often requires the visualization of geo-referenced data. Creating visualizations should be fast, attractive, flexible, easily applicable and easily reproducible. There is a wide range of software tools available for visualizing raster data, but they often are inaccessible to many users (e.g. because they are difficult to use in a script or have low flexibility). In order to facilitate easy visualization of geo-referenced data, we developed a new framework called "psyplot," which can aid earth system scientists with their daily work. It is purely written in the programming language Python and primarily built upon the python packages matplotlib, cartopy and xray. The package can visualize data stored on the hard disk (e.g. NetCDF, GeoTIFF, any other file format supported by the xray package), or directly from the memory or Climate Data Operators (CDOs). Furthermore, data can be visualized on a rectangular grid (following or not following the CF Conventions) and on a triangular grid (following the CF or UGRID Conventions). Psyplot visualizes 2D scalar and vector fields, enabling the user to easily manage and format multiple plots at the same time, and to export the plots into all common picture formats and movies covered by the matplotlib package. The package can currently be used in an interactive python session or in python scripts, and will soon be developed for use with a graphical user interface (GUI). Finally, the psyplot framework enables flexible configuration, allows easy integration into other scripts that uses matplotlib, and provides a flexible foundation for further development.

Impact of genotyping errors on statistical power of association tests in genomic analyses: A case study

PubMed Central

Hou, Lin; Sun, Ning; Mane, Shrikant; Sayward, Fred; Rajeevan, Nallakkandi; Cheung, Kei-Hoi; Cho, Kelly; Pyarajan, Saiju; Aslan, Mihaela; Miller, Perry; Harvey, Philip D.; Gaziano, J. Michael; Concato, John; Zhao, Hongyu

2017-01-01

A key step in genomic studies is to assess high throughput measurements across millions of markers for each participant’s DNA, either using microarrays or sequencing techniques. Accurate genotype calling is essential for downstream statistical analysis of genotype-phenotype associations, and next generation sequencing (NGS) has recently become a more common approach in genomic studies. How the accuracy of variant calling in NGS-based studies affects downstream association analysis has not, however, been studied using empirical data in which both microarrays and NGS were available. In this article, we investigate the impact of variant calling errors on the statistical power to identify associations between single nucleotides and disease, and on associations between multiple rare variants and disease. Both differential and nondifferential genotyping errors are considered. Our results show that the power of burden tests for rare variants is strongly influenced by the specificity in variant calling, but is rather robust with regard to sensitivity. By using the variant calling accuracies estimated from a substudy of a Cooperative Studies Program project conducted by the Department of Veterans Affairs, we show that the power of association tests is mostly retained with commonly adopted variant calling pipelines. An R package, GWAS.PC, is provided to accommodate power analysis that takes account of genotyping errors (http://zhaocenter.org/software/). PMID:28019059

SEMModComp: An R Package for Calculating Likelihood Ratio Tests for Mean and Covariance Structure Models

ERIC Educational Resources Information Center

Levy, Roy

2010-01-01

SEMModComp, a software package for conducting likelihood ratio tests for mean and covariance structure modeling is described. The package is written in R and freely available for download or on request.

The design, deployment, and testing of kriging models in GEOframe with SIK-0.9.8

NASA Astrophysics Data System (ADS)

Bancheri, Marialaura; Serafin, Francesco; Bottazzi, Michele; Abera, Wuletawu; Formetta, Giuseppe; Rigon, Riccardo

2018-06-01

This work presents a software package for the interpolation of climatological variables, such as temperature and precipitation, using kriging techniques. The purposes of the paper are (1) to present a geostatistical software that is easy to use and easy to plug in to a hydrological model; (2) to provide a practical example of an accurately designed software from the perspective of reproducible research; and (3) to demonstrate the goodness of the results of the software and so have a reliable alternative to other, more traditional tools. A total of 11 types of theoretical semivariograms and four types of kriging were implemented and gathered into Object Modeling System-compliant components. The package provides real-time optimization for semivariogram and kriging parameters. The software was tested using a year's worth of hourly temperature readings and a rain storm event (11 h) recorded in 2008 and retrieved from 97 meteorological stations in the Isarco River basin, Italy. For both the variables, good interpolation results were obtained and then compared to the results from the R package gstat.

Advanced Software Development Workstation Project

NASA Technical Reports Server (NTRS)

Lee, Daniel

1989-01-01

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

Identification of triacylglycerol using automated annotation of high resolution multistage mass spectral trees.

PubMed

Wang, Xiupin; Peng, Qingzhi; Li, Peiwu; Zhang, Qi; Ding, Xiaoxia; Zhang, Wen; Zhang, Liangxiao

2016-10-12

High complexity of identification for non-target triacylglycerols (TAGs) is a major challenge in lipidomics analysis. To identify non-target TAGs, a powerful tool named accurate MS(n) spectrometry generating so-called ion trees is used. In this paper, we presented a technique for efficient structural elucidation of TAGs on MS(n) spectral trees produced by LTQ Orbitrap MS(n), which was implemented as an open source software package, or TIT. The TIT software was used to support automatic annotation of non-target TAGs on MS(n) ion trees from a self-built fragment ion database. This database includes 19108 simulate TAG molecules from a random combination of fatty acids and corresponding 500582 self-built multistage fragment ions (MS ≤ 3). Our software can identify TAGs using a "stage-by-stage elimination" strategy. By utilizing the MS(1) accurate mass and referenced RKMD, the TIT software can discriminate unique elemental composition candidates. The regiospecific isomers of fatty acyl chains will be distinguished using MS(2) and MS(3) fragment spectra. We applied the algorithm to the selection of 45 TAG standards and demonstrated that the molecular ions could be 100% correctly assigned. Therefore, the TIT software could be applied to TAG identification in complex biological samples such as mouse plasma extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

MAMA User Guide v2.0.1

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

Gaschen, Brian Keith; Bloch, Jeffrey Joseph; Porter, Reid

Morphological signatures of bulk SNM materials have significant promise, but these potential signatures are not fully utilized. This document describes software tools, collectively called the MAMA (Morphological Analysis for Material Attribution) software that can help provide robust and accurate quantification of morphological features in bulk material microscopy images (Optical, SEM). Although many of the specific tools are not unique to Mama, the software package has been designed specifically for nuclear material morphological analysis, and is at a point where it can be easily adapted (by Los Alamos or by collaborators) in response to new, different, or changing forensics needs. Themore » current release of the MAMA software only includes the image quantification, descriptions, and annotation functionality. Only limited information on a sample, its pedigree, and its chemistry are recorded inside this part of the software. This was decision based on initial feedback and the fact that there are several analytical chemistry databases being developed within the community. Currently MAMA is a standalone program that can export quantification results in a basic text format that can be imported into other programs such as Excel and Access. There is also a basic report generating feature that produces HTML formatted pages of the same information. We will be working with collaborators to provide better integration of MAMA into their particular systems, databases and workflows.« less

Prowess - A Software Model for the Ooty Wide Field Array

NASA Astrophysics Data System (ADS)

Marthi, Visweshwar Ram

2017-03-01

One of the scientific objectives of the Ooty Wide Field Array (OWFA) is to observe the redshifted H i emission from z ˜ 3.35. Although predictions spell out optimistic outcomes in reasonable integration times, these studies were based purely on analytical assumptions, without accounting for limiting systematics. A software model for OWFA has been developed with a view to understanding the instrument-induced systematics, by describing a complete software model for the instrument. This model has been implemented through a suite of programs, together called Prowess, which has been conceived with the dual role of an emulator as well as observatory data analysis software. The programming philosophy followed in building Prowess enables a general user to define an own set of functions and add new functionality. This paper describes a co-ordinate system suitable for OWFA in which the baselines are defined. The foregrounds are simulated from their angular power spectra. The visibilities are then computed from the foregrounds. These visibilities are then used for further processing, such as calibration and power spectrum estimation. The package allows for rich visualization features in multiple output formats in an interactive fashion, giving the user an intuitive feel for the data. Prowess has been extensively used for numerical predictions of the foregrounds for the OWFA H i experiment.

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.

ELF/VLF/LF Radio Propagation and Systems Aspects (La Propagation des Ondes Radio ELF/VLF/LF et les Aspects Systemes)

DTIC Science & Technology

1993-05-01

limitation of the software package would not allow DATE/I’ME FREQUENCY (kHz) the program to run over 2359 to 0001 UT. This was 18.1 19.0 21.4 24.0...Capability (LWPC), software package devel- oped at NOSC (FERGUSON et al 1989) and adapted by us to the Macintosh personal computer. We find that this... software works very well. Our investigations are to I evaluate and devise geophysical models to be used with . LWPC in assessing VLF communications and

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

PubMed Central

Höhna, Sebastian; Landis, Michael J.

2016-01-01

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com. [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.] PMID:27235697

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

PubMed

Höhna, Sebastian; Landis, Michael J; Heath, Tracy A; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R; Huelsenbeck, John P; Ronquist, Fredrik

2016-07-01

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

The GRIDView Visualization Package

NASA Astrophysics Data System (ADS)

Kent, B. R.

2011-07-01

Large three-dimensional data cubes, catalogs, and spectral line archives are increasingly important elements of the data discovery process in astronomy. Visualization of large data volumes is of vital importance for the success of large spectral line surveys. Examples of data reduction utilizing the GRIDView software package are shown. The package allows users to manipulate data cubes, extract spectral profiles, and measure line properties. The package and included graphical user interfaces (GUIs) are designed with pipeline infrastructure in mind. The software has been used with great success analyzing spectral line and continuum data sets obtained from large radio survey collaborations. The tools are also important for multi-wavelength cross-correlation studies and incorporate Virtual Observatory client applications for overlaying database information in real time as cubes are examined by users.

The Planck Legacy Archive

NASA Astrophysics Data System (ADS)

Dupac, X.; Arviset, C.; Fernandez Barreiro, M.; Lopez-Caniego, M.; Tauber, J.

2015-12-01

The Planck Collaboration has released in 2015 their second major dataset through the Planck Legacy Archive (PLA). It includes cosmological, Extragalactic and Galactic science data in temperature (intensity) and polarization. Full-sky maps are provided with unprecedented angular resolution and sensitivity, together with a large number of ancillary maps, catalogues (generic, SZ clusters and Galactic cold clumps), time-ordered data and other information. The extensive cosmological likelihood package allows cosmologists to fully explore the plausible parameters of the Universe. A new web-based PLA user interface is made public since Dec. 2014, allowing easier and faster access to all Planck data, and replacing the previous Java-based software. Numerous additional improvements to the PLA are also being developed through the so-called PLA Added-Value Interface, making use of an external contract with the Planetek Hellas and Expert Analytics software companies. This will allow users to process time-ordered data into sky maps, separate astrophysical components in existing maps, simulate the microwave and infrared sky through the Planck Sky Model, and use a number of other functionalities.

jmzTab: a java interface to the mzTab data standard.

PubMed

Xu, Qing-Wei; Griss, Johannes; Wang, Rui; Jones, Andrew R; Hermjakob, Henning; Vizcaíno, Juan Antonio

2014-06-01

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches. We here present an open-source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files. In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com. © 2014 The Authors PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design and Implementation of a C++ Software Package to scan for and parse Tsunami Messages issued by the Tsunami Warning Centers for Operational use at the Pacific Tsunami Warning Center

NASA Astrophysics Data System (ADS)

Sardina, V.

2012-12-01

The US Tsunami Warning Centers (TWCs) have traditionally generated their tsunami message products primarily as blocks of text then tagged with headers that identify them on each particular communications' (comms) circuit. Each warning center has a primary area of responsibility (AOR) within which it has an authoritative role regarding parameters such as earthquake location and magnitude. This means that when a major tsunamigenic event occurs the other warning centers need to quickly access the earthquake parameters issued by the authoritative warning center before issuing their message products intended for customers in their own AOR. Thus, within the operational context of the TWCs the scientists on duty have an operational need to access the information contained in the message products issued by other warning centers as quickly as possible. As a solution to this operational problem we designed and implemented a C++ software package that allows scanning for and parsing the entire suite of tsunami message products issued by the Pacific Tsunami Warning Center (PTWC), the West Coast and Alaska Tsunami Warning Center (WCATWC), and the Japan Meteorological Agency (JMA). The scanning and parsing classes composing the resulting C++ software package allow parsing both non-official message products(observatory messages) routinely issued by the TWCs, and all official tsunami message products such as tsunami advisories, watches, and warnings. This software package currently allows scientists on duty at the PTWC to automatically retrieve the parameters contained in tsunami messages issued by WCATWC, JMA, or PTWC itself. Extension of the capabilities of the classes composing the software package would make it possible to generate XML and CAP compliant versions of the TWCs' message products until new messaging software natively adds this capabilities. Customers who receive the TWCs' tsunami message products could also use the package to automatically retrieve information from messages sent via any text-based communications' circuit currently used by the TWCs to disseminate their tsunami message products.

21 CFR 801.50 - Labeling requirements for stand-alone software.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Labeling requirements for stand-alone software....50 Labeling requirements for stand-alone software. (a) Stand-alone software that is not distributed... in packaged form, stand-alone software regulated as a medical device must provide its unique device...

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.

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.

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

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.

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

EPA Science Inventory

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

Common Ada (tradename) Missile Package (CAMP) Project. Missile Software Parts. Volume 8. Detail Design Document

DTIC Science & Technology

1988-03-01

PACKAGE BODY ) TLCSC P661 (CATALOG #P106-0) This package contains the CAMP parts required to do the vaypoint steering portion of navigation. The...3.3.4.1.6 PROCESSING The following describes the processing performed by this part: package body WaypointSteering is package body ...Steering_Vector_Operations is separate; package body Steering_Vector_Operations_with_Arcsin is separate; procedure Compute Turn_Angle_and Direction (UnitNormal C

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.

An image-processing software package: UU and Fig for optical metrology applications

NASA Astrophysics Data System (ADS)

Chen, Lujie

2013-06-01

Modern optical metrology applications are largely supported by computational methods, such as phase shifting [1], Fourier Transform [2], digital image correlation [3], camera calibration [4], etc, in which image processing is a critical and indispensable component. While it is not too difficult to obtain a wide variety of image-processing programs from the internet; few are catered for the relatively special area of optical metrology. This paper introduces an image-processing software package: UU (data processing) and Fig (data rendering) that incorporates many useful functions to process optical metrological data. The cross-platform programs UU and Fig are developed based on wxWidgets. At the time of writing, it has been tested on Windows, Linux and Mac OS. The userinterface is designed to offer precise control of the underline processing procedures in a scientific manner. The data input/output mechanism is designed to accommodate diverse file formats and to facilitate the interaction with other independent programs. In terms of robustness, although the software was initially developed for personal use, it is comparably stable and accurate to most of the commercial software of similar nature. In addition to functions for optical metrology, the software package has a rich collection of useful tools in the following areas: real-time image streaming from USB and GigE cameras, computational geometry, computer vision, fitting of data, 3D image processing, vector image processing, precision device control (rotary stage, PZT stage, etc), point cloud to surface reconstruction, volume rendering, batch processing, etc. The software package is currently used in a number of universities for teaching and research.

Validating module network learning algorithms using simulated data.

PubMed

Michoel, Tom; Maere, Steven; Bonnet, Eric; Joshi, Anagha; Saeys, Yvan; Van den Bulcke, Tim; Van Leemput, Koenraad; van Remortel, Piet; Kuiper, Martin; Marchal, Kathleen; Van de Peer, Yves

2007-05-03

In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Despite the demonstrated success of such algorithms in uncovering biologically relevant regulatory relations, further developments in the area are hampered by a lack of tools to compare the performance of alternative module network learning strategies. Here, we demonstrate the use of the synthetic data generator SynTReN for the purpose of testing and comparing module network learning algorithms. We introduce a software package for learning module networks, called LeMoNe, which incorporates a novel strategy for learning regulatory programs. Novelties include the use of a bottom-up Bayesian hierarchical clustering to construct the regulatory programs, and the use of a conditional entropy measure to assign regulators to the regulation program nodes. Using SynTReN data, we test the performance of LeMoNe in a completely controlled situation and assess the effect of the methodological changes we made with respect to an existing software package, namely Genomica. Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance. Overall, application of Genomica and LeMoNe to simulated data sets gave comparable results. However, LeMoNe offers some advantages, one of them being that the learning process is considerably faster for larger data sets. Additionally, we show that the location of the regulators in the LeMoNe regulation programs and their conditional entropy may be used to prioritize regulators for functional validation, and that the combination of the bottom-up clustering strategy with the conditional entropy-based assignment of regulators improves the handling of missing or hidden regulators. We show that data simulators such as SynTReN are very well suited for the purpose of developing, testing and improving module network algorithms. We used SynTReN data to develop and test an alternative module network learning strategy, which is incorporated in the software package LeMoNe, and we provide evidence that this alternative strategy has several advantages with respect to existing methods.

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

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.

PubMed

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-05-28

Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4-15.9 times faster, while Unphased jobs performed 1.1-18.6 times faster compared to the accumulated computation duration. Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance.

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

PubMed Central

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-01-01

Background Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Results Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4–15.9 times faster, while Unphased jobs performed 1.1–18.6 times faster compared to the accumulated computation duration. Conclusion Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance. PMID:18541045

The application of virtual reality systems as a support of digital manufacturing and logistics

NASA Astrophysics Data System (ADS)

Golda, G.; Kampa, A.; Paprocka, I.

2016-08-01

Modern trends in development of computer aided techniques are heading toward the integration of design competitive products and so-called "digital manufacturing and logistics", supported by computer simulation software. All phases of product lifecycle: starting from design of a new product, through planning and control of manufacturing, assembly, internal logistics and repairs, quality control, distribution to customers and after-sale service, up to its recycling or utilization should be aided and managed by advanced packages of product lifecycle management software. Important problems for providing the efficient flow of materials in supply chain management of whole product lifecycle, using computer simulation will be described on that paper. Authors will pay attention to the processes of acquiring relevant information and correct data, necessary for virtual modeling and computer simulation of integrated manufacturing and logistics systems. The article describes possibilities of use an applications of virtual reality software for modeling and simulation the production and logistics processes in enterprise in different aspects of product lifecycle management. The authors demonstrate effective method of creating computer simulations for digital manufacturing and logistics and show modeled and programmed examples and solutions. They pay attention to development trends and show options of the applications that go beyond enterprise.

Informed-Proteomics: open-source software package for top-down proteomics

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

Park, Jungkap; Piehowski, Paul D.; Wilkins, Christopher

Top-down proteomics involves the analysis of intact proteins. This approach is very attractive as it allows for analyzing proteins in their endogenous form without proteolysis, preserving valuable information about post-translation modifications, isoforms, proteolytic processing or their combinations collectively called proteoforms. Moreover, the quality of the top-down LC-MS/MS datasets is rapidly increasing due to advances in the liquid chromatography and mass spectrometry instrumentation and sample processing protocols. However, the top-down mass spectra are substantially more complex compare to the more conventional bottom-up data. To take full advantage of the increasing quality of the top-down LC-MS/MS datasets there is an urgent needmore » to develop algorithms and software tools for confident proteoform identification and quantification. In this study we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer. The presented tool along with several other popular tools were evaluated using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.« less

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.

Courseware Review.

ERIC Educational Resources Information Center

Risley, John, Ed.

1988-01-01

Compares the features of the sonic rangers available from HRM Software, MICROMEASUREMENTS, NAGAWTIS Software Research, and PASCO Scientific for demonstrations and experiments in mechanics. Presents the advantages of the sonic rangers and the typical graphics displayed by each software package. (YP)

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.

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.

Attributes and Behaviors of Performance-Centered Systems.

ERIC Educational Resources Information Center

Gery, Gloria

1995-01-01

Examines attributes, characteristics, and behaviors of performance-centered software packages that are emerging in the consumer software marketplace and compares them with large-scale systems software being designed by internal information systems staffs and vendors of large-scale software designed for financial, manufacturing, processing, and…

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

MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data.

PubMed

Yavorska, Olena O; Burgess, Stephen

2017-12-01

MendelianRandomization is a software package for the R open-source software environment that performs Mendelian randomization analyses using summarized data. The core functionality is to implement the inverse-variance weighted, MR-Egger and weighted median methods for multiple genetic variants. Several options are available to the user, such as the use of robust regression, fixed- or random-effects models and the penalization of weights for genetic variants with heterogeneous causal estimates. Extensions to these methods, such as allowing for variants to be correlated, can be chosen if appropriate. Graphical commands allow summarized data to be displayed in an interactive graph, or the plotting of causal estimates from multiple methods, for comparison. Although the main method of data entry is directly by the user, there is also an option for allowing summarized data to be incorporated from the PhenoScanner database of genotype-phenotype associations. We hope to develop this feature in future versions of the package. The R software environment is available for download from [https://www.r-project.org/]. The MendelianRandomization package can be downloaded from the Comprehensive R Archive Network (CRAN) within R, or directly from [https://cran.r-project.org/web/packages/MendelianRandomization/]. Both R and the MendelianRandomization package are released under GNU General Public Licenses (GPL-2|GPL-3). © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

The MeqTrees software system and its use for third-generation calibration of radio interferometers

NASA Astrophysics Data System (ADS)

Noordam, J. E.; Smirnov, O. M.

2010-12-01

Context. The formulation of the radio interferometer measurement equation (RIME) for a generic radio telescope by Hamaker et al. has provided us with an elegant mathematical apparatus for better understanding, simulation and calibration of existing and future instruments. The calibration of the new radio telescopes (LOFAR, SKA) would be unthinkable without the RIME formalism, and new software to exploit it. Aims: The MeqTrees software system is designed to implement numerical models, and to solve for arbitrary subsets of their parameters. It may be applied to many problems, but was originally geared towards implementing Measurement Equations in radio astronomy for the purposes of simulation and calibration. The technical goal of MeqTrees is to provide a tool for rapid implementation of such models, while offering performance comparable to hand-written code. We are also pursuing the wider goal of increasing the rate of evolution of radio astronomical software, by offering a tool that facilitates rapid experimentation, and exchange of ideas (and scripts). Methods: MeqTrees is implemented as a Python-based front-end called the meqbrowser, and an efficient (C++-based) computational back-end called the meqserver. Numerical models are defined on the front-end via a Python-based Tree Definition Language (TDL), then rapidly executed on the back-end. The use of TDL facilitates an extremely short turn-around time (hours rather than weeks or months) for experimentation with new ideas. This is also helped by unprecedented visualization capabilities for all final and intermediate results. A flexible data model and a number of important optimizations in the back-end ensures that the numerical performance is comparable to that of hand-written code. Results: MeqTrees is already widely used as the simulation tool for new instruments (LOFAR, SKA) and technologies (focal plane arrays). It has demonstrated that it can achieve a noise-limited dynamic range in excess of a million, on WSRT data. It is the only package that is specifically designed to handle what we propose to call third-generation calibration (3GC), which is needed for the new generation of giant radio telescopes, but can also improve the calibration of existing instruments.

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

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

MANN, F.M.

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

An 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

Advanced Simulation in Undergraduate Pilot Training: Automatic Instructional System

DTIC Science & Technology

1975-10-01

an addressable reel-to--reel audio tape recorder, a random access audio memory drum , and an interactive software package which permits the user to...audio memory drum , and an interactive software package which permits the user to develop preptogtahmed exercises. Figure 2 illustrates overall...Data Recprding System consists of two elements; an overlay program which performs the real-time sampling of specified variables and stores data to disc

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus.

PubMed

Condon, David E; Tran, Phu V; Lien, Yu-Chin; Schug, Jonathan; Georgieff, Michael K; Simmons, Rebecca A; Won, Kyoung-Jae

2018-02-05

Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.

On Bayesian methods of exploring qualitative interactions for targeted treatment.

PubMed

Chen, Wei; Ghosh, Debashis; Raghunathan, Trivellore E; Norkin, Maxim; Sargent, Daniel J; Bepler, Gerold

2012-12-10

Providing personalized treatments designed to maximize benefits and minimizing harms is of tremendous current medical interest. One problem in this area is the evaluation of the interaction between the treatment and other predictor variables. Treatment effects in subgroups having the same direction but different magnitudes are called quantitative interactions, whereas those having opposite directions in subgroups are called qualitative interactions (QIs). Identifying QIs is challenging because they are rare and usually unknown among many potential biomarkers. Meanwhile, subgroup analysis reduces the power of hypothesis testing and multiple subgroup analyses inflate the type I error rate. We propose a new Bayesian approach to search for QI in a multiple regression setting with adaptive decision rules. We consider various regression models for the outcome. We illustrate this method in two examples of phase III clinical trials. The algorithm is straightforward and easy to implement using existing software packages. We provide a sample code in Appendix A. Copyright © 2012 John Wiley & Sons, Ltd.

Investigation of the effects of aeroelastic deformations on the radar cross section of aircraft

NASA Astrophysics Data System (ADS)

McKenzie, Samuel D.

1991-12-01

The effects of aeroelastic deformations on the radar cross section (RCS) of a T-38 trainer jet and a C-5A transport aircraft are examined and characterized. Realistic representations of structural wing deformations are obtained from a mechanical/computer aided design software package called NASTRAN. NASTRAN is used to evaluate the structural parameters of the aircraft as well as the restraints and loads associated with realistic flight conditions. Geometries for both the non-deformed and deformed airframes are obtained from the NASTRAN models and translated into RCS models. The RCS is analyzed using a numerical modeling code called the Radar Cross Section - Basic Scattering Code, version 2 which was developed at the Ohio State University and is based on the uniform geometric theory of diffraction. The code is used to analyze the effects of aeroelastic deformations on the RCS of the aircraft by comparing the computed RCS representing the deformed airframe to that of the non-deformed airframe and characterizing the differences between them.

AXAF user interfaces for heterogeneous analysis environments

NASA Technical Reports Server (NTRS)

Mandel, Eric; Roll, John; Ackerman, Mark S.

1992-01-01

The AXAF Science Center (ASC) will develop software to support all facets of data center activities and user research for the AXAF X-ray Observatory, scheduled for launch in 1999. The goal is to provide astronomers with the ability to utilize heterogeneous data analysis packages, that is, to allow astronomers to pick the best packages for doing their scientific analysis. For example, ASC software will be based on IRAF, but non-IRAF programs will be incorporated into the data system where appropriate. Additionally, it is desired to allow AXAF users to mix ASC software with their own local software. The need to support heterogeneous analysis environments is not special to the AXAF project, and therefore finding mechanisms for coordinating heterogeneous programs is an important problem for astronomical software today. The approach to solving this problem has been to develop two interfaces that allow the scientific user to run heterogeneous programs together. The first is an IRAF-compatible parameter interface that provides non-IRAF programs with IRAF's parameter handling capabilities. Included in the interface is an application programming interface to manipulate parameters from within programs, and also a set of host programs to manipulate parameters at the command line or from within scripts. The parameter interface has been implemented to support parameter storage formats other than IRAF parameter files, allowing one, for example, to access parameters that are stored in data bases. An X Windows graphical user interface called 'agcl' has been developed, layered on top of the IRAF-compatible parameter interface, that provides a standard graphical mechanism for interacting with IRAF and non-IRAF programs. Users can edit parameters and run programs for both non-IRAF programs and IRAF tasks. The agcl interface allows one to communicate with any command line environment in a transparent manner and without any changes to the original environment. For example, the authors routinely layer the GUI on top of IRAF, ksh, SMongo, and IDL. The agcl, based on the facilities of a system called Answer Garden, also has sophisticated support for examining documentation and help files, asking questions of experts, and developing a knowledge base of frequently required information. Thus, the GUI becomes a total environment for running programs, accessing information, examining documents, and finding human assistance. Because the agcl can communicate with any command-line environment, most projects can make use of it easily. New applications are continually being found for these interfaces. It is the authors' intention to evolve the GUI and its underlying parameter interface in response to these needs - from users as well as developers - throughout the astronomy community. This presentation describes the capabilities and technology of the above user interface mechanisms and tools. It also discusses the design philosophies guiding the work, as well as hopes for the future.

Evaluation of Agricultural Accounting Software. Improved Decision Making. Third Edition.

ERIC Educational Resources Information Center

Lovell, Ashley C., Comp.

Following a discussion of the evaluation criteria for choosing accounting software, this guide contains reviews of 27 accounting software programs that could be used by farm or ranch business managers. The information in the reviews was provided by the software vendors and covers the following points for each software package: general features,…

Sustaining Software-Intensive Systems

DTIC Science & Technology

2006-05-01

2.2 Multi- Service Operational Test and Evaluation .......................................4 2.3 Stable Software Baseline...or equivalent document • completed Multi- Service Operational Test and Evaluation (MOT&E) for the potential production software package (or OT&E if...not multi- service ) • stable software production baseline • complete and current software documentation • Authority to Operate (ATO) for an

Nuclear Data Online Services at Peking University

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

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

2005-05-24

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

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

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

2005-05-01

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

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

tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics.

PubMed

Becker, Alexander D; Grenfell, Bryan T

2017-01-01

tsiR is an open source software package implemented in the R programming language designed to analyze infectious disease time-series data. The software extends a well-studied and widely-applied algorithm, the time-series Susceptible-Infected-Recovered (TSIR) model, to infer parameters from incidence data, such as contact seasonality, and to forward simulate the underlying mechanistic model. The tsiR package aggregates a number of different fitting features previously described in the literature in a user-friendly way, providing support for their broader adoption in infectious disease research. Also included in tsiR are a number of diagnostic tools to assess the fit of the TSIR model. This package should be useful for researchers analyzing incidence data for fully-immunizing infectious diseases.

Aspects on Transfer of Aided - Design Files

NASA Astrophysics Data System (ADS)

Goanta, A. M.; Anghelache, D. G.

2016-08-01

At this stage of development of hardware and software, each company that makes design software packages has a certain type of file created and customized in time to distinguish that company from its competitors. Thus today are widely known the DWG files belonging AutoCAD, IPT / IAM belonging to Inventor, PAR / ASM of Solid Edge's, PRT from the NX and so on. Behind every type of file there is a mathematical model which is common to more types of files. A specific aspect of the computer -aided design is that all softwares are working with both individual parts and assemblies, but their approach is different in that some use the same type of file both for each part and for the whole (PRT ), while others use different types of files (IPT / IAM, PAR / ASM, etc.). Another aspect of the computer -aided design is to transfer files between different companies which use different software packages or even the same software package but in different versions. Each of these situations generates distinct issues. Thus, to solve the partial reading by a project different from the native one, transfer files of STEP and IGES type are used

7 CFR 1944.52 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... subpart L of part 1940 of this chapter. Complete application package (hereafter called package). The package submitted to the appropriate FmHA or its successor agency under Public Law 103-354 office which is... the Administrator that equals the customary and reasonable costs incurred in preparing a package for a...

7 CFR 1944.52 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... subpart L of part 1940 of this chapter. Complete application package (hereafter called package). The package submitted to the appropriate FmHA or its successor agency under Public Law 103-354 office which is... the Administrator that equals the customary and reasonable costs incurred in preparing a package for a...

7 CFR 1944.52 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... subpart L of part 1940 of this chapter. Complete application package (hereafter called package). The package submitted to the appropriate FmHA or its successor agency under Public Law 103-354 office which is... the Administrator that equals the customary and reasonable costs incurred in preparing a package for a...

7 CFR 1944.52 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... subpart L of part 1940 of this chapter. Complete application package (hereafter called package). The package submitted to the appropriate FmHA or its successor agency under Public Law 103-354 office which is... the Administrator that equals the customary and reasonable costs incurred in preparing a package for a...

7 CFR 1944.52 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... subpart L of part 1940 of this chapter. Complete application package (hereafter called package). The package submitted to the appropriate FmHA or its successor agency under Public Law 103-354 office which is... the Administrator that equals the customary and reasonable costs incurred in preparing a package for a...

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Ghysels, Pieter; Li, Xiaoye S.; Rouet, Francois -Henry

Here, we present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which have low-rank off-diagonal blocks, to approximate the frontal matrices. For HSS matrix construction, a randomized sampling algorithm is used together with interpolative decompositions. The combination of the randomized compression with a fast ULV HSS factoriz ation leads to a solver with lower computational complexity than the standard multifrontal method for many applications, resulting in speedups up to 7 fold for problems in our test suite.more » The implementation targets many-core systems by using task parallelism with dynamic runtime scheduling. Numerical experiments show performance improvements over state-of-the-art sparse direct solvers. The implementation achieves high performance and good scalability on a range of modern shared memory parallel systems, including the Intel Xeon Phi (MIC). The code is part of a software package called STRUMPACK - STRUctured Matrices PACKage, which also has a distributed memory component for dense rank-structured matrices.« less

An Efficient Multicore Implementation of a Novel HSS-Structured Multifrontal Solver Using Randomized Sampling

DOE PAGES

Ghysels, Pieter; Li, Xiaoye S.; Rouet, Francois -Henry; ...

2016-10-27

Here, we present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which have low-rank off-diagonal blocks, to approximate the frontal matrices. For HSS matrix construction, a randomized sampling algorithm is used together with interpolative decompositions. The combination of the randomized compression with a fast ULV HSS factoriz ation leads to a solver with lower computational complexity than the standard multifrontal method for many applications, resulting in speedups up to 7 fold for problems in our test suite.more » The implementation targets many-core systems by using task parallelism with dynamic runtime scheduling. Numerical experiments show performance improvements over state-of-the-art sparse direct solvers. The implementation achieves high performance and good scalability on a range of modern shared memory parallel systems, including the Intel Xeon Phi (MIC). The code is part of a software package called STRUMPACK - STRUctured Matrices PACKage, which also has a distributed memory component for dense rank-structured matrices.« less

Identification of pathogen genomic variants through an integrated pipeline

PubMed Central

2014-01-01

Background Whole-genome sequencing represents a powerful experimental tool for pathogen research. We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for finding single nucleotide and copy number variants as well as recombination events. Results We have validated our pipeline using four sets of Plasmodium falciparum drug resistant data containing 26 clones from 3D7 and Dd2 background strains, identifying an average of 11 single nucleotide variants per clone. We also identify 8 copy number variants with contributions to resistance, and report for the first time that all analyzed amplification events are in tandem. Conclusions The Platypus pipeline provides malaria researchers with a powerful tool to analyze short read sequencing data. It provides an accurate way to detect SNVs using known software packages, and a novel methodology for detection of CNVs, though it does not currently support detection of small indels. We have validated that the pipeline detects known SNVs in a variety of samples while filtering out spurious data. We bundle the methods into a freely available package. PMID:24589256

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

PubMed

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

2015-07-15

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

Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

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

ERIC Educational Resources Information Center

Evermann, Joerg

2010-01-01

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

LANZ: Software solving the large sparse symmetric generalized eigenproblem

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1990-01-01

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

Weaves as an Interconnection Fabric for ASIM's and Nanosatellites

NASA Technical Reports Server (NTRS)

Gorlick, Michael M.

1995-01-01

Many of the micromachines under consideration require computer support, indeed, one of the appeals of this technology is the ability to intermix mechanical, optical, analog, and digital devices on the same substrate. The amount of computer power is rarely an issue, the sticking point is the complexity of the software required to make effective use of these devices. Micromachines are the nano-technologist's equivalent of 'golden screws'. In other words, they will be piece parts in larger assemblages. For example, a nano-satellite may be composed of stacked silicon wafers where each wafer contains hundreds to thousands of micromachines, digital controllers, general purpose computers, memories, and high-speed bus interconnects. Comparatively few of these devices will be custom designed, most will be stock parts selected from libraries and catalogs. The novelty will lie in the interconnections. For example, a digital accelerometer may be a component part in an adaptive suspension, a monitoring element embedded in the wrapper of a package, or a portion of the smart skin of a launch vehicle. In each case, this device must inter-operate with other devices and probes for the purposes of command, control, and communication. We propose a software technology called 'weaves' that will permit large collections of micromachines and their attendant computers to freely intercommunicate while preserving modularity, transparency, and flexibility. Weaves are composed of networks of communicating software components. The network, and the components comprising it, may be changed even while the software, and the devices it controls, are executing. This unusual degree of software plasticity permits micromachines to dynamically adapt the software to changing conditions and allows system engineers to rapidly and inexpensively develop special purpose software by assembling stock software components in custom configurations.

Evidence for soft bounds in Ubuntu package sizes and mammalian body masses.

PubMed

Gherardi, Marco; Mandrà, Salvatore; Bassetti, Bruno; Cosentino Lagomarsino, Marco

2013-12-24

The development of a complex system depends on the self-coordinated action of a large number of agents, often determining unexpected global behavior. The case of software evolution has great practical importance: knowledge of what is to be considered atypical can guide developers in recognizing and reacting to abnormal behavior. Although the initial framework of a theory of software exists, the current theoretical achievements do not fully capture existing quantitative data or predict future trends. Here we show that two elementary laws describe the evolution of package sizes in a Linux-based operating system: first, relative changes in size follow a random walk with non-Gaussian jumps; second, each size change is bounded by a limit that is dependent on the starting size, an intriguing behavior that we call "soft bound." Our approach is based on data analysis and on a simple theoretical model, which is able to reproduce empirical details without relying on any adjustable parameter and generates definite predictions. The same analysis allows us to formulate and support the hypothesis that a similar mechanism is shaping the distribution of mammalian body sizes, via size-dependent constraints during cladogenesis. Whereas generally accepted approaches struggle to reproduce the large-mass shoulder displayed by the distribution of extant mammalian species, this is a natural consequence of the softly bounded nature of the process. Additionally, the hypothesis that this model is valid has the relevant implication that, contrary to a common assumption, mammalian masses are still evolving, albeit very slowly.

FLIMX: A Software Package to Determine and Analyze the Fluorescence Lifetime in Time-Resolved Fluorescence Data from the Human Eye

PubMed Central

Klemm, Matthias; Schweitzer, Dietrich; Peters, Sven; Sauer, Lydia; Hammer, Martin; Haueisen, Jens

2015-01-01

Fluorescence lifetime imaging ophthalmoscopy (FLIO) is a new technique for measuring the in vivo autofluorescence intensity decays generated by endogenous fluorophores in the ocular fundus. Here, we present a software package called FLIM eXplorer (FLIMX) for analyzing FLIO data. Specifically, we introduce a new adaptive binning approach as an optimal tradeoff between the spatial resolution and the number of photons required per pixel. We also expand existing decay models (multi-exponential, stretched exponential, spectral global analysis, incomplete decay) to account for the layered structure of the eye and present a method to correct for the influence of the crystalline lens fluorescence on the retina fluorescence. Subsequently, the Holm-Bonferroni method is applied to FLIO measurements to allow for group comparisons between patients and controls on the basis of fluorescence lifetime parameters. The performance of the new approaches was evaluated in five experiments. Specifically, we evaluated static and adaptive binning in a diabetes mellitus patient, we compared the different decay models in a healthy volunteer and performed a group comparison between diabetes patients and controls. An overview of the visualization capabilities and a comparison of static and adaptive binning is shown for a patient with macular hole. FLIMX’s applicability to fluorescence lifetime imaging microscopy is shown in the ganglion cell layer of a porcine retina sample, obtained by a laser scanning microscope using two-photon excitation. PMID:26192624

DATAMAP upgrade version 4.0

NASA Technical Reports Server (NTRS)

Watts, Michael E.; Dejpour, Shabob R.

1989-01-01

The changes made on the data analysis and management program DATAMAP (Data from Aeromechanics Test and Analytics - Management and Analysis Package) are detailed. These changes are made to Version 3.07 (released February, 1981) and are called Version 4.0. Version 4.0 improvements were performed by Sterling Software under contract to NASA Ames Research Center. The increased capabilities instituted in this version include the breakout of the source code into modules for ease of modification, addition of a more accurate curve fit routine, ability to handle higher frequency data, additional data analysis features, and improvements in the functionality of existing features. These modification will allow DATAMAP to be used on more data sets and will make future modifications and additions easier to implement.

Incorporating Spatial Data into Enterprise Applications

NASA Astrophysics Data System (ADS)

Akiki, Pierre; Maalouf, Hoda

The main goal of this chapter is to discuss the usage of spatial data within enterprise as well as smaller line-of-business applications. In particular, this chapter proposes new methodologies for storing and manipulating vague spatial data and provides methods for visualizing both crisp and vague spatial data. It also provides a comparison between different types of spatial data, mainly 2D crisp and vague spatial data, and their respective fields of application. Additionally, it compares existing commercial relational database management systems, which are the most widely used with enterprise applications, and discusses their deficiencies in terms of spatial data support. A new spatial extension package called Spatial Extensions (SPEX) is provided in this chapter and is tested on a software prototype.

Fly ash system technology improves opacity

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

NONE

2007-06-15

Unit 3 of the Dave Johnston Power Plant east of Glenrock, WY, USA had problems staying at or below the opacity limits set by the state. The unit makes use of a Lodge Cottrell precipitator. When the plant changed to burning Power River Basin coal, ash buildup became a significant issue as the fly ash control system was unable to properly evacuate hoppers on the unit. To overcome the problem, the PLC on the unit was replaced with a software optimization package called SmartAsh for the precipitator fly ash control system, at a cost of $500,000. After the upgrade, theremore » have been no plugged hoppers and the opacity has been reduced from around 20% to 3-5%. 2 figs.« less

Genetic mapping in the presence of genotyping errors.

PubMed

Cartwright, Dustin A; Troggio, Michela; Velasco, Riccardo; Gutin, Alexander

2007-08-01

Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Each individual marker is assigned an error rate, which is inferred from the data, just as the genetic distances are. We have developed a software package, called TMAP, which uses this model to find maximum-likelihood maps for phase-known pedigrees. We have tested our methods using a data set in Vitis and on simulated data and confirmed that our method dramatically reduces the inflationary effect caused by increasing the number of markers and leads to more accurate orders.

Genetic Mapping in the Presence of Genotyping Errors

PubMed Central

Cartwright, Dustin A.; Troggio, Michela; Velasco, Riccardo; Gutin, Alexander

2007-01-01

Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Each individual marker is assigned an error rate, which is inferred from the data, just as the genetic distances are. We have developed a software package, called TMAP, which uses this model to find maximum-likelihood maps for phase-known pedigrees. We have tested our methods using a data set in Vitis and on simulated data and confirmed that our method dramatically reduces the inflationary effect caused by increasing the number of markers and leads to more accurate orders. PMID:17277374

Educational Software for Illustration of Drainage, Evapotranspiration, and Crop Yield.

ERIC Educational Resources Information Center

Khan, A. H.; And Others

1996-01-01

Describes a study that developed a software package for illustrating drainage, evapotranspiration, and crop yield as influenced by water conditions. The software is a tool for depicting water's influence on crop production in western Kansas. (DDR)

Modelling robotic systems with DADS

NASA Technical Reports Server (NTRS)

Churchill, L. W.; Sharf, I.

1993-01-01

With the appearance of general off-the-shelf software packages for the simulation of mechanical systems, modelling and simulation of mechanisms has become an easier task. The authors have recently used one such package, DADS, to model the dynamics of rigid and flexible-link robotic manipulators. In this paper, we present this overview of our learning experiences with DADS, in the hope that it will shorten the learning process for others interested in this software.

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.

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.

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform

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

Huang, Renke; Jin, Shuangshuang; Chen, Yousu

This paper presents a faster-than-real-time dynamic simulation software package that is designed for large-size power system dynamic simulation. It was developed on the GridPACKTM high-performance computing (HPC) framework. The key features of the developed software package include (1) faster-than-real-time dynamic simulation for a WECC system (17,000 buses) with different types of detailed generator, controller, and relay dynamic models, (2) a decoupled parallel dynamic simulation algorithm with optimized computation architecture to better leverage HPC resources and technologies, (3) options for HPC-based linear and iterative solvers, (4) hidden HPC details, such as data communication and distribution, to enable development centered on mathematicalmore » models and algorithms rather than on computational details for power system researchers, and (5) easy integration of new dynamic models and related algorithms into the software package.« less

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/ .

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)

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.

[Microcomputer control of a LED stimulus display device].

PubMed

Ohmoto, S; Kikuchi, T; Kumada, T

1987-02-01

A visual stimulus display system controlled by a microcomputer was constructed at low cost. The system consists of a LED stimulus display device, a microcomputer, two interface boards, a pointing device (a "mouse") and two kinds of software. The first software package is written in BASIC. Its functions are: to construct stimulus patterns using the mouse, to construct letter patterns (alphabet, digit, symbols and Japanese letters--kanji, hiragana, katakana), to modify the patterns, to store the patterns on a floppy disc, to translate the patterns into integer data which are used to display the patterns in the second software. The second software package, written in BASIC and machine language, controls display of a sequence of stimulus patterns in predetermined time schedules in visual experiments.

LHCb Build and Deployment Infrastructure for run 2

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.

2015-12-01

After the successful run 1 of the LHC, the LHCb Core software team has taken advantage of the long shutdown to consolidate and improve its build and deployment infrastructure. Several of the related projects have already been presented like the build system using Jenkins, as well as the LHCb Performance and Regression testing infrastructure. Some components are completely new, like the Software Configuration Database (using the Graph DB Neo4j), or the new packaging installation using RPM packages. Furthermore all those parts are integrated to allow easier and quicker releases of the LHCb Software stack, therefore reducing the risk of operational errors. Integration and Regression tests are also now easier to implement, allowing to improve further the software checks.

MathBrowser: Web-Enabled Mathematical Software with Application to the Chemistry Curriculum, v 1.0

NASA Astrophysics Data System (ADS)

Goldsmith, Jack G.

1997-10-01

MathSoft: Cambridge, MA, 1996; free via ftp from www.mathsoft.com. The movement to provide computer-based applications in chemistry has come to focus on three main areas: software aimed at specific applications (drawing, simulation, data analysis, etc.), multimedia applications designed to assist in the presentation of conceptual information, and packages to be used in conjunction with a particular textbook at a specific point in the chemistry curriculum. The result is a situation where no single software package devoted to problem solving can be used across a large segment of the curriculum. Adoption of World Wide Web (WWW) technology by a manufacturer of mathematical software, however, has produced software that provides an attractive means of providing a problem-solving resource to students in courses from freshman through senior level.

MINDS: A microcomputer interactive data system for 8086-based controllers

NASA Technical Reports Server (NTRS)

Soeder, J. F.

1985-01-01

A microcomputer interactive data system (MINDS) software package for the 8086 family of microcomputers is described. To enhance program understandability and ease of code maintenance, the software is written in PL/M-86, Intel Corporation's high-level system implementation language. The MINDS software is intended to run in residence with real-time digital control software to provide displays of steady-state and transient data. In addition, the MINDS package provides classic monitor capabilities along with extended provisions for debugging an executing control system. The software uses the CP/M-86 operating system developed by Digital Research, Inc., to provide program load capabilities along with a uniform file structure for data and table storage. Finally, a library of input and output subroutines to be used with consoles equipped with PL/M-86 and assembly language is described.

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.

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

Science.gov Websites

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

TADtool: visual parameter identification for TAD-calling algorithms.

PubMed

Kruse, Kai; Hug, Clemens B; Hernández-Rodríguez, Benjamín; Vaquerizas, Juan M

2016-10-15

Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility. TADtool is available as a Python package from GitHub (https://github.com/vaquerizaslab/tadtool) or can be installed directly via PyPI, the Python package index (tadtool). kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

PubMed Central

2014-01-01

Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

Surface infrastructure functions, requirements and subsystems for a manned Mars mission

NASA Technical Reports Server (NTRS)

Fairchild, Kyle

1986-01-01

Planning and development for a permanently manned scientific outpost on Mars requires an in-depth understanding and analysis of the functions the outpost is expected to perform. The optimum configuration that accomplishes these functions then arises during the trade studies process. In a project this complex, it becomes necessary to use a formal methodology to document the design and planning process. The method chosen for this study is called top-down functional decomposition. This method is used to determine the functions that are needed to accomplish the overall mission, then determine what requirements and systems are needed to do each of the functions. This method facilitates automation of the trades and options process. In the example, this was done with an off-the shelf software package called TK! olver. The basic functions that a permanently manned outpost on Mars must accomplish are: (1) Establish the Life Critical Systems; (2) Support Planetary Sciences and Exploration; and (3) Develop and Maintain Long-term Support Functions, including those systems needed towards self-sufficiency. The top-down functional decomposition methology, combined with standard spread sheet software, offers a powerful tool to quickly assess various design trades and analyze options. As the specific subsystems, and the relational rule algorithms are further refined, it will be possible to very accurately determine the implications of continually evolving mission requirements.

Progress in the Development of a Prototype Reuse Enablement System

NASA Astrophysics Data System (ADS)

Marshall, J. J.; Downs, R. R.; Gilliam, L. J.; Wolfe, R. E.

2008-12-01

An important part of promoting software reuse is to ensure that reusable software assets are readily available to the software developers who want to use them. Through dialogs with the community, the NASA Earth Science Data Systems Software Reuse Working Group has learned that the lack of a centralized, domain- specific software repository or catalog system addressing the needs of the Earth science community is a major barrier to software reuse within the community. The Working Group has proposed the creation of such a reuse enablement system, which would provide capabilities for contributing and obtaining reusable software, to remove this barrier. The Working Group has recommended the development of a Reuse Enablement System to NASA and has performed a trade study to review systems with similar capabilities and to identify potential platforms for the proposed system. This was followed by an architecture study to determine an expeditious and cost-effective solution for this system. A number of software packages and systems were examined through both creating prototypes and examining existing systems that use the same software packages and systems. Based on the results of the architecture study, the Working Group developed a prototype of the proposed system using the recommended software package, through an iterative process of identifying needed capabilities and improving the system to provide those capabilities. Policies for the operation and maintenance of the system are being established for the system, and the identification of system policies also has contributed to the development process. Additionally, a test plan is being developed for formal testing of the prototype, to ensure that it meets all of the requirements previously developed by the Working Group. This poster summarizes the results of our work to date, focusing on the most recent activities.

New optical package and algorithms for accurate estimation and interactive recording of the cloud cover information over land and sea

NASA Astrophysics Data System (ADS)

Krinitskiy, Mikhail; Sinitsyn, Alexey; Gulev, Sergey

2014-05-01

Cloud fraction is a critical parameter for the accurate estimation of short-wave and long-wave radiation - one of the most important surface fluxes over sea and land. Massive estimates of the total cloud cover as well as cloud amount for different layers of clouds are available from visual observations, satellite measurements and reanalyses. However, these data are subject of different uncertainties and need continuous validation against highly accurate in-situ measurements. Sky imaging with high resolution fish eye camera provides an excellent opportunity for collecting cloud cover data supplemented with additional characteristics hardly available from routine visual observations (e.g. structure of cloud cover under broken cloud conditions, parameters of distribution of cloud dimensions). We present operational automatic observational package which is based on fish eye camera taking sky images with high resolution (up to 1Hz) in time and a spatial resolution of 968x648px. This spatial resolution has been justified as an optimal by several sensitivity experiments. For the use of the package at research vessel when the horizontal positioning becomes critical, a special extension of the hardware and software to the package has been developed. These modules provide the explicit detection of the optimal moment for shooting. For the post processing of sky images we developed a software realizing the algorithm of the filtering of sunburn effect in case of small and moderate could cover and broken cloud conditions. The same algorithm accurately quantifies the cloud fraction by analyzing color mixture for each point and introducing the so-called "grayness rate index" for every pixel. The accuracy of the algorithm has been tested using the data collected during several campaigns in 2005-2011 in the North Atlantic Ocean. The collection of images included more than 3000 images for different cloud conditions supplied with observations of standard parameters. The system is fully autonomous and has a block for digital data collection at the hard disk. The system has been tested for a wide range of open ocean cloud conditions and we will demonstrate some pilot results of data processing and physical interpretation of fractional cloud cover estimation.

A Freeware Path to Neutron Computed Tomography

NASA Astrophysics Data System (ADS)

Schillinger, Burkhard; Craft, Aaron E.

Neutron computed tomography has become a routine method at many neutron sources due to the availability of digital detection systems, powerful computers and advanced software. The commercial packages Octopus by Inside Matters and VGStudio by Volume Graphics have been established as a quasi-standard for high-end computed tomography. However, these packages require a stiff investment and are available to the users only on-site at the imaging facility to do their data processing. There is a demand from users to have image processing software at home to do further data processing; in addition, neutron computed tomography is now being introduced even at smaller and older reactors. Operators need to show a first working tomography setup before they can obtain a budget to build an advanced tomography system. Several packages are available on the web for free; however, these have been developed for X-rays or synchrotron radiation and are not immediately useable for neutron computed tomography. Three reconstruction packages and three 3D-viewers have been identified and used even for Gigabyte datasets. This paper is not a scientific publication in the classic sense, but is intended as a review to provide searchable help to make the described packages usable for the tomography community. It presents the necessary additional preprocessing in ImageJ, some workarounds for bugs in the software, and undocumented or badly documented parameters that need to be adapted for neutron computed tomography. The result is a slightly complicated, but surprisingly high-quality path to neutron computed tomography images in 3D, but not a replacement for the even more powerful commercial software mentioned above.

Parallel computation and the Basis system

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

Smith, G.R.

1992-12-16

A software package has been written that can facilitate efforts to develop powerful, flexible, and easy-to-use programs that can run in single-processor, massively parallel, and distributed computing environments. Particular attention has been given to the difficulties posed by a program consisting of many science packages that represent subsystems of a complicated, coupled system. Methods have been found to maintain independence of the packages by hiding data structures without increasing the communication costs in a parallel computing environment. Concepts developed in this work are demonstrated by a prototype program that uses library routines from two existing software systems, Basis and Parallelmore » Virtual Machine (PVM). Most of the details of these libraries have been encapsulated in routines and macros that could be rewritten for alternative libraries that possess certain minimum capabilities. The prototype software uses a flexible master-and-slaves paradigm for parallel computation and supports domain decomposition with message passing for partitioning work among slaves. Facilities are provided for accessing variables that are distributed among the memories of slaves assigned to subdomains. The software is named PROTOPAR.« less

Parallel computation and the basis system

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

Smith, G.R.

1993-05-01

A software package has been written that can facilitate efforts to develop powerful, flexible, and easy-to use programs that can run in single-processor, massively parallel, and distributed computing environments. Particular attention has been given to the difficulties posed by a program consisting of many science packages that represent subsystems of a complicated, coupled system. Methods have been found to maintain independence of the packages by hiding data structures without increasing the communications costs in a parallel computing environment. Concepts developed in this work are demonstrated by a prototype program that uses library routines from two existing software systems, Basis andmore » Parallel Virtual Machine (PVM). Most of the details of these libraries have been encapsulated in routines and macros that could be rewritten for alternative libraries that possess certain minimum capabilities. The prototype software uses a flexible master-and-slaves paradigm for parallel computation and supports domain decomposition with message passing for partitioning work among slaves. Facilities are provided for accessing variables that are distributed among the memories of slaves assigned to subdomains. The software is named PROTOPAR.« less

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

WinTRAX: A raytracing software package for the design of multipole focusing systems

NASA Astrophysics Data System (ADS)

Grime, G. W.

2013-07-01

The software package TRAX was a simulation tool for modelling the path of charged particles through linear cylindrical multipole fields described by analytical expressions and was a development of the earlier OXRAY program (Grime and Watt, 1983; Grime et al., 1982) [1,2]. In a 2005 comparison of raytracing software packages (Incerti et al., 2005) [3], TRAX/OXRAY was compared with Geant4 and Zgoubi and was found to give close agreement with the more modern codes. TRAX was a text-based program which was only available for operation in a now rare VMS workstation environment, so a new program, WinTRAX, has been developed for the Windows operating system. This implements the same basic computing strategy as TRAX, and key sections of the code are direct translations from FORTRAN to C++, but the Windows environment is exploited to make an intuitive graphical user interface which simplifies and enhances many operations including system definition and storage, optimisation, beam simulation (including with misaligned elements) and aberration coefficient determination. This paper describes the program and presents comparisons with other software and real installations.

ICEG2D: An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils with Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson, David S.; Soni, Bharat K.

2000-01-01

An integrated software package, ICEG2D, was developed to automate computational fluid dynamics (CFD) simulations for single-element airfoils with ice accretion. ICEG2D is designed to automatically perform three primary functions: (1) generating a grid-ready, surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generating a high-quality grid using the generated surface point distribution, and (3) generating the input and restart files needed to run the general purpose CFD solver NPARC. ICEG2D can be executed in batch mode using a script file or in an interactive mode by entering directives from a command line. This report summarizes activities completed in the first year of a three-year research and development program to address issues related to CFD simulations for aircraft components with ice accretion. Specifically, this document describes the technology employed in the software, the installation procedure, and a description of the operation of the software package. Validation of the geometry and grid generation modules of ICEG2D is also discussed.

PINT, A Modern Software Package for Pulsar Timing

NASA Astrophysics Data System (ADS)

Luo, Jing; Ransom, Scott M.; Demorest, Paul; Ray, Paul S.; Stovall, Kevin; Jenet, Fredrick; Ellis, Justin; van Haasteren, Rutger; Bachetti, Matteo; NANOGrav PINT developer team

2018-01-01

Pulsar timing, first developed decades ago, has provided an extremely wide range of knowledge about our universe. It has been responsible for many important discoveries, such as the discovery of the first exoplanet and the orbital period decay of double neutron star systems. Currently pulsar timing is the leading technique for detecting low frequency (about 10^-9 Hertz) gravitational waves (GW) using an array of pulsars as the detectors. To achieve this goal, high precision pulsar timing data, at about nanoseconds level, is required. Most high precision pulsar timing data are analyzed using the widely adopted software TEMPO/TEMPO2. But for a robust and believable GW detection, it is important to have independent software that can cross-check the result. In this poster we present the new generation pulsar timing software PINT. This package will provide a robust system to cross check high-precision timing results, completely independent of TEMPO and TEMPO2. In addition, PINT is designed to be a package that is easy to extend and modify, through use of flexible code architecture and a modern programming language, Python, with modern technology and libraries.