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.

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

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

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

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.

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)

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.

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…

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 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.

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.

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.

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.

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.

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

Software Reviews.

ERIC Educational Resources Information Center

Classroom Computer Learning, 1988

1988-01-01

Provides reviews of three software packages including "MusicShapes,""For Comment," and "Colortrope," which were developed for music, writing, and science, respectively. Includes information on grade levels, publishers, hardware needed, and cost. (TW)

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…

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.

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

Evaluation of copy number variation detection for a SNP array platform

PubMed Central

2014-01-01

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

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)…

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

PubMed

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

2017-10-01

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

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

Salama, A.; Mikhail, M.

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

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.

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

Smith, W. Spencer; Zeng, Zheng; Carette, Jacques

2018-05-01

We analyzed the state of practice for software development in the seismology domain by comparing 30 software packages on four aspects: product, implementation, design, and process. We found room for improvement in most seismology software packages. The principal areas of concern include a lack of adequate requirements and design specification documents, a lack of test data to assess reliability, a lack of examples to get new users started, and a lack of technological tools to assist with managing the development process. To assist going forward, we provide recommendations for a document-driven development process that includes a problem statement, development plan, requirement specification, verification and validation (V&V) plan, design specification, code, V&V report, and a user manual. We also provide advice on tool use, including issue tracking, version control, code documentation, and testing tools.

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

Smith, W. Spencer; Zeng, Zheng; Carette, Jacques

2018-02-01

We analyzed the state of practice for software development in the seismology domain by comparing 30 software packages on four aspects: product, implementation, design, and process. We found room for improvement in most seismology software packages. The principal areas of concern include a lack of adequate requirements and design specification documents, a lack of test data to assess reliability, a lack of examples to get new users started, and a lack of technological tools to assist with managing the development process. To assist going forward, we provide recommendations for a document-driven development process that includes a problem statement, development plan, requirement specification, verification and validation (V&V) plan, design specification, code, V&V report, and a user manual. We also provide advice on tool use, including issue tracking, version control, code documentation, and testing tools.

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.

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.

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.

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/.

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)

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.

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.

''Do-it-yourself'' software program calculates boiler efficiency

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

Not Available

1984-03-01

An easy-to-use software package is described which runs on the IBM Personal Computer. The package calculates boiler efficiency, an important parameter of operating costs and equipment wellbeing. The program stores inputs and calculated results for 20 sets of boiler operating data, called cases. Cases can be displayed and modified on the CRT screen through multiple display pages or copied to a printer. All intermediate calculations are performed by this package. They include: steam enthalpy; water enthalpy; air humidity; gas, oil, coal, and wood heat capacity; and radiation losses.

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.

Software Reviews.

ERIC Educational Resources Information Center

Kimball, Jeffrey P.; And Others

1987-01-01

Describes a variety of computer software. The packages reviewed include a variety of simulations, a spread sheet, a printer driver and an alternative operating system for DBM.PCs and compatible programs. (BSR)

CIP's Eighth Annual Educational Software Contest: The Winners.

ERIC Educational Resources Information Center

Donnelly, Denis

1997-01-01

Announces the winners of an annual software contest for innovative software in physics education. Winning entries include an application to help students visualize the origin of energy bands in a solid, a package on the radioastronomy of pulsars, and a school-level science simulation program. Also includes student winners, honorable mentions,…

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

Railroads and Riddles Highlight New Software.

ERIC Educational Resources Information Center

Kinnamon, J. C.

1988-01-01

Six software products are reviewed including multimedia packages for history/geography and science. Other products include a coloring program, riddle-maker, word puzzle generator, a lesson on counting money, and a math game equipped with animation and sound effects. (IAH)

Software.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1989

1989-01-01

Presented are reviews of two computer software packages for Apple II computers; "Organic Spectroscopy," and "Videodisc Display Program" for use with "The Periodic Table Videodisc." A sample spectrograph from "Organic Spectroscopy" is included. (CW)

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1990-01-01

Reviewed are six computer software packages including "Lunar Greenhouse,""Dyno-Quest,""How Weather Works,""Animal Trackers,""Personal Science Laboratory," and "The Skeletal and Muscular Systems." Availability, functional, and hardware requirements are discussed. (CW)

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1988-01-01

Reviews seven instructional software packages covering a variety of topics. Includes: "Science Square-Off"; "The Desert"; "Science Courseware: Physical Science"; "Odell Lake"; "Safety First"; "An Experience in Artificial Intelligence"; and "Master Mapper." (TW)

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.

Report of AAPM Task Group 162: Software for planar image quality metrology.

PubMed

Samei, Ehsan; Ikejimba, Lynda C; Harrawood, Brian P; Rong, John; Cunningham, Ian A; Flynn, Michael J

2018-02-01

The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE). First, a methodological framework is provided to highlight the theoretical basis of the work. Then, a step-by-step guide is included to assist in proper execution of each component of the code. Lastly, an evaluation of the method is included to validate its accuracy against model-based and experimental data. The code was built using a Macintosh OSX operating system. The software package contains all the source codes to permit an experienced user to build the suite on a Linux or other *nix type system. The package further includes manuals and sample images and scripts to demonstrate use of the software for new users. The results of the code are in close alignment with theoretical expectations and published results of experimental data. The methodology and the software package offered in AAPM TG162 can be used as baseline for characterization of inherent image quality attributes of planar imaging systems. © 2017 American Association of Physicists in Medicine.

Software Reviews.

ERIC Educational Resources Information Center

Mathematics and Computer Education, 1988

1988-01-01

Presents reviews of six software packages. Includes (1) "Plain Vanilla Statistics"; (2) "MathCAD 2.0"; (3) "GrFx"; (4) "Trigonometry"; (5) "Algebra II"; (6) "Algebra Drill and Practice I, II, and III." (PK)

Software Reviews.

ERIC Educational Resources Information Center

Dwyer, Donna; And Others

1989-01-01

Reviewed are seven software packages for Apple and IBM computers. Included are: "Toxicology"; "Science Corner: Space Probe"; "Alcohol and Pregnancy"; "Science Tool Kit Plus"; Computer Investigations: Plant Growth"; "Climatrolls"; and "Animal Watch: Whales." (CW)

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.

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

National Collegiate Software Clearinghouse Software for the Humanities and Social Sciences. Summer 1989 Catalog.

ERIC Educational Resources Information Center

National Collegiate Software Clearinghouse, Durham, NC.

Over 250 microcomputer software packages, intended for use on MS-DOS machines by scholars and teachers in the humanities and social sciences, are included in this catalog. The clearinghouse's first Macintosh listing is included, with many more Macintosh programs and data sets being planned and tested for future inclusion. Most programs were…

Selecting Really Excellent Software for Young Adults.

ERIC Educational Resources Information Center

Polly, Jean Armour

1985-01-01

This article discusses criteria of a good computer software package to aid the public librarian in the building, weeding, and maintenance of a software collection for young adults. Highlights include manuals or documentation; bells, whistles, and color; and the true test of time. (EJS)

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.

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.

Real time flight simulation methodology

NASA Technical Reports Server (NTRS)

Parrish, E. A.; Cook, G.; Mcvey, E. S.

1977-01-01

Substitutional methods for digitization, input signal-dependent integrator approximations, and digital autopilot design were developed. The software framework of a simulator design package is described. Included are subroutines for iterative designs of simulation models and a rudimentary graphics package.

MicroSIFT Courseware Evaluations (199-222). Set 10. Including Subject and Title Indexes Covering Sets 1-10.

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

This document consists of 24 microcomputer software package evaluations prepared by the MicroSIFT (Microcomputer Software and Information for Teachers) Clearinghouse at the Northwest Regional Educational Laboratory. Each software review lists source, cost, ability level, subject, topic, medium of transfer, required hardware, required software,…

The Organization of a Computer Software Collection Using an Information Storage and Retrieval Software Package.

ERIC Educational Resources Information Center

Davies, Denise M.

1985-01-01

Discusses design, development, and use of a database to provide organization and access to a computer software collection at the University of Hawaii School of Library Studies. Field specifications, samples of report forms, and a description of the physical organization of the software collection are included. (MBR)

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.

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.

Mathematical and Statistical Software Index. Final Report.

ERIC Educational Resources Information Center

Black, Doris E., Comp.

Brief descriptions are provided of general-purpose mathematical and statistical software, including 27 "stand-alone" programs, three subroutine systems, and two nationally recognized statistical packages, which are available in the Air Force Human Resources Laboratory (AFHRL) software library. This index was created to enable researchers…

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;

Canputer Science and Technology: Introduction to Software Packages

DTIC Science & Technology

1984-04-01

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

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1990

1990-01-01

Reviewed are seven computer software packages for IBM and/or Apple Computers. Included are "Windows on Science: Volume 1--Physical Science"; "Science Probe--Physical Science"; "Wildlife Adventures--Grizzly Bears"; "Science Skills--Development Programs"; "The Clean Machine"; "Rock Doctor";…

Software Reviews.

ERIC Educational Resources Information Center

Classroom Computer Learning, 1990

1990-01-01

Reviewed are three computer software packages including "Martin Luther King, Jr.: Instant Replay of History,""Weeds to Trees," and "The New Print Shop, School Edition." Discussed are hardware requirements, costs, grade levels, availability, emphasis, strengths, and weaknesses. (CW)

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

PubMed

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

2011-01-01

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

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.

PubMed

Hill, Jon; Davis, Katie E

2014-01-01

Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.

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.

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.

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.

Design Optimization Toolkit: Users' Manual

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

Aguilo Valentin, Miguel Alejandro

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

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.

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1989

1989-01-01

Reviews of seven software packages are presented including "The Environment I: Habitats and EcoSystems; II Cycles and Interactions"; "Super Sign Maker"; "The Great Knowledge Race: Substance Abuse"; "Exploring Science: Temperature"; "Fast Food Calculator and RD Aide"; "The Human Body:…

Cyber-Ed.

ERIC Educational Resources Information Center

Ruben, Barbara

1994-01-01

Reviews a number of interactive environmental computer education networks and software packages. Computer networks include National Geographic Kids Network, Global Lab, and Global Rivers Environmental Education Network. Computer software involve environmental decision making, simulation games, tropical rainforests, the ocean, the greenhouse…

Reviews: Software.

ERIC Educational Resources Information Center

Mackenzie, Norma N.; And Others

1988-01-01

Reviews four computer software packages including: "The Physical Science Series: Sound" which demonstrates making waves, speed of sound, doppler effect, and human hearing; "Andromeda" depicting celestial motions in any direction; "Biology Quiz: Humans" covering chemistry, cells, viruses, and human biology; and…

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

ERIC Educational Resources Information Center

Bantz, David A.; And Others

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

Science for the Home: New Products Tackle Such Weighty Subjects as Immunology, Chemistry.

ERIC Educational Resources Information Center

Mace, Scott

1984-01-01

Discusses trends in science software for home and educational use. Examples of software on various science topics are provided, including packages which revolve around such television shows as "Nova" and "Voyage of the Mimi" and those produced by the Human Engineering Software. (JN)

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

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

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

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

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

Reviews five software packages for use with school age children. Includes "Science Toolkit Module 2: Earthquake Lab"; "Adaptations and Identification"; "Geoworld"; "Body Systems II Series: The Blood System: A Liquid of Life," all for Apple II, and "Science Courseware: Life Science/Biology" for…

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

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

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

PubMed Central

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

2011-01-01

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

Software For Clear-Air Doppler-Radar Display

NASA Technical Reports Server (NTRS)

Johnston, Bruce W.

1990-01-01

System of software developed to present plan-position-indicator scans of clear-air Doppler radar station on color graphical cathode-ray-tube display. Designed to incorporate latest accepted standards for equipment, computer programs, and meteorological data bases. Includes use of Ada programming language, of "Graphical-Kernel-System-like" graphics interface, and of Common Doppler Radar Exchange Format. Features include portability and maintainability. Use of Ada software packages produced number of software modules reused on other related projects.

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.

College Explorer.

ERIC Educational Resources Information Center

Ahl, David H.

1985-01-01

The "College Explorer" is a software package (for the 64K Apple II, IBM PC, TRS-80 model III and 4 microcomputers) which aids in choosing a college. The major features of this package (manufactured by The College Board) are described and evaluated. Sample input/output is included. (JN)

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.

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

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.

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

PubMed

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

2015-10-20

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

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

PubMed Central

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

2015-01-01

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

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.

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

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.

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.

Software Reviews.

ERIC Educational Resources Information Center

Kinnaman, Daniel E.; And Others

1988-01-01

Reviews four educational software packages for Apple, IBM, and Tandy computers. Includes "How the West was One + Three x Four,""Mavis Beacon Teaches Typing,""Math and Me," and "Write On." Reviews list hardware requirements, emphasis, levels, publisher, purchase agreements, and price. Discusses the strengths…

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1990-01-01

Reviewed are six software packages for Apple and/or IBM computers. Included are "Autograph,""The New Game Show,""Science Probe-Earth Science,""Pollution Patrol,""Investigating Plant Growth," and "AIDS: The Investigation." Discussed are the grade level, function, availability, cost, and hardware requirements of each. (CW)

Computerizing the Accounting Curriculum.

ERIC Educational Resources Information Center

Nash, John F.; England, Thomas G.

1986-01-01

Discusses the use of computers in college accounting courses. Argues that the success of new efforts in using computers in teaching accounting is dependent upon increasing instructors' computer skills, and choosing appropriate hardware and software, including commercially available business software packages. (TW)

School Microware: A Directory of Educational Software. Over 500 Programs/Packages for APPLE, PET, TRS-80.

ERIC Educational Resources Information Center

Dresden Associates, Dresden, ME.

This preliminary directory represents the offerings of 45 software suppliers and information about instructional software currently available for three microcomputers widely used in schools. It is geared towards a wide variety of users including school planners contemplating microcomputer acquisition, teachers planning courses and curricula, media…

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction

PubMed Central

2014-01-01

Abstract Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work. PMID:24891820

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

PubMed

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

2009-04-01

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

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

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

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

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.

Reviews, Software.

ERIC Educational Resources Information Center

Science Teacher, 1988

1988-01-01

Reviews two computer software packages for use in physical science, physics, and chemistry classes. Includes "Physics of Model Rocketry" for Apple II, and "Black Box" for Apple II and IBM compatible computers. "Black Box" is designed to help students understand the concept of indirect evidence. (CW)

Software Reviews.

ERIC Educational Resources Information Center

Teles, Elizabeth, Ed.; And Others

1990-01-01

Reviewed are two computer software packages for Macintosh microcomputers including "Phase Portraits," an exploratory graphics tool for studying first-order planar systems; and "MacMath," a set of programs for exploring differential equations, linear algebra, and other mathematical topics. Features, ease of use, cost, availability, and hardware…

Hop, Skip and Jump: Animation Software.

ERIC Educational Resources Information Center

Eiser, Leslie

1986-01-01

Discusses the features of animation software packages, reviewing eight commercially available programs. Information provided for each program includes name, publisher, current computer(s) required, cost, documentation, input device, import/export capabilities, printing possibilities, what users can originate, types of image manipulation possible,…

Tips for Good Electronic Presentations.

ERIC Educational Resources Information Center

Strasser, Dennis

1996-01-01

Describes library uses of presentation graphics software and offers tips for creating electronic presentations. Tips include: audience retention; visual aid options; software package options; presentation planning; presentation showing; and use of text, colors, and graphics. Sidebars note common presentation errors and popular presentation…

Original Courseware for Introductory Psychology: Implementation and Evaluation.

ERIC Educational Resources Information Center

Slotnick, Robert S.

1988-01-01

Describes the implementation and field testing of PsychWare, a courseware package for introductory psychology developed and field tested at New York Institute of Technology. Highlights include the courseware package (10 software programs, a faculty manual, and a student workbook), and instructional design features (simulations, real-time…

Open-source Software for Exoplanet Atmospheric Modeling

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Blecic, Jasmina; Harrington, Joseph

2018-01-01

I will present a suite of self-standing open-source tools to model and retrieve exoplanet spectra implemented for Python. These include: (1) a Bayesian-statistical package to run Levenberg-Marquardt optimization and Markov-chain Monte Carlo posterior sampling, (2) a package to compress line-transition data from HITRAN or Exomol without loss of information, (3) a package to compute partition functions for HITRAN molecules, (4) a package to compute collision-induced absorption, and (5) a package to produce radiative-transfer spectra of transit and eclipse exoplanet observations and atmospheric retrievals.

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

PubMed

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

2018-03-01

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

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

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.

GP Workbench Manual: Technical Manual, User's Guide, and Software Guide

USGS Publications Warehouse

Oden, Charles P.; Moulton, Craig W.

2006-01-01

GP Workbench is an open-source general-purpose geophysical data processing software package written primarily for ground penetrating radar (GPR) data. It also includes support for several USGS prototype electromagnetic instruments such as the VETEM and ALLTEM. The two main programs in the package are GP Workbench and GP Wave Utilities. GP Workbench has routines for filtering, gridding, and migrating GPR data; as well as an inversion routine for characterizing UXO (unexploded ordinance) using ALLTEM data. GP Workbench provides two-dimensional (section view) and three-dimensional (plan view or time slice view) processing for GPR data. GP Workbench can produce high-quality graphics for reports when Surfer 8 or higher (Golden Software) is installed. GP Wave Utilities provides a wide range of processing algorithms for single waveforms, such as filtering, correlation, deconvolution, and calculating GPR waveforms. GP Wave Utilities is used primarily for calibrating radar systems and processing individual traces. Both programs also contain research features related to the calibration of GPR systems and calculating subsurface waveforms. The software is written to run on the Windows operating systems. GP Workbench can import GPR data file formats used by major commercial instrument manufacturers including Sensors and Software, GSSI, and Mala. The GP Workbench native file format is SU (Seismic Unix), and subsequently, files generated by GP Workbench can be read by Seismic Unix as well as many other data processing packages.

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.

Mass decomposition of galaxies using DECA software package

NASA Astrophysics Data System (ADS)

Mosenkov, A. V.

2014-01-01

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

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.

Software Review.

ERIC Educational Resources Information Center

McGrath, Diane, Ed.

1989-01-01

Reviewed is a computer software package entitled "Audubon Wildlife Adventures: Grizzly Bears" for Apple II and IBM microcomputers. Included are availability, hardware requirements, cost, and a description of the program. The murder-mystery flavor of the program is stressed in this program that focuses on illegal hunting and game…

Computer Aided Teaching of Digital Signal Processing.

ERIC Educational Resources Information Center

Castro, Ian P.

1990-01-01

Describes a microcomputer-based software package developed at the University of Surrey for teaching digital signal processing to undergraduate science and engineering students. Menu-driven software capabilities are explained, including demonstration of qualitative concepts and experimentation with quantitative data, and examples are given of…

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.

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

PubMed

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

2011-01-01

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

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.

A new vector radiative transfer model as a part of SCIATRAN 3.0 software package.

NASA Astrophysics Data System (ADS)

Rozanov, Alexei; Rozanov, Vladimir; Burrows, John P.

The SCIATRAN 3.0 package is a result of further development of the SCIATRAN 2.x software family which, similar to previous versions, comprises a radiative transfer model and a retrieval block. A major improvement was achieved in comparison to previous software versions by adding the vector mode to the radiative transfer model. Thus, the well-established Discrete Ordinate solver can now be run in the vector mode to calculate the scattered solar radiation including polarization, i.e., to simulate all four components of the Stockes vector. Similar to the scalar version, the simulations can be performed for any viewing geometry typical for atmospheric observations in the UV-Vis-NIR spectral range (nadir, limb, off-axis, etc.) as well as for any observer position within or outside the Earth's atmosphere. Similar to the precursor version, the new model is freely available for non-commercial use via the web page of the University of Bremen. In this presentation a short description of the software package, especially of the new vector radiative transfer model will be given, including remarks on the availability for the scientific community. Furthermore, comparisons to other vector models will be shown and some example problems will be considered where the polarization of the observed radiation must be accounted for to obtain high quality results.

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

NASA Astrophysics Data System (ADS)

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

2013-08-01

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

Software Package Completed for Alloy Design at the Atomic Level

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

SIRU utilization. Volume 2: Software description and program documentation

NASA Technical Reports Server (NTRS)

Oehrle, J.; Whittredge, R.

1973-01-01

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

The Environmental Data Initiative data repository: Trustworthy practices that foster preservation, fitness, and reuse for environmental and ecological data

NASA Astrophysics Data System (ADS)

Servilla, M. S.; Brunt, J.; Costa, D.; Gries, C.; Grossman-Clarke, S.; Hanson, P. C.; O'Brien, M.; Smith, C.; Vanderbilt, K.; Waide, R.

2017-12-01

The Environmental Data Initiative (EDI) is an outgrowth of more than 30 years of information management experience and technology from LTER Network data practitioners. EDI builds upon the PASTA data repository software used by the LTER Network Information System and manages more than 42,000 data packages, containing tabular data, imagery, and other formats. Development of the repository was a community process beginning in 2009 that included numerous working groups for generating use cases, system requirements, and testing of completed software, thereby creating a vested interested in its success and transparency in design. All software is available for review on GitHub, and refinements and new features are ongoing. Documentation is also available on Read-the-docs, including a comprehensive description of all web-service API methods. PASTA is metadata driven and uses the Ecological Metadata Language (EML) standard for describing environmental and ecological data; a simplified Dublin Core document is also available for each data package. Data are aggregated into packages consisting of metadata and other related content described by an OAI-ORE document. Once archived, each data package becomes immutable and permanent; updates are possible through the addition of new revisions. Components of each data package are accessible through a unique identifier, while the entire data package receives a DOI that is registered in DataCite. Preservation occurs through a combination of DataONE synchronization/replication and by a series of local and remote backup strategies, including daily uploads to AWS Glacier storage. Checksums are computed for all data at initial upload, with random verification occurring on a continuous basis, thus ensuring the integrity of data. PASTA incorporates a series of data quality tests to ensure that data are correctly documented with EML before data are archived; data packages that fail any test are forbidden in the repository. These tests are a measure data fitness, which ultimately increases confidence in data reuse and synthesis. The EDI data repository is recognized by multiple organizations, including EarthCube's Council of Data Facilities, the United States Geological Survey, FAIRsharing.org, re3data.org, and is a PLOS and Nature recommended data repository.

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.

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

PubMed Central

2015-01-01

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

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

PubMed

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

2014-09-22

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

Microcomputer Materials from MEP. An Annotated Directory of Packages of Interest to Further Education. An Occasional Paper.

ERIC Educational Resources Information Center

Gilbert, Leslie

Designed to disseminate information to the post-school sector of United Kingdom education, this directory provides information on 50 microcomputer software packages developed by the Microelectronics Education Program (MEP) and available through educational publishers. Subject areas represented include accountancy, biology, business education,…

Teacher's Corner: Structural Equation Modeling with the Sem Package in R

ERIC Educational Resources Information Center

Fox, John

2006-01-01

R is free, open-source, cooperatively developed software that implements the S statistical programming language and computing environment. The current capabilities of R are extensive, and it is in wide use, especially among statisticians. The sem package provides basic structural equation modeling facilities in R, including the ability to fit…

An open and extensible framework for spatially explicit land use change modelling: the lulcc R package

NASA Astrophysics Data System (ADS)

Moulds, S.; Buytaert, W.; Mijic, A.

2015-10-01

We present the lulcc software package, an object-oriented framework for land use change modelling written in the R programming language. The contribution of the work is to resolve the following limitations associated with the current land use change modelling paradigm: (1) the source code for model implementations is frequently unavailable, severely compromising the reproducibility of scientific results and making it impossible for members of the community to improve or adapt models for their own purposes; (2) ensemble experiments to capture model structural uncertainty are difficult because of fundamental differences between implementations of alternative models; and (3) additional software is required because existing applications frequently perform only the spatial allocation of change. The package includes a stochastic ordered allocation procedure as well as an implementation of the CLUE-S algorithm. We demonstrate its functionality by simulating land use change at the Plum Island Ecosystems site, using a data set included with the package. It is envisaged that lulcc will enable future model development and comparison within an open environment.

From Workstation to Teacher Support System: A Tool to Increase Productivity.

ERIC Educational Resources Information Center

Chen, J. Wey

1989-01-01

Describes a teacher support system which is a computer-based workstation that provides support for teachers and administrators by integrating teacher utility programs, instructional management software, administrative packages, and office automation tools. Hardware is described and software components are explained, including database managers,…

DoD Application Store: Enabling C2 Agility?

DTIC Science & Technology

2014-06-01

Framework, will include automated delivery of software patches, web applications, widgets and mobile application packages. The envisioned DoD...Marketplace within the Ozone Widget Framework, will include automated delivery of software patches, web applications, widgets and mobile application...current needs. DoD has started to make inroads within this environment with several Programs of Record (PoR) embracing widgets and other mobile

The LARSYS Educational Package: Instructor's Notes for Use with the Data 100

NASA Technical Reports Server (NTRS)

Lindenlaub, J. C.; Russell, J. D.

1977-01-01

The LARSYS Educational Package is a set of instructional materials developed to train people to analyze remotely sensed multispectral data using LARSYS, a computer software system. The materials included in this volume have been designed to assist LARSYS instructors as they guide students through the LARSYS Educational Package. All of the materials have been updated from the previous version to reflect the use of a Data 100 Remote Terminal.

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.

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

PubMed Central

Solernou, Albert

2018-01-01

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

The Next Generation in Subsidence and Aquifer-System Compaction Modeling within the MODFLOW Software Family: A New Package for MODFLOW-2005 and MODFLOW-OWHM

NASA Astrophysics Data System (ADS)

Boyce, S. E.; Leake, S. A.; Hanson, R. T.; Galloway, D. L.

2015-12-01

The Subsidence and Aquifer-System Compaction Packages, SUB and SUB-WT, for MODFLOW are two currently supported subsidence packages within the MODFLOW family of software. The SUB package allows the calculation of instantaneous and delayed releases of water from distributed interbeds (relatively more compressible fine-grained sediments) within a saturated aquifer system or discrete confining beds. The SUB-WT package does not include delayed releases, but does perform a more rigorous calculation of vertical stresses that can vary the effective stress that causes compaction. This calculation of instantaneous compaction can include the effect of water-table fluctuations for unconfined aquifers on effective stress, and can optionally adjust the elastic and inelastic storage properties based on the changes in effective stress. The next generation of subsidence modeling in MODFLOW is under development, and will merge and enhance the capabilities of the SUB and SUB-WT Packages for MODFLOW-2005 and MODFLOW-OWHM. This new version will also provide some additional features such as stress dependent vertical hydraulic conductivity of interbeds, time-varying geostatic loads, and additional attributes related to aquifer-system compaction and subsidence that will broaden the class of problems that can be simulated. The new version will include a redesigned source code, a new user friendly input file structure, more output options, and new subsidence solution options. This presentation will discuss progress in developing the new package and the new features being implemented and their potential applications. By Stanley Leake, Scott E. Boyce, Randall T. Hanson, and Devin Galloway

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

Klusters, NeuroScope, NDManager: a free software suite for neurophysiological data processing and visualization.

PubMed

Hazan, Lynn; Zugaro, Michaël; Buzsáki, György

2006-09-15

Recent technological advances now allow for simultaneous recording of large populations of anatomically distributed neurons in behaving animals. The free software package described here was designed to help neurophysiologists process and view recorded data in an efficient and user-friendly manner. This package consists of several well-integrated applications, including NeuroScope (http://neuroscope.sourceforce.net), an advanced viewer for electrophysiological and behavioral data with limited editing capabilities, Klusters (http://klusters.sourceforge.net), a graphical cluster cutting application for manual and semi-automatic spike sorting, NDManager (GPL,see http://www.gnu.org/licenses/gpl.html), an experimental parameter and data processing manager. All of these programs are distributed under the GNU General Public License (GPL, see ), which gives its users legal permission to copy, distribute and/or modify the software. Also included are extensive user manuals and sample data, as well as source code and documentation.

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…

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

Software Reviews. Programs Worth a Second Look.

ERIC Educational Resources Information Center

Schneider, Roxanne; Eiser, Leslie

1989-01-01

Reviewed are three computer software packages for use in middle/high school classrooms. Included are "MacWrite II," a word-processing program for MacIntosh computers; "Super Story Tree," a word-processing program for Apple and IBM computers; and "Math Blaster Mystery," for IBM, Apple, and Tandy computers. (CW)

Computers as Teaching Tools: Some Examples and Guidelines.

ERIC Educational Resources Information Center

Beins, Bernard C.

The use of computers in the classroom has been touted as an important innovation in education. This article features some recently developed software for use in teaching psychology and different approaches to classroom computer use. Uses of software packages for psychological research designs are included as are applications and limitations of…

Desktop Publishing: A Brave New World and Publishing from the Desktop.

ERIC Educational Resources Information Center

Lormand, Robert; Rowe, Jane J.

1988-01-01

The first of two articles presents basic selection criteria for desktop publishing software packages, including discussion of expectations, required equipment, training costs, publication size, desired software features, additional equipment needed, and quality control. The second provides a brief description of desktop publishing using the Apple…

International Inventory of Software Packages in the Information Field.

ERIC Educational Resources Information Center

Keren, Carl, Ed.; Sered, Irina, Ed.

Designed to provide guidance in selecting appropriate software for library automation, information storage and retrieval, or management of bibliographic databases, this inventory describes 188 computer software packages. The information was obtained through a questionnaire survey of 600 software suppliers and developers who were asked to describe…

ATLAS software configuration and build tool optimisation

NASA Astrophysics Data System (ADS)

Rybkin, Grigory; Atlas Collaboration

2014-06-01

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

CSAM Metrology Software Tool

NASA Technical Reports Server (NTRS)

Vu, Duc; Sandor, Michael; Agarwal, Shri

2005-01-01

CSAM Metrology Software Tool (CMeST) is a computer program for analysis of false-color CSAM images of plastic-encapsulated microcircuits. (CSAM signifies C-mode scanning acoustic microscopy.) The colors in the images indicate areas of delamination within the plastic packages. Heretofore, the images have been interpreted by human examiners. Hence, interpretations have not been entirely consistent and objective. CMeST processes the color information in image-data files to detect areas of delamination without incurring inconsistencies of subjective judgement. CMeST can be used to create a database of baseline images of packages acquired at given times for comparison with images of the same packages acquired at later times. Any area within an image can be selected for analysis, which can include examination of different delamination types by location. CMeST can also be used to perform statistical analyses of image data. Results of analyses are available in a spreadsheet format for further processing. The results can be exported to any data-base-processing software.

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

PubMed Central

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

2016-01-01

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

Detection And Mapping (DAM) package. Volume 4B: Software System Manual, part 2

NASA Technical Reports Server (NTRS)

Schlosser, E. H.

1980-01-01

Computer programs, graphic devices, and an integrated set of manual procedures designed for efficient production of precisely registered and formatted maps from digital data are presented. The software can be used on any Univac 1100 series computer. The software includes pre-defined spectral limits for use in classifying and mapping surface water for LANDSAT-1, LANDSAT-2, and LANDSAT-3.

Digital PIV (DPIV) Software Analysis System

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

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

The Venus Balloon Project telemetry processing

NASA Technical Reports Server (NTRS)

Urech, J. M.; Chamarro, A.; Morales, J. L.; Urech, M. A.

1986-01-01

The peculiarities of the Venus Balloon telemetry system required the development of a new methodology for the telemetry processing, since the capabilities of the Deep Space Network (DSN) telemetry system do not include burst processing of short frames with two different bit rates and first bit acquisition. A software package was produced for the non-real time detection, demodulation, and decoding of the telemetry streams obtained from an open loop recording utilizing the DSN spectrum processing subsystem-radio science (DSP-RS). A general description of the resulting software package (DMO-5539-SP) and its adaptability to the real mission's variations is contained.

Quantum Computing Architectural Design

NASA Astrophysics Data System (ADS)

West, Jacob; Simms, Geoffrey; Gyure, Mark

2006-03-01

Large scale quantum computers will invariably require scalable architectures in addition to high fidelity gate operations. Quantum computing architectural design (QCAD) addresses the problems of actually implementing fault-tolerant algorithms given physical and architectural constraints beyond those of basic gate-level fidelity. Here we introduce a unified framework for QCAD that enables the scientist to study the impact of varying error correction schemes, architectural parameters including layout and scheduling, and physical operations native to a given architecture. Our software package, aptly named QCAD, provides compilation, manipulation/transformation, multi-paradigm simulation, and visualization tools. We demonstrate various features of the QCAD software package through several examples.

RNAbrowse: RNA-Seq de novo assembly results browser.

PubMed

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

2014-01-01

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

SUBOPT: A CAD program for suboptimal linear regulators

NASA Technical Reports Server (NTRS)

Fleming, P. J.

1985-01-01

An interactive software package which provides design solutions for both standard linear quadratic regulator (LQR) and suboptimal linear regulator problems is described. Intended for time-invariant continuous systems, the package is easily modified to include sampled-data systems. LQR designs are obtained by established techniques while the large class of suboptimal problems containing controller and/or performance index options is solved using a robust gradient minimization technique. Numerical examples demonstrate features of the package and recent developments are described.

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.

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…

Design Tool

NASA Technical Reports Server (NTRS)

1993-01-01

Developed under a Small Business Innovation Research (SBIR) contract, RAMPANT is a CFD software package for computing flow around complex shapes. The package is flexible, fast and easy to use. It has found a great number of applications, including computation of air flow around a Nordic ski jumper, prediction of flow over an airfoil and computation of the external aerodynamics of motor vehicles.

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.

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

PubMed

Karabatsos, George

2017-02-01

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

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.

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…

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

Integrated software system for low level waste management

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

Worku, G.

1995-12-31

In the continually changing and uncertain world of low level waste management, many generators in the US are faced with the prospect of having to store their waste on site for the indefinite future. This consequently increases the set of tasks performed by the generators in the areas of packaging, characterizing, classifying, screening (if a set of acceptance criteria applies), and managing the inventory for the duration of onsite storage. When disposal sites become available, it is expected that the work will require re-evaluating the waste packages, including possible re-processing, re-packaging, or re-classifying in preparation for shipment for disposal undermore » the regulatory requirements of the time. In this day and age, when there is wide use of computers and computer literacy is at high levels, an important waste management tool would be an integrated software system that aids waste management personnel in conducting these tasks quickly and accurately. It has become evident that such an integrated radwaste management software system offers great benefits to radwaste generators both in the US and other countries. This paper discusses one such approach to integrated radwaste management utilizing some globally accepted radiological assessment software applications.« less

Trend Monitoring System (TMS) graphics software

NASA Technical Reports Server (NTRS)

Brown, J. S.

1979-01-01

A prototype bus communications systems, which is being used to support the Trend Monitoring System (TMS) and to evaluate the bus concept is considered. A set of FORTRAN-callable graphics subroutines for the host MODCOMP comuter, and an approach to splitting graphics work between the host and the system's intelligent graphics terminals are described. The graphics software in the MODCOMP and the operating software package written for the graphics terminals are included.

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

PubMed

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

2015-09-01

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

Control Systems

NASA Technical Reports Server (NTRS)

1984-01-01

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

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.

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,…

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

ERIC Educational Resources Information Center

Weaver, Dave

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

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.

Substructured multibody molecular dynamics.

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

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

2006-11-01

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

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

ERIC Educational Resources Information Center

Suen, Che-yin; Pok, Yang-ming

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

DSISoft—a MATLAB VSP data processing package

NASA Astrophysics Data System (ADS)

Beaty, K. S.; Perron, G.; Kay, I.; Adam, E.

2002-05-01

DSISoft is a public domain vertical seismic profile processing software package developed at the Geological Survey of Canada. DSISoft runs under MATLAB version 5.0 and above and hence is portable between computer operating systems supported by MATLAB (i.e. Unix, Windows, Macintosh, Linux). The package includes processing modules for reading and writing various standard seismic data formats, performing data editing, sorting, filtering, and other basic processing modules. The processing sequence can be scripted allowing batch processing and easy documentation. A structured format has been developed to ensure future additions to the package are compatible with existing modules. Interactive modules have been created using MATLAB's graphical user interface builder for displaying seismic data, picking first break times, examining frequency spectra, doing f- k filtering, and plotting the trace header information. DSISoft modular design facilitates the incorporation of new processing algorithms as they are developed. This paper gives an overview of the scope of the software and serves as a guide for the addition of new modules.

Software archeology: a case study in software quality assurance and design

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

Macdonald, John M; Lloyd, Jane A; Turner, Cameron J

2009-01-01

Ideally, quality is designed into software, just as quality is designed into hardware. However, when dealing with legacy systems, demonstrating that the software meets required quality standards may be difficult to achieve. As the need to demonstrate the quality of existing software was recognized at Los Alamos National Laboratory (LANL), an effort was initiated to uncover and demonstrate that legacy software met the required quality standards. This effort led to the development of a reverse engineering approach referred to as software archaeology. This paper documents the software archaeology approaches used at LANL to document legacy software systems. A case studymore » for the Robotic Integrated Packaging System (RIPS) software is included.« less

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.

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…

Radar Unix: a complete package for GPR data processing

NASA Astrophysics Data System (ADS)

Grandjean, Gilles; Durand, Herve

1999-03-01

A complete package for ground penetrating radar data interpretation including data processing, forward modeling and a case history database consultation is presented. Running on an Unix operating system, its architecture consists of a graphical user interface generating batch files transmitted to a library of processing routines. This design allows a better software maintenance and the possibility for the user to run processing or modeling batch files by itself and differed in time. A case history data base is available and consists of an hypertext document which can be consulted by using a standard HTML browser. All the software specifications are presented through a realistic example.

RNAbrowse: RNA-Seq De Novo Assembly Results Browser

PubMed Central

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

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

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 Upgrade of the Aeroheating Software "MINIVER"

NASA Technical Reports Server (NTRS)

Louderback, Pierce

2013-01-01

Many software packages assist engineers with performing flight vehicle analysis, but some of these packages have gone many years without updates or significant improvements to their workflows. One such software package, known as MINIVER, is a powerful yet lightweight tool used for aeroheating analyses. However, it is an aging program that has not seen major improvements within the past decade. As part of a collaborative effort with the Florida Institute of Technology, MINIVER has received a major user interface overhaul, a change in program language, and will be continually receiving updates to improve its capabilities. The user interface update includes a migration from a command-line interface to that of a graphical user interface supported in the Windows operating system. The organizational structure of the pre-processor has been transformed to clearly defined categories to provide ease of data entry. Helpful tools have been incorporated, including the ability to copy sections of cases as well as a generalized importer which aids in bulk data entry. A visual trajectory editor has been included, as well as a CAD Editor which allows the user to input simplified geometries in order to generate MINIVER cases in bulk. To demonstrate its continued effectiveness, a case involving the JAXA OREX flight vehicle will be included, providing comparisons to captured flight data as well as other computational solutions. The most recent upgrade effort incorporated the use of the CAD Editor, and current efforts are investigating methods to link MINIVER projects with SINDA/Fluint and Thermal Desktop.

Reviews.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Reviews three computer software packages for chemistry education including "Osmosis and Diffusion" and "E.M.E. Titration Lab" for Apple II and "Simplex-V: An Interactive Computer Program for Experimental Optimization" for IBM PC. Summary ratings include ease of use, content, pedagogic value, student reaction, and…

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.

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.

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

CONRAD—A software framework for cone-beam imaging in radiology

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

Maier, Andreas; Choi, Jang-Hwan; Riess, Christian

2013-11-15

Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform withmore » extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.« less

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.

ControlShell: A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Chen, Vincent W.; Pardo-Castellote, Gerardo

1994-01-01

The ControlShell system is a programming environment that enables the development and implementation of complex real-time software. It includes many building tools for complex systems, such as a graphical finite state machine (FSM) tool to provide strategic control. ControlShell has a component-based design, providing interface definitions and mechanisms for building real-time code modules along with providing basic data management. Some of the system-building tools incorporated in ControlShell are a graphical data flow editor, a component data requirement editor, and a state-machine editor. It also includes a distributed data flow package, an execution configuration manager, a matrix package, and an object database and dynamic binding facility. This paper presents an overview of ControlShell's architecture and examines the functions of several of its tools.

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…

SeaShark and Starfish opertional data processing schemes for AVHRR and SeaWiFs

NASA Astrophysics Data System (ADS)

Flowerdew, R. J.; Corlyon, Anaa M.; Greer, W. A. D.; Newby, Steve J.; Winder, C. P.

1997-02-01

SeaShark is an operational software package for processing, archiving and cataloguing AVHRR and SeaWiFS data using an operator friendly GUI. Upon receipt of a customer order, it produces standard AVHRR data products, including Sea Surface Temperature (SST) and it has recently been modified to include SeaWiFS level 2 data processing. This uses an atmospheric correction scheme developed by the Plymouth Marine Laboratory, UK (PML) that builds upon the standard Gordon and Wang approach to be applicable over both case 1 and case 2 waters. Higher level products are then generated using PML algorithms, including chlorophyll a, a CZCS-type pigment, Kd, and suspended particulate matter. Outputs are in CEOS-compatible format. The software also produces fast delivery products (FDPs) of chlorophyll a and SST. These FDPs are combined in the StarFish software package to provide maps indicating potential location of phytoplankton and the preferred thermal environment of certain pelagic fish species. Fishing vessels may obtain these maps over Inmarsat, allowing them to achieve a greater efficiency hence lower cost.

Investigating Deaf Students' Use of Visual Multimedia Resources in Reading Comprehension

ERIC Educational Resources Information Center

Nikolaraizi, Magda; Vekiri, Ioanna; Easterbrooks, Susan R.

2013-01-01

A mixed research design was used to examine how deaf students used the visual resources of a multimedia software package that was designed to support reading comprehension. The viewing behavior of 8 deaf students, ages 8-12 years, was recorded during their interaction with multimedia software that included narrative texts enriched with Greek Sign…

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

PubMed

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

2014-01-01

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

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.

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

NASA Technical Reports Server (NTRS)

Stefanski, Philip L.

2015-01-01

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

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)

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

Waste Management Information System (WMIS) User Guide

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

R. E. Broz

2008-12-22

This document provides the user of the Waste Management Information System (WMIS) instructions on how to use the WMIS software. WMIS allows users to initiate, track, and close waste packages. The modular design supports integration and utilization of data throuh the various stages of waste management. The phases of the waste management work process include generation, designation, packaging, container management, procurement, storage, treatment, transportation, and disposal.

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

Browndye: A software package for Brownian dynamics

NASA Astrophysics Data System (ADS)

Huber, Gary A.; McCammon, J. Andrew

2010-11-01

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. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

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.

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.

Unidata: 30 Years of FOSS for the Geosciences

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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.

gr-MRI: A software package for magnetic resonance imaging using software defined radios

NASA Astrophysics Data System (ADS)

Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

2016-09-01

The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

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.

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.

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.

The igmspec database of public spectra probing the intergalactic medium

NASA Astrophysics Data System (ADS)

Prochaska, J. X.

2017-04-01

We describe v02 of igmspec, a database of publicly available ultraviolet, optical, and near-infrared spectra that probe the intergalactic medium (IGM). This database, a child of the specdb repository in the specdb github organization, comprises 403 277 unique sources and 434 686 spectra obtained with the world's greatest observatories. All of these data are distributed in a single ≈ 25GB HDF5 file maintained at the University of California Observatories and the University of California, Santa Cruz. The specdb software package includes Python scripts and modules for searching the source catalog and spectral datasets, and software links to the linetools package for spectral analysis. The repository also includes software to generate private spectral datasets that are compliant with International Virtual Observatory Alliance (IVOA) protocols and a Python-based interface for IVOA Simple Spectral Access queries. Future versions of igmspec will ingest other sources (e.g. gamma-ray burst afterglows) and other surveys as they become publicly available. The overall goal is to include every spectrum that effectively probes the IGM. Future databases of specdb may include publicly available galaxy spectra (exgalspec) and published supernovae spectra (snspec). The community is encouraged to join the effort on github: https://github.com/specdb.

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

PubMed

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

2010-01-11

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

Tarjetas v.1.2015.7.23

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

Burchard, Ross L.; Pierson, Kathleen P.; Trumbo, Derek

Tarjetas is used to generate requirements from source documents. These source documents are in a hierarchical XML format that have been produced from PDF documents processed through the “Reframe” software package. The software includes the ability to create Topics and associate text Snippets with those topics. Requirements are then generated and text Snippets with their associated Topics are referenced to the requirement. The software maintains traceability from the requirement ultimately to the source document that produced the snippet

UFMulti: A new parallel processing software system for HEP

NASA Astrophysics Data System (ADS)

Avery, Paul; White, Andrew

1989-12-01

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

System and Method for Providing a Climate Data Persistence Service

NASA Technical Reports Server (NTRS)

Schnase, John L. (Inventor); Ripley, III, William David (Inventor); Duffy, Daniel Q. (Inventor); Thompson, John H. (Inventor); Strong, Savannah L. (Inventor); McInerney, Mark (Inventor); Sinno, Scott (Inventor); Tamkin, Glenn S. (Inventor); Nadeau, Denis (Inventor)

2018-01-01

A system, method and computer-readable storage devices for providing a climate data persistence service. A system configured to provide the service can include a climate data server that performs data and metadata storage and management functions for climate data objects, a compute-storage platform that provides the resources needed to support a climate data server, provisioning software that allows climate data server instances to be deployed as virtual climate data servers in a cloud computing environment, and a service interface, wherein persistence service capabilities are invoked by software applications running on a client device. The climate data objects can be in various formats, such as International Organization for Standards (ISO) Open Archival Information System (OAIS) Reference Model Submission Information Packages, Archive Information Packages, and Dissemination Information Packages. The climate data server can enable scalable, federated storage, management, discovery, and access, and can be tailored for particular use cases.

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

PubMed

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

2015-02-01

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

MNE software for processing MEG and EEG data

PubMed Central

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

2013-01-01

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

General-Purpose Ada Software Packages

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.

1991-01-01

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

Advance Directives and Do Not Resuscitate Orders

MedlinePlus

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

Nested Cohort - R software package

Cancer.gov

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

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

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

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

Case Study: Audio-Guided Learning, with Computer Graphics.

ERIC Educational Resources Information Center

Koumi, Jack; Daniels, Judith

1994-01-01

Describes teaching packages which involve the use of audiotape recordings with personal computers in Open University (United Kingdom) mathematics courses. Topics addressed include software development; computer graphics; pedagogic principles for distance education; feedback, including course evaluations and student surveys; and future plans.…

Multi-canister overpack project -- verification and validation, MCNP 4A

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

Goldmann, L.H.

This supporting document contains the software verification and validation (V and V) package used for Phase 2 design of the Spent Nuclear Fuel Multi-Canister Overpack. V and V packages for both ANSYS and MCNP are included. Description of Verification Run(s): This software requires that it be compiled specifically for the machine it is to be used on. Therefore to facilitate ease in the verification process the software automatically runs 25 sample problems to ensure proper installation and compilation. Once the runs are completed the software checks for verification by performing a file comparison on the new output file and themore » old output file. Any differences between any of the files will cause a verification error. Due to the manner in which the verification is completed a verification error does not necessarily indicate a problem. This indicates that a closer look at the output files is needed to determine the cause of the error.« less

AOFlagger: RFI Software

NASA Astrophysics Data System (ADS)

Offringa, A. R.

2010-10-01

The RFI software presented here can automatically flag data and can be used to analyze the data in a measurement. The purpose of flagging is to mark samples that are affected by interfering sources such as radio stations, airplanes, electrical fences or other transmitting interferers. The tools in the package are meant for offline use. The software package contains a graphical interface ("rfigui") that can be used to visualize a measurement set and analyze mitigation techniques. It also contains a console flagger ("rficonsole") that can execute a script of mitigation functions without the overhead of a graphical environment. All tools were written in C++. The software has been tested extensively on low radio frequencies (150 MHz or lower) produced by the WSRT and LOFAR telescopes. LOFAR is the Low Frequency Array that is built in and around the Netherlands. Higher frequencies should work as well. Some of the methods implemented are the SumThreshold, the VarThreshold and the singular value decomposition (SVD) method. Included also are several surface fitting algorithms. The software is published under the GNU General Public License version 3.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

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

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

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…

Real-Time Data Processing Onboard Remote Sensor Platforms: Annual Review #3 Data Package

NASA Technical Reports Server (NTRS)

Cook, Sid; Harsanyi, Joe

2003-01-01

The current program status reviewed by this viewgraph presentation includes: 1) New Evaluation Results; 2) Algorithm Improvement Investigations; 3) Electronic Hardware Design; 4) Software Hardware Interface Design.

Headway Separation Assurance Subsystem (HSAS)

DOT National Transportation Integrated Search

1975-07-01

This report discusses the design, fabrication, test and evaluation of a Headway Separation Assurance Subsystem (HSAS) capable of reliable, failsafe performance in PRT systems. The items designed include both hardware and software packages. These pack...

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.

Computing and software

USGS Publications Warehouse

White, Gary C.; Hines, J.E.

2004-01-01

The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methodsavailable. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them.In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented.Rotella et al. (2004) compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004).Efford et al. (2004) present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years.Barker & White (2004) discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine pieces of likelihood functions together to generate estimates. The idea is interesting, and maybe some bright young statistician can work out the specifics to implement the procedure.Choquet et al. (2004) describe MSURGE, a software package that implements the multistate capture–recapture models. The unique feature of MSURGE is that the design matrix is constructed with an interpreted language called GEMACO. Because MSURGE is limited to just multistate models, the special requirements of these likelihoods can be provided.The software and methods presented in these papers gives biologists and wildlife managers an expanding range of possibilities for data analysis. Although ease–of–use is generally getting better, it does not replace the need for understanding of the requirements and structure of the models being computed. The internet provides access to many free software packages as well as user–discussion groups to share knowledge and ideas. (A starting point for wildlife–related applications is (http://www.phidot.org).

Pizza.py Toolkit

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

Plimpton, Steve; Jones, Matt; Crozier, Paul

2006-01-01

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

Implementation of Audio Computer-Assisted Interviewing Software in HIV/AIDS Research

PubMed Central

Pluhar, Erika; Yeager, Katherine A.; Corkran, Carol; McCarty, Frances; Holstad, Marcia McDonnell; Denzmore-Nwagbara, Pamela; Fielder, Bridget; DiIorio, Colleen

2007-01-01

Computer assisted interviewing (CAI) has begun to play a more prominent role in HIV/AIDS prevention research. Despite the increased popularity of CAI, particularly audio computer assisted self-interviewing (ACASI), some research teams are still reluctant to implement ACASI technology due to lack of familiarity with the practical issues related to using these software packages. The purpose of this paper is to describe the implementation of one particular ACASI software package, the Questionnaire Development System™ (QDS™), in several nursing and HIV/AIDS prevention research settings. We present acceptability and satisfaction data from two large-scale public health studies in which we have used QDS with diverse populations. We also address issues related to developing and programming a questionnaire, discuss practical strategies related to planning for and implementing ACASI in the field, including selecting equipment, training staff, and collecting and transferring data, and summarize advantages and disadvantages of computer assisted research methods. PMID:17662924

A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package.

PubMed

Lan, Hongzhi; Updegrove, Adam; Wilson, Nathan M; Maher, Gabriel D; Shadden, Shawn C; Marsden, Alison L

2018-02-01

Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid-structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, W. A.; Lepicovsky, J.

1992-01-01

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

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, William A.

1992-01-01

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

Reviews.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Reviews three computer software packages for Apple II computers. Includes "Simulation of Hemoglobin Function,""Solution Equilibrium Problems," and "Thin-Layer Chromatography." Contains ratings of ease of use, subject matter content, pedagogic value, and student reaction according to two separate reviewers for each…

Do Drills Make Drones?

ERIC Educational Resources Information Center

McKibbin, Wendy Lea

1986-01-01

Examines the shift in schools toward using software that teaches critical thinking skills. A list of 14 packages is also provided, with each entry including name, recommended age level(s), current cost, source, and a brief description. (JN)

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

PubMed

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

2017-06-01

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

Radiative transfer modeling through terrestrial atmosphere and ocean accounting for inelastic processes: Software package SCIATRAN

NASA Astrophysics Data System (ADS)

Rozanov, V. V.; Dinter, T.; Rozanov, A. V.; Wolanin, A.; Bracher, A.; Burrows, J. P.

2017-06-01

SCIATRAN is a comprehensive software package which is designed to model radiative transfer processes in the terrestrial atmosphere and ocean in the spectral range from the ultraviolet to the thermal infrared (0.18-40 μm). It accounts for multiple scattering processes, polarization, thermal emission and ocean-atmosphere coupling. The main goal of this paper is to present a recently developed version of SCIATRAN which takes into account accurately inelastic radiative processes in both the atmosphere and the ocean. In the scalar version of the coupled ocean-atmosphere radiative transfer solver presented by Rozanov et al. [61] we have implemented the simulation of the rotational Raman scattering, vibrational Raman scattering, chlorophyll and colored dissolved organic matter fluorescence. In this paper we discuss and explain the numerical methods used in SCIATRAN to solve the scalar radiative transfer equation including trans-spectral processes, and demonstrate how some selected radiative transfer problems are solved using the SCIATRAN package. In addition we present selected comparisons of SCIATRAN simulations with those published benchmark results, independent radiative transfer models, and various measurements from satellite, ground-based, and ship-borne instruments. The extended SCIATRAN software package along with a detailed User's Guide is made available for scientists and students, who are undertaking their own research typically at universities, via the web page of the Institute of Environmental Physics (IUP), University of Bremen: http://www.iup.physik.uni-bremen.de.

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.

Reusable software parts and the semi-abstract data type

NASA Technical Reports Server (NTRS)

Cohen, Sanford G.

1986-01-01

The development of reuable software parts has been an area of intense discussion within the software community for many years. An approach is described for developing reusable parts for the applications of missile guidance, navigation and control which meet the following criteria: (1) Reusable; (2) Tailorable; (3) Efficient; (4) Simple to use; and (5) Protected against misuse. Validating the feasibility of developing reusable parts which possess these characteristics is the basis of the Common Ada Missile Packages Program (CAMP). Under CAMP, over 200 reusable software parts were developed, including part for navigation, Kalman filter, signal processing and autopilot. Six different methods are presented for designing reusable software parts.

Criteria for the Evaluation of Microcomputer Courseware.

ERIC Educational Resources Information Center

Cohen, Vicki Blum

1983-01-01

Discusses attributes which are offered as set of standards to judge instructional software--those unique to design of microcomputer courseware and those included in design of all instruction. Curriculum role, modes of interaction, computer managed instruction, graphics, feedback, packaging, and manuals are noted. Fourteen references are included.…

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.

Analyzing qualitative data with computer software.

PubMed Central

Weitzman, E A

1999-01-01

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

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

NASA Astrophysics Data System (ADS)

Ramkilowan, A.; Griffith, D. J.

2017-10-01

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

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.

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.

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).

Lessons Learned from Autonomous Sciencecraft Experiment

NASA Technical Reports Server (NTRS)

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

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.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A new computer code for discrete fracture network modelling

NASA Astrophysics Data System (ADS)

Xu, Chaoshui; Dowd, Peter

2010-03-01

The authors describe a comprehensive software package for two- and three-dimensional stochastic rock fracture simulation using marked point processes. Fracture locations can be modelled by a Poisson, a non-homogeneous, a cluster or a Cox point process; fracture geometries and properties are modelled by their respective probability distributions. Virtual sampling tools such as plane, window and scanline sampling are included in the software together with a comprehensive set of statistical tools including histogram analysis, probability plots, rose diagrams and hemispherical projections. The paper describes in detail the theoretical basis of the implementation and provides a case study in rock fracture modelling to demonstrate the application of the software.

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

Pavement profile viewer and analyzer : product brief.

DOT National Transportation Integrated Search

2003-06-01

Pavement Profile Viewer and Analyzer, or ProVAL, is a software package that imports, displays, and analyzes the characteristics of pavement profiles from many different sources. ProVAL can analyze pavement profiles using several methods, including In...

PAVECHECK : training material updated user's manual including GPS.

DOT National Transportation Integrated Search

2009-01-01

PAVECHECK is a software package used to integrate nondestructive test data from various testing systems to provide the pavement engineer with a comprehensive evaluation of both surface and subsurface conditions. This User's Manual is intended to demo...

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

NASA Technical Reports Server (NTRS)

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

1983-01-01

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

Cross-platform validation and analysis environment for particle physics

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

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

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

Mold heating and cooling microprocessor conversion. Final report

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

Hoffman, D.P.

Conversion of the microprocessors and software for the Mold Heating and Cooling (MHAC) pump package control systems was initiated to allow required system enhancements and provide data communications capabilities with the Plastics Information and Control System (PICS). The existing microprocessor-based control systems for the pump packages use an Intel 8088-based microprocessor board with a maximum of 64 Kbytes of program memory. The requirements for the system conversion were developed, and hardware has been selected to allow maximum reuse of existing hardware and software while providing the required additional capabilities and capacity. The new hardware will incorporate an Intel 80286-based microprocessormore » board with an 80287 math coprocessor, the system includes additional memory, I/O, and RS232 communication ports.« less

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.

XAPiir: A recursive digital filtering package

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

Harris, D.

1990-09-21

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

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....

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

The Computational Infrastructure for Geodynamics: An Example of Software Curation and Citation in the Geodynamics Community

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2017-12-01

Curation of software promotes discoverability and accessibility and works hand in hand with scholarly citation to ascribe value to, and provide recognition for software development. To meet this challenge, the Computational Infrastructure for Geodynamics (CIG) maintains a community repository built on custom and open tools to promote discovery, access, identification, credit, and provenance of research software for the geodynamics community. CIG (geodynamics.org) originated from recognition of the tremendous effort required to develop sound software and the need to reduce duplication of effort and to sustain community codes. CIG curates software across 6 domains and has developed and follows software best practices that include establishing test cases, documentation, and a citable publication for each software package. CIG software landing web pages provide access to current and past releases; many are also accessible through the CIG community repository on github. CIG has now developed abc - attribution builder for citation to enable software users to give credit to software developers. abc uses zenodo as an archive and as the mechanism to obtain a unique identifier (DOI) for scientific software. To assemble the metadata, we searched the software's documentation and research publications and then requested the primary developers to verify. In this process, we have learned that each development community approaches software attribution differently. The metadata gathered is based on guidelines established by groups such as FORCE11 and OntoSoft. The rollout of abc is gradual as developers are forward-looking, rarely willing to go back and archive prior releases in zenodo. Going forward all actively developed packages will utilize the zenodo and github integration to automate the archival process when a new release is issued. How to handle legacy software, multi-authored libraries, and assigning roles to software remain open issues.

’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,…

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

NASA Astrophysics Data System (ADS)

Duffy, Alan; Yates, Brian; Takacs, Peter

2012-09-01

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

Evaluation of Emergency Vehicle Signal Preemption on the Route 7 Virginia Corridor

DOT National Transportation Integrated Search

1999-07-01

This study analyzed the impact of emergency vehicle traffic signal preemption across three coordinated intersections on Route 7 (Leesburg Pike near Landsdowne) in Virginia. FHWA's Traffic Software Integrated System (TSIS) package, which includes the ...

Cenozoic Antarctic DiatomWare/BugCam: An aid for research and teaching

USGS Publications Warehouse

Wise, S.W.; Olney, M.; Covington, J.M.; Egerton, V.M.; Jiang, S.; Ramdeen, D.K.; ,; Schrader, H.; Sims, P.A.; Wood, A.S.; Davis, A.; Davenport, D.R.; Doepler, N.; Falcon, W.; Lopez, C.; Pressley, T.; Swedberg, O.L.; Harwood, D.M.

2007-01-01

Cenozoic Antarctic DiatomWare/BugCam© is an interactive, icon-driven digital-image database/software package that displays over 500 illustrated Cenozoic Antarctic diatom taxa along with original descriptions (including over 100 generic and 20 family-group descriptions). This digital catalog is designed primarily for use by micropaleontologists working in the field (at sea or on the Antarctic continent) where hard-copy literature resources are limited. This new package will also be useful for classroom/lab teaching as well as for any paleontologists making or refining taxonomic identifications at the microscope. The database (Cenozoic Antarctic DiatomWare) is displayed via a custom software program (BugCam) written in Visual Basic for use on PCs running Windows 95 or later operating systems. BugCam is a flexible image display program that utilizes an intuitive thumbnail “tree” structure for navigation through the database. The data are stored on Micrsosoft EXCEL spread sheets, hence no separate relational database program is necessary to run the package

VS2DI: Model use, calibration, and validation

USGS Publications Warehouse

Healy, Richard W.; Essaid, Hedeff I.

2012-01-01

VS2DI is a software package for simulating water, solute, and heat transport through soils or other porous media under conditions of variable saturation. The package contains a graphical preprocessor for constructing simulations, a postprocessor for displaying simulation results, and numerical models that solve for flow and solute transport (VS2DT) and flow and heat transport (VS2DH). Flow is described by the Richards equation, and solute and heat transport are described by advection-dispersion equations; the finite-difference method is used to solve these equations. Problems can be simulated in one, two, or three (assuming radial symmetry) dimensions. This article provides an overview of calibration techniques that have been used with VS2DI; included is a detailed description of calibration procedures used in simulating the interaction between groundwater and a stream fed by drainage from agricultural fields in central Indiana. Brief descriptions of VS2DI and the various types of problems that have been addressed with the software package are also presented.

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

Introducing a New Software for Geodetic Analysis

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Separation in Logistic Regression: Causes, Consequences, and Control.

PubMed

Mansournia, Mohammad Ali; Geroldinger, Angelika; Greenland, Sander; Heinze, Georg

2018-04-01

Separation is encountered in regression models with a discrete outcome (such as logistic regression) where the covariates perfectly predict the outcome. It is most frequent under the same conditions that lead to small-sample and sparse-data bias, such as presence of a rare outcome, rare exposures, highly correlated covariates, or covariates with strong effects. In theory, separation will produce infinite estimates for some coefficients. In practice, however, separation may be unnoticed or mishandled because of software limits in recognizing and handling the problem and in notifying the user. We discuss causes of separation in logistic regression and describe how common software packages deal with it. We then describe methods that remove separation, focusing on the same penalized-likelihood techniques used to address more general sparse-data problems. These methods improve accuracy, avoid software problems, and allow interpretation as Bayesian analyses with weakly informative priors. We discuss likelihood penalties, including some that can be implemented easily with any software package, and their relative advantages and disadvantages. We provide an illustration of ideas and methods using data from a case-control study of contraceptive practices and urinary tract infection.

Optomechanical design software for segmented mirrors

NASA Astrophysics Data System (ADS)

Marrero, Juan

2016-08-01

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

gr-MRI: A software package for magnetic resonance imaging using software defined radios.

PubMed

Hasselwander, Christopher J; Cao, Zhipeng; Grissom, William A

2016-09-01

The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately $2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs. Copyright © 2016. Published by Elsevier Inc.

Software Models Impact Stresses

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

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

2015-01-01

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

Kassiopeia: a modern, extensible C++ particle tracking package

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

Furse, Daniel; Groh, Stefan; Trost, Nikolaus

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease-of-use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur inmore » flight such as bulk scattering and decay, and stochastic surface processes occurring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopeia.« less

Kassiopeia: a modern, extensible C++ particle tracking package

DOE PAGES

Furse, Daniel; Groh, Stefan; Trost, Nikolaus; ...

2017-05-16

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease-of-use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur inmore » flight such as bulk scattering and decay, and stochastic surface processes occurring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopeia.« less

Kassiopeia: a modern, extensible C++ particle tracking package

NASA Astrophysics Data System (ADS)

Furse, Daniel; Groh, Stefan; Trost, Nikolaus; Babutzka, Martin; Barrett, John P.; Behrens, Jan; Buzinsky, Nicholas; Corona, Thomas; Enomoto, Sanshiro; Erhard, Moritz; Formaggio, Joseph A.; Glück, Ferenc; Harms, Fabian; Heizmann, Florian; Hilk, Daniel; Käfer, Wolfgang; Kleesiek, Marco; Leiber, Benjamin; Mertens, Susanne; Oblath, Noah S.; Renschler, Pascal; Schwarz, Johannes; Slocum, Penny L.; Wandkowsky, Nancy; Wierman, Kevin; Zacher, Michael

2017-05-01

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease-of-use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occurring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle’s state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopeia.

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.

Advances in the REDCAT software package

PubMed Central

2013-01-01

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

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

NASA Technical Reports Server (NTRS)

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

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

PubMed

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

2008-10-06

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

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

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

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

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…

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

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

PubMed Central

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

2015-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

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.

International MODIS and AIRS Processing Package (IMAPP) Implementation of Infusion of Satellite Data into Environmental Applications-International (IDEA-I) for Air Quality Forecasts using Suomi-NPP, Terra and Aqua Aerosol Retrievals

NASA Astrophysics Data System (ADS)

Davies, J. E.; Strabala, K.; Pierce, R. B.; Huang, A.

2016-12-01

Fine mode aerosols play a significant role in public health through their impact on respiratory and cardiovascular disease. IDEA-I (Infusion of Satellite Data into Environmental Applications-International) is a real-time system for trajectory-based forecasts of aerosol dispersion that can assist in the prediction of poor air quality events. We released a direct broadcast version of IDEA-I for aerosol trajectory forecasts in June 2012 under the International MODIS and AIRS Processing Package (IMAPP). In January 2014 we updated this application with website software to display multi-satellite products. Now we have added VIIRS aerosols from Suomi National Polar-orbiting Partnership (S-NPP). IMAPP is a NASA-funded and freely-distributed software package developed at Space Science and Engineering Center of University of Wisconsin-Madison that has over 2,300 registered users worldwide. With IMAPP, any ground station capable of receiving direct broadcast from Terra or Aqua can produce calibrated and geolocated radiances and a suite of environmental products. These products include MODIS AOD required for IDEA-I. VIIRS AOD for IDEA-I can be generated by Community Satellite Processing Package (CSPP) VIIRS EDR Version 2.0 Software for Suomi NPP. CSPP is also developed and distributed by Space Science & Engineering Center. This presentation describes our updated IMAPP implementation of IDEA-I through an example of its operation in a region known for episodic poor air quality events.

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.

PubMed

Tregouet, D A; Garelle, V

2007-04-15

THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.

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.

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)

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

PubMed

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

2016-01-01

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

The IDL astronomy user's library

NASA Technical Reports Server (NTRS)

Landsman, W. B.

1992-01-01

IDL (Interactive Data Language) is a commercial programming, plotting, and image display language, which is widely used in astronomy. The IDL Astronomy User's Library is a central repository of over 400 astronomy-related IDL procedures accessible via anonymous FTP. The author will overview the use of IDL within the astronomical community and discuss recent enhancements at the IDL astronomy library. These enhancements include a fairly complete I/O package for FITS images and tables, an image deconvolution package and an image mosaic package, and access to IDL Open Windows/Motif widgets interface. The IDL Astronomy Library is funded by NASA through the Astrophysics Software and Research Aids Program.

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

The use of applied software for the professional training of students studying humanities

NASA Astrophysics Data System (ADS)

Sadchikova, A. S.; Rodin, M. M.

2017-01-01

Research practice is an integral part of humanities students' training process. In this regard the training process is to include modern information techniques of the training process of students studying humanities. This paper examines the most popular applied software products used for data processing in social science. For testing purposes we selected the most commonly preferred professional packages: MS Excel, IBM SPSS Statistics, STATISTICA, STADIA. Moreover the article contains testing results of a specialized software Prikladnoy Sotsiolog that is applicable for the preparation stage of the research. The specialised software were tested during one term in groups of students studying humanities.

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.

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

PubMed

Crowell, Kevin L; Slysz, Gordon W; Baker, Erin S; LaMarche, Brian L; Monroe, Matthew E; Ibrahim, Yehia M; Payne, Samuel H; Anderson, Gordon A; Smith, Richard D

2013-11-01

The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing. We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension. LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README). rds@pnnl.gov. Supplementary data are available at Bioinformatics online.

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.

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 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…

The Cloud Feedback Model Intercomparison Project Observational Simulator Package: Version 2

NASA Astrophysics Data System (ADS)

Swales, Dustin J.; Pincus, Robert; Bodas-Salcedo, Alejandro

2018-01-01

The Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) gathers together a collection of observation proxies or satellite simulators that translate model-simulated cloud properties to synthetic observations as would be obtained by a range of satellite observing systems. This paper introduces COSP2, an evolution focusing on more explicit and consistent separation between host model, coupling infrastructure, and individual observing proxies. Revisions also enhance flexibility by allowing for model-specific representation of sub-grid-scale cloudiness, provide greater clarity by clearly separating tasks, support greater use of shared code and data including shared inputs across simulators, and follow more uniform software standards to simplify implementation across a wide range of platforms. The complete package including a testing suite is freely available.

Implementation of Altimetry Data in the GIPSY POD Software Package

NASA Technical Reports Server (NTRS)

Stauch, Jason R.; Gold, Kenn; Born, George H.

2001-01-01

Altimetry data has been used extensively to acquire data about characteristics of the Earth, the Moon, and Mars. More recently, the idea of using altimetry for orbit determination has also been explored. This report discusses modifications to JPL's GIPSY/OASIS II software to include altimetry data as an observation type for precise orbit determination. The mathematical foundation of using altimetry for the purpose of orbit determination is presented, along with results.

Digital Topographic Support System (DTSS).

DTIC Science & Technology

1987-07-29

effects applications software, a word processing package and a Special Purpose Product Builder ( SPPB ) in terms common to his Job. Through the MI, the...communicating with the TA in terms he understands, the applications software, the SPPB and the GIS form the underlying tools which perform the computations and...displayed on the monitors or plotted on paper or Mylar. The SPPB will guide the TA enabling him to design products which are not included in the applications

Strehl-constrained reconstruction of post-adaptive optics data and the Software Package AIRY, v. 6.1

NASA Astrophysics Data System (ADS)

Carbillet, Marcel; La Camera, Andrea; Deguignet, Jérémy; Prato, Marco; Bertero, Mario; Aristidi, Éric; Boccacci, Patrizia

2014-08-01

We first briefly present the last version of the Software Package AIRY, version 6.1, a CAOS-based tool which includes various deconvolution methods, accelerations, regularizations, super-resolution, boundary effects reduction, point-spread function extraction/extrapolation, stopping rules, and constraints in the case of iterative blind deconvolution (IBD). Then, we focus on a new formulation of our Strehl-constrained IBD, here quantitatively compared to the original formulation for simulated near-infrared data of an 8-m class telescope equipped with adaptive optics (AO), showing their equivalence. Next, we extend the application of the original method to the visible domain with simulated data of an AO-equipped 1.5-m telescope, testing also the robustness of the method with respect to the Strehl ratio estimation.

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by UAH and provide versions of the software in a Macintosh and Windows compatible format.

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.

Organizational Response to the Introduction of New Computer Software Technology

DTIC Science & Technology

1991-07-01

the documentation to be much use at all." Another said that "the tutorial did a good job, but ... the manual did an average job." The Lotus Manuscript...when they have a specific use in mind and believe they can find the information easily in the manual . 12 The AutoCAD users were also split on their...AutoCAD user with AutoLISP , a programming language included in the package. (Some CADD packages come with these features and others as part of the

A CAD approach to magnetic bearing design

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

Implementation of audio computer-assisted interviewing software in HIV/AIDS research.

PubMed

Pluhar, Erika; McDonnell Holstad, Marcia; Yeager, Katherine A; Denzmore-Nwagbara, Pamela; Corkran, Carol; Fielder, Bridget; McCarty, Frances; Diiorio, Colleen

2007-01-01

Computer-assisted interviewing (CAI) has begun to play a more prominent role in HIV/AIDS prevention research. Despite the increased popularity of CAI, particularly audio computer-assisted self-interviewing (ACASI), some research teams are still reluctant to implement ACASI technology because of lack of familiarity with the practical issues related to using these software packages. The purpose of this report is to describe the implementation of one particular ACASI software package, the Questionnaire Development System (QDS; Nova Research Company, Bethesda, MD), in several nursing and HIV/AIDS prevention research settings. The authors present acceptability and satisfaction data from two large-scale public health studies in which they have used QDS with diverse populations. They also address issues related to developing and programming a questionnaire; discuss practical strategies related to planning for and implementing ACASI in the field, including selecting equipment, training staff, and collecting and transferring data; and summarize advantages and disadvantages of computer-assisted research methods.

Probabilistic Design and Analysis Framework

NASA Technical Reports Server (NTRS)

Strack, William C.; Nagpal, Vinod K.

2010-01-01

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

A Digital Control Algorithm for Magnetic Suspension Systems

NASA Technical Reports Server (NTRS)

Britton, Thomas C.

1996-01-01

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

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

NASA Technical Reports Server (NTRS)

Mcgary, M. C.

1982-01-01

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

Reviewing and Viewing.

ERIC Educational Resources Information Center

Clements, Douglas H., Ed.; And Others

1988-01-01

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

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

DOT National Transportation Integrated Search

1982-11-01

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

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

ERIC Educational Resources Information Center

Leach, James A.; Gull, Randall L.

1990-01-01

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

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.

Assessment of Dose to the Nursing Infant from Radionuclides in Breast Milk

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

Leggett, Richard Wayne; Eckerman, Keith F

A computer software package was developed to predict tissue doses to an infant due to intake of radionuclides in breast milk based on bioassay measurements and exposure data for the mother. The package is intended mainly to aid in decisions regarding the safety of breast feeding by a mother who has been acutely exposed to a radionuclide during lactation or pregnancy, but it may be applied to previous intakes during the mother s adult life. The package includes biokinetic and dosimetric information needed to address intake of Co-60, Sr-90, Cs-134, Cs-137, Ir-192, Pu-238, Pu-239, Am-241, or Cf-252 by the mother.more » It has been designed so that the library of biokinetic and dosimetric files can be expanded to address a more comprehensive set of radionuclides without modifying the basic computational module. The methods and models build on the approach used in Publication 95 of the International Commission on Radiological Protection (ICRP 2004), Doses to Infants from Ingestion of Radionuclides in Mothers Milk . The software package allows input of case-specific information or judgments such as chemical form or particle size of an inhaled aerosol. The package is expected to be more suitable than ICRP Publication 95 for dose assessment for real events or realistic planning scenarios in which measurements of the mother s excretion or body burden are available.« less

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina

2018-04-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel , designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel , designed to facilitate the exploration of novel research questions for advanced modelers.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks

PubMed Central

Jenness, Samuel M.; Goodreau, Steven M.; Morris, Martina

2018-01-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers. PMID:29731699

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.

Painting a picture across the landscape with ModelMap

Treesearch

Brian Cooke; Elizabeth Freeman; Gretchen Moisen; Tracey Frescino

2017-01-01

Scientists and statisticians working for the Rocky Mountain Research Station have created a software package that simplifies and automates many of the processes needed for converting models into maps. This software package, called ModelMap, has helped a variety of specialists and land managers to quickly convert data into easily understood graphical images. The...

"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…

Active Mirror Predictive and Requirements Verification Software (AMP-ReVS)

NASA Technical Reports Server (NTRS)

Basinger, Scott A.

2012-01-01

This software is designed to predict large active mirror performance at various stages in the fabrication lifecycle of the mirror. It was developed for 1-meter class powered mirrors for astronomical purposes, but is extensible to other geometries. The package accepts finite element model (FEM) inputs and laboratory measured data for large optical-quality mirrors with active figure control. It computes phenomenological contributions to the surface figure error using several built-in optimization techniques. These phenomena include stresses induced in the mirror by the manufacturing process and the support structure, the test procedure, high spatial frequency errors introduced by the polishing process, and other process-dependent deleterious effects due to light-weighting of the mirror. Then, depending on the maturity of the mirror, it either predicts the best surface figure error that the mirror will attain, or it verifies that the requirements for the error sources have been met once the best surface figure error has been measured. The unique feature of this software is that it ties together physical phenomenology with wavefront sensing and control techniques and various optimization methods including convex optimization, Kalman filtering, and quadratic programming to both generate predictive models and to do requirements verification. This software combines three distinct disciplines: wavefront control, predictive models based on FEM, and requirements verification using measured data in a robust, reusable code that is applicable to any large optics for ground and space telescopes. The software also includes state-of-the-art wavefront control algorithms that allow closed-loop performance to be computed. It allows for quantitative trade studies to be performed for optical systems engineering, including computing the best surface figure error under various testing and operating conditions. After the mirror manufacturing process and testing have been completed, the software package can be used to verify that the underlying requirements have been met.

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.

Atrioventricular junction (AVJ) motion tracking: a software tool with ITK/VTK/Qt.

PubMed

Pengdong Xiao; Shuang Leng; Xiaodan Zhao; Hua Zou; Ru San Tan; Wong, Philip; Liang Zhong

2016-08-01

The quantitative measurement of the Atrioventricular Junction (AVJ) motion is an important index for ventricular functions of one cardiac cycle including systole and diastole. In this paper, a software tool that can conduct AVJ motion tracking from cardiovascular magnetic resonance (CMR) images is presented by using Insight Segmentation and Registration Toolkit (ITK), The Visualization Toolkit (VTK) and Qt. The software tool is written in C++ by using Visual Studio Community 2013 integrated development environment (IDE) containing both an editor and a Microsoft complier. The software package has been successfully implemented. From the software engineering practice, it is concluded that ITK, VTK, and Qt are very handy software systems to implement automatic image analysis functions for CMR images such as quantitative measure of motion by visual tracking.

Methodology of functionality selection for water management software and examples of its application.

PubMed

Vasilyev, K N

2013-01-01

When developing new software products and adapting existing software, project leaders have to decide which functionalities to keep, adapt or develop. They have to consider that the cost of making errors during the specification phase is extremely high. In this paper a formalised approach is proposed that considers the main criteria for selecting new software functions. The application of this approach minimises the chances of making errors in selecting the functions to apply. Based on the work on software development and support projects in the area of water resources and flood damage evaluation in economic terms at CH2M HILL (the developers of the flood modelling package ISIS), the author has defined seven criteria for selecting functions to be included in a software product. The approach is based on the evaluation of the relative significance of the functions to be included into the software product. Evaluation is achieved by considering each criterion and the weighting coefficients of each criterion in turn and applying the method of normalisation. This paper includes a description of this new approach and examples of its application in the development of new software products in the are of the water resources management.

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

Introducing a New Software for Geodetic Analysis

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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.

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.

National Computer Security Conference (13th) Held in Washington, DC on 1-4 October, 1990. Procedings. Volume 1: Information Systems Security: Standards - The Key to the Future

DTIC Science & Technology

1990-10-04

methods Category 6: Cryptographic methods (hard/ software ) - Tested countermeasures and standard means - Acknowledgements As the number of antivirus ...Skulason), only our own antiviruses have been mentioned in the catalog. We hope to include the major antivirus packages in the future. The current...Center GTE SRI International Trusted Information Systems, Inc. Grumann Data Systems SRI International Software Engineering Institute Trusted

Considerations for choosing an electronic medical record for an ophthalmology practice.

PubMed

DeBry, P W

2001-04-01

To give a brief overview of issues pertinent to selecting an ophthalmic electronic medical record (EMR) program and to outline the company demographics and software capabilities of the major vendors in this area. Software companies shipping an EMR package were contacted to obtain information on their software and company demographics. The focus was on companies selectively marketing to ophthalmology practices, and, therefore, most were selected based on their representation at the 1998 and/or 1999 American Academy of Ophthalmology meeting. Software companies that responded to repeated inquiries in a timely fashion were included. Sixteen companies were evaluated. Electronic medical records packages ranged from $3000 to $80 000 (mean, approximately $30 000). Company demographics revealed a range from 1 to 1600 employees (mean, 204). Most of these companies have been in business for 6 years or less (range, 1-15 years; mean, 6 years). My opinions concerning various aspects of the EMR are presented. There is a wide range of EMR products available for the ophthalmology practice. Computer technology has matured to a point at which the graphical demands of the ophthalmology EMR can be satisfied. Weaknesses do exist in the inherent difficulty of recording an ophthalmology encounter, the relative adolescence of software companies, and the lack of standards in the industry.

The experience factory: Can it make you a 5? or what is its relationship to other quality and improvement concepts?

NASA Technical Reports Server (NTRS)

Basili, Victor R.

1992-01-01

The concepts of quality improvements have permeated many businesses. It is clear that the nineties will be the quality era for software and there is a growing need to develop or adapt quality improvement approaches to the software business. Thus we must understand software as an artifact and software as a business. Since the business we are dealing with is software, we must understand the nature of software and software development. The software discipline is evolutionary and experimental; it is a laboratory science. Software is development not production. The technologies of the discipline are human based. There is a lack of models that allow us to reason about the process and the product. All software is not the same; process is a variable, goals are variable, etc. Packaged, reusable, experiences require additional resources in the form of organization, processes, people, etc. There have been a variety of organizational frameworks proposed to improve quality for various businesses. The ones discussed in this presentation include: Plan-Do-Check-Act, a quality improvement process based upon a feedback cycle for optimizing a single process model/production line; the Experience Factory/Quality Improvement Paradigm, continuous improvements through the experimentation, packaging, and reuse of experiences based upon a business's needs; Total Quality Management, a management approach to long term success through customer satisfaction based on the participation of all members of an organization; the SEI capability maturity model, a staged process improvement based upon assessment with regard to a set of key process areas until you reach a level 5 which represents a continuous process improvement; and Lean (software) Development, a principle supporting the concentration of the production on 'value added' activities and the elimination of reduction of 'not value added' activities.

AstroBlend: An astrophysical visualization package for Blender

NASA Astrophysics Data System (ADS)

Naiman, J. P.

2016-04-01

The rapid growth in scale and complexity of both computational and observational astrophysics over the past decade necessitates efficient and intuitive methods for examining and visualizing large datasets. Here, I present AstroBlend, an open-source Python library for use within the three dimensional modeling software, Blender. While Blender has been a popular open-source software among animators and visual effects artists, in recent years it has also become a tool for visualizing astrophysical datasets. AstroBlend combines the three dimensional capabilities of Blender with the analysis tools of the widely used astrophysical toolset, yt, to afford both computational and observational astrophysicists the ability to simultaneously analyze their data and create informative and appealing visualizations. The introduction of this package includes a description of features, work flow, and various example visualizations. A website - www.astroblend.com - has been developed which includes tutorials, and a gallery of example images and movies, along with links to downloadable data, three dimensional artistic models, and various other resources.

State-of-the-art software for window energy-efficiency rating and labeling

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

Arasteh, D.; Finlayson, E.; Huang, J.

1998-07-01

Measuring the thermal performance of windows in typical residential buildings is an expensive proposition. Not only is laboratory testing expensive, but each window manufacturer typically offers hundreds of individual products, each of which has different thermal performance properties. With over a thousand window manufacturers nationally, a testing-based rating system would be prohibitively expensive to the industry and to consumers. Beginning in the early 1990s, simulation software began to be used as part of a national program for rating window U-values. The rating program has since been expanded to include Solar Hear Gain Coefficients and is now being extended to annualmore » energy performance. This paper describes four software packages available to the public from Lawrence Berkeley National Laboratory (LBNL). These software packages are used to evaluate window thermal performance: RESFEN (for evaluating annual energy costs), WINDOW (for calculating a product`s thermal performance properties), THERM (a preprocessor for WINDOW that determines two-dimensional heat-transfer effects), and Optics (a preprocessor for WINDOW`s glass database). Software not only offers a less expensive means than testing to evaluate window performance, it can also be used during the design process to help manufacturers produce windows that will meet target specifications. In addition, software can show small improvements in window performance that might not be detected in actual testing because of large uncertainties in test procedures.« less

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.; Olariu, Stephen

1995-01-01

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

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/ .

'tomo_display' and 'vol_tools': IDL VM Packages for Tomography Data Reconstruction, Processing, and Visualization

NASA Astrophysics Data System (ADS)

Rivers, M. L.; Gualda, G. A.

2009-05-01

One of the challenges in tomography is the availability of suitable software for image processing and analysis in 3D. We present here 'tomo_display' and 'vol_tools', two packages created in IDL that enable reconstruction, processing, and visualization of tomographic data. They complement in many ways the capabilities offered by Blob3D (Ketcham 2005 - Geosphere, 1: 32-41, DOI: 10.1130/GES00001.1) and, in combination, allow users without programming knowledge to perform all steps necessary to obtain qualitative and quantitative information using tomographic data. The package 'tomo_display' was created and is maintained by Mark Rivers. It allows the user to: (1) preprocess and reconstruct parallel beam tomographic data, including removal of anomalous pixels, ring artifact reduction, and automated determination of the rotation center, (2) visualization of both raw and reconstructed data, either as individual frames, or as a series of sequential frames. The package 'vol_tools' consists of a series of small programs created and maintained by Guilherme Gualda to perform specific tasks not included in other packages. Existing modules include simple tools for cropping volumes, generating histograms of intensity, sample volume measurement (useful for porous samples like pumice), and computation of volume differences (for differential absorption tomography). The module 'vol_animate' can be used to generate 3D animations using rendered isosurfaces around objects. Both packages use the same NetCDF format '.volume' files created using code written by Mark Rivers. Currently, only 16-bit integer volumes are created and read by the packages, but floating point and 8-bit data can easily be stored in the NetCDF format as well. A simple GUI to convert sequences of tiffs into '.volume' files is available within 'vol_tools'. Both 'tomo_display' and 'vol_tools' include options to (1) generate onscreen output that allows for dynamic visualization in 3D, (2) save sequences of tiffs to disk, and (3) generate MPEG movies for inclusion in presentations, publications, websites, etc. Both are freely available as run-time ('.sav') versions that can be run using the free IDL Virtual Machine TM, available from ITT Visual Information Solutions: http://www.ittvis.com/ProductServices/IDL/VirtualMachine.aspx The run-time versions of 'tomo_display' and 'vol_tools' can be downloaded from: http://cars.uchicago.edu/software/idl/tomography.html http://sites.google.com/site/voltools/

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

Cluster-lensing: A Python Package for Galaxy Clusters and Miscentering

NASA Astrophysics Data System (ADS)

Ford, Jes; VanderPlas, Jake

2016-12-01

We describe a new open source package for calculating properties of galaxy clusters, including Navarro, Frenk, and White halo profiles with and without the effects of cluster miscentering. This pure-Python package, cluster-lensing, provides well-documented and easy-to-use classes and functions for calculating cluster scaling relations, including mass-richness and mass-concentration relations from the literature, as well as the surface mass density {{Σ }}(R) and differential surface mass density {{Δ }}{{Σ }}(R) profiles, probed by weak lensing magnification and shear. Galaxy cluster miscentering is especially a concern for stacked weak lensing shear studies of galaxy clusters, where offsets between the assumed and the true underlying matter distribution can lead to a significant bias in the mass estimates if not accounted for. This software has been developed and released in a public GitHub repository, and is licensed under the permissive MIT license. The cluster-lensing package is archived on Zenodo. Full documentation, source code, and installation instructions are available at http://jesford.github.io/cluster-lensing/.

TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.

PubMed

Cuadros-Inostroza, Alvaro; Caldana, Camila; Redestig, Henning; Kusano, Miyako; Lisec, Jan; Peña-Cortés, Hugo; Willmitzer, Lothar; Hannah, Matthew A

2009-12-16

Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data.

TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data

PubMed Central

2009-01-01

Background Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. Results We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. Conclusions TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data. PMID:20015393

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.

ELSA: An integrated, semi-automated nebular abundance package

NASA Astrophysics Data System (ADS)

Johnson, Matthew D.; Levitt, Jesse S.; Henry, Richard B. C.; Kwitter, Karen B.

We present ELSA, a new modular software package, written in C, to analyze and manage spectroscopic data from emission-line objects. In addition to calculating plasma diagnostics and abundances from nebular emission lines, the software provides a number of convenient features including the ability to ingest logs produced by IRAF's splot task, to semi-automatically merge spectra in different wavelength ranges, and to automatically generate various data tables in machine-readable or LaTeX format. ELSA features a highly sophisticated interstellar reddening correction scheme that takes into account temperature and density effects as well as He II contamination of the hydrogen Balmer lines. Abundance calculations are performed using a 5-level atom approximation with recent atomic data, based on R. Henry's ABUN program. Downloading and detailed documentation for all aspects of ELSA are available at the following URL:

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.

Overview of Current Activities in Combustion Instability

DTIC Science & Technology

2015-10-02

and avoid liquid rocket engine combustion stability problems Approach:  1) Develop a  SOA  combustion stability software package  called Stable...phase II will invest in Multifidelity Tools and Methodologies – CSTD will develop a SOA combustion stability software package called Stable Combustion

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.

SEL's Software Process-Improvement Program

NASA Technical Reports Server (NTRS)

Basili, Victor; Zelkowitz, Marvin; McGarry, Frank; Page, Jerry; Waligora, Sharon; Pajerski, Rose

1995-01-01

The goals and operations of the Software Engineering Laboratory (SEL) is reviewed. For nearly 20 years the SEL has worked to understand, assess, and improve software and the development process within the production environment of the Flight Dynamics Division (FDD) of NASA's Goddard Space Flight Center. The SEL was established in 1976 with the goals of reducing: (1) the defect rate of delivered software, (2) the cost of software to support flight projects, and (3) the average time to produce mission-support software. After studying over 125 projects of FDD, the results have guided the standards, management practices, technologies, and the training within the division. The results of the studies have been a 75 percent reduction in defects, a 50 percent reduction in cost, and a 25 percent reduction in development time. Over time the goals of SEL have been clarified. The goals are now stated as: (1) Understand baseline processes and product characteristics, (2) Assess improvements that have been incorporated into the development projects, (3) Package and infuse improvements into the standard SEL process. The SEL improvement goal is to demonstrate continual improvement of the software process by carrying out analysis, measurement and feedback to projects with in the FDD environment. The SEL supports the understanding of the process by study of several processes including, the effort distribution, and error detection rates. The SEL assesses and refines the processes. Once the assessment and refinement of a process is completed, the SEL packages the process by capturing the process in standards, tools and training.

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)

Object-oriented design of medical imaging software.

PubMed

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

1994-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Electronic Router

NASA Technical Reports Server (NTRS)

Crusan, Jason

2005-01-01

Electronic Router (E-Router) is an application program for routing documents among the cognizant individuals in a government agency or other organization. E-Router supplants a prior 14 NASA Tech Briefs, May 2005 system in which paper documents were routed physically in packages by use of paper slips, packages could be lost, routing times were unacceptably long, tracking of packages was difficult, and there was a need for much photocopying. E-Router enables a user to create a digital package to be routed. Input accepted by E-Router includes the title of the package, the person(s) to whom the package is to be routed, attached files, and comments to reviewers. Electronic mail is used to notify reviewers of needed actions. The creator of the package can, at any time, see the status of the package in the routing structure. At the end of the routing process, E-Router keeps a record of the package and of approvals and/or concurrences of the reviewers. There are commercial programs that perform the general functions of E-Router, but they are more complicated. E-Router is Web-based, easy to use, and does not require the installation or use of client software.

The Resource Directory: Designing Your Success.

ERIC Educational Resources Information Center

Bowers, Richard A.

1995-01-01

Discusses computer software and system design in the information industry and provides an annotated bibliography of 31 resources that address the issue of design. Highlights include competition, color use, hardware and presentation design, content and packaging, screen design, graphics, and interactive multimedia. A sidebar reviews and rates seven…

Computer Series, 89.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1988-01-01

Describes five computer software packages; four for MS-DOS Systems and one for Apple II. Included are SPEC20, an interactive simulation of a Bausch and Lomb Spectronic-20; a database for laboratory chemicals and programs for visualizing Boltzmann-like distributions, orbital plot for the hydrogen atom and molecular orbital theory. (CW)

SIMWEST: A simulation model for wind and photovoltaic energy storage systems (CDC user's manual), volume 1

NASA Technical Reports Server (NTRS)

Warren, A. W.; Esinger, A. W.

1979-01-01

Procedures are given for using the SIMWEST program on CDC 6000 series computers. This expanded software package includes wind and/or photovoltaic systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel, and pneumatic).

HAL/S-FC compiler system functional specification

NASA Technical Reports Server (NTRS)

1974-01-01

Compiler organization is discussed, including overall compiler structure, internal data transfer, compiler development, and code optimization. The user, system, and SDL interfaces are described, along with compiler system requirements. Run-time software support package and restrictions and dependencies are also considered of the HAL/S-FC system.

Technology Trends: Buying a Computer.

ERIC Educational Resources Information Center

Strot, Melody; Benno, Mark

1997-01-01

Provides guidelines for buying computers for parents of gifted children. Steps for making decisions include deciding who will use the computer, deciding its purposes and what software packages will be used, determining current and future needs, setting a budget, and reviewing needs with salespersons and school-based technology specialists. (CR)

Scilab software package for the study of dynamical systems

NASA Astrophysics Data System (ADS)

Bordeianu, C. C.; Beşliu, C.; Jipa, Al.; Felea, D.; Grossu, I. V.

2008-05-01

This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE. Program summaryProgram title: Chaos Catalogue identifier: AEAP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 885 No. of bytes in distributed program, including test data, etc.: 5925 Distribution format: tar.gz Programming language: Scilab 3.1.1 Computer: PC-compatible running Scilab on MS Windows or Linux Operating system: Windows XP, Linux RAM: below 100 Megabytes Classification: 6.2 Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE). Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies. Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem. Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE and Lyapunov exponents calculation.

Spinors: A Mathematica package for doing spinor calculus in General Relativity

NASA Astrophysics Data System (ADS)

Gómez-Lobo, Alfonso García-Parrado; Martín-García, José M.

2012-10-01

The Spinors software is a Mathematica package which implements 2-component spinor calculus as devised by Penrose for General Relativity in dimension 3+1. The Spinors software is part of the xAct system, which is a collection of Mathematica packages to do tensor analysis by computer. In this paper we give a thorough description of Spinors and present practical examples of use. Program summary Program title: Spinors Catalogue identifier: AEMQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 117039 No. of bytes in distributed program, including test data, etc.: 300404 Distribution format: tar.gz Programming language: Mathematica. Computer: Any computer running Mathematica 7.0 or higher. Operating system: Any operating system compatible with Mathematica 7.0 or higher. RAM: 94Mb in Mathematica 8.0. Classification: 1.5. External routines: Mathematica packages xCore, xPerm and xTensor which are part of the xAct system. These can be obtained at http://www.xact.es. Nature of problem: Manipulation and simplification of spinor expressions in General Relativity. Solution method: Adaptation of the tensor functionality of the xAct system for the specific situation of spinor calculus in four dimensional Lorentzian geometry. Restrictions: The software only works on 4-dimensional Lorentzian space-times with metric of signature (1, -1, -1, -1). There is no direct support for Dirac spinors. Unusual features: Easy rules to transform tensor expressions into spinor ones and back. Seamless integration of abstract index manipulation of spinor expressions with component computations. Running time: Under one second to handle and canonicalize standard spinorial expressions with a few dozen indices. (These expressions arise naturally in the transformation of a spinor expression into a tensor one or vice versa.)

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.

HashDist: Reproducible, Relocatable, Customizable, Cross-Platform Software Stacks for Open Hydrological Science

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Developing scientific software is a continuous balance between not reinventing the wheel and getting fragile codes to interoperate with one another. Binary software distributions such as Anaconda provide a robust starting point for many scientific software packages, but this solution alone is insufficient for many scientific software developers. HashDist provides a critical component of the development workflow, enabling highly customizable, source-driven, and reproducible builds for scientific software stacks, available from both the IPython Notebook and the command line. To address these issues, the Coastal and Hydraulics Laboratory at the US Army Engineer Research and Development Center has funded the development of HashDist in collaboration with Simula Research Laboratories and the University of Texas at Austin. HashDist is motivated by a functional approach to package build management, and features intelligent caching of sources and builds, parametrized build specifications, and the ability to interoperate with system compilers and packages. HashDist enables the easy specification of "software stacks", which allow both the novice user to install a default environment and the advanced user to configure every aspect of their build in a modular fashion. As an advanced feature, HashDist builds can be made relocatable, allowing the easy redistribution of binaries on all three major operating systems as well as cloud, and supercomputing platforms. As a final benefit, all HashDist builds are reproducible, with a build hash specifying exactly how each component of the software stack was installed. This talk discusses the role of HashDist in the hydrological sciences, including its use by the Coastal and Hydraulics Laboratory in the development and deployment of the Proteus Toolkit as well as the Rapid Operational Access and Maneuver Support project. We demonstrate HashDist in action, and show how it can effectively support development, deployment, teaching, and reproducibility for scientists working in the hydrological sciences. The HashDist documentation is available from: http://hashdist.readthedocs.org/en/latest/ HashDist is currently hosted at: https://github.com/hashdist/hashdist

The CUORE slow monitoring systems

NASA Astrophysics Data System (ADS)

Gladstone, L.; Biare, D.; Cappelli, L.; Cushman, J. S.; Del Corso, F.; Fujikawa, B. K.; Hickerson, K. P.; Moggi, N.; Pagliarone, C. E.; Schmidt, B.; Wagaarachchi, S. L.; Welliver, B.; Winslow, L. A.

2017-09-01

CUORE is a cryogenic experiment searching primarily for neutrinoless double decay in 130Te. It will begin data-taking operations in 2016. To monitor the cryostat and detector during commissioning and data taking, we have designed and developed Slow Monitoring systems. In addition to real-time systems using LabVIEW, we have an alarm, analysis, and archiving website that uses MongoDB, AngularJS, and Bootstrap software. These modern, state of the art software packages make the monitoring system transparent, easily maintainable, and accessible on many platforms including mobile devices.

Development of a CCD based solar speckle imaging system

NASA Astrophysics Data System (ADS)

Nisenson, Peter; Stachnik, Robert V.; Noyes, Robert W.

1986-02-01

A program to develop software and hardware for the purpose of obtaining high angular resolution images of the solar surface is described. The program included the procurement of a Charge Coupled Devices imaging system; an extensive laboratory and remote site testing of the camera system; the development of a software package for speckle image reconstruction which was eventually installed and tested at the Sacramento Peak Observatory; and experiments of the CCD system (coupled to an image intensifier) for low light level, narrow spectral band solar imaging.

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Earth Global Reference Atmospheric Model (Earth-GRAM) GRAM Virtual Meeting

NASA Technical Reports Server (NTRS)

White, Patrick

2017-01-01

What is Earth-GRAM? Provide monthly mean and standard deviation for any point in atmosphere; Monthly, Geographic, and Altitude Variation. Earth-GRAM is a C++ software package; Currently distributed as Earth-GRAM 2016. Atmospheric variables included: pressure, density, temperature, horizontal and vertical winds, speed of sound, and atmospheric constituents. Used by engineering community because of ability to create dispersions inatmosphere at a rapid runtime; Often embedded in trajectory simulation software. Not a forecast model. Does not readily capture localized atmospheric effects.

Program Aids Design Of Fluid-Circulating Systems

NASA Technical Reports Server (NTRS)

Bacskay, Allen; Dalee, Robert

1992-01-01

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

Ada (Trade Name) Foundation Technology. Volume 4. Software Requirements for WIS (WWMCCS (World Wide Military Command and Control System) Information System) Text Processing Prototypes

DTIC Science & Technology

1986-12-01

graphics : The package allows a character set which can be defined by users giving the picture for a character by designating its pixels. Such characters...type lonts and gsei-oriented "help" messages tailored to the operations being performed and user expertise In general, critical design issues...other volumes include command language, software design , description and analysis tools, database management system operating systems; planning and

Evaluation and Selection of a Telecommunication System at the Naval Postgraduate School BOQ

DTIC Science & Technology

1991-03-01

software, and operating system software as a part of a complete package. An internal modem must be included for remote diagnostic and programming...2 service delivery will follow the CCITT V.35 recommendation for physical, functional and electrical interfaces. Type 1 & 2 will transfer data at 56K ...by a dedicated access line at 4.8 kbs and 9.6 Kbps and 56k /64Kbps. PSS will follow the CCITT X.25 recommendations. E-mail service may be provided on

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

A knowledge-based approach to improving optimization techniques in system planning

NASA Technical Reports Server (NTRS)

Momoh, J. A.; Zhang, Z. Z.

1990-01-01

A knowledge-based (KB) approach to improve mathematical programming techniques used in the system planning environment is presented. The KB system assists in selecting appropriate optimization algorithms, objective functions, constraints and parameters. The scheme is implemented by integrating symbolic computation of rules derived from operator and planner's experience and is used for generalized optimization packages. The KB optimization software package is capable of improving the overall planning process which includes correction of given violations. The method was demonstrated on a large scale power system discussed in the paper.

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.

Bending of I-beam with the transvers shear effect included - FEM calculated

NASA Astrophysics Data System (ADS)

Grygorowicz, Magdalena; Lewiński, Jerzy

2016-06-01

The paper is devoted to three-point bending of an I-beam with include of transvers shear effect. Numerical calculations were conducted independently with the use of the SolidWorks system and the multi-purpose software package ANSYS The results of FEM study conducted with the use of two systems were compared and presented in tables and figures.

Bending of I-beam with the transvers shear effect included – FEM calculated

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

Grygorowicz, Magdalena; Lewiński, Jerzy

2016-06-08

The paper is devoted to three-point bending of an I-beam with include of transvers shear effect. Numerical calculations were conducted independently with the use of the SolidWorks system and the multi-purpose software package ANSYS The results of FEM study conducted with the use of two systems were compared and presented in tables and figures.

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.

[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.

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.

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by University of Alabama in Huntsville (UAH) and provide versions of the software in a Macintosh and Windows compatible format. Appendix 1 science requirements document (SRD) Users Manual is attached.

Traduccion automatica mediante el ordenador (Automatic Translation Using a Computer).

ERIC Educational Resources Information Center

Bueno, Julian L.

This report on machine translation contains a brief history of the field; a description of the processes involved; a discussion of systems currently in use, including three software packages on the market (Teaching Assistant, Translate, and Globalink); reflections on implications for teaching; observations of results obtained when elements of…

26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., etc. Section 197 intangibles include any patent, copyright, formula, process, design, pattern, know-how, format, package design, computer software (as defined in paragraph (c)(4)(iv) of this section... agreement that provides one of the parties to the agreement with the right to distribute, sell, or provide...

Non Contacting Evaluation of Strains and Cracking Using Optical and Infrared Imaging Techniques

DTIC Science & Technology

1988-08-22

Compatible Zenith Z-386 microcomputer with plotter II. 3-D Motion Measurinq System 1. Complete OPTOTRAK three dimensional digitizing system. System includes...acquisition unit - 16 single ended analog input channels 3. Data Analysis Package software (KINEPLOT) 4. Extra OPTOTRAK Camera (max 224 per system

Robo-Sensei's NLP-Based Error Detection and Feedback Generation

ERIC Educational Resources Information Center

Nagata, Noriko

2009-01-01

This paper presents a new version of Robo-Sensei's NLP (Natural Language Processing) system which updates the version currently available as the software package "ROBO-SENSEI: Personal Japanese Tutor" (Nagata, 2004). Robo-Sensei's NLP system includes a lexicon, a morphological generator, a word segmentor, a morphological parser, a syntactic…

Reporting Subscores Using R: A Software Review

ERIC Educational Resources Information Center

Dai, Shenghai; Svetina, Dubravka; Wang, Xiaolin

2017-01-01

There is an increasing interest in reporting test subscores for diagnostic purposes. In this article, we review nine popular R packages (subscore, mirt, TAM, sirt, CDM, NPCD, lavaan, sem, and OpenMX) that are capable of implementing subscore-reporting methods within one or more frameworks including classical test theory, multidimensional item…

The importance of data curation on QSAR Modeling - PHYSPROP open data as a case study. (QSAR 2016)

EPA Science Inventory

During the last few decades many QSAR models and tools have been developed at the US EPA, including the widely used EPISuite. During this period the arsenal of computational capabilities supporting cheminformatics has broadened dramatically with multiple software packages. These ...

The Expanded Capabilities Of The Cementitious Barriers Partnership Software Toolbox Version 2.0 - 14331

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

Burns, Heather; Flach, Greg; Smith, Frank

2014-01-10

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. The CBP Software Toolbox – “Version 1.0” was released early in FY2013 and was used to support DOE-EM performance assessments in evaluating various degradation mechanisms that included sulfate attack, carbonation and constituent leaching. The sulfate attackmore » analysis predicted the extent and damage that sulfate ingress will have on concrete vaults over extended time (i.e., > 1000 years) and the carbonation analysis provided concrete degradation predictions from rebar corrosion. The new release “Version 2.0” includes upgraded carbonation software and a new software module to evaluate degradation due to chloride attack. Also included in the newer version are a dual regime module allowing evaluation of contaminant release in two regimes – both fractured and un-fractured. The integrated software package has also been upgraded with new plotting capabilities and many other features that increase the “user-friendliness” of the package. Experimental work has been generated to provide data to calibrate the models to improve the credibility of the analysis and reduce the uncertainty. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox is and will continue to produce tangible benefits to the working DOE Performance Assessment (PA) community.« less

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

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.

Intelligent sensor and controller framework for the power grid

DOEpatents

Akyol, Bora A.; Haack, Jereme Nathan; Craig, Jr., Philip Allen; Tews, Cody William; Kulkarni, Anand V.; Carpenter, Brandon J.; Maiden, Wendy M.; Ciraci, Selim

2015-07-28

Disclosed below are representative embodiments of methods, apparatus, and systems for monitoring and using data in an electric power grid. For example, one disclosed embodiment comprises a sensor for measuring an electrical characteristic of a power line, electrical generator, or electrical device; a network interface; a processor; and one or more computer-readable storage media storing computer-executable instructions. In this embodiment, the computer-executable instructions include instructions for implementing an authorization and authentication module for validating a software agent received at the network interface; instructions for implementing one or more agent execution environments for executing agent code that is included with the software agent and that causes data from the sensor to be collected; and instructions for implementing an agent packaging and instantiation module for storing the collected data in a data container of the software agent and for transmitting the software agent, along with the stored data, to a next destination.

Intelligent sensor and controller framework for the power grid

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

Akyol, Bora A.; Haack, Jereme Nathan; Craig, Jr., Philip Allen

Disclosed below are representative embodiments of methods, apparatus, and systems for monitoring and using data in an electric power grid. For example, one disclosed embodiment comprises a sensor for measuring an electrical characteristic of a power line, electrical generator, or electrical device; a network interface; a processor; and one or more computer-readable storage media storing computer-executable instructions. In this embodiment, the computer-executable instructions include instructions for implementing an authorization and authentication module for validating a software agent received at the network interface; instructions for implementing one or more agent execution environments for executing agent code that is included with themore » software agent and that causes data from the sensor to be collected; and instructions for implementing an agent packaging and instantiation module for storing the collected data in a data container of the software agent and for transmitting the software agent, along with the stored data, to a next destination.« less

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.

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

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

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

NASA Astrophysics Data System (ADS)

Fadakar Alghalandis, Younes

2017-05-01

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

An Upgrade of the Aeroheating Software "MINIVER"

NASA Technical Reports Server (NTRS)

Louderback, Pierce M.

2013-01-01

Many software packages assist engineers with performing flight vehicle analysis, but some of these packages have gone many years without updates or significant improvements to their workflows. One such software, known as MINIVER, is a powerful yet lightweight tool that is used for aeroheating analyses. However, it is an aging program that has not seen major improvements within the past decade. As part of a collaborative effort with Florida Institute of Technology, MINIVER has received a major user interface overhaul, a change in program language, and will be continually receiving updates to improve its capabilities. The user interface update includes a migration from a command-line interface to that of a graphical user interface supported in the Windows operating system. The organizational structure of the preprocessor has been transformed to clearly defined categories to provide ease of data entry. Helpful tools have been incorporated, including the ability to copy sections of cases as well as a generalized importer which aids in bulk data entry. A visual trajectory editor has been included, as well as a CAD Editor which allows the user to input simplified geometries in order to generate MINIVER cases in bulk. To demonstrate its continued effectiveness, a case involving the JAXA OREX flight vehicle will be included, providing comparisons to captured flight data as well as other computational solutions. The most recent upgrade effort incorporated the use of the CAD Editor, and current efforts are investigating methods to link MINIVER projects with SINDA/Fluint and Thermal Desktop.

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."

Web-Based Mapping Puts the World at Your Fingertips

NASA Technical Reports Server (NTRS)

2008-01-01

NASA's award-winning Earth Resources Laboratory Applications Software (ELAS) package was developed at Stennis Space Center. Since 1978, ELAS has been used worldwide for processing satellite and airborne sensor imagery data of the Earth's surface into readable and usable information. DATASTAR Inc., of Picayune, Mississippi, has used ELAS software in the DATASTAR Image Processing Exploitation (DIPEx) desktop and Internet image processing, analysis, and manipulation software. The new DIPEx Version III includes significant upgrades and improvements compared to its esteemed predecessor. A true World Wide Web application, this product evolved with worldwide geospatial dimensionality and numerous other improvements that seamlessly support the World Wide Web version.

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

NASA Technical Reports Server (NTRS)

Smart, Christian

1998-01-01

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

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

Using GDAL to Convert NetCDF 4 CF 1.6 to GeoTIFF: Interoperability Problems and Solutions for Data Providers and Distributors

NASA Astrophysics Data System (ADS)

Haran, T. M.; Brodzik, M. J.; Nordgren, B.; Estilow, T.; Scott, D. J.

2015-12-01

An increasing number of new Earth science datasets are being producedby data providers in self-describing, machine-independent file formatsincluding Hierarchical Data Format version 5 (HDF5) and NetworkCommon Data Form version 4 (netCDF-4). Furthermore data providers maybe producing netCDF-4 files that follow the conventions for Climateand Forecast metadata version 1.6 (CF 1.6) which, for datasets mappedto a projected raster grid covering all or a portion of the earth,includes the Coordinate Reference System (CRS) used to define howlatitude and longitude are mapped to grid coordinates, i.e. columnsand rows, and vice versa. One problem that users may encounter is thattheir preferred visualization and analysis tool may not yet includesupport for one of these newer formats. Moreover, data distributorssuch as NASA's NSIDC DAAC may not yet include support for on-the-flyconversion of data files for all data sets produced in a new format toa preferred older distributed format.There do exist open source solutions to this dilemma in the form ofsoftware packages that can translate files in one of the new formatsto one of the preferred formats. However these software packagesrequire that the file to be translated conform to the specificationsof its respective format. Although an online CF-Convention compliancechecker is available from cfconventions.org, a recent NSIDC userservices incident described here in detail involved an NSIDC-supporteddata set that passed the (then current) CF Checker Version 2.0.6, butwas in fact lacking two variables necessary for conformance. Thisproblem was not detected until GDAL, a software package which reliedon the missing variables, was employed by a user in an attempt totranslate the data into a different file format, namely GeoTIFF.This incident indicates that testing a candidate data product with oneor more software products written to accept the advertised conventionsis proposed as a practice which improves interoperability. Differencesbetween data file contents and software package expectations areexposed, affording an opportunity to improve conformance of software,data or both. The incident can also serve as a demonstration that dataproviders, distributors, and users can work together to improve dataproduct quality and interoperability.

PIV/HPIV Film Analysis Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

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

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

Open Source Software to Control Bioflo Bioreactors

PubMed Central

Burdge, David A.; Libourel, Igor G. L.

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

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

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

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

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

NASA Technical Reports Server (NTRS)

Witzberger, Kevin E.; Zeiler, Tom

2012-01-01

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

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...

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.

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.

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 .

Variational Trajectory Optimization Tool Set: Technical description and user's manual

NASA Technical Reports Server (NTRS)

Bless, Robert R.; Queen, Eric M.; Cavanaugh, Michael D.; Wetzel, Todd A.; Moerder, Daniel D.

1993-01-01

The algorithms that comprise the Variational Trajectory Optimization Tool Set (VTOTS) package are briefly described. The VTOTS is a software package for solving nonlinear constrained optimal control problems from a wide range of engineering and scientific disciplines. The VTOTS package was specifically designed to minimize the amount of user programming; in fact, for problems that may be expressed in terms of analytical functions, the user needs only to define the problem in terms of symbolic variables. This version of the VTOTS does not support tabular data; thus, problems must be expressed in terms of analytical functions. The VTOTS package consists of two methods for solving nonlinear optimal control problems: a time-domain finite-element algorithm and a multiple shooting algorithm. These two algorithms, under the VTOTS package, may be run independently or jointly. The finite-element algorithm generates approximate solutions, whereas the shooting algorithm provides a more accurate solution to the optimization problem. A user's manual, some examples with results, and a brief description of the individual subroutines are included.

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

Scalable computing for evolutionary genomics.

PubMed

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

2012-01-01

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

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.

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.

An R package for simulating growth and organic wastage in aquaculture farms in response to environmental conditions and husbandry practices

PubMed Central

Baldan, Damiano; Porporato, Erika Maria Diletta; Pastres, Roberto

2018-01-01

A new R software package, RAC, is presented. RAC allows to simulate the rearing cycle of 4 species, finfish and shellfish, highly important in terms of production in the Mediterranean Sea. The package works both at the scale of the individual and of the farmed population. Mathematical models included in RAC were all validated in previous works, and account for growth and metabolism, based on input data characterizing the forcing functions—water temperature, and food quality/quantity. The package provides a demo dataset of forcings for each species, as well as a typical set of husbandry parameters for Mediterranean conditions. The present work illustrates RAC main features, and its current capabilities/limitations. Three test cases are presented as a proof of concept of RAC applicability, and to demonstrate its potential for integrating different open products nowadays provided by remote sensing and operational oceanography. PMID:29723208

SBML Level 3 package: Groups, Version 1 Release 1

PubMed Central

Hucka, Michael; Smith, Lucian P.

2017-01-01

Summary Biological models often contain components that have relationships with each other, or that modelers want to treat as belonging to groups with common characteristics or shared metadata. The SBML Level 3 Version 1 Core specification does not provide an explicit mechanism for expressing such relationships, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Groups package for SBML Level 3 adds the necessary features to SBML to allow grouping of model components to be expressed. Such groups do not affect the mathematical interpretation of a model, but they do provide a way to add information that can be useful for modelers and software tools. The SBML Groups package enables a modeler to include definitions of groups and nested groups, each of which may be annotated to convey why that group was created, and what it represents. PMID:28187406

Comparing and characterizing three-dimensional point clouds derived by structure from motion photogrammetry

NASA Astrophysics Data System (ADS)

Schwind, Michael

Structure from Motion (SfM) is a photogrammetric technique whereby three-dimensional structures (3D) are estimated from overlapping two-dimensional (2D) image sequences. It is studied in the field of computer vision and utilized in fields such as archeology, engineering, and the geosciences. Currently, many SfM software packages exist that allow for the generation of 3D point clouds. Little work has been done to show how topographic data generated from these software differ over varying terrain types and why they might produce different results. This work aims to compare and characterize the differences between point clouds generated by three different SfM software packages: two well-known proprietary solutions (Pix4D, Agisoft PhotoScan) and one open source solution (OpenDroneMap). Five terrain types were imaged utilizing a DJI Phantom 3 Professional small unmanned aircraft system (sUAS). These terrain types include a marsh environment, a gently sloped sandy beach and jetties, a forested peninsula, a house, and a flat parking lot. Each set of imagery was processed with each software and then directly compared to each other. Before processing the sets of imagery, the software settings were analyzed and chosen in a manner that allowed for the most similar settings to be set across the three software types. This was done in an attempt to minimize point cloud differences caused by dissimilar settings. The characteristics of the resultant point clouds were then compared with each other. Furthermore, a terrestrial light detection and ranging (LiDAR) survey was conducted over the flat parking lot using a Riegl VZ- 400 scanner. This data served as ground truth in order to conduct an accuracy assessment of the sUAS-SfM point clouds. Differences were found between the different results, apparent not only in the characteristics of the clouds, but also the accuracy. This study allows for users of SfM photogrammetry to have a better understanding of how different processing software compare and the inherent sensitivity of SfM automation in 3D reconstruction. Because this study used mostly default settings within the software, it would be beneficial for further research to investigate the effects of changing parameters have on the fidelity of point cloud datasets generated from different SfM software packages.

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.

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.

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

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.