Tool & Die and EDM Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 2-year vocational training program to prepare students for entry-level employment as tool and die makers. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi volume begins with…

Lessons Learned in Cyberspace Security

DTIC Science & Technology

2014-06-01

software; something undesirable is packaged together with something desirable. A classic example was Elf Bowling attachment, which ran rampant through...the authors’ former school. It combined a fun program featuring elves as bowling pins, however it was packaged with SubSeven (Sub7) malware that...allowed remote access to the infected machine. IExpress, which is delivered in the Windows OS, is one of the legitimate tools for packaging multiple

T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

PubMed Central

Monnier, Stéphanie; Cox, David G; Albion, Tim; Canzian, Federico

2005-01-01

Background Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS. PMID:16221298

'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/

The Future of Earthquake Relocation Tools

NASA Astrophysics Data System (ADS)

Lecocq, T.; Caudron, C.

2010-12-01

Many scientists around the world use earthquake relocation software for their research. Some use "known" software like HYPODD or COMPLOC, while others use their own algorithms and codes. Often, beginners struggle to get one tool running or to properly configure input parameters. This Poster will be witness of debates that will take place during the Meeting, for example adressing questions like "Which program for which application?" ; "Standardized In/Outs?" , "Tectonic / Volcanic / Other ?" ; "All programs inside one single Super-Package?" ; "Common/Base Bibliography for the Relocation-Beginner?" ; "Continuous or Layered Velocity Model?" etc... We will also present the scheme of a Super-Package we are working on, grouping HYPODD [Waldhauser 2001], COMPLOC [Lin&Shearer 2006], LOTOS [Koulakov 2009] ; allowing standard in/outs for the 3 programs, and thus, the comparison of their outputs.

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

The ViennaRNA web services.

PubMed

Gruber, Andreas R; Bernhart, Stephan H; Lorenz, Ronny

2015-01-01

The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detection. The ViennaRNA web services can be used free of charge and can be accessed via http://rna.tbi.univie.ac.at.

ENergy and Power Evaluation Program

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

NONE

1996-11-01

In the late 1970s, national and international attention began to focus on energy issues. Efforts were initiated to design and test analytical tools that could be used to assist energy planners in evaluating energy systems, particularly in developing countries. In 1984, the United States Department of Energy (DOE) commissioned Argonne National Laboratory`s Decision and Information Sciences Division (DIS) to incorporate a set of analytical tools into a personal computer-based package for distribution in developing countries. The package developed by DIS staff, the ENergy and Power Evaluation Program (ENPEP), covers the range of issues that energy planners must face: economic development,more » energy demand projections, supply-and-demand balancing, energy system expansion, and environmental impact analysis. Following the original DOE-supported development effort, the International Atomic Energy Agency (IAEA), with the assistance from the US Department of State (DOS) and the US Department of Energy (DOE), provided ENPEP training, distribution, and technical support to many countries. ENPEP is now in use in over 60 countries and is an international standard for energy planning tools. More than 500 energy experts have been trained in the use of the entire ENPEP package or some of its modules during the international training courses organized by the IAEA in collaboration with Argonne`s Decision and Information Sciences (DIS) Division and the Division of Educational Programs (DEP). This report contains the ENPEP program which can be download from the internet. Described in this report is the description of ENPEP Program, news, forums, online support and contacts.« less

From Numerical Problem Solving to Model-Based Experimentation Incorporating Computer-Based Tools of Various Scales into the ChE Curriculum

ERIC Educational Resources Information Center

Shacham, Mordechai; Cutlip, Michael B.; Brauner, Neima

2009-01-01

A continuing challenge to the undergraduate chemical engineering curriculum is the time-effective incorporation and use of computer-based tools throughout the educational program. Computing skills in academia and industry require some proficiency in programming and effective use of software packages for solving 1) single-model, single-algorithm…

A PHARMACOKINETIC PROGRAM (PKFIT) FOR R

EPA Science Inventory

The purpose of this study was to create a nonlinear regression (including a genetic algorithm) program (R script) to deal with data fitting for pharmacokinetics (PK) in R environment using its available packages. We call this tool as PKfit.

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

The Implications of Cognitive Psychology for Computer-Based Learning Tools.

ERIC Educational Resources Information Center

Kozma, Robert B.

1987-01-01

Defines cognitive computer tools as software programs that use the control capabilities of computers to amplify, extend, or enhance human cognition; suggests seven ways in which computers can aid learning; and describes the "Learning Tool," a software package for the Apple Macintosh microcomputer that is designed to aid learning of…

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

NASA Astrophysics Data System (ADS)

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

2007-05-01

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

Hypercard Another Computer Tool.

ERIC Educational Resources Information Center

Geske, Joel

1991-01-01

Describes "Hypercard," a computer application package usable in all three modes of instructional computing: tutor, tool, and tutee. Suggests using Hypercard in scholastic journalism programs to teach such topics as news, headlines, design, photography, and advertising. Argues that the ability to access, organize, manipulate, and comprehend…

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

PubMed

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

2010-09-21

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

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

Computer-Aided Drafting and Design Series. Educational Resources for the Machine Tool Industry, Course Syllabi, [and] Instructor's Handbook. Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 2-year vocational training program to prepare students for entry-level employment in computer-aided drafting and design in the machine tool industry. The program was developed through a modification of the DACUM (Developing a Curriculum)…

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

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

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

Enhancing Linkages Between Healthy Diets, Local Agriculture, and Sustainable Food Systems: The School Meals Planner Package in Ghana.

PubMed

Fernandes, Meenakshi; Galloway, Rae; Gelli, Aulo; Mumuni, Daniel; Hamdani, Salha; Kiamba, Josephine; Quarshie, Kate; Bhatia, Rita; Aurino, Elisabetta; Peel, Francis; Drake, Lesley

2016-12-01

Interventions that enhance linkages between healthy diets and local agriculture can promote sustainable food systems. Home-grown school feeding programs present a promising entry point for such interventions, through the delivery of nutritious menus and meals. To describe the adaptation of the School Meals Planner Package to the programmatic and environmental reality in Ghana during the 2014 to 2015 school year. Guided by a conceptual framework highlighting key considerations and trade-offs in menu design, an open-source software was developed that could be easily understood by program implementers. Readily available containers from markets were calibrated into "handy measures" to support the provision of adequate quantities of food indicated by menus. Schools and communities were sensitized to the benefits of locally sourced, nutrient-rich diets. A behavior change communication campaign including posters and songs promoting healthy diets was designed and disseminated in schools and communities. The School Meals Planner Package was introduced in 42 districts in Ghana, reaching more than 320 000 children. Monitoring reports and feedback on its use were positive, demonstrating how the tool can be used by planners and implementers alike to deliver nutritious, locally-sourced meals to schoolchildren. The value of the tool has been recognized at the highest levels by Ghana's government who have adopted it as official policy. The School Meals Planner Package supported the design of nutritious, locally sourced menus for the school feeding program in Ghana. The tool can be similarly adapted for other countries to meet context-specific needs. © The Author(s) 2016.

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.

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,…

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

NASA Astrophysics Data System (ADS)

Solano-Altamirano, J. M.; Hernández-Pérez, Julio M.

2015-11-01

DensToolKit is a suite of cross-platform, optionally parallelized, programs for analyzing the molecular electron density (ρ) and several fields derived from it. Scalar and vector fields, such as the gradient of the electron density (∇ρ), electron localization function (ELF) and its gradient, localized orbital locator (LOL), region of slow electrons (RoSE), reduced density gradient, localized electrons detector (LED), information entropy, molecular electrostatic potential, kinetic energy densities K and G, among others, can be evaluated on zero, one, two, and three dimensional grids. The suite includes a program for searching critical points and bond paths of the electron density, under the framework of Quantum Theory of Atoms in Molecules. DensToolKit also evaluates the momentum space electron density on spatial grids, and the reduced density matrix of order one along lines joining two arbitrary atoms of a molecule. The source code is distributed under the GNU-GPLv3 license, and we release the code with the intent of establishing an open-source collaborative project. The style of DensToolKit's code follows some of the guidelines of an object-oriented program. This allows us to supply the user with a simple manner for easily implement new scalar or vector fields, provided they are derived from any of the fields already implemented in the code. In this paper, we present some of the most salient features of the programs contained in the suite, some examples of how to run them, and the mathematical definitions of the implemented fields along with hints of how we optimized their evaluation. We benchmarked our suite against both a freely-available program and a commercial package. Speed-ups of ˜2×, and up to 12× were obtained using a non-parallel compilation of DensToolKit for the evaluation of fields. DensToolKit takes similar times for finding critical points, compared to a commercial package. Finally, we present some perspectives for the future development and growth of the suite.

Promoter classifier: software package for promoter database analysis.

PubMed

Gershenzon, Naum I; Ioshikhes, Ilya P

2005-01-01

Promoter Classifier is a package of seven stand-alone Windows-based C++ programs allowing the following basic manipulations with a set of promoter sequences: (i) calculation of positional distributions of nucleotides averaged over all promoters of the dataset; (ii) calculation of the averaged occurrence frequencies of the transcription factor binding sites and their combinations; (iii) division of the dataset into subsets of sequences containing or lacking certain promoter elements or combinations; (iv) extraction of the promoter subsets containing or lacking CpG islands around the transcription start site; and (v) calculation of spatial distributions of the promoter DNA stacking energy and bending stiffness. All programs have a user-friendly interface and provide the results in a convenient graphical form. The Promoter Classifier package is an effective tool for various basic manipulations with eukaryotic promoter sequences that usually are necessary for analysis of large promoter datasets. The program Promoter Divider is described in more detail as a representative component of the package.

SIMULATION TOOL KIT FOR INDOOR AIR QUALITY AND INHALATION EXPOSURE (IAQX) VERSION 1.0 USER'S GUIDE

EPA Science Inventory

The User's Guide describes a Microsoft Windows-based indoor air quality (IAQ) simulation software package designed Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short. This software complements and supplements existing IAQ simulation programs and...

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.

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.

Fragman: an R package for fragment analysis.

PubMed

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

2016-04-21

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

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

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

Dunn, W.N.

1998-03-01

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

NY TBO Research: Integrated Demand Management (IDM): IDM Concept, Tools, and Training Package

NASA Technical Reports Server (NTRS)

Smith, Nancy

2016-01-01

A series of human-in-the-loop simulation sessions were conducted in the Airspace Operations Laboratory (AOL) to evaluate a new traffic management concept called Integrated Demand Management (IDM). The simulation explored how to address chronic equity, throughput and delay issues associated with New Yorks high-volume airports by operationally integrating three current and NextGen capabilities the Collaborative Trajectory Options Program (CTOP), Time-Based Flow Management (TBFM) and Required Time of Arrival (RTA) in order to better manage traffic demand within the National Air Traffic System. A package of presentation slides was developed to describe the concept, tools, and training materials used in the simulation sessions. The package will be used to outbrief our stakeholders by both presenting orally and disseminating of the materials via email.

Survey of visualization and analysis tools

NASA Technical Reports Server (NTRS)

Meyer, P. J.

1994-01-01

A large number of commercially available visualization and analysis tools are available to the researcher. Some of the strengths and limitations of some of these tools, from the viewpoint of the earth sciences discipline, are discussed. Visualization and analysis tools fall into one of two categories: those that are designed to a specific purpose and are non-extensive and those that are generic visual programming tools that are extensible. Most of the extensible packages examined incorporate a data flow paradigm.

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

PubMed Central

Chu, Vu T; Gottardo, Raphael; Raftery, Adrian E; Bumgarner, Roger E; Yeung, Ka Yee

2008-01-01

We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R packages and provides users with point and click access to traditionally command line driven tools written in R. We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA. PMID:18652698

Chapter 14. New tools to assess nitrogen management for conservation of our biosphere

USDA-ARS?s Scientific Manuscript database

There are several tools that can be used to assess the effects of management on nitrogen (N) losses to the environment. The Nitrogen Loss and Environmental Assessment Package (NLEAP) is an improved and renamed version of the DOS program that was called the Nitrate Leaching and Economic Analysis Pack...

FIESTA—An R estimation tool for FIA analysts

Treesearch

Tracey S. Frescino; Paul L. Patterson; Gretchen G. Moisen; Elizabeth A. Freeman

2015-01-01

FIESTA (Forest Inventory ESTimation for Analysis) is a user-friendly R package that was originally developed to support the production of estimates consistent with current tools available for the Forest Inventory and Analysis (FIA) National Program, such as FIDO (Forest Inventory Data Online) and EVALIDator. FIESTA provides an alternative data retrieval and reporting...

Early Childhood Classrooms and Computers: Programs with Promise.

ERIC Educational Resources Information Center

Hoot, James L.; Kimler, Michele

Word processing and the LOGO programing language are two microcomputer applications that are beginning to show benefits as learning tools in elementary school classrooms. Word processing packages are especially useful with beginning writers, whose lack of motor coordination often slows down their acquisition of competence in written communication.…

Test Generators: Teacher's Tool or Teacher's Headache?

ERIC Educational Resources Information Center

Eiser, Leslie

1988-01-01

Discusses the advantages and disadvantages of test generation programs. Includes setting up, printing exams and "bells and whistles." Reviews eight computer packages for Apple and IBM personal computers. Compares features, costs, and usage. (CW)

Computer aided system engineering and analysis (CASE/A) modeling package for ECLS systems - An overview

NASA Technical Reports Server (NTRS)

Dalee, Robert C.; Bacskay, Allen S.; Knox, James C.

1990-01-01

An overview of the CASE/A-ECLSS series modeling package is presented. CASE/A is an analytical tool that has supplied engineering productivity accomplishments during ECLSS design activities. A components verification program was performed to assure component modeling validity based on test data from the Phase II comparative test program completed at the Marshall Space Flight Center. An integrated plotting feature has been added to the program which allows the operator to analyze on-screen data trends or get hard copy plots from within the CASE/A operating environment. New command features in the areas of schematic, output, and model management, and component data editing have been incorporated to enhance the engineer's productivity during a modeling program.

Computerized power supply analysis: State equation generation and terminal models

NASA Technical Reports Server (NTRS)

Garrett, S. J.

1978-01-01

To aid engineers that design power supply systems two analysis tools that can be used with the state equation analysis package were developed. These tools include integration routines that start with the description of a power supply in state equation form and yield analytical results. The first tool uses a computer program that works with the SUPER SCEPTRE circuit analysis program and prints the state equation for an electrical network. The state equations developed automatically by the computer program are used to develop an algorithm for reducing the number of state variables required to describe an electrical network. In this way a second tool is obtained in which the order of the network is reduced and a simpler terminal model is obtained.

Integrated Network Decompositions and Dynamic Programming for Graph Optimization (INDDGO)

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

The INDDGO software package offers a set of tools for finding exact solutions to graph optimization problems via tree decompositions and dynamic programming algorithms. Currently the framework offers serial and parallel (distributed memory) algorithms for finding tree decompositions and solving the maximum weighted independent set problem. The parallel dynamic programming algorithm is implemented on top of the MADNESS task-based runtime.

VTGRAPH - GRAPHIC SOFTWARE TOOL FOR VT TERMINALS

NASA Technical Reports Server (NTRS)

Wang, C.

1994-01-01

VTGRAPH is a graphics software tool for DEC/VT or VT compatible terminals which are widely used by government and industry. It is a FORTRAN or C-language callable library designed to allow the user to deal with many computer environments which use VT terminals for window management and graphic systems. It also provides a PLOT10-like package plus color or shade capability for VT240, VT241, and VT300 terminals. The program is transportable to many different computers which use VT terminals. With this graphics package, the user can easily design more friendly user interface programs and design PLOT10 programs on VT terminals with different computer systems. VTGRAPH was developed using the ReGis Graphics set which provides a full range of graphics capabilities. The basic VTGRAPH capabilities are as follows: window management, PLOT10 compatible drawing, generic program routines for two and three dimensional plotting, and color graphics or shaded graphics capability. The program was developed in VAX FORTRAN in 1988. VTGRAPH requires a ReGis graphics set terminal and a FORTRAN compiler. The program has been run on a DEC MicroVAX 3600 series computer operating under VMS 5.0, and has a virtual memory requirement of 5KB.

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

PubMed

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

PubMed

Luo, Weijun; Brouwer, Cory

2013-07-15

Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. luo_weijun@yahoo.com Supplementary data are available at Bioinformatics online.

[Is there life beyond SPSS? Discover R].

PubMed

Elosua Oliden, Paula

2009-11-01

R is a GNU statistical and programming environment with very high graphical capabilities. It is very powerful for research purposes, but it is also an exceptional tool for teaching. R is composed of more than 1400 packages that allow using it for simple statistics and applying the most complex and most recent formal models. Using graphical interfaces like the Rcommander package, permits working in user-friendly environments which are similar to the graphical environment used by SPSS. This last characteristic allows non-statisticians to overcome the obstacle of accessibility, and it makes R the best tool for teaching. Is there anything better? Open, free, affordable, accessible and always on the cutting edge.

Transportable Applications Environment Plus, Version 5.1

NASA Technical Reports Server (NTRS)

1994-01-01

Transportable Applications Environment Plus (TAE+) computer program providing integrated, portable programming environment for developing and running application programs based on interactive windows, text, and graphical objects. Enables both programmers and nonprogrammers to construct own custom application interfaces easily and to move interfaces and application programs to different computers. Used to define corporate user interface, with noticeable improvements in application developer's and end user's learning curves. Main components are; WorkBench, What You See Is What You Get (WYSIWYG) software tool for design and layout of user interface; and WPT (Window Programming Tools) Package, set of callable subroutines controlling user interface of application program. WorkBench and WPT's written in C++, and remaining code written in C.

New and revised fire effects tools for fire management

Treesearch

Robert E. Keane; Greg Dillon; Stacy Drury; Robin Innes; Penny Morgan; Duncan Lutes; Susan J. Prichard; Jane Smith; Eva Strand

2014-01-01

Announcing the release of new software packages for application in wildland fire science and management, two fields that are already fully saturated with computer technology, may seem a bit too much to many managers. However, there have been some recent releases of new computer programs and revisions of existing software and information tools that deserve mention...

Mathematical Modeling with MyMaps and Spreadsheets

ERIC Educational Resources Information Center

Weber, Victoria; Fortune, Nicholas; Williams, Derek; Whitehead, Ashley

2016-01-01

Software programs such as Tinkerplots ® or Geometer's Sketchpad ® can help students solve problems in mathematics classes, but may not be available to them after high school. In contrast, many students who become familiar with Internet tools and programs in office packages (word processing, spreadsheets, etc.) may use them daily to enhance their…

Programming Languages or Generic Software Tools, for Beginners' Courses in Computer Literacy?

ERIC Educational Resources Information Center

Neuwirth, Erich

1987-01-01

Discussion of methods that can be used to teach beginner courses in computer literacy focuses on students aged 10-12. The value of using a programing language versus using a generic software package is highlighted; Logo and Prolog are reviewed; and the use of databases is discussed. (LRW)

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

PubMed

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

2012-06-08

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

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.

PubMed

Simillion, Cedric; Janssens, Koen; Sterck, Lieven; Van de Peer, Yves

2008-01-01

i-ADHoRe is a software tool that combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. The new version offers, besides a significant increase in performance, several optimizations to the algorithm, most importantly to the profile alignment routine. As a result, the annotations of multiple genomes, or parts thereof, can be fed simultaneously into the program, after which it will report all regions of homology, both within and between genomes. The i-ADHoRe 2.0 package contains the C++ source code for the main program as well as various Perl scripts and a fully documented Perl API to facilitate post-processing. The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http://bioinformatics.psb.ugent.be/

QDENSITY—A Mathematica quantum computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2009-03-01

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. New version program summaryProgram title: QDENSITY 2.0 Catalogue identifier: ADXH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_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.: 26 055 No. of bytes in distributed program, including test data, etc.: 227 540 Distribution format: tar.gz Programming language: Mathematica 6.0 Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Catalogue identifier of previous version: ADXH_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914 Classification: 4.15 Does the new version supersede the previous version?: Offers an alternative, more up to date, implementation Nature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters. Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0 Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0 Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.

The Affordance Template ROS Package for Robot Task Programming

NASA Technical Reports Server (NTRS)

Hart, Stephen; Dinh, Paul; Hambuchen, Kimberly

2015-01-01

This paper introduces the Affordance Template ROS package for quickly programming, adjusting, and executing robot applications in the ROS RViz environment. This package extends the capabilities of RViz interactive markers by allowing an operator to specify multiple end-effector waypoint locations and grasp poses in object-centric coordinate frames and to adjust these waypoints in order to meet the run-time demands of the task (specifically, object scale and location). The Affordance Template package stores task specifications in a robot-agnostic XML description format such that it is trivial to apply a template to a new robot. As such, the Affordance Template package provides a robot-generic ROS tool appropriate for building semi-autonomous, manipulation-based applications. Affordance Templates were developed by the NASA-JSC DARPA Robotics Challenge (DRC) team and have since successfully been deployed on multiple platforms including the NASA Valkyrie and Robonaut 2 humanoids, the University of Texas Dreamer robot and the Willow Garage PR2. In this paper, the specification and implementation of the affordance template package is introduced and demonstrated through examples for wheel (valve) turning, pick-and-place, and drill grasping, evincing its utility and flexibility for a wide variety of robot applications.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community. The current trends for customized biomedical software tools are highlighted in this short review.

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.

Industrial Maintenance Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 1-year vocational training program to prepare students for entry-level employment as industrial maintenance technicians. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi…

Students' Reactions to the Use of Animals as Instructional Tools for Science

ERIC Educational Resources Information Center

Gurzau, Vickie Anne

2013-01-01

Teaching science to students with special needs requires different approaches. A program at the study site supplemented packaged science kits with animal-assisted instruction, but such an approach was never evaluated. The purpose of this study was to provide a formative program evaluation documenting students' reactions to the use of animals…

Language games: Advanced R & R packages: Book Review

DOE PAGES

Hraber, Peter Thomas

2016-03-23

Readers who wrangle answers from data by extended refinement of available computational tools have many options and resources available. Inevitably, they will develop their own methods tailored to the problem at hand.Two new books have recently been published, each of which is useful addition to the library for a scientist who programs with data. The two books reviewed are both written by H. Wickham. The titles are ''Advanced R'' and ''R Packages'', both published in 2015.

Language games: Advanced R & R packages: Book Review

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

Hraber, Peter Thomas

Readers who wrangle answers from data by extended refinement of available computational tools have many options and resources available. Inevitably, they will develop their own methods tailored to the problem at hand.Two new books have recently been published, each of which is useful addition to the library for a scientist who programs with data. The two books reviewed are both written by H. Wickham. The titles are ''Advanced R'' and ''R Packages'', both published in 2015.

GAPIT: genome association and prediction integrated tool.

PubMed

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

2012-09-15

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

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.

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

PubMed Central

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-01-01

Background The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. Results We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. Conclusion By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development. PMID:16740163

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.

PubMed

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-06-01

The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.

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.

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…

Calibration data Analysis Package (CAP): An IDL based widget application for analysis of X-ray calibration data

NASA Astrophysics Data System (ADS)

Vaishali, S.; Narendranath, S.; Sreekumar, P.

An IDL (interactive data language) based widget application developed for the calibration of C1XS (Narendranath et al., 2010) instrument on Chandrayaan-1 is modified to provide a generic package for the analysis of data from x-ray detectors. The package supports files in ascii as well as FITS format. Data can be fitted with a list of inbuilt functions to derive the spectral redistribution function (SRF). We have incorporated functions such as `HYPERMET' (Philips & Marlow 1976) including non Gaussian components in the SRF such as low energy tail, low energy shelf and escape peak. In addition users can incorporate additional models which may be required to model detector specific features. Spectral fits use a routine `mpfit' which uses Leven-Marquardt least squares fitting method. The SRF derived from this tool can be fed into an accompanying program to generate a redistribution matrix file (RMF) compatible with the X-ray spectral analysis package XSPEC. The tool provides a user friendly interface of help to beginners and also provides transparency and advanced features for experts.

A suite of R packages for web-enabled modeling and analysis of surface waters

NASA Astrophysics Data System (ADS)

Read, J. S.; Winslow, L. A.; Nüst, D.; De Cicco, L.; Walker, J. I.

2014-12-01

Researchers often create redundant methods for downloading, manipulating, and analyzing data from online resources. Moreover, the reproducibility of science can be hampered by complicated and voluminous data, lack of time for documentation and long-term maintenance of software, and fear of exposing programming skills. The combination of these factors can encourage unshared one-off programmatic solutions instead of openly provided reusable methods. Federal and academic researchers in the water resources and informatics domains have collaborated to address these issues. The result of this collaboration is a suite of modular R packages that can be used independently or as elements in reproducible analytical workflows. These documented and freely available R packages were designed to fill basic needs for the effective use of water data: the retrieval of time-series and spatial data from web resources (dataRetrieval, geoknife), performing quality assurance and quality control checks of these data with robust statistical methods (sensorQC), the creation of useful data derivatives (including physically- and biologically-relevant indices; GDopp, LakeMetabolizer), and the execution and evaluation of models (glmtools, rLakeAnalyzer). Here, we share details and recommendations for the collaborative coding process, and highlight the benefits of an open-source tool development pattern with a popular programming language in the water resources discipline (such as R). We provide examples of reproducible science driven by large volumes of web-available data using these tools, explore benefits of accessing packages as standardized web processing services (WPS) and present a working platform that allows domain experts to publish scientific algorithms in a service-oriented architecture (WPS4R). We assert that in the era of open data, tools that leverage these data should also be freely shared, transparent, and developed in an open innovation environment.

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.

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

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

Laser Machining Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 1-year vocational training program to prepare students for entry-level employment as laser machining technicians. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi volume…

Automated Equipment Repair Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 1-year vocational training program to prepare students for entry-level employment as automated equipment repair technicians. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi…

Advanced CNC and CAM Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and student laboratory manual for a 1-year vocational training program to prepare students for entry-level positions as advanced computer numerical control (CNC) and computer-assisted manufacturing (CAM) technicians.. The program was developed through a modification of the DACUM…

Mold Making Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of a course syllabi, an instructor's handbook, and a student laboratory manual for a 2-year vocational training program to prepare students for entry-level employment as mold makers. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi volume begins with the…

Manufacturing Technology Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 2-year vocational training program to prepare students for entry-level employment as manufacturing technicians. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi volume begins…

Welding Series. Educational Resources for the Machine Tool Industry. Course Syllabi, Instructor's Handbook, [and] Student Laboratory Manual.

ERIC Educational Resources Information Center

Texas State Technical Coll. System, Waco.

This package consists of course syllabi, an instructor's handbook, and a student laboratory manual for a 2-year vocational training program to prepare students for entry-level employment as welders. The program was developed through a modification of the DACUM (Developing a Curriculum) technique. The course syllabi volume begins with the MASTER…

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.

PubMed

Molnos, Sophie; Baumbach, Clemens; Wahl, Simone; Müller-Nurasyid, Martina; Strauch, Konstantin; Wang-Sattler, Rui; Waldenberger, Melanie; Meitinger, Thomas; Adamski, Jerzy; Kastenmüller, Gabi; Suhre, Karsten; Peters, Annette; Grallert, Harald; Theis, Fabian J; Gieger, Christian

2017-09-29

Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associations between genetic variants and metabolite levels. However, only considering genetic variants and their effects on one trait ignores the possible interplay between different "omics" layers. Existing tools only consider single-nucleotide polymorphism (SNP)-SNP interactions, and no practical tool is available for large-scale investigations of the interactions between pairs of arbitrary quantitative variables. We developed an R package called pulver to compute p-values for the interaction term in a very large number of linear regression models. Comparisons based on simulated data showed that pulver is much faster than the existing tools. This is achieved by using the correlation coefficient to test the null-hypothesis, which avoids the costly computation of inversions. Additional tricks are a rearrangement of the order, when iterating through the different "omics" layers, and implementing this algorithm in the fast programming language C++. Furthermore, we applied our algorithm to data from the German KORA study to investigate a real-world problem involving the interplay among DNA methylation, genetic variants, and metabolite levels. The pulver package is a convenient and rapid tool for screening huge numbers of linear regression models for significant interaction terms in arbitrary pairs of quantitative variables. pulver is written in R and C++, and can be downloaded freely from CRAN at https://cran.r-project.org/web/packages/pulver/ .

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)

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

USGS Publications Warehouse

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

2012-01-01

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

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.

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

NASA Technical Reports Server (NTRS)

Dejong, Frederik J.; Thoren, Stephen J.

1993-01-01

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

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

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

PubMed

Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid

2012-08-15

Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future. The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html

Space transfer vehicle concepts and requirements study. Volume 3: Program cost estimates. Book 2: WBS and dictionary

NASA Technical Reports Server (NTRS)

Peffley, A. F.

1991-01-01

This document describes the products and services to be developed, tested, produced, and operated for the Space Transfer Vehicle (STV) Program. The Work Breakdown Structure (WBS) and WBS Dictionary are program management tools used to catalog, account by task, and summarize work packages of a space system program. The products or services to be delivered or accomplished during the STV C/D phase are the primary focus of this work breakdown structure document.

PyCMSXiO: an external interface to script treatment plans for the Elekta® CMS XiO treatment planning system

NASA Astrophysics Data System (ADS)

Xing, Aitang; Arumugam, Sankar; Holloway, Lois; Goozee, Gary

2014-03-01

Scripting in radiotherapy treatment planning systems not only simplifies routine planning tasks but can also be used for clinical research. Treatment planning scripting can only be utilized in a system that has a built-in scripting interface. Among the commercially available treatment planning systems, Pinnacle (Philips) and Raystation (Raysearch Lab.) have inherent scripting functionality. CMS XiO (Elekta) is a widely used treatment planning system in radiotherapy centres around the world, but it does not have an interface that allows the user to script radiotherapy plans. In this study an external scripting interface, PyCMSXiO, was developed for XiO using the Python programming language. The interface was implemented as a python package/library using a modern object-oriented programming methodology. The package was organized as a hierarchy of different classes (objects). Each class (object) corresponds to a plan object such as the beam of a clinical radiotherapy plan. The interface of classes was implemented as object functions. Scripting in XiO using PyCMSXiO is comparable with Pinnacle scripting. This scripting package has been used in several research projects including commissioning of a beam model, independent three-dimensional dose verification for IMRT plans and a setup-uncertainty study. Ease of use and high-level functions provided in the package achieve a useful research tool. It was released as an open-source tool that may benefit the medical physics community.

The Impact of New Technology on Accounting Education.

ERIC Educational Resources Information Center

Shaoul, Jean

The introduction of computers in the Department of Accounting and Finance at Manchester University is described. General background outlining the increasing need for microcomputers in the accounting curriculum (including financial modelling tools and decision support systems such as linear programming, statistical packages, and simulation) is…

Carpentry Specialist.

ERIC Educational Resources Information Center

Air Force Training Command, Sheppard AFB, TX.

This instructional package is intended for use in training Air Force personnel enrolled in a program for apprentice carpenters. Training includes an introduction to carpentry and provides instruction in the use of carpentry hand, portable power, and shop tools; construction and maintenance of wood structures; installation of building hardware; and…

Enhancing the prospective biology teachers’ Pedagogical Content Knowledge (PCK) through a peer coaching based model

NASA Astrophysics Data System (ADS)

Anwar, Yenny

2018-05-01

This paper presents the results of implementation Peer Coaching Based Model that was implemented in development and Packaging Learning Tool program aimed at developing a Pedagogical Content Knowledge prospective teachers’ capabilities. Development and Packaging Learning Tool is a training program that applies various knowledge, attitude, and skill of students in order to form professional teacher. A need assessment was conducted to identify prospective teachers’ professional needs, especially PCK ability. Tests, questionnaires, interviews, field notes and video recordings were used in this research. The result indicated that the ability of Prospective teachers’ PCK has increased. This can be shown from the N-Gain that included in the medium category. This increase shows that there is integration of pedagogy and content; they have used varied strategies and can explain the reasons for its used. This means that the pattern belongs to the lower limit of the growing- PCK category. It is recommended to use peer coaching model during peer teaching.

fluff: exploratory analysis and visualization of high-throughput sequencing data

PubMed Central

Georgiou, Georgios

2016-01-01

Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff. PMID:27547532

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

SWMPr: An R Package for Retrieving, Organizing, and ...

EPA Pesticide Factsheets

The System-Wide Monitoring Program (SWMP) was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, andanalysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to estimate rates of ecosystem metabolism using the open-water method. The SWMPr package has facilitated a cross-reserve comparison of water quality trends and links quantitative information with analysis tools that have use for more generic applications to environmental time series. The manuscript describes a software package that was recently developed to retrieve, organize, and analyze monitoring data from the National Estuarine Research Reserve System. Functions are explained in detail, including recent applications for trend analysis of ecosystem metabolism.

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.

Air Markets Program Data (AMPD)

EPA Pesticide Factsheets

The Air Markets Program Data tool allows users to search EPA data to answer scientific, general, policy, and regulatory questions about industry emissions. Air Markets Program Data (AMPD) is a web-based application that allows users easy access to both current and historical data collected as part of EPA's emissions trading programs. This site allows you to create and view reports and to download emissions data for further analysis. AMPD provides a query tool so users can create custom queries of industry source emissions data, allowance data, compliance data, and facility attributes. In addition, AMPD provides interactive maps, charts, reports, and pre-packaged datasets. AMPD does not require any additional software, plug-ins, or security controls and can be accessed using a standard web browser.

Computers in medical education 1: evaluation of a problem-orientated learning package.

PubMed

Devitt, P; Palmer, E

1998-04-01

A computer-based learning package has been developed, aimed at expanding students' knowledge base, as well as improving data-handling abilities and clinical problem-solving skills. The program was evaluated by monitoring its use by students, canvassing users' opinions and measuring its effectiveness as a learning tool compared to tutorials on the same material. Evaluation was undertaken using three methods: initially, by a questionnaire on computers as a learning tool and the applicability of the content: second, through monitoring by the computer of student use, decisions and performance; finally, through pre- and post-test assessment of fifth-year students who either used a computer package or attended a tutorial on equivalent material. Most students provided positive comments on the learning material and expressed a willingness to see computer-aided learning (CAL) introduced into the curriculum. Over a 3-month period, 26 modules in the program were used on 1246 occasions. Objective measurement showed a significant gain in knowledge, data handling and problem-solving skills. Computer-aided learning is a valuable learning resource that deserves better attention in medical education. When used appropriately, the computer can be an effective learning resource, not only for the delivery of knowledge. but also to help students develop their problem-solving skills.

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.

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

PubMed Central

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

2012-01-01

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

Radio Astronomy Tools in Python: Spectral-cube, pvextractor, and more

NASA Astrophysics Data System (ADS)

Ginsburg, A.; Robitaille, T.; Beaumont, C.; Rosolowsky, E.; Leroy, A.; Brogan, C.; Hunter, T.; Teuben, P.; Brisbin, D.

2015-12-01

The radio-astro-tools organization has been established to facilitate development of radio and millimeter analysis tools by the scientific community. The first packages developed under its umbrella are: • The spectral-cube package, for reading, writing, and analyzing spectral data cubes • The pvextractor package for extracting position-velocity slices from position-position-velocity cubes along aribitrary paths • The radio-beam package to handle gaussian beams in the context of the astropy quantity and unit framework • casa-python to enable installation of these packages - and any other - into users' CASA environments without conflicting with the underlying CASA package. Community input in the form of code contributions, suggestions, questions and commments is welcome on all of these tools. They can all be found at http://radio-astro-tools.github.io.

Masonry Specialist.

ERIC Educational Resources Information Center

Air Force Training Command, Sheppard AFB, TX.

This instructional package is intended for use in training Air Force personnel enrolled in a program for apprentice masons. Training includes an introduction to masonry and provides instruction in the use of masons' hand, portable power, and shop tools; construction and maintenance of masonry structures using brick, concrete block, and tile;…

ExGUtils: A Python Package for Statistical Analysis With the ex-Gaussian Probability Density.

PubMed

Moret-Tatay, Carmen; Gamermann, Daniel; Navarro-Pardo, Esperanza; Fernández de Córdoba Castellá, Pedro

2018-01-01

The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density. In order to validate the package, we present an extensive analysis of fits obtained with it, discuss advantages and differences between the least squares and maximum likelihood methods and quantitatively evaluate the goodness of the obtained fits (which is usually an overlooked point in most literature in the area). The analysis done allows one to identify outliers in the empirical datasets and criteriously determine if there is a need for data trimming and at which points it should be done.

ExGUtils: A Python Package for Statistical Analysis With the ex-Gaussian Probability Density

PubMed Central

Moret-Tatay, Carmen; Gamermann, Daniel; Navarro-Pardo, Esperanza; Fernández de Córdoba Castellá, Pedro

2018-01-01

The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density. In order to validate the package, we present an extensive analysis of fits obtained with it, discuss advantages and differences between the least squares and maximum likelihood methods and quantitatively evaluate the goodness of the obtained fits (which is usually an overlooked point in most literature in the area). The analysis done allows one to identify outliers in the empirical datasets and criteriously determine if there is a need for data trimming and at which points it should be done. PMID:29765345

Making software get along: integrating optical and mechanical design programs

NASA Astrophysics Data System (ADS)

Shackelford, Christie J.; Chinnock, Randal B.

2001-03-01

As modern optomechanical engineers, we have the good fortune of having very sophisticated software programs available to us. The current optical design, mechanical design, industrial design, and CAM programs are very powerful tools with some very desirable features. However, no one program can do everything necessary to complete an entire optomechanical system design. Each program has a unique set of features and benefits, and typically two or mo re will be used during the product development process. At a minimum, an optical design program and a mechanical CAD package will be employed. As we strive for efficient, cost-effective, and rapid progress in our development projects, we must use these programs to their full advantage, while keeping redundant tasks to a minimum. Together, these programs offer the promise of a `seamless' flow of data from concept all the way to the download of part designs directly to the machine shop for fabrication. In reality, transferring data from one software package to the next is often frustrating. Overcoming these problems takes some know-how, a bit of creativity, and a lot of persistence. This paper describes a complex optomechanical development effort in which a variety of software tools were used from the concept stage to prototyping. It will describe what software was used for each major design task, how we learned to use them together to best advantage, and how we overcame the frustrations of software that didn't get along.

Chimera Grid Tools

NASA Technical Reports Server (NTRS)

Chan, William M.; Rogers, Stuart E.; Nash, Steven M.; Buning, Pieter G.; Meakin, Robert

2005-01-01

Chimera Grid Tools (CGT) is a software package for performing computational fluid dynamics (CFD) analysis utilizing the Chimera-overset-grid method. For modeling flows with viscosity about geometrically complex bodies in relative motion, the Chimera-overset-grid method is among the most computationally cost-effective methods for obtaining accurate aerodynamic results. CGT contains a large collection of tools for generating overset grids, preparing inputs for computer programs that solve equations of flow on the grids, and post-processing of flow-solution data. The tools in CGT include grid editing tools, surface-grid-generation tools, volume-grid-generation tools, utility scripts, configuration scripts, and tools for post-processing (including generation of animated images of flows and calculating forces and moments exerted on affected bodies). One of the tools, denoted OVERGRID, is a graphical user interface (GUI) that serves to visualize the grids and flow solutions and provides central access to many other tools. The GUI facilitates the generation of grids for a new flow-field configuration. Scripts that follow the grid generation process can then be constructed to mostly automate grid generation for similar configurations. CGT is designed for use in conjunction with a computer-aided-design program that provides the geometry description of the bodies, and a flow-solver program.

The effect of a simulation training package on skill acquisition for duplex arterial stenosis detection.

PubMed

Jaffer, Usman; Normahani, Pasha; Singh, Prashant; Aslam, Mohammed; Standfield, Nigel J

2015-01-01

In vascular surgery, duplex ultrasonography is a valuable diagnostic tool in patients with peripheral vascular disease, and there is increasing demand for vascular surgeons to be able to perform duplex scanning. This study evaluates the role of a novel simulation training package on vascular ultrasound (US) skill acquisition. A total of 19 novices measured predefined stenosis in a simulated pulsatile vessel using both peak systolic velocity ratio (PSVR) and diameter reduction (DR) methods before and after a short period of training using a simulated training package. The training package consisted of a simulated pulsatile vessel phantom, a set of instructional videos, duplex ultrasound objective structured assessment of technical skills (DUOSATS) tool, and a portable US scanner. Quantitative metrics (procedure time, percentage error using PSVR and DR methods, DUOSAT scores, and global rating scores) before and after training were compared. Subjects spent a median time of 144 mins (IQR: 60-195) training using the simulation package. Subjects exhibited statistically significant improvements when comparing pretraining and posttraining DUOSAT scores (pretraining = 17 [16-19.3] vs posttraining = 30 [27.8-31.8]; p < 0.01), global rating score (pretraining = 1 [1-2] vs posttraining = 4 [3.8-4]; p < 0.01), percentage error using both the DR (pretraining = 12.6% [9-29.6] vs posttraining = 10.3% [8.9-11.1]; p = 0.03) and PSVR (pretraining = 60% [40-60] vs posttraining = 20% [6.7-20]; p < 0.01) methods. In this study, subjects with no previous practical US experience developed the ability to both acquire and interpret arterial duplex images in a pulsatile simulated phantom following a short period of goal direct training using a simulation training package. A simulation training package may be a valuable tool for integration into a vascular training program. However, further work is needed to explore whether these newly attained skills are translated into clinical assessment. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2007-07-01

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

COD::CIF::Parser: an error-correcting CIF parser for the Perl language.

PubMed

Merkys, Andrius; Vaitkus, Antanas; Butkus, Justas; Okulič-Kazarinas, Mykolas; Kairys, Visvaldas; Gražulis, Saulius

2016-02-01

A syntax-correcting CIF parser, COD::CIF::Parser , is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser , the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.

Risk Management for Weapon Systems Acquisition: A Decision Support System

DTIC Science & Technology

1985-02-28

includes the program evaluation and review technique (PERT) for network analysis, the PMRM for quantifying risk , an optimization package for generating...Despite the inclusion of uncertainty in time, PERT can at best be considered as a tool for quantifying risk with regard to the time element only. Moreover

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

A postdoctoral position is available in the Viral Recombination Section (VRS), HIV Dynamics and Replication Program, CCR.  The VRS studies retroviral replication using human immunodeficiency viruses and other retroviruses, with a particular emphasis on the mechanisms of viral RNA biology, specific RNA packaging, virus assembly, and HIV replication.  Molecular tools and

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.

Using Data to Improve Programs: Assessment of a Data Quality and Use Intervention Package for Integrated Community Case Management in Malawi.

PubMed

Hazel, Elizabeth; Chimbalanga, Emmanuel; Chimuna, Tiyese; Nsona, Humphreys; Mtimuni, Angella; Kaludzu, Ernest; Gilroy, Kate; Guenther, Tanya

2017-09-27

Health Surveillance Assistants (HSAs) have been providing integrated community case management (iCCM) for sick children in Malawi since 2008. HSAs report monthly iCCM program data but, at the time of this study, little of it was being used for service improvement. Additionally, HSAs and facility health workers did not have the tools to compile and visualize the data they collected to make evidence-based program decisions. From 2012 to 2013, we worked with Ministry of Health staff and partners to develop and pilot a program in Dowa and Kasungu districts to improve data quality and use at the health worker level. We developed and distributed wall chart templates to display and visualize data, provided training to 426 HSAs and supervisors on data analysis using the templates, and engaged health workers in program improvement plans as part of a data quality and use (DQU) package. We assessed the package through baseline and endline surveys of the HSAs and facility and district staff in the study areas, focusing specifically on availability of reporting forms, completeness of the forms, and consistency of the data between different levels of the health system as measured through results verification ratio (RVR). We found evidence of significant improvements in reporting consistency for suspected pneumonia illness (from overreporting cases at baseline [RVR=0.82] to no reporting inconsistency at endline [RVR=1.0]; P =.02). Other non-significant improvements were measured for fever illness and gender of the patient. Use of the data-display wall charts was high; almost all HSAs and three-fourths of the health facilities had completed all months since January 2013. Some participants reported the wall charts helped them use data for program improvement, such as to inform community health education activities and to better track stock-outs. Since this study, the DQU package has been scaled up in Malawi and expanded to 2 other countries. Unfortunately, without the sustained support and supervision provided in this project, use of the tools in the Malawi scale-up is lower than during the pilot period. Nevertheless, this pilot project shows community and facility health workers can use data to improve programs at the local level given the opportunity to access and visualize the data along with supervision support. © Hazel et al.

EggLib: processing, analysis and simulation tools for population genetics and genomics

PubMed Central

2012-01-01

Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded. PMID:22494792

EggLib: processing, analysis and simulation tools for population genetics and genomics.

PubMed

De Mita, Stéphane; Siol, Mathieu

2012-04-11

With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.

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

PubMed Central

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

2006-01-01

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

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

PubMed

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

2006-10-13

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

JGromacs: a Java package for analyzing protein simulations.

PubMed

Münz, Márton; Biggin, Philip C

2012-01-23

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

JGromacs: A Java Package for Analyzing Protein Simulations

PubMed Central

2011-01-01

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

General MACOS Interface for Modeling and Analysis for Controlled Optical Systems

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

Tolerant (parallel) Programming

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Bailey, David H. (Technical Monitor)

1997-01-01

In order to be truly portable, a program must be tolerant of a wide range of development and execution environments, and a parallel program is just one which must be tolerant of a very wide range. This paper first defines the term "tolerant programming", then describes many layers of tools to accomplish it. The primary focus is on F-Nets, a formal model for expressing computation as a folded partial-ordering of operations, thereby providing an architecture-independent expression of tolerant parallel algorithms. For implementing F-Nets, Cooperative Data Sharing (CDS) is a subroutine package for implementing communication efficiently in a large number of environments (e.g. shared memory and message passing). Software Cabling (SC), a very-high-level graphical programming language for building large F-Nets, possesses many of the features normally expected from today's computer languages (e.g. data abstraction, array operations). Finally, L2(sup 3) is a CASE tool which facilitates the construction, compilation, execution, and debugging of SC programs.

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

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

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

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

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

1989-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

pROC: an open-source package for R and S+ to analyze and compare ROC curves.

PubMed

Robin, Xavier; Turck, Natacha; Hainard, Alexandre; Tiberti, Natalia; Lisacek, Frédérique; Sanchez, Jean-Charles; Müller, Markus

2011-03-17

Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.

Supercomputing '91; Proceedings of the 4th Annual Conference on High Performance Computing, Albuquerque, NM, Nov. 18-22, 1991

NASA Technical Reports Server (NTRS)

1991-01-01

Various papers on supercomputing are presented. The general topics addressed include: program analysis/data dependence, memory access, distributed memory code generation, numerical algorithms, supercomputer benchmarks, latency tolerance, parallel programming, applications, processor design, networks, performance tools, mapping and scheduling, characterization affecting performance, parallelism packaging, computing climate change, combinatorial algorithms, hardware and software performance issues, system issues. (No individual items are abstracted in this volume)

Evaluation of a TB infection control implementation initiative in out-patient HIV clinics in Zambia and Botswana.

PubMed

Emerson, C; Lipke, V; Kapata, N; Mwananyambe, N; Mwinga, A; Garekwe, M; Lanje, S; Moshe, Y; Pals, S L; Nakashima, A K; Miller, B

2016-07-01

Out-patient human immunodeficiency virus (HIV) care and treatment clinics in Zambia and Botswana, countries with a high burden of HIV and TB infection. To develop a tuberculosis infection control (TB IC) training and implementation package and evaluate the implementation of TB IC activities in facilities implementing the package. Prospective program evaluation of a TB IC training and implementation package using a standardized facility risk assessment tool, qualitative interviews with facility health care workers and measures of pre- and post-test performance. A composite measure of facility performance in TB IC improved from 32% at baseline to 50% at 1 year among eight facilities in Zambia, and from 27% to 80% at 6 months among 10 facilities in Botswana. Although there was marked improvement in indicators of managerial, administrative and environmental controls, key ongoing challenges remained in ensuring access to personal protective equipment and implementing TB screening in health care workers. TB IC activities at out-patient HIV clinics in Zambia and Botswana improved after training using the implementation package. Continued infrastructure support, as well as monitoring and evaluation, are needed to support the scale-up and sustainability of TB IC programs in facilities in low-resource countries.

Where in Louisiana [with] Teacher Manual.

ERIC Educational Resources Information Center

Gillan, Bob; Williams, Ross

The first part of this document is a report describing "Where in Louisiana," a program model using IBM LinkWay (i.e., a multimedia software package providing tools to merge text and graphics) that was created as a cooperative learning activity to enhance and expand state studies. The introductory report discusses ways the model promotes…

METAPHOR: Programmer's guide, Version 1

NASA Technical Reports Server (NTRS)

Furchtgott, D. G.

1979-01-01

The internal structure of the Michigan Evaluation Aid for Perphormability (METAPHOR), an interactive software package to facilitate performability modeling and evaluation is described. Revised supplemented guides are prepared in order to maintain an up-to-date documentation of the system. Programmed tools to facilitate each step of performability model construction and model solution are given.

A Virtual Environment for Process Management. A Step by Step Implementation

ERIC Educational Resources Information Center

Mayer, Sergio Valenzuela

2003-01-01

In this paper it is presented a virtual organizational environment, conceived with the integration of three computer programs: a manufacturing simulation package, an automation of businesses processes (workflows), and business intelligence (Balanced Scorecard) software. It was created as a supporting tool for teaching IE, its purpose is to give…

Technological Tools in the Introductory Statistics Classroom: Effects on Student Understanding of Inferential Statistics

ERIC Educational Resources Information Center

Meletiou-Mavrotheris, Maria

2004-01-01

While technology has become an integral part of introductory statistics courses, the programs typically employed are professional packages designed primarily for data analysis rather than for learning. Findings from several studies suggest that use of such software in the introductory statistics classroom may not be very effective in helping…

iPat: intelligent prediction and association tool for genomic research.

PubMed

Chen, Chunpeng James; Zhang, Zhiwu

2018-06-01

The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills. Non-programmers struggle to use them efficiently because of the steep learning curves and zero tolerance for data formats and mistakes when inputting keywords and parameters. To address these problems, this study developed a software package, named the Intelligent Prediction and Association Tool (iPat), with a user-friendly graphical user interface. With iPat, GWAS or GS can be performed using a pointing device to simply drag and/or click on graphical elements to specify input data files, choose input parameters and select analytical models. Models available to users include those implemented in third party CLI packages such as GAPIT, PLINK, FarmCPU, BLINK, rrBLUP and BGLR. Users can choose any data format and conduct analyses with any of these packages. File conversions are automatically conducted for specified input data and selected packages. A GWAS-assisted genomic prediction method was implemented to perform genomic prediction using any GWAS method such as FarmCPU. iPat was written in Java for adaptation to multiple operating systems including Windows, Mac and Linux. The iPat executable file, user manual, tutorials and example datasets are freely available at http://zzlab.net/iPat. zhiwu.zhang@wsu.edu.

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

NASA Technical Reports Server (NTRS)

Maul, William A.; Fulton, Christopher E.

2011-01-01

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

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

PubMed

Couvin, David; Bernheim, Aude; Toffano-Nioche, Claire; Touchon, Marie; Michalik, Juraj; Néron, Bertrand; C Rocha, Eduardo P; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

2018-05-22

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

Modeling Quantum Teleportation with Quantum Tools in Python (QuTiP)

DTIC Science & Technology

2017-12-01

FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM-YYYY) December 2017 2. REPORT TYPE Technical Report 3. DATES COVERED (From - To) June 1, 2017... technical report we evaluate one in particular, the Quantum Tools in Python (QuTiP) package, to determine its suitability for use in the simulation of...found that QuTiP is technically sound in that it is able to reproduce several published findings, and that it saves significant program design time due

Solid Modeling Aerospace Research Tool (SMART) user's guide, version 2.0

NASA Technical Reports Server (NTRS)

Mcmillin, Mark L.; Spangler, Jan L.; Dahmen, Stephen M.; Rehder, John J.

1993-01-01

The Solid Modeling Aerospace Research Tool (SMART) software package is used in the conceptual design of aerospace vehicles. It provides a highly interactive and dynamic capability for generating geometries with Bezier cubic patches. Features include automatic generation of commonly used aerospace constructs (e.g., wings and multilobed tanks); cross-section skinning; wireframe and shaded presentation; area, volume, inertia, and center-of-gravity calculations; and interfaces to various aerodynamic and structural analysis programs. A comprehensive description of SMART and how to use it is provided.

R-SWAT-FME user's guide

USGS Publications Warehouse

Wu, Yiping; Liu, Shu-Guang

2012-01-01

R program language-Soil and Water Assessment Tool-Flexible Modeling Environment (R-SWAT-FME) (Wu and Liu, 2012) is a comprehensive modeling framework that adopts an R package, Flexible Modeling Environment (FME) (Soetaert and Petzoldt, 2010), for the Soil and Water Assessment Tool (SWAT) model (Arnold and others, 1998; Neitsch and others, 2005). This framework provides the functionalities of parameter identifiability, model calibration, and sensitivity and uncertainty analysis with instant visualization. This user's guide shows how to apply this framework for a customized SWAT project.

'spup' - an R package for uncertainty propagation in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2016-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected static and interactive visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2017-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

Plato: A localised orbital based density functional theory code

NASA Astrophysics Data System (ADS)

Kenny, S. D.; Horsfield, A. P.

2009-12-01

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_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.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater-Koster tables for accuracy. Running time: Test cases will run in a few minutes, large calculations may run for several days.

A systematic review of substance misuse assessment packages.

PubMed

Sweetman, Jennifer; Raistrick, Duncan; Mdege, Noreen D; Crosby, Helen

2013-07-01

Health-care systems globally are moving away from process measures of performance to payments for outcomes achieved. It follows that there is a need for a selection of proven quality tools that are suitable for undertaking comprehensive assessments and outcomes assessments. This review aimed to identify and evaluate existing comprehensive assessment packages. The work is part of a national program in the UK, Collaborations in Leadership of Applied Health Research and Care. Systematic searches were carried out across major databases to identify instruments designed to assess substance misuse. For those instruments identified, searches were carried out using the Cochrane Library, Embase, Ovid MEDLINE(®) and PsychINFO to identify articles reporting psychometric data. From 595 instruments, six met the inclusion criteria: Addiction Severity Index; Chemical Use, Abuse and Dependence Scale; Form 90; Maudsley Addiction Profile; Measurements in the Addictions for Triage and Evaluation; and Substance Abuse Outcomes Module. The most common reasons for exclusion were that instruments were: (i) designed for a specific substance (239); (ii) not designed for use in addiction settings (136); (iii) not providing comprehensive assessment (89); and (iv) not suitable as an outcome measure (20). The six packages are very different and suited to different uses. No package had adequate evaluation of their properties and so the emphasis should be on refining a small number of tools with very general application rather than creating new ones. An alternative to using 'off-the-shelf' packages is to create bespoke packages from well-validated, single-construct scales. [ © 2013 Australasian Professional Society on Alcohol and other Drugs.

User’s guide for MapMark4GUI—A graphical user interface for the MapMark4 R package

USGS Publications Warehouse

Shapiro, Jason

2018-05-29

MapMark4GUI is an R graphical user interface (GUI) developed by the U.S. Geological Survey to support user implementation of the MapMark4 R statistical software package. MapMark4 was developed by the U.S. Geological Survey to implement probability calculations for simulating undiscovered mineral resources in quantitative mineral resource assessments. The GUI provides an easy-to-use tool to input data, run simulations, and format output results for the MapMark4 package. The GUI is written and accessed in the R statistical programming language. This user’s guide includes instructions on installing and running MapMark4GUI and descriptions of the statistical output processes, output files, and test data files.

An electronic clinical decision support tool to assist primary care providers in cardiovascular disease risk management: development and mixed methods evaluation.

PubMed

Peiris, David P; Joshi, Rohina; Webster, Ruth J; Groenestein, Patrick; Usherwood, Tim P; Heeley, Emma; Turnbull, Fiona M; Lipman, Alexandra; Patel, Anushka A

2009-12-17

Challenges remain in translating the well-established evidence for management of cardiovascular disease (CVD) risk into clinical practice. Although electronic clinical decision support (CDS) systems are known to improve practitioner performance, their development in Australian primary health care settings is limited. Study aims were to (1) develop a valid CDS tool that assists Australian general practitioners (GPs) in global CVD risk management, and (2) preliminarily evaluate its acceptability to GPs as a point-of-care resource for both general and underserved populations. CVD risk estimation (based on Framingham algorithms) and risk-based management advice (using recommendations from six Australian guidelines) were programmed into a software package. Tool validation: Data from 137 patients attending a physician's clinic were analyzed to compare the tool's risk scores with those obtained from an independently programmed algorithm in a separate statistics package. The tool's management advice was compared with a physician's recommendations based on a manual review of the guidelines. Field test: The tool was then tested with 21 GPs from eight general practices and three Aboriginal Medical Services. Customized CDS-based recommendations were generated for 200 routinely attending patients (33% Aboriginal) using information extracted from the health record by a research assistant. GPs reviewed these recommendations during each consultation. Changes in CVD risk factor measurement and management were recorded. In-depth interviews with GPs were conducted. Validation testing: the tool's risk assessment algorithm correlated very highly with the independently programmed version in the separate statistics package (intraclass correlation coefficient 0.999). For management advice, there were only two cases of disagreement between the tool and the physician. Field test: GPs found 77% (153/200) of patient outputs easy to understand and agreed with screening and prescribing recommendations in 72% and 64% of outputs, respectively; 26% of patients had their CVD risk factor history updated; 73% had at least one CVD risk factor measured or tests ordered. For people assessed at high CVD risk (n = 82), 10% and 9%, respectively, had lipid-lowering and BP-lowering medications commenced or dose adjustments made, while 7% newly commenced anti-platelet medications. Three key qualitative findings emerged: (1) GPs found the tool enabled a systematic approach to care; (2) the tool greatly influenced CVD risk communication; (3) successful implementation into routine care would require integration with practice software, minimal data entry, regular revision with updated guidelines, and a self-auditing feature. There were no substantive differences in study findings for Aboriginal Medical Services GPs, and the tool was generally considered appropriate for use with Aboriginal patients. A fully-integrated, self-populating, and potentially Internet-based CDS tool could contribute to improved global CVD risk management in Australian primary health care. The findings from this study will inform a large-scale trial intervention.

Graphics Software For VT Terminals

NASA Technical Reports Server (NTRS)

Wang, Caroline

1991-01-01

VTGRAPH graphics software tool for DEC/VT computer terminal or terminals compatible with it, widely used by government and industry. Callable in FORTRAN or C language, library program enabling user to cope with many computer environments in which VT terminals used for window management and graphic systems. Provides PLOT10-like package plus color or shade capability for VT240, VT241, and VT300 terminals. User can easily design more-friendly user-interface programs and design PLOT10 programs on VT terminals with different computer systems. Requires ReGis graphics set terminal and FORTRAN compiler.

C-mii: a tool for plant miRNA and target identification.

PubMed

Numnark, Somrak; Mhuantong, Wuttichai; Ingsriswang, Supawadee; Wichadakul, Duangdao

2012-01-01

MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.

C-mii: a tool for plant miRNA and target identification

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. Results To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. Conclusions C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms. PMID:23281648

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations

NASA Astrophysics Data System (ADS)

Laloo, Jalal Z. A.; Laloo, Nassirah; Rhyman, Lydia; Ramasami, Ponnadurai

2017-07-01

The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations.

PubMed

Laloo, Jalal Z A; Laloo, Nassirah; Rhyman, Lydia; Ramasami, Ponnadurai

2017-07-01

The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.

MOFA Software for the COBRA Toolbox

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

Griesemer, Marc; Navid, Ali

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

Three Applications of Automated Test Assembly within a User-Friendly Modeling Environment

ERIC Educational Resources Information Center

Cor, Ken; Alves, Cecilia; Gierl, Mark

2009-01-01

While linear programming is a common tool in business and industry, there have not been many applications in educational assessment and only a handful of individuals have been actively involved in conducting psychometric research in this area. Perhaps this is due, at least in part, to the complexity of existing software packages. This article…

Management of an affiliated Physics Residency Program using a commercial software tool.

PubMed

Zacarias, Albert S; Mills, Michael D

2010-06-01

A review of commercially available allied health educational management software tools was performed to evaluate their capacity to manage program data associated with a CAMPEP-accredited Therapy Physics Residency Program. Features of these software tools include: a) didactic course reporting and organization, b) competency reporting by topic, category and didactic course, c) student time management and accounting, and d) student patient case reporting by topic, category and course. The software package includes features for recording school administrative information; setting up lists of courses, faculty, clinical sites, categories, competencies, and time logs; and the inclusion of standardized external documents. There are provisions for developing evaluation and survey instruments. The mentors and program may be evaluated by residents, and residents may be evaluated by faculty members using this feature. Competency documentation includes the time spent on the problem or with the patient, time spent with the mentor, date of the competency, and approval by the mentor and program director. Course documentation includes course and lecture title, lecturer, topic information, date of lecture and approval by the Program Director. These software tools have the facility to include multiple clinical sites, with local subadministrators having the ability to approve competencies and attendance at clinical conferences. In total, these software tools have the capability of managing all components of a CAMPEP-accredited residency program. The application database lends the software to the support of multiple affiliated clinical sites within a single residency program. Such tools are a critical and necessary component if the medical physics profession is to meet the projected needs for qualified medical physicists in future years.

Supersonic civil airplane study and design: Performance and sonic boom

NASA Technical Reports Server (NTRS)

Cheung, Samson

1995-01-01

Since aircraft configuration plays an important role in aerodynamic performance and sonic boom shape, the configuration of the next generation supersonic civil transport has to be tailored to meet high aerodynamic performance and low sonic boom requirements. Computational fluid dynamics (CFD) can be used to design airplanes to meet these dual objectives. The work and results in this report are used to support NASA's High Speed Research Program (HSRP). CFD tools and techniques have been developed for general usages of sonic boom propagation study and aerodynamic design. Parallel to the research effort on sonic boom extrapolation, CFD flow solvers have been coupled with a numeric optimization tool to form a design package for aircraft configuration. This CFD optimization package has been applied to configuration design on a low-boom concept and an oblique all-wing concept. A nonlinear unconstrained optimizer for Parallel Virtual Machine has been developed for aerodynamic design and study.

Mac OS X for Astronomy

NASA Astrophysics Data System (ADS)

Pierfederici, F.; Pirzkal, N.; Hook, R. N.

Mac OS X is the new Unix based version of the Macintosh operating system. It combines a high performance DisplayPDF user interface with a standard BSD UNIX subsystem and provides users with simultaneous access to a broad range of applications which were not previously available on a single system such as Microsoft Office and Adobe Photoshop, as well as legacy X11-based scientific tools and packages like IRAF, SuperMongo, MIDAS, etc. The combination of a modern GUI layered on top of a familiar UNIX environment paves the way for new, more flexible and powerful astronomical tools to be developed while assuring compatibility with already existing, older programs. In this paper, we outline the strengths of the Mac OS X platform in a scientific environment, astronomy in particular, and point to the numerous astronomical software packages available for this platform; most notably the Scisoft collection which we have compiled.

CWDPRNP: A tool for cervid prion sequence analysis in program R

USGS Publications Warehouse

Miller, William L.; Walter, W. David

2017-01-01

Chronic wasting disease is a fatal, neurological disease caused by an infectious prion protein, which affects economically and ecologically important members of the family Cervidae. Single nucleotide polymorphisms within the prion protein gene have been linked to differential susceptibility to the disease in many species. Wildlife managers are seeking to determine the frequencies of disease-associated alleles and genotypes and delineate spatial genetic patterns. The CWDPRNP package, implemented in program R, provides a unified framework for analyzing prion protein gene variability and spatial structure.

Building Computer-Based Experiments in Psychology without Programming Skills.

PubMed

Ruisoto, Pablo; Bellido, Alberto; Ruiz, Javier; Juanes, Juan A

2016-06-01

Research in Psychology usually requires to build and run experiments. However, although this task has required scripting, recent computer tools based on graphical interfaces offer new opportunities in this field for researchers with non-programming skills. The purpose of this study is to illustrate and provide a comparative overview of two of the main free open source "point and click" software packages for building and running experiments in Psychology: PsychoPy and OpenSesame. Recommendations for their potential use are further discussed.

Hypertext-based computer vision teaching packages

NASA Astrophysics Data System (ADS)

Marshall, A. David

1994-10-01

The World Wide Web Initiative has provided a means for providing hypertext and multimedia based information across the whole INTERNET. Many applications have been developed on such http servers. At Cardiff we have developed a http hypertext based multimedia server, the Cardiff Information Server, using the widely available Mosaic system. The server provides a variety of information ranging from the provision of teaching modules, on- line documentation, timetables for departmental activities to more light hearted hobby interests. One important and novel development to the server has been the development of courseware facilities. This ranges from the provision of on-line lecture notes, exercises and their solutions to more interactive teaching packages. A variety of disciplines have benefitted notably Computer Vision, and Image Processing but also C programming, X Windows, Computer Graphics and Parallel Computing. This paper will address the issues of the implementation of the Computer Vision and Image Processing packages, the advantages gained from using a hypertext based system and also will relate practical experiences of using the packages in a class environment. The paper addresses issues of how best to provide information in such a hypertext based system and how interactive image processing packages can be developed and integrated into courseware. The suite of tools developed facilitates a flexible and powerful courseware package that has proved popular in the classroom and over the Internet. The paper will also detail many future developments we see possible. One of the key points raised in the paper is that Mosaic's hypertext language (html) is extremely powerful and yet relatively straightforward to use. It is also possible to link in Unix calls so that programs and shells can be executed. This provides a powerful suite of utilities that can be exploited to develop many packages.

Design Package for Fuel Retrieval System Fuel Handling Tool Modification

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

TEDESCHI, D.J.

This design package documents design, fabrication, and testing of new stinger tool design. Future revisions will document further development of the stinger tool and incorporate various developmental stages, and final test results.

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.

Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box (TTB)

NASA Technical Reports Server (NTRS)

Doyle, Monica; ONeil, Daniel A.; Christensen, Carissa B.

2005-01-01

The Advanced Technology Lifecycle Analysis System (ATLAS) is a decision support tool designed to aid program managers and strategic planners in determining how to invest technology research and development dollars. It is an Excel-based modeling package that allows a user to build complex space architectures and evaluate the impact of various technology choices. ATLAS contains system models, cost and operations models, a campaign timeline and a centralized technology database. Technology data for all system models is drawn from a common database, the ATLAS Technology Tool Box (TTB). The TTB provides a comprehensive, architecture-independent technology database that is keyed to current and future timeframes.

Pipe Flow Simulation Software: A Team Approach to Solve an Engineering Education Problem.

ERIC Educational Resources Information Center

Engel, Renata S.; And Others

1996-01-01

A computer simulation program for use in the study of fluid mechanics is described. The package is an interactive tool to explore the fluid flow characteristics of a pipe system by manipulating the physical construction of the system. The motivation, software design requirements, and specific details on how its objectives were met are presented.…

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

NASA Technical Reports Server (NTRS)

1981-01-01

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

Development of a Spacecraft Materials Selector Expert System

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Engaging Undergraduate Math Majors in Geoscience Research using Interactive Simulations and Computer Art

NASA Astrophysics Data System (ADS)

Matott, L. S.; Hymiak, B.; Reslink, C. F.; Baxter, C.; Aziz, S.

2012-12-01

As part of the NSF-sponsored 'URGE (Undergraduate Research Group Experiences) to Compute' program, Dr. Matott has been collaborating with talented Math majors to explore the design of cost-effective systems to safeguard groundwater supplies from contaminated sites. Such activity is aided by a combination of groundwater modeling, simulation-based optimization, and high-performance computing - disciplines largely unfamiliar to the students at the outset of the program. To help train and engage the students, a number of interactive and graphical software packages were utilized. Examples include: (1) a tutorial for exploring the behavior of evolutionary algorithms and other heuristic optimizers commonly used in simulation-based optimization; (2) an interactive groundwater modeling package for exploring alternative pump-and-treat containment scenarios at a contaminated site in Billings, Montana; (3) the R software package for visualizing various concepts related to subsurface hydrology; and (4) a job visualization tool for exploring the behavior of numerical experiments run on a large distributed computing cluster. Further engagement and excitement in the program was fostered by entering (and winning) a computer art competition run by the Coalition for Academic Scientific Computation (CASC). The winning submission visualizes an exhaustively mapped optimization cost surface and dramatically illustrates the phenomena of artificial minima - valley locations that correspond to designs whose costs are only partially optimal.

KERNELHR: A program for estimating animal home ranges

USGS Publications Warehouse

Seaman, D.E.; Griffith, B.; Powell, R.A.

1998-01-01

Kernel methods are state of the art for estimating animal home-range area and utilization distribution (UD). The KERNELHR program was developed to provide researchers and managers a tool to implement this extremely flexible set of methods with many variants. KERNELHR runs interactively or from the command line on any personal computer (PC) running DOS. KERNELHR provides output of fixed and adaptive kernel home-range estimates, as well as density values in a format suitable for in-depth statistical and spatial analyses. An additional package of programs creates contour files for plotting in geographic information systems (GIS) and estimates core areas of ranges.

Control system design and analysis using the INteractive Controls Analysis (INCA) program

NASA Technical Reports Server (NTRS)

Bauer, Frank H.; Downing, John P.

1987-01-01

The INteractive Controls Analysis (INCA) program was developed at the Goddard Space Flight Center to provide a user friendly efficient environment for the design and analysis of linear control systems. Since its inception, INCA has found extensive use in the design, development, and analysis of control systems for spacecraft, instruments, robotics, and pointing systems. Moreover, the results of the analytic tools imbedded in INCA have been flight proven with at least three currently orbiting spacecraft. This paper describes the INCA program and illustrates, using a flight proven example, how the package can perform complex design analyses with relative ease.

CSOLNP: Numerical Optimization Engine for Solving Non-linearly Constrained Problems.

PubMed

Zahery, Mahsa; Maes, Hermine H; Neale, Michael C

2017-08-01

We introduce the optimizer CSOLNP, which is a C++ implementation of the R package RSOLNP (Ghalanos & Theussl, 2012, Rsolnp: General non-linear optimization using augmented Lagrange multiplier method. R package version, 1) alongside some improvements. CSOLNP solves non-linearly constrained optimization problems using a Sequential Quadratic Programming (SQP) algorithm. CSOLNP, NPSOL (a very popular implementation of SQP method in FORTRAN (Gill et al., 1986, User's guide for NPSOL (version 4.0): A Fortran package for nonlinear programming (No. SOL-86-2). Stanford, CA: Stanford University Systems Optimization Laboratory), and SLSQP (another SQP implementation available as part of the NLOPT collection (Johnson, 2014, The NLopt nonlinear-optimization package. Retrieved from http://ab-initio.mit.edu/nlopt)) are three optimizers available in OpenMx package. These optimizers are compared in terms of runtimes, final objective values, and memory consumption. A Monte Carlo analysis of the performance of the optimizers was performed on ordinal and continuous models with five variables and one or two factors. While the relative difference between the objective values is less than 0.5%, CSOLNP is in general faster than NPSOL and SLSQP for ordinal analysis. As for continuous data, none of the optimizers performs consistently faster than the others. In terms of memory usage, we used Valgrind's heap profiler tool, called Massif, on one-factor threshold models. CSOLNP and NPSOL consume the same amount of memory, while SLSQP uses 71 MB more memory than the other two optimizers.

Development and validation of an open source quantification tool for DSC-MRI studies.

PubMed

Gordaliza, P M; Mateos-Pérez, J M; Montesinos, P; Guzmán-de-Villoria, J A; Desco, M; Vaquero, J J

2015-03-01

This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots). An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license. Copyright © 2015 Elsevier Ltd. All rights reserved.

An Electronic Clinical Decision Support Tool to Assist Primary Care Providers in Cardiovascular Disease Risk Management: Development and Mixed Methods Evaluation

PubMed Central

Joshi, Rohina; Webster, Ruth J; Groenestein, Patrick; Usherwood, Tim P; Heeley, Emma; Turnbull, Fiona M; Lipman, Alexandra; Patel, Anushka A

2009-01-01

Background Challenges remain in translating the well-established evidence for management of cardiovascular disease (CVD) risk into clinical practice. Although electronic clinical decision support (CDS) systems are known to improve practitioner performance, their development in Australian primary health care settings is limited. Objectives Study aims were to (1) develop a valid CDS tool that assists Australian general practitioners (GPs) in global CVD risk management, and (2) preliminarily evaluate its acceptability to GPs as a point-of-care resource for both general and underserved populations. Methods CVD risk estimation (based on Framingham algorithms) and risk-based management advice (using recommendations from six Australian guidelines) were programmed into a software package. Tool validation: Data from 137 patients attending a physician’s clinic were analyzed to compare the tool’s risk scores with those obtained from an independently programmed algorithm in a separate statistics package. The tool’s management advice was compared with a physician’s recommendations based on a manual review of the guidelines. Field test: The tool was then tested with 21 GPs from eight general practices and three Aboriginal Medical Services. Customized CDS-based recommendations were generated for 200 routinely attending patients (33% Aboriginal) using information extracted from the health record by a research assistant. GPs reviewed these recommendations during each consultation. Changes in CVD risk factor measurement and management were recorded. In-depth interviews with GPs were conducted. Results Validation testing: The tool’s risk assessment algorithm correlated very highly with the independently programmed version in the separate statistics package (intraclass correlation coefficient 0.999). For management advice, there were only two cases of disagreement between the tool and the physician. Field test: GPs found 77% (153/200) of patient outputs easy to understand and agreed with screening and prescribing recommendations in 72% and 64% of outputs, respectively; 26% of patients had their CVD risk factor history updated; 73% had at least one CVD risk factor measured or tests ordered. For people assessed at high CVD risk (n = 82), 10% and 9%, respectively, had lipid-lowering and BP-lowering medications commenced or dose adjustments made, while 7% newly commenced anti-platelet medications. Three key qualitative findings emerged: (1) GPs found the tool enabled a systematic approach to care; (2) the tool greatly influenced CVD risk communication; (3) successful implementation into routine care would require integration with practice software, minimal data entry, regular revision with updated guidelines, and a self-auditing feature. There were no substantive differences in study findings for Aboriginal Medical Services GPs, and the tool was generally considered appropriate for use with Aboriginal patients. Conclusion A fully-integrated, self-populating, and potentially Internet-based CDS tool could contribute to improved global CVD risk management in Australian primary health care. The findings from this study will inform a large-scale trial intervention. PMID:20018588

[Not Available].

PubMed

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2009-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

PubMed

Bunk, Boyke; Kucklick, Martin; Jonas, Rochus; Münch, Richard; Schobert, Max; Jahn, Dieter; Hiller, Karsten

2006-12-01

MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

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.

CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data.

PubMed

Maenhout, Steven; De Baets, Bernard; Haesaert, Geert

2009-10-15

Phenotypic data collected in breeding programs and marker-trait association studies are often analyzed by means of linear mixed models. In these models, the covariance between the genetic background effects of all genotypes under study is modeled by means of pairwise coefficients of coancestry. Several marker-based coancestry estimation procedures allow to estimate this covariance matrix, but generally introduce a certain amount of bias when the examined genotypes are part of a breeding program. CoCoa implements the most commonly used marker-based coancestry estimation procedures and as such, allows to select the best fitting covariance structure for the phenotypic data at hand. This better model fit translates into an increased power and improved type I error control in association studies and an improved accuracy in phenotypic prediction studies. The presented software package also provides an implementation of the new Weighted Alikeness in State (WAIS) estimator for use in hybrid breeding programs. Besides several matrix manipulation tools, CoCoa implements two different bending heuristics, in case the inverse of an ill-conditioned coancestry matrix estimate is needed. The software package CoCoa is freely available at http://webs.hogent.be/cocoa. Source code, manual, binaries for 32 and 64-bit Linux systems and an installer for Microsoft Windows are provided. The core components of CoCoa are written in C++, while the graphical user interface is written in Java.

`spup' - An R Package for Analysis of Spatial Uncertainty Propagation and Application to Trace Gas Emission Simulations

NASA Astrophysics Data System (ADS)

Sawicka, K.; Breuer, L.; Houska, T.; Santabarbara Ruiz, I.; Heuvelink, G. B. M.

2016-12-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Advances in uncertainty propagation analysis and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the `spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo techniques, as well as several uncertainty visualization functions. Here we will demonstrate that the 'spup' package is an effective and easy-to-use tool to be applied even in a very complex study case, and that it can be used in multi-disciplinary research and model-based decision support. As an example, we use the ecological LandscapeDNDC model to analyse propagation of uncertainties associated with spatial variability of the model driving forces such as rainfall, nitrogen deposition and fertilizer inputs. The uncertainty propagation is analysed for the prediction of emissions of N2O and CO2 for a German low mountainous, agriculturally developed catchment. The study tests the effect of spatial correlations on spatially aggregated model outputs, and could serve as an advice for developing best management practices and model improvement strategies.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Parallel Adaptive Mesh Refinement Library

NASA Technical Reports Server (NTRS)

Mac-Neice, Peter; Olson, Kevin

2005-01-01

Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.

The IBM PC at NASA Ames

NASA Technical Reports Server (NTRS)

Peredo, James P.

1988-01-01

Like many large companies, Ames relies very much on its computing power to get work done. And, like many other large companies, finding the IBM PC a reliable tool, Ames uses it for many of the same types of functions as other companies. Presentation and clarification needs demand much of graphics packages. Programming and text editing needs require simpler, more-powerful packages. The storage space needed by NASA's scientists and users for the monumental amounts of data that Ames needs to keep demand the best database packages that are large and easy to use. Availability to the Micom Switching Network combines the powers of the IBM PC with the capabilities of other computers and mainframes and allows users to communicate electronically. These four primary capabilities of the PC are vital to the needs of NASA's users and help to continue and support the vast amounts of work done by the NASA employees.

Rule-based optimization and multicriteria decision support for packaging a truck chassis

NASA Astrophysics Data System (ADS)

Berger, Martin; Lindroth, Peter; Welke, Richard

2017-06-01

Trucks are highly individualized products where exchangeable parts are flexibly combined to suit different customer requirements, this leading to a great complexity in product development. Therefore, an optimization approach based on constraint programming is proposed for automatically packaging parts of a truck chassis by following packaging rules expressed as constraints. A multicriteria decision support system is developed where a database of truck layouts is computed, among which interactive navigation then can be performed. The work has been performed in cooperation with Volvo Group Trucks Technology (GTT), from which specific rules have been used. Several scenarios are described where the methods developed can be successfully applied and lead to less time-consuming manual work, fewer mistakes, and greater flexibility in configuring trucks. A numerical evaluation is also presented showing the efficiency and practical relevance of the methods, which are implemented in a software tool.

An Introduction to Benefit-Cost Analysis for Evaluating Public Expenditure Alternatives. Learning Packages in the Policy Sciences, PS-22.

ERIC Educational Resources Information Center

LaPlante, Josephine M.; Durham, Taylor R.

A revised edition of PS-14, "An Introduction to Benefit-Cost Analysis for Evaluating Public Programs," presents concepts and techniques of benefit-cost analysis as tools that can be used to assist in deciding between alternatives. The goals of the new edition include teaching students to think about the possible benefits and costs of each…

Computer Program Development Specification for Ada Integrated Environment: KAPSE (Kernel Ada Programming Support Environment)/Database, Type B5, B5-AIE(1).KAPSE(1).

DTIC Science & Technology

1982-11-12

File 1/0 Prgram Invocation Other Access M and Control Services KAPSE/Host Interface most Operating System Peripherals/ 01 su ?eetworks 6282318-2 Figure 3...3.2.4.3.8.5 Transitory Windows The TRANSITORY flag is used to prevent permanent dependence on temporary windows created simply for focusing on a part of the...KAPSE/Tool interfaces in terms of these low-level host-independent interfaces. In addition, the KAPSE/Host interface packages prevent the application

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.

AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

NASA Astrophysics Data System (ADS)

Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

2010-06-01

A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Program summaryProgram title: AFMPB: Adaptive fast multipole Poisson-Boltzmann solver Catalogue identifier: AEGB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 453 649 No. of bytes in distributed program, including test data, etc.: 8 764 754 Distribution format: tar.gz Programming language: Fortran Computer: Any Operating system: Any RAM: Depends on the size of the discretized biomolecular system Classification: 3 External routines: Pre- and post-processing tools are required for generating the boundary elements and for visualization. Users can use MSMS ( http://www.scripps.edu/~sanner/html/msms_home.html) for pre-processing, and VMD ( http://www.ks.uiuc.edu/Research/vmd/) for visualization. Sub-programs included: An iterative Krylov subspace solvers package from SPARSKIT by Yousef Saad ( http://www-users.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html), and the fast multipole methods subroutines from FMMSuite ( http://www.fastmultipole.org/). Nature of problem: Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions. Solution method: A novel node-patch scheme is used to discretize the well-conditioned boundary integral equation formulation of the linearized Poisson-Boltzmann equation. Various Krylov subspace solvers can be subsequently applied to solve the resulting linear system, with a bounded number of iterations independent of the number of discretized unknowns. The matrix-vector multiplication at each iteration is accelerated by the adaptive new versions of fast multipole methods. The AFMPB solver requires other stand-alone pre-processing tools for boundary mesh generation, post-processing tools for data analysis and visualization, and can be conveniently coupled with different time stepping methods for dynamics simulation. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/~lubz/afmpb.html and http://mccammon.ucsd.edu/ for updates and changes. Running time: The running time varies with the number of discretized elements ( N) in the system and their distributions. In most cases, it scales linearly as a function of N.

Improvements in Spectrum's fit to program data tool.

PubMed

Mahiane, Severin G; Marsh, Kimberly; Grantham, Kelsey; Crichlow, Shawna; Caceres, Karen; Stover, John

2017-04-01

The Joint United Nations Program on HIV/AIDS-supported Spectrum software package (Glastonbury, Connecticut, USA) is used by most countries worldwide to monitor the HIV epidemic. In Spectrum, HIV incidence trends among adults (aged 15-49 years) are derived by either fitting to seroprevalence surveillance and survey data or generating curves consistent with program and vital registration data, such as historical trends in the number of newly diagnosed infections or people living with HIV and AIDS related deaths. This article describes development and application of the fit to program data (FPD) tool in Joint United Nations Program on HIV/AIDS' 2016 estimates round. In the FPD tool, HIV incidence trends are described as a simple or double logistic function. Function parameters are estimated from historical program data on newly reported HIV cases, people living with HIV or AIDS-related deaths. Inputs can be adjusted for proportions undiagnosed or misclassified deaths. Maximum likelihood estimation or minimum chi-squared distance methods are used to identify the best fitting curve. Asymptotic properties of the estimators from these fits are used to estimate uncertainty. The FPD tool was used to fit incidence for 62 countries in 2016. Maximum likelihood and minimum chi-squared distance methods gave similar results. A double logistic curve adequately described observed trends in all but four countries where a simple logistic curve performed better. Robust HIV-related program and vital registration data are routinely available in many middle-income and high-income countries, whereas HIV seroprevalence surveillance and survey data may be scarce. In these countries, the FPD tool offers a simpler, improved approach to estimating HIV incidence trends.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.

1992-01-01

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

The efieldbook program: A teaching resource for geology

NASA Astrophysics Data System (ADS)

Vacas Peña, José Manuel; Chamoso, José M.; Urones, Carmen

2011-04-01

The eFieldBook program is a geology teaching tool with high didactic potential that guides a student's work in the field using multimedia and other resources. This program allows the collection of geo-referenced geological information as well as its storage and transmission, if necessary, as soon as it is collected. The data can be collected as in traditional field notebooks or on maps and photographs. The information can be used as soon as it is collected and can be exported to other programs such as Word, Excel, Georient or statistical packages. eFieldBook safely stores and backs up user information by sending any data collected to a selected Internet target at regular time intervals.

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

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

Automated Reporting of DXA Studies Using a Custom-Built Computer Program.

PubMed

England, Joseph R; Colletti, Patrick M

2018-06-01

Dual-energy x-ray absorptiometry (DXA) scans are a critical population health tool and relatively simple to interpret but can be time consuming to report, often requiring manual transfer of bone mineral density and associated statistics into commercially available dictation systems. We describe here a custom-built computer program for automated reporting of DXA scans using Pydicom, an open-source package built in the Python computer language, and regular expressions to mine DICOM tags for patient information and bone mineral density statistics. This program, easy to emulate by any novice computer programmer, has doubled our efficiency at reporting DXA scans and has eliminated dictation errors.

Classroom Drama as an Instructional Tool. Learning Package No. 42.

ERIC Educational Resources Information Center

Simic, Marge, Comp.; Smith, Carl, Ed.

Originally developed as part of a project for the Department of Defense Schools (DoDDS) system, this learning package on classroom drama as an instructional tool is designed for teachers who wish to upgrade or expand their teaching skills on their own. The package includes an overview of the project; a comprehensive search of the ERIC database; a…

AutoMicromanager: A microscopy scripting toolkit for LABVIEW and other programming environments

NASA Astrophysics Data System (ADS)

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

AutoMicromanager: a microscopy scripting toolkit for LABVIEW and other programming environments.

PubMed

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

78 FR 29016 - Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

... Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material AGENCY: Nuclear..., ``Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material.'' This draft... regulations for the packaging and transportation of radioactive material in Part 71 of Title 10 of the Code of...

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

PC Software for Artificial Intelligence Applications.

PubMed

Epp, H; Kalin, M; Miller, D

1988-05-06

Our review has emphasized that AI tools are programming languages inspired by some problem-solving paradigm. We want to underscore their status as programming languages; even if an AI tool seems to fit a problem perfectly, its proficient use still requires the training and practice associated with any programming language. The programming manuals for PC-Plus, Smalltalk/ V, and Nexpert Object are all tutorial in nature, and the corresponding software packages come with sample applications. We find the manuals to be uniformly good introductions that try to anticipate the problems of a user who is new to the technology. All three vendors offer free technical support by telephone to licensed users. AI tools are sometimes oversold as a way to make programming easy or to avoid it altogether. The truth is that AI tools demand programming-but programming that allows you to concentrate on the essentials of the problem. If we had to implement a diagnostic system, we would look first to a product such as PC-Plus rather than BASIC or C, because PC-Plus is designed specifically for such a problem, whereas these conventional languages are not. If we had to implement a system that required graphical interfaces and could benefit from inheritance, we would look first to an object-oriented system such as Smalltalk/V that provides built-in mechanisms for both. If we had to implement an expert system that called for some mix of AI and conventional techniques, we would look first to a product such as Nexpert Object that integrates various problem-solving technologies. Finally, we might use FORTRAN if we were concerned primarily with programming a well-defined numerical algorithm. AI tools are a valuable complement to traditional languages.

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

XCAT/DRASIM: a realistic CT/human-model simulation package

NASA Astrophysics Data System (ADS)

Fung, George S. K.; Stierstorfer, Karl; Segars, W. Paul; Taguchi, Katsuyuki; Flohr, Thomas G.; Tsui, Benjamin M. W.

2011-03-01

The aim of this research is to develop a complete CT/human-model simulation package by integrating the 4D eXtended CArdiac-Torso (XCAT) phantom, a computer generated NURBS surface based phantom that provides a realistic model of human anatomy and respiratory and cardiac motions, and the DRASIM (Siemens Healthcare) CT-data simulation program. Unlike other CT simulation tools which are based on simple mathematical primitives or voxelized phantoms, this new simulation package has the advantages of utilizing a realistic model of human anatomy and physiological motions without voxelization and with accurate modeling of the characteristics of clinical Siemens CT systems. First, we incorporated the 4D XCAT anatomy and motion models into DRASIM by implementing a new library which consists of functions to read-in the NURBS surfaces of anatomical objects and their overlapping order and material properties in the XCAT phantom. Second, we incorporated an efficient ray-tracing algorithm for line integral calculation in DRASIM by computing the intersection points of the rays cast from the x-ray source to the detector elements through the NURBS surfaces of the multiple XCAT anatomical objects along the ray paths. Third, we evaluated the integrated simulation package by performing a number of sample simulations of multiple x-ray projections from different views followed by image reconstruction. The initial simulation results were found to be promising by qualitative evaluation. In conclusion, we have developed a unique CT/human-model simulation package which has great potential as a tool in the design and optimization of CT scanners, and the development of scanning protocols and image reconstruction methods for improving CT image quality and reducing radiation dose.

Transducer Analysis and ATILA++ Model Development

DTIC Science & Technology

2016-10-10

the ATILA finite element software package. This will greatly enhance the state-of-the-art in transducer performance prediction and provide a tool...refereed publication. 15 IMPACT/APPLICATIONS This work is helping to enable the expansion of the functionality of the A TILA ++ finite element ...Sb. GRANT NUMBER N00014-13-1-0196 Sc. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Sd. PROJECT NUMBER Richard J. Meyer, Jr. 20675 Douglas C. Markley Se

Searching for 'Unknown Unknowns'

NASA Technical Reports Server (NTRS)

Parsons, Vickie S.

2005-01-01

The NASA Engineering and Safety Center (NESC) was established to improve safety through engineering excellence within NASA programs and projects. As part of this goal, methods are being investigated to enable the NESC to become proactive in identifying areas that may be precursors to future problems. The goal is to find unknown indicators of future problems, not to duplicate the program-specific trending efforts. The data that is critical for detecting these indicators exist in a plethora of dissimilar non-conformance and other databases (without a common format or taxonomy). In fact, much of the data is unstructured text. However, one common database is not required if the right standards and electronic tools are employed. Electronic data mining is a particularly promising tool for this effort into unsupervised learning of common factors. This work in progress began with a systematic evaluation of available data mining software packages, based on documented decision techniques using weighted criteria. The four packages, which were perceived to have the most promise for NASA applications, are being benchmarked and evaluated by independent contractors. Preliminary recommendations for "best practices" in data mining and trending are provided. Final results and recommendations should be available in the Fall 2005. This critical first step in identifying "unknown unknowns" before they become problems is applicable to any set of engineering or programmatic data.

An evaluation of the documented requirements of the SSP UIL and a review of commercial software packages for the development and testing of UIL prototypes

NASA Technical Reports Server (NTRS)

Gill, Esther Naomi

1986-01-01

A review was conducted of software packages currently on the market which might be integrated with the interface language and aid in reaching the objectives of customization, standardization, transparency, reliability, maintainability, language substitutions, expandability, portability, and flexibility. Recommendations are given for best choices in hardware and software acquisition for inhouse testing of these possible integrations. Software acquisition in the line of tools to aid expert-system development and/or novice program development, artificial intelligent voice technology and touch screen or joystick or mouse utilization as well as networking were recommended. Other recommendations concerned using the language Ada for the user interface language shell because of its high level of standardization, structure, and ability to accept and execute programs written in other programming languages, its DOD ownership and control, and keeping the user interface language simple so that multiples of users will find the commercialization of space within their realm of possibility which is, after all, the purpose of the Space Station.

KISS for STRAP: user extensions for a protein alignment editor.

PubMed

Gille, Christoph; Lorenzen, Stephan; Michalsky, Elke; Frömmel, Cornelius

2003-12-12

The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool. JAVA-1.4 or higher. http://www.charite.de/bioinf/strap/

THE CAUSAL ANALYSIS / DIAGNOSIS DECISION ...

EPA Pesticide Factsheets

CADDIS is an on-line decision support system that helps investigators in the regions, states and tribes find, access, organize, use and share information to produce causal evaluations in aquatic systems. It is based on the US EPA's Stressor Identification process which is a formal method for identifying causes of impairments in aquatic systems. CADDIS 2007 increases access to relevant information useful for causal analysis and provides methods and tools that practitioners can use to analyze their own data. The new Candidate Cause section provides overviews of commonly encountered causes of impairments to aquatic systems: metals, sediments, nutrients, flow alteration, temperature, ionic strength, and low dissolved oxygen. CADDIS includes new Conceptual Models that illustrate the relationships from sources to stressors to biological effects. An Interactive Conceptual Model for phosphorus links the diagram with supporting literature citations. The new Analyzing Data section helps practitioners analyze their data sets and interpret and use those results as evidence within the USEPA causal assessment process. Downloadable tools include a graphical user interface statistical package (CADStat), and programs for use with the freeware R statistical package, and a Microsoft Excel template. These tools can be used to quantify associations between causes and biological impairments using innovative methods such as species-sensitivity distributions, biological inferenc

Software Comparison for Renewable Energy Deployment in a Distribution Network

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

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

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

simuwatt - A Tablet Based Electronic Auditing Tool

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

Macumber, Daniel; Parker, Andrew; Lisell, Lars

2014-05-08

'simuwatt Energy Auditor' (TM) is a new tablet-based electronic auditing tool that is designed to dramatically reduce the time and cost to perform investment-grade audits and improve quality and consistency. The tool uses the U.S. Department of Energy's OpenStudio modeling platform and integrated Building Component Library to automate modeling and analysis. simuwatt's software-guided workflow helps users gather required data, and provides the data in a standard electronic format that is automatically converted to a baseline OpenStudio model for energy analysis. The baseline energy model is calibrated against actual monthly energy use to ASHRAE Standard 14 guidelines. Energy conservation measures frommore » the Building Component Library are then evaluated using OpenStudio's parametric analysis capability. Automated reporting creates audit documents that describe recommended packages of energy conservation measures. The development of this tool was partially funded by the U.S. Department of Defense's Environmental Security Technology Certification Program. As part of this program, the tool is being tested at 13 buildings on 5 Department of Defense sites across the United States. Results of the first simuwatt audit tool demonstration are presented in this paper.« less

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.

Inspection of the Math Model Tools for On-Orbit Assessment of Impact Damage Report

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Raju, Ivatury S.; Piascik, Robert S> ; KramerWhite, Julie A.; KramerWhite, Julie A.; Labbe, Steve G.; Rotter, Hank A.

2007-01-01

In Spring of 2005, the NASA Engineering Safety Center (NESC) was engaged by the Space Shuttle Program (SSP) to peer review the suite of analytical tools being developed to support the determination of impact and damage tolerance of the Orbiter Thermal Protection Systems (TPS). The NESC formed an independent review team with the core disciplines of materials, flight sciences, structures, mechanical analysis and thermal analysis. The Math Model Tools reviewed included damage prediction and stress analysis, aeroheating analysis, and thermal analysis tools. Some tools are physics-based and other tools are empirically-derived. Each tool was created for a specific use and timeframe, including certification, real-time pre-launch assessments. In addition, the tools are used together in an integrated strategy for assessing the ramifications of impact damage to tile and RCC. The NESC teams conducted a peer review of the engineering data package for each Math Model Tool. This report contains the summary of the team observations and recommendations from these reviews.

Destructive examination of shipping package 9975-02101

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

Daugherty, W. L.

Destructive and non-destructive examinations have been performed on the components of shipping package 9975-02101 as part of the comprehensive Model 9975 package surveillance program. This package is one of ten high-wattage packages that were selected for field surveillance in FY15, and was identified to contain several non-conforming conditions. Most of these conditions (mold, stains, drum corrosion, calculated fiberboard dimensions and fiberboard damage) relate to the accumulation of water in the outer and lower portions of the cane fiberboard assembly. In the short term, this causes local but reversible changes in the fiberboard properties. Long-term effects can include the permanent lossmore » of fiberboard properties (thus far observed only in the bottom fiberboard layers) and reduced drum integrity due to corrosion. The observed conditions must be fully evaluated by KAC to ensure the safety function of the package is being maintained. Three of the other nine FY15 high-wattage packages examined in the K-Area Complex showed similar behavior. Corrosion of the overpack drum has been seen primarily in those packages with relatively severe fiberboard degradation. Visual examination of the drums in storage for external corrosion should be considered as a screening tool to identify additional packages with potential fiberboard degradation. Where overpack drum corrosion has been observed, it is typically heaviest adjacent to the stitch welds along the bottom edge. It is possible that changes to the stitch weld design would reduce the degree of corrosion in this area, but would not eliminate it. Several factors can contribute to the concentration of moisture in the fiberboard, including higher than average initial moisture content, higher internal temperature (due to internal heat load and placement with the array of packages), and the creation of additional moisture as the fiberboard begins to degrade.« less

Computer program documentation modified version of the JA70 aerodynamic heating computer program H800 (MINIVER with a DISSPLA plot package

NASA Technical Reports Server (NTRS)

Olmedo, L.

1980-01-01

The changes, modifications, and inclusions which were adapted to the current version of the MINIVER program are discussed. Extensive modifications were made to various subroutines, and a new plot package added. This plot package is the Johnson Space Center DISSPLA Graphics System currently driven under an 1110 EXEC 8 configuration. User instructions on executing the MINIVER program are provided and the plot package is described.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_IM_KP_0161

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

2000-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_KP_0192

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

2001-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_KP_0139

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

1999-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_IM_KP_0185

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

2000-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

The Ndynamics package—Numerical analysis of dynamical systems and the fractal dimension of boundaries

NASA Astrophysics Data System (ADS)

Avellar, J.; Duarte, L. G. S.; da Mota, L. A. C. P.; de Melo, N.; Skea, J. E. F.

2012-09-01

A set of Maple routines is presented, fully compatible with the new releases of Maple (14 and higher). The package deals with the numerical evolution of dynamical systems and provide flexible plotting of the results. The package also brings an initial conditions generator, a numerical solver manager, and a focusing set of routines that allow for better analysis of the graphical display of the results. The novelty that the package presents an optional C interface is maintained. This allows for fast numerical integration, even for the totally inexperienced Maple user, without any C expertise being required. Finally, the package provides the routines to calculate the fractal dimension of boundaries (via box counting). New version program summary Program Title: Ndynamics Catalogue identifier: %Leave blank, supplied by Elsevier. Licensing provisions: no. Programming language: Maple, C. Computer: Intel(R) Core(TM) i3 CPU M330 @ 2.13 GHz. Operating system: Windows 7. RAM: 3.0 GB Keywords: Dynamical systems, Box counting, Fractal dimension, Symbolic computation, Differential equations, Maple. Classification: 4.3. Catalogue identifier of previous version: ADKH_v1_0. Journal reference of previous version: Comput. Phys. Commun. 119 (1999) 256. Does the new version supersede the previous version?: Yes. Nature of problem Computation and plotting of numerical solutions of dynamical systems and the determination of the fractal dimension of the boundaries. Solution method The default method of integration is a fifth-order Runge-Kutta scheme, but any method of integration present on the Maple system is available via an argument when calling the routine. A box counting [1] method is used to calculate the fractal dimension [2] of the boundaries. Reasons for the new version The Ndynamics package met a demand of our research community for a flexible and friendly environment for analyzing dynamical systems. All the user has to do is create his/her own Maple session, with the system to be studied, and use the commands on the package to (for instance) calculate the fractal dimension of a certain boundary, without knowing or worrying about a single line of C programming. So the package combines the flexibility and friendly aspect of Maple with the fast and robust numerical integration of the compiled (for example C) basin. The package is old, but the problems it was designed to dealt with are still there. Since Maple evolved, the package stopped working, and we felt compelled to produce this version, fully compatible with the latest version of Maple, to make it again available to the Maple user. Summary of revisions Deprecated Maple Packages and Commands: Paraphrasing the Maple in-built help files, "Some Maple commands and packages are deprecated. A command (or package) is deprecated when its functionality has been replaced by an improved implementation. The newer command is said to supersede the older one, and use of the newer command is strongly recommended". So, we have examined our code to see if some of these occurrences could be dangerous for it. For example, the "readlib" command is unnecessary, and we have removed its occurrences from our code. We have checked and changed all the necessary commands in order for us to be safe in respect to danger from this source. Another change we had to make was related to the tools we have implemented in order to use the interface for performing the numerical integration in C, externally, via the use of the Maple command "ssystem". In the past, we had used, for the external C integration, the DJGPP system. But now we present the package with (free) Borland distribution. The compilation and compiling commands are now slightly changed. For example, to compile only, we had used "gcc-c"; now, we use "bcc32-c", etc. All this installation (Borland) is explained on a "README" file we are submitting here to help the potential user. Restrictions Besides the inherent restrictions of numerical integration methods, this version of the package only deals with systems of first-order differential equations. Unusual features This package provides user-friendly software tools for analyzing the character of a dynamical system, whether it displays chaotic behaviour, and so on. Options within the package allow the user to specify characteristics that separate the trajectories into families of curves. In conjunction with the facilities for altering the user's viewpoint, this provides a graphical interface for the speedy and easy identification of regions with interesting dynamics. An unusual characteristic of the package is its interface for performing the numerical integrations in C using a fifth-order Runge-Kutta method (default). This potentially improves the speed of the numerical integration by some orders of magnitude and, in cases where it is necessary to calculate thousands of graphs in regions of difficult integration, this feature is very desirable. Besides that tool, somewhat more experienced users can produce their own C integrator and, by using the commands available in the package, use it as the C integrator provided with the package as long as the new integrator manages the input and output in the same format as the default one does. Running time This depends strongly on the dynamical system. With an Intel® Core™ i3 CPU M330 @ 2.13 GHz, the integration of 50 graphs, for a system of two first-order equations, typically takes less than a second to run (with the C integration interface). Without the C interface, it takes a few seconds. In order to calculate the fractal dimension, where we typically use 10,000 points to integrate, using the C interface it takes from 20 to 30 s. Without the C interface, it becomes really impractical, taking, sometimes, for the same case, almost an hour. For some cases, it takes many hours.

MPI_XSTAR: MPI-based parallelization of XSTAR program

NASA Astrophysics Data System (ADS)

Danehkar, A.

2017-12-01

MPI_XSTAR parallelizes execution of multiple XSTAR runs using Message Passing Interface (MPI). XSTAR (ascl:9910.008), part of the HEASARC's HEAsoft (ascl:1408.004) package, calculates the physical conditions and emission spectra of ionized gases. MPI_XSTAR invokes XSTINITABLE from HEASoft to generate a job list of XSTAR commands for given physical parameters. The job list is used to make directories in ascending order, where each individual XSTAR is spawned on each processor and outputs are saved. HEASoft's XSTAR2TABLE program is invoked upon the contents of each directory in order to produce table model FITS files for spectroscopy analysis tools.

MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes.

PubMed

Ardin, Maude; Cahais, Vincent; Castells, Xavier; Bouaoun, Liacine; Byrnes, Graham; Herceg, Zdenko; Zavadil, Jiri; Olivier, Magali

2016-04-18

The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called MutSpec. MutSpec includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the COSMIC database and other sources. MutSpec offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. MutSpec may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. MutSpec offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. MutSpec can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.

ZBB--a new skill for the financial manager.

PubMed

Thompson, G B; Pyhrr, P A

1979-03-01

Zero-based budgeting (ZBB) is a management decision-making tool currently gaining wide acceptance. ZBB is a budgeting approach which is useful for planning, controlling and coordinating financial and human resources. It involves the re-evaluation of all budgeted activities in terms of priorities established by the management. The traditional process of incremental budgeting differs from ZBB in that only the planned changes are evaluated in the former. In incremental budgeting, the base budget is considered authorized and required little attention. The ZBB process focuses on the whol budget. This is accomplished by: (1) identifying decision units; (2) evaluating each decision unit in terms of performance, costs, benefits, and alternate means of accomplishiing the objectives; (3) ranking the decision packages; and (4) preparing a budget for the highest priority decision packages. The effect of the ZBB approach is that new high priority programs may be funded by eliminating or reducing existing lower-priority programs. ZBB is viewed as a logical process which can combine many of the elements of good management.

PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python

PubMed Central

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2008-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations. PMID:19543450

A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

DOE PAGES

Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

2008-01-01

Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

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

PubMed

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

2004-07-01

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

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.

NASA EEE Parts and NASA Electronic Parts and Packaging (NEPP) Program Update 2018

NASA Technical Reports Server (NTRS)

Label, Kenneth A.; Sampson, Michael J.; Pellish, Jonathan A.; Majewicz, Peter J.

2018-01-01

NASA Electronic Parts and Packaging (NEPP) Program and NASA Electronic Parts Assurance Group (NEPAG) are NASAs point-of-contacts for reliability and radiation tolerance of EEE parts and their packages. This presentation includes an FY18 program overview.

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.

PubMed

Sauro, Herbert M; Hucka, Michael; Finney, Andrew; Wellock, Cameron; Bolouri, Hamid; Doyle, John; Kitano, Hiroaki

2003-01-01

Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.

Development of a computer-assisted learning software package on dental traumatology.

PubMed

Tolidis, K; Crawford, P; Stephens, C; Papadogiannis, Y; Plakias, C

1998-10-01

The development of computer-assisted learning software packages is a relatively new field of computer application. The progress made in personal computer technology toward more user-friendly operating systems has stimulated the academic community to develop computer-assisted learning for pre- and postgraduate students. The ability of computers to combine audio and visual data in an interactive form provides a powerful educational tool. The purpose of this study was to develop and evaluate a computer-assisted learning package on dental traumatology. This program contains background information on the diagnosis, classification, and management of dental injuries in both the permanent and the deciduous dentitions. It is structured into chapters according to the nature of the injury and whether injury has occurred in the primary or permanent dentition. At the end of each chapter there is a self-assessment questionnaire as well as references to relevant literature. Extensive use of pictures and video provides a comprehensive overview of the subject.

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.

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

msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data.

PubMed

Pérez-Figueroa, A

2013-05-01

In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses. © 2013 Blackwell Publishing Ltd.

Dynamic optimization case studies in DYNOPT tool

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

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

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2010 CFR

2010-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2011 CFR

2011-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

10 CFR 60.143 - Monitoring and testing waste packages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... package monitoring program shall include laboratory experiments which focus on the internal condition of... the laboratory experiments. (d) The waste package monitoring program shall continue as long as...

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

PubMed

Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L; Du, Meijun; Kohli, Manish; Boardman, Lisa; Thibodeau, Stephen N; Wang, Liang

2014-03-05

RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module "mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module "Target screening" provides expression profiling analyses and graphic visualization. The module "Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality. eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

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.

Performance Assessment and Translation of Physiologically Based Pharmacokinetic Models From acslX to Berkeley Madonna, MATLAB, and R Language: Oxytetracycline and Gold Nanoparticles As Case Examples.

PubMed

Lin, Zhoumeng; Jaberi-Douraki, Majid; He, Chunla; Jin, Shiqiang; Yang, Raymond S H; Fisher, Jeffrey W; Riviere, Jim E

2017-07-01

Many physiologically based pharmacokinetic (PBPK) models for environmental chemicals, drugs, and nanomaterials have been developed to aid risk and safety assessments using acslX. However, acslX has been rendered sunset since November 2015. Alternative modeling tools and tutorials are needed for future PBPK applications. This forum article aimed to: (1) demonstrate the performance of 4 PBPK modeling software packages (acslX, Berkeley Madonna, MATLAB, and R language) tested using 2 existing models (oxytetracycline and gold nanoparticles); (2) provide a tutorial of PBPK model code conversion from acslX to Berkeley Madonna, MATLAB, and R language; (3) discuss the advantages and disadvantages of each software package in the implementation of PBPK models in toxicology, and (4) share our perspective about future direction in this field. Simulation results of plasma/tissue concentrations/amounts of oxytetracycline and gold from different models were compared visually and statistically with linear regression analyses. Simulation results from the original models were correlated well with results from the recoded models, with time-concentration/amount curves nearly superimposable and determination coefficients of 0.86-1.00. Step-by-step explanations of the recoding of the models in different software programs are provided in the Supplementary Data. In summary, this article presents a tutorial of PBPK model code conversion for a small molecule and a nanoparticle among 4 software packages, and a performance comparison of these software packages in PBPK model implementation. This tutorial helps beginners learn PBPK modeling, provides suggestions for selecting a suitable tool for future projects, and may lead to the transition from acslX to alternative modeling tools. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Online learning tools in an M.Ed. in Earth Sciences program

NASA Astrophysics Data System (ADS)

Richardson, E.

2011-12-01

Penn State's Master of Education in Earth Sciences program is a fully online 30-credit degree program serving mid-career secondary science teachers. Teachers in the program have a diverse background in science and math, are usually many years removed from their most recent degree, and are often deficient in the same geoscience skills as are beginning undergraduates. For example, they habitually assign incorrect causal relationships to concepts that are taught at the same time (such as sea-floor spreading and magnetic field reversals), and they have trouble with both object and spatial visualization. Program faculty also observe anecdotally that many teachers enter the program lacking the ability to describe their mental model of a given Earth science process, making it difficult to identify teachers' knowledge gaps. We have implemented many technical strategies to enhance program content delivery while trying to minimize the inherent barriers to completing quantitative assignments online and at a distance. These barriers include competence with and access to sophisticated data analysis and plotting programs commonly used by scientists. Here, I demonstrate two technical tools I use frequently to strengthen online content delivery and assessment. The first, Jing, is commercially-available, free, and platform-independent. Jing allows the user to make screencasts with narration and embed them into a web page as a flash movie or as an external link. The second is a set of simple sketching tools I have created using the programming language Processing, which is a free, open source, platform-independent language built on Java. The integration of easy-to-use drawing tools into problem sets and other assessments has enabled faculty to appraise a learner's grasp of the material without the steep technical learning curve and expense inherent in most computer graphics packages. A serendipitous benefit of teaching with these tools is that they are easy to learn and freely available and so the teachers in the program learn to use them, too. Qualitative assessment of feedback from the teachers in the program shows that they find the explanations, screencasts, animations, and discussions arising from these tools not only enhance their own learning but also inspire them to try them in their classrooms.

ATK-ForceField: a new generation molecular dynamics software package

NASA Astrophysics Data System (ADS)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

Program Instrumentation and Trace Analysis

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Goldberg, Allen; Filman, Robert; Rosu, Grigore; Koga, Dennis (Technical Monitor)

2002-01-01

Several attempts have been made recently to apply techniques such as model checking and theorem proving to the analysis of programs. This shall be seen as a current trend to analyze real software systems instead of just their designs. This includes our own effort to develop a model checker for Java, the Java PathFinder 1, one of the very first of its kind in 1998. However, model checking cannot handle very large programs without some kind of abstraction of the program. This paper describes a complementary scalable technique to handle such large programs. Our interest is turned on the observation part of the equation: How much information can be extracted about a program from observing a single execution trace? It is our intention to develop a technology that can be applied automatically and to large full-size applications, with minimal modification to the code. We present a tool, Java PathExplorer (JPaX), for exploring execution traces of Java programs. The tool prioritizes scalability for completeness, and is directed towards detecting errors in programs, not to prove correctness. One core element in JPaX is an instrumentation package that allows to instrument Java byte code files to log various events when executed. The instrumentation is driven by a user provided script that specifies what information to log. Examples of instructions that such a script can contain are: 'report name and arguments of all called methods defined in class C, together with a timestamp'; 'report all updates to all variables'; and 'report all acquisitions and releases of locks'. In more complex instructions one can specify that certain expressions should be evaluated and even that certain code should be executed under various conditions. The instrumentation package can hence be seen as implementing Aspect Oriented Programming for Java in the sense that one can add functionality to a Java program without explicitly changing the code of the original program, but one rather writes an aspect and compiles it into the original program using the instrumentation. Another core element of JPaX is an observation package that supports the analysis of the generated event stream. Two kinds of analysis are currently supported. In temporal analysis the execution trace is evaluated against formulae written in temporal logic. We have implemented a temporal logic evaluator on finite traces using the Maude rewriting system from SRI International, USA. Temporal logic is defined in Maude by giving its syntax as a signature and its semantics as rewrite equations. The resulting semantics is extremely efficient and can handle event streams of hundreds of millions events in few minutes. Furthermore, the implementation is very succinct. The second form of even stream analysis supported is error pattern analysis where an execution trace is analyzed using various error detection algorithms that can identify error-prone programming practices that may potentially lead to errors in some different executions. Two such algorithms focusing on concurrency errors have been implemented in JPaX, one for deadlocks and the other for data races. It is important to note, that a deadlock or data race potential does not need to occur in order for its potential to be detected with these algorithms. This is what makes them very scalable in practice. The data race algorithm implemented is the Eraser algorithm from Compaq, however adopted to Java. The tool is currently being applied to a code base for controlling a spacecraft by the developers of that software in order to evaluate its applicability.

The Physics Portal through Physics Connection Website: It's a new way to Stay Connected!

NASA Astrophysics Data System (ADS)

Jacome, D. Z.; Mato, P.; Lopez, J. L.; Zhu, W.; Dong, D.

2011-12-01

Our project involves connecting all level of students to science with limited funding available and having necessary resources to keep them updated. Students gain the opportunity to interact with others without having to leave the comfort of their schools. Through the Physics Portal, a door is automatically opened linking students to projects worldwide and expanding their knowledge each day. Through the funds provided we would purchase 2 laptops, a projector, speakers, a microphone, and an HD webcam. This package includes all of the tools needed to communicate and have an interactive experience with other institutions in our local area. Schools receive packages in the mail with every component needed to connect via conferencing to other students, teachers or professors in the field. Information can be recorded on each laptop, reactions of the students, and questions asked to later be updated on the Physics Connection webpage. Physics Connection allows the science community to explore through each recorded session and make recommendations to increase the efficiently of the program. Several applications on the website allow for groups to connect, discuss general ideas, or contact students for admissions to schools. Interviews, event participation, networking, and communication tools are all linked into one complete interactive package. When the experience ends for one student, it begins for another one. The process continues until the majority becomes informed.

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.

PubMed

Joyce, Brendan; Lee, Danny; Rubio, Alex; Ogurtsov, Aleksey; Alves, Gelio; Yu, Yi-Kuo

2018-03-15

RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. We have constructed a graphical user interface to facilitate the use of RAId on users' local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html .

Unified, Cross-Platform, Open-Source Library Package for High-Performance Computing

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

Kozacik, Stephen

Compute power is continually increasing, but this increased performance is largely found in sophisticated computing devices and supercomputer resources that are difficult to use, resulting in under-utilization. We developed a unified set of programming tools that will allow users to take full advantage of the new technology by allowing them to work at a level abstracted away from the platform specifics, encouraging the use of modern computing systems, including government-funded supercomputer facilities.

Accounting utility for determining individual usage of production level software systems

NASA Technical Reports Server (NTRS)

Garber, S. C.

1984-01-01

An accounting package was developed which determines the computer resources utilized by a user during the execution of a particular program and updates a file containing accumulated resource totals. The accounting package is divided into two separate programs. The first program determines the total amount of computer resources utilized by a user during the execution of a particular program. The second program uses these totals to update a file containing accumulated totals of computer resources utilized by a user for a particular program. This package is useful to those persons who have several other users continually accessing and running programs from their accounts. The package provides the ability to determine which users are accessing and running specified programs along with their total level of usage.

Computer Simulation Is an Undervalued Tool for Genetic Analysis: A Historical View and Presentation of SHIMSHON – A Web-Based Genetic Simulation Package

PubMed Central

Greenberg, David A.

2011-01-01

Computer simulation methods are under-used tools in genetic analysis because simulation approaches have been portrayed as inferior to analytic methods. Even when simulation is used, its advantages are not fully exploited. Here, I present SHIMSHON, our package of genetic simulation programs that have been developed, tested, used for research, and used to generated data for Genetic Analysis Workshops (GAW). These simulation programs, now web-accessible, can be used by anyone to answer questions about designing and analyzing genetic disease studies for locus identification. This work has three foci: (1) the historical context of SHIMSHON's development, suggesting why simulation has not been more widely used so far. (2) Advantages of simulation: computer simulation helps us to understand how genetic analysis methods work. It has advantages for understanding disease inheritance and methods for gene searches. Furthermore, simulation methods can be used to answer fundamental questions that either cannot be answered by analytical approaches or cannot even be defined until the problems are identified and studied, using simulation. (3) I argue that, because simulation was not accepted, there was a failure to grasp the meaning of some simulation-based studies of linkage. This may have contributed to perceived weaknesses in linkage analysis; weaknesses that did not, in fact, exist. PMID:22189467

The R package 'icosa' for coarse resolution global triangular and penta-hexagonal gridding

NASA Astrophysics Data System (ADS)

Kocsis, Adam T.

2017-04-01

With the development of the internet and the computational power of personal computers, open source programming environments have become indispensable for science in the past decade. This includes the increase of the GIS capacity of the free R environment, which was originally developed for statistical analyses. The flexibility of R made it a preferred programming tool in a multitude of disciplines from the area of the biological and geological sciences. Many of these subdisciplines operate with incidence (occurrence) data that are in a large number of cases to be grained before further analyses can be conducted. This graining is executed mostly by gridding data to cells of a Gaussian grid of various resolutions to increase the density of data in a single unit of the analyses. This method has obvious shortcomings despite the ease of its application: well-known systematic biases are induced to cell sizes and shapes that can interfere with the results of statistical procedures, especially if the number of incidence points influences the metrics in question. The 'icosa' package employs a common method to overcome this obstacle by implementing grids with roughly equal cell sizes and shapes that are based on tessellated icosahedra. These grid objects are essentially polyhedra with xyz Cartesian vertex data that are linked to tables of faces and edges. At its current developmental stage, the package uses a single method of tessellation which balances grid cell size and shape distortions, but its structure allows the implementation of various other types of tessellation algorithms. The resolution of the grids can be set by the number of breakpoints inserted into a segment forming an edge of the original icosahedron. Both the triangular and their inverted penta-hexagonal grids are available for creation with the package. The package also incorporates functions to look up coordinates in the grid very effectively and data containers to link data to the grid structure. The classes defined in the package are communicating with classes of the 'sp' and 'raster' packages and functions are supplied that allow resolution change and type conversions. Three-dimensional rendering is made available with the 'rgl' package and two-dimensional projections can be calculated using 'sp' and 'rgdal'. The package was developed as part of a project funded by the Deutsche Forschungsgemeinschaft (KO - 5382/1-1).

Fuzzy Logic Engine

NASA Technical Reports Server (NTRS)

Howard, Ayanna

2005-01-01

The Fuzzy Logic Engine is a software package that enables users to embed fuzzy-logic modules into their application programs. Fuzzy logic is useful as a means of formulating human expert knowledge and translating it into software to solve problems. Fuzzy logic provides flexibility for modeling relationships between input and output information and is distinguished by its robustness with respect to noise and variations in system parameters. In addition, linguistic fuzzy sets and conditional statements allow systems to make decisions based on imprecise and incomplete information. The user of the Fuzzy Logic Engine need not be an expert in fuzzy logic: it suffices to have a basic understanding of how linguistic rules can be applied to the user's problem. The Fuzzy Logic Engine is divided into two modules: (1) a graphical-interface software tool for creating linguistic fuzzy sets and conditional statements and (2) a fuzzy-logic software library for embedding fuzzy processing capability into current application programs. The graphical- interface tool was developed using the Tcl/Tk programming language. The fuzzy-logic software library was written in the C programming language.

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

Approaching Suspicious Substances Safely

NASA Technical Reports Server (NTRS)

2004-01-01

A mineral identification tool that was developed for NASA's Mars Rover Technology Development program is now serving as a powerful tool for U.S. law enforcement agencies and military personnel to identify suspicious liquid and solid substances. The tool can measure unknown substances through glass and plastic packaging materials with the RamanProbe(TradeMark) focused fiber-optic probe. The probe length can be extended up to 200 meters to enable users to analyze potentially dangerous substances at a safe distance. In many cases, the spectrometer and personnel are kept in a safe zone while the probe is positioned next to the sample being analyzed. Being able to identify chemicals in remote locations also saves users time and labor, since otherwise the samples would need to be collected, transported, and prepared prior to measurement in the laboratory.

eXtended CASA Line Analysis Software Suite (XCLASS)

NASA Astrophysics Data System (ADS)

Möller, T.; Endres, C.; Schilke, P.

2017-02-01

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

A practical tool for monitoring the performance of measuring systems in a laboratory network: report of an ACB Working Group.

PubMed

Ayling, Pete; Hill, Robert; Jassam, Nuthar; Kallner, Anders; Khatami, Zahra

2017-11-01

Background A logical consequence of the introduction of robotics and high-capacity analysers has seen a consolidation to larger units. This requires new structures and quality systems to ensure that laboratories deliver consistent and comparable results. Methods A spreadsheet program was designed to accommodate results from up to 12 different instruments/laboratories and present IQC data, i.e. Levey-Jennings and Youden plots and comprehensive numerical tables of the performance of each item. Input of data was made possible by a 'data loader' by which IQC data from the individual instruments could be transferred to the spreadsheet program on line. Results A set of real data from laboratories is used to populate the data loader and the networking software program. Examples are present from the analysis of variance components, the Levey-Jennings and Youden plots. Conclusions This report presents a software package that allows the simultaneous management and detailed monitoring of the performance of up to 12 different instruments/laboratories in a fully interactive mode. The system allows a quality manager of networked laboratories to have a continuous updated overview of the performance. This software package has been made available at the ACB website.

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

Almond, P.; Livingston, R.; Traver, L.

The Savannah River National Laboratory (SRNL) 3013 destructive examination program performs surveillances on 3013 containers originating from multiple sites across the DOE complex. The bases for the packaging, storage, and surveillance activities are derived from the Department of Energy's 3013 Standard (DOE-STD-3013-2004). During destructive examination, headspace gas samples are obtained from the 3013 inner container and the annulus between the outer and inner containers. To characterize gas species, the samples are analyzed by gas chromatography (GC), direct-inlet mass spectrometry (DIMS), and Fourier-transform infrared spectroscopy (FTIR). The GC results, as well as other parameters, are utilized as input into the gasmore » evaluation software tool (GEST) program for computation of pre-puncture gas compositions and pressures. Over 30 containers from the Hanford Site and the Rocky Flats Environmental Technology Site (RFETS) have been examined in the first three years of the surveillance program. Several containers were shown to have appreciable hydrogen content (some greater than 30 mol %), yet little or no oxygen was detected in any of the containers, including those exhibiting high hydrogen concentrations. Characteristics including moisture content, surface area, and material composition, along with the headspace gas composition, are utilized in an attempt to explain the chemical behavior of the packaged materials.« less

The NASA Electronic Parts and Packaging (NEPP) Program: Overview and Update FY15 and Beyond

NASA Technical Reports Server (NTRS)

LaBel, Kenneth A.; Sampson, Michael J.

2016-01-01

The NASA Electronic Parts and Packaging (NEPP) program, and its subset the NASA Electronic Parts Assurance Group (NEPAG), are NASA's point-of-contacts for reliability and radiation tolerance of electrical, electronic, and electromechanical (EEE) parts and their packages. This presentation includes a Fiscal Year 2015 program overview.

78 FR 17777 - Tax Counseling for the Elderly (TCE) Program Availability of Application Packages

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-22

... DEPARTMENT OF THE TREASURY Internal Revenue Service Tax Counseling for the Elderly (TCE) Program...: This document provides notice of the availability of Application Packages for the 2014 Tax Counseling... for submitting an application package to the IRS for the Tax Counseling for the Elderly (TCE) Program...

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…

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.

PubMed

Banerjee, Shyamashree; Gupta, Parth Sarthi Sen; Nayek, Arnab; Das, Sunit; Sur, Vishma Pratap; Seth, Pratyay; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal K

2015-01-01

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics. PHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users.

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2

PubMed Central

Banerjee, Shyamashree; Gupta, Parth Sarthi Sen; Nayek, Arnab; Das, Sunit; Sur, Vishma Pratap; Seth, Pratyay; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal K

2015-01-01

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics. Availability PHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users. PMID:26339154

A permanent seismic station beneath the Ocean Bottom

NASA Astrophysics Data System (ADS)

Harris, David; Cessaro, Robert K.; Duennebier, Fred K.; Byrne, David A.

1987-03-01

The Hawaii Institute of Geophysics began development of the Ocean Subbottom Seisometer (OSS) system in 1978, and OSS systems were installed in four locations between 1979 and 1982. The OSS system is a permanent, deep ocean borehole seismic recording system composed of a borehole sensor package (tool), an electromechanical cable, recorder package, and recovery system. Installed near the bottom of a borehole (drilled by the D/V Glomar Challenger), the tool contains three orthogonal, 4.5-Hz geophones, two orthogonal tilt meters; and a temperature sensor. Signals from these sensors are multiplexed, digitized (with a floating point technique), and telemetered through approximately 10 km of electromechanical cable to a recorder package located near the ocean bottom. Electrical power for the tool is supplied from the recorder package. The digital seismic signals are demultiplexed, converted back to analog form, processed through an automatic gain control (AGC) circuit, and recorded along with a time code on magnetic tape cassettes in the recorder package. Data may be recorded continuously for up to two months in the self-contained recorder package. Data may also be recorded in real time (digital formal) during the installation and subsequent recorder package servicing. The recorder package is connected to a submerged recovery buoy by a length of bouyant polypropylene rope. The anchor on the recovery buoy is released by activating either of the acoustical command releases. The polypropylene rope may also be seized with a grappling hook to effect recovery. The recorder package may be repeatedly serviced as long as the tool remains functional A wide range of data has been recovered from the OSS system. Recovered analog records include signals from natural seismic sources such as earthquakes (teleseismic and local), man-made seismic sources such as refraction seismic shooting (explosives and air cannons), and nuclear tests. Lengthy continuous recording has permitted analysis of wideband noise levels, and the slowly varying parameters, temperature and tilt.

Inspection of the Math Model Tools for On-Orbit Assessment of Impact Damage Report. Version 1.0

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Raju, Ivatury S.; Piascik, Robert S.; Kramer White, Julie; Labbe, Steve G.; Rotter, Hank A.

2005-01-01

In Spring of 2005, the NASA Engineering Safety Center (NESC) was engaged by the Space Shuttle Program (SSP) to peer review the suite of analytical tools being developed to support the determination of impact and damage tolerance of the Orbiter Thermal Protection Systems (TPS). The NESC formed an independent review team with the core disciplines of materials, flight sciences, structures, mechanical analysis and thermal analysis. The Math Model Tools reviewed included damage prediction and stress analysis, aeroheating analysis, and thermal analysis tools. Some tools are physics-based and other tools are empirically-derived. Each tool was created for a specific use and timeframe, including certification, real-time pre-launch assessments, and real-time on-orbit assessments. The tools are used together in an integrated strategy for assessing the ramifications of impact damage to tile and RCC. The NESC teams conducted a peer review of the engineering data package for each Math Model Tool. This report contains the summary of the team observations and recommendations from these reviews.

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.

SAHARA: A package of PC computer programs for estimating both log-hyperbolic grain-size parameters and standard moments

NASA Astrophysics Data System (ADS)

Christiansen, Christian; Hartmann, Daniel

This paper documents a package of menu-driven POLYPASCAL87 computer programs for handling grouped observations data from both sieving (increment data) and settling tube procedures (cumulative data). The package is designed deliberately for use on IBM-compatible personal computers. Two of the programs solve the numerical problem of determining the estimates of the four (main) parameters of the log-hyperbolic distribution and their derivatives. The package also contains a program for determining the mean, sorting, skewness. and kurtosis according to the standard moments. Moreover, the package contains procedures for smoothing and grouping of settling tube data. A graphic part of the package plots the data in a log-log plot together with the estimated log-hyperbolic curve. Along with the plot follows all estimated parameters. Another graphic option is a plot of the log-hyperbolic shape triangle with the (χ,ζ) position of the sample.

ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

PubMed

Huntley, Melanie A; Larson, Jessica L; Chaivorapol, Christina; Becker, Gabriel; Lawrence, Michael; Hackney, Jason A; Kaminker, Joshua S

2013-12-15

It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.

POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

NASA Astrophysics Data System (ADS)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

Method for simulating paint mixing on computer monitors

NASA Astrophysics Data System (ADS)

Carabott, Ferdinand; Lewis, Garth; Piehl, Simon

2002-06-01

Computer programs like Adobe Photoshop can generate a mixture of two 'computer' colors by using the Gradient control. However, the resulting colors diverge from the equivalent paint mixtures in both hue and value. This study examines why programs like Photoshop are unable to simulate paint or pigment mixtures, and offers a solution using Photoshops existing tools. The article discusses how a library of colors, simulating paint mixtures, is created from 13 artists' colors. The mixtures can be imported into Photoshop as a color swatch palette of 1248 colors and as 78 continuous or stepped gradient files, all accessed in a new software package, Chromafile.

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats

PubMed Central

2014-01-01

Background Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). Results BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. Conclusions BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication. PMID:24955110

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats

USGS Publications Warehouse

Erickson, Richard A.; Thogmartin, Wayne E.; Szymanski, Jennifer A.

2014-01-01

Background: Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). Results: BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. Conclusions: BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication.

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats.

PubMed

Erickson, Richard A; Thogmartin, Wayne E; Szymanski, Jennifer A

2014-01-01

Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication.

Tool for use in lifting pin supported objects

NASA Technical Reports Server (NTRS)

Marzek, R. A.; Read, W. S. (Inventor)

1974-01-01

A tool for use in lifting a pin-supported, electronic package mounted in juxtaposition with the surface of an electronic circuit board is described. The tool is configured to be received beneath a pin-supported package and is characterized by a manually operable linkage, including an elongated, rigid link is supported for axial reciprocation and a pivotal link pinned to the body and supported for oscillation induced in response to axial motion imparted to the rigid link. A lifting plate is pivotally coupled to the distal end of the pivotal link so that oscillatory motion imparted to the pivotal link serves to move the plate vertically for elevating the plate into lifting engagement with the electronic package positioned thereabove.

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).

Novel technique for tracking manpower and work packages: a useful tool for the team and management

NASA Astrophysics Data System (ADS)

Gill, R.; Gracia, G.; Lupton, R. H.; O'Mullane, W.

2014-08-01

In these times of austerity it is becoming more and more important to justify the need for manpower to management. Additionally, with the fast pace of today's projects the need for tools that facilitate teams to not only plan, but also track their work, are essential. The practice of planning work packages and the associated manpower has been about for a while but little is done to really cross-check that planning against reality. In this paper these elements are brought together through a number of tools that make up the end to end process of planning, tracking and reporting of work package progress and manpower usage.

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data.

PubMed

Mayne, Benjamin T; Leemaqz, Shalem Y; Buckberry, Sam; Rodriguez Lopez, Carlos M; Roberts, Claire T; Bianco-Miotto, Tina; Breen, James

2018-02-01

Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package ( https://bioconductor.org/packages/release/bioc/html/msgbsR.html ).

Function Package for Computing Quantum Resource Measures

NASA Astrophysics Data System (ADS)

Huang, Zhiming

2018-05-01

In this paper, we present a function package for to calculate quantum resource measures and dynamics of open systems. Our package includes common operators and operator lists, frequently-used functions for computing quantum entanglement, quantum correlation, quantum coherence, quantum Fisher information and dynamics in noisy environments. We briefly explain the functions of the package and illustrate how to use the package with several typical examples. We expect that this package is a useful tool for future research and education.

Sequence Segmentation with changeptGUI.

PubMed

Tasker, Edward; Keith, Jonathan M

2017-01-01

Many biological sequences have a segmental structure that can provide valuable clues to their content, structure, and function. The program changept is a tool for investigating the segmental structure of a sequence, and can also be applied to multiple sequences in parallel to identify a common segmental structure, thus providing a method for integrating multiple data types to identify functional elements in genomes. In the previous edition of this book, a command line interface for changept is described. Here we present a graphical user interface for this package, called changeptGUI. This interface also includes tools for pre- and post-processing of data and results to facilitate investigation of the number and characteristics of segment classes.

Developing the online survey.

PubMed

Gordon, Jeffry S; McNew, Ryan

2008-12-01

Institutions of higher education are now using Internet-based technology tools to conduct surveys for data collection. Research shows that the type and quality of responses one receives with online surveys are comparable with what one receives in paper-based surveys. Data collection can take place on Web-based surveys, e-mail-based surveys, and personal digital assistants/Smartphone devices. Web surveys can be subscription templates, software packages installed on one's own server, or created from scratch using Web programming development tools. All of these approaches have their advantages and disadvantages. The survey owner must make informed decisions as to the right technology to implement. The correct choice can save hours of work in sorting, organizing, and analyzing data.

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Visualization of International Solar-Terrestrial Physics Program (ISTP) data

NASA Technical Reports Server (NTRS)

Kessel, Ramona L.; Candey, Robert M.; Hsieh, Syau-Yun W.; Kayser, Susan

1995-01-01

The International Solar-Terrestrial Physics Program (ISTP) is a multispacecraft, multinational program whose objective is to promote further understanding of the Earth's complex plasma environment. Extensive data sharing and data analysis will be needed to ensure the success of the overall ISTP program. For this reason, there has been a special emphasis on data standards throughout ISTP. One of the key tools will be the common data format (CDF), developed, maintained, and evolved at the National Space Science Data Center (NSSDC), with the set of ISTP implementation guidelines specially designed for space physics data sets by the Space Physics Data Facility (associated with the NSSDC). The ISTP guidelines were developed to facilitate searching, plotting, merging, and subsetting of data sets. We focus here on the plotting application. A prototype software package was developed to plot key parameter (KP) data from the ISTP program at the Science Planning and Operations Facility (SPOF). The ISTP Key Parameter Visualization Tool is based on the Interactive Data Language (IDL) and is keyed to the ISTP guidelines, reading data stored in CDF. With the combination of CDF, the ISTP guidelines, and the visualization software, we can look forward to easier and more effective data sharing and use among ISTP scientists.

Computational thinking in life science education.

PubMed

Rubinstein, Amir; Chor, Benny

2014-11-01

We join the increasing call to take computational education of life science students a step further, beyond teaching mere programming and employing existing software tools. We describe a new course, focusing on enriching the curriculum of life science students with abstract, algorithmic, and logical thinking, and exposing them to the computational "culture." The design, structure, and content of our course are influenced by recent efforts in this area, collaborations with life scientists, and our own instructional experience. Specifically, we suggest that an effective course of this nature should: (1) devote time to explicitly reflect upon computational thinking processes, resisting the temptation to drift to purely practical instruction, (2) focus on discrete notions, rather than on continuous ones, and (3) have basic programming as a prerequisite, so students need not be preoccupied with elementary programming issues. We strongly recommend that the mere use of existing bioinformatics tools and packages should not replace hands-on programming. Yet, we suggest that programming will mostly serve as a means to practice computational thinking processes. This paper deals with the challenges and considerations of such computational education for life science students. It also describes a concrete implementation of the course and encourages its use by others.

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.

Floating-Point Units and Algorithms for field-programmable gate arrays

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

Underwood, Keith D.; Hemmert, K. Scott

2005-11-01

The software that we are attempting to copyright is a package of floating-point unit descriptions and example algorithm implementations using those units for use in FPGAs. The floating point units are best-in-class implementations of add, multiply, divide, and square root floating-point operations. The algorithm implementations are sample (not highly flexible) implementations of FFT, matrix multiply, matrix vector multiply, and dot product. Together, one could think of the collection as an implementation of parts of the BLAS library or something similar to the FFTW packages (without the flexibility) for FPGAs. Results from this work has been published multiple times and wemore » are working on a publication to discuss the techniques we use to implement the floating-point units, For some more background, FPGAS are programmable hardware. "Programs" for this hardware are typically created using a hardware description language (examples include Verilog, VHDL, and JHDL). Our floating-point unit descriptions are written in JHDL, which allows them to include placement constraints that make them highly optimized relative to some other implementations of floating-point units. Many vendors (Nallatech from the UK, SRC Computers in the US) have similar implementations, but our implementations seem to be somewhat higher performance. Our algorithm implementations are written in VHDL and models of the floating-point units are provided in VHDL as well. FPGA "programs" make multiple "calls" (hardware instantiations) to libraries of intellectual property (IP), such as the floating-point unit library described here. These programs are then compiled using a tool called a synthesizer (such as a tool from Synplicity, Inc.). The compiled file is a netlist of gates and flip-flops. This netlist is then mapped to a particular type of FPGA by a mapper and then a place- and-route tool. These tools assign the gates in the netlist to specific locations on the specific type of FPGA chip used and constructs the required routes between them. The result is a "bitstream" that is analogous to a compiled binary. The bitstream is loaded into the FPGA to create a specific hardware configuration.« less

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services

PubMed Central

Castaño-Díez, Daniel

2017-01-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance. PMID:28580909

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services.

PubMed

Castaño-Díez, Daniel

2017-06-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.

3DRT-MPASS

NASA Technical Reports Server (NTRS)

Lickly, Ben

2005-01-01

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

VLSI Design Tools, Reference Manual, Release 2.0.

DTIC Science & Technology

1984-08-01

eder. 2.3 ITACV: Libary ofC readne. far oesumdg a layoit 1-,, tiling. V ~2.4 "QUILT: CeinS"Wbesa-i-M-8euar ray f atwok til 2.5 "TIL: Tockmeleff...8217patterns package was added so that complex and repetitive digital waveforms could be generated far more easily. The recently written program MTP (Multiple...circuit model to estimate timing delays through digital circuits. It also has a mode that allows it to be used as a switch (gate) level simulator

Scientific Workflow Management in Proteomics

PubMed Central

de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

2012-01-01

Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

A postdoctoral position is available in the Viral Recombination Section (VRS), HIV Dynamics and Replication Program, CCR.  The VRS studies retroviral replication using human immunodeficiency viruses and other retroviruses, with a particular emphasis on the mechanisms of viral RNA biology, specific RNA packaging, virus assembly, and HIV replication.  Molecular tools and advanced imaging approaches are used to dissect various aspects of viral replication mechanisms.  A more complete description of the projects can be found at http://home.ncifcrf.gov/hivdrp/Hu_res.html.

Social Network Collaboration for Crisis Response Operations: Developing a Situational Awareness (SA) Tool to Improve Haiti’s Interagency Relief Efforts

DTIC Science & Technology

2011-06-01

and interpret patterns of social ties among actors, either multitudinous or relatively few (de Nooy, Mrvar , & Batagelj , 2005, p. 5). An aspect of...millions of vertices [aka nodes] ( Batagelj & Mrvar , 2003). With its ability to process large networks, it is considered an excellent social-network...8217Vladimir Batagelj and Andrej Mrvar —program package Pajek: http://vlado.fmf.uni-lj.si/pub/networks/pajek/’ name=’generator’/> </head> <Scene

GT-SUPREEM: the Georgia Tech summer undergraduate packaging research and engineering experience for minorities

NASA Astrophysics Data System (ADS)

May, Gary S.

1996-07-01

The Georgia Tech SUmmer Undergraduate Packaging Research and Engineering Experience for Minorities (GT-SUPREEM) is an eight-week summer program designed to attract qualified minority students to pursue graduate degrees in packaging- related disciplines. The program is conducted under the auspices of the Georgia Tech Engineering Research Center in Low-Cost Electronic Packaging, which is sponsored by the National Science Foundation. In this program, nine junior and senior level undergraduate students are selected on a nationwide basis and paired with a faculty advisor to undertake research projects in the Packaging Research CEnter. The students are housed on campus and provided with a $DLR3,000 stipend and a travel allowance. At the conclusion of the program, the students present both oral and written project summaries. It is anticipated that this experience will motivate these students to become applicants for graduate study in ensuring years. This paper will provide an overview of the GT-SUPREEM program, including student research activities, success stories, lessons learned, and overall program outlook.

MutAIT: an online genetic toxicology data portal and analysis tools.

PubMed

Avancini, Daniele; Menzies, Georgina E; Morgan, Claire; Wills, John; Johnson, George E; White, Paul A; Lewis, Paul D

2016-05-01

Assessment of genetic toxicity and/or carcinogenic activity is an essential element of chemical screening programs employed to protect human health. Dose-response and gene mutation data are frequently analysed by industry, academia and governmental agencies for regulatory evaluations and decision making. Over the years, a number of efforts at different institutions have led to the creation and curation of databases to house genetic toxicology data, largely, with the aim of providing public access to facilitate research and regulatory assessments. This article provides a brief introduction to a new genetic toxicology portal called Mutation Analysis Informatics Tools (MutAIT) (www.mutait.org) that provides easy access to two of the largest genetic toxicology databases, the Mammalian Gene Mutation Database (MGMD) and TransgenicDB. TransgenicDB is a comprehensive collection of transgenic rodent mutation data initially compiled and collated by Health Canada. The updated MGMD contains approximately 50 000 individual mutation spectral records from the published literature. The portal not only gives access to an enormous quantity of genetic toxicology data, but also provides statistical tools for dose-response analysis and calculation of benchmark dose. Two important R packages for dose-response analysis are provided as web-distributed applications with user-friendly graphical interfaces. The 'drsmooth' package performs dose-response shape analysis and determines various points of departure (PoD) metrics and the 'PROAST' package provides algorithms for dose-response modelling. The MutAIT statistical tools, which are currently being enhanced, provide users with an efficient and comprehensive platform to conduct quantitative dose-response analyses and determine PoD values that can then be used to calculate human exposure limits or margins of exposure. © The Author 2015. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Basis System

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

Dubois, P.F.

1989-05-16

This paper discusses the basis system. Basis is a program development system for scientific programs. It has been developed over the last five years at Lawrence Livermore National Laboratory (LLNL), where it is now used in about twenty major programming efforts. The Basis System includes two major components, a program development system and a run-time package. The run-time package provides the Basis Language interpreter, through which the user does input, output, plotting, and control of the program's subroutines and functions. Variables in the scientific packages are known to this interpreter, so that the user may arbitrarily print, plot, and calculatemore » with, any major program variables. Also provided are facilities for dynamic memory management, terminal logs, error recovery, text-file i/o, and the attachment of non-Basis-developed packages.« less

Rural Programs: Vocational Education Resource Package.

ERIC Educational Resources Information Center

Evaluation and Training Inst., Los Angeles, CA.

Designed to assist community college administrators and faculty in enhancing vocational education programs and services, this resource package on rural college programs contains information about successful program strategies and ideas currently in use in vocational education programs at rural schools within the California Community Colleges…

Language, Literacy and Numeracy in National Training Packages: Case Studies in Aged Care and Hospitality.

ERIC Educational Resources Information Center

Haines, Christine; Brand, Jennie Bickmore

The implementation and effectiveness of the inclusion of literacy and numeracy in industry training packages was examined in case studies of three programs in Western Australia. Two were certificate programs in cooking and food and beverage as specified in the hospitality training package, and the third was an aged care program based on the…

Shielding Calculations on Waste Packages - The Limits and Possibilities of different Calculation Methods by the example of homogeneous and inhomogeneous Waste Packages

NASA Astrophysics Data System (ADS)

Adams, Mike; Smalian, Silva

2017-09-01

For nuclear waste packages the expected dose rates and nuclide inventory are beforehand calculated. Depending on the package of the nuclear waste deterministic programs like MicroShield® provide a range of results for each type of packaging. Stochastic programs like "Monte-Carlo N-Particle Transport Code System" (MCNP®) on the other hand provide reliable results for complex geometries. However this type of program requires a fully trained operator and calculations are time consuming. The problem here is to choose an appropriate program for a specific geometry. Therefore we compared the results of deterministic programs like MicroShield® and stochastic programs like MCNP®. These comparisons enable us to make a statement about the applicability of the various programs for chosen types of containers. As a conclusion we found that for thin-walled geometries deterministic programs like MicroShield® are well suited to calculate the dose rate. For cylindrical containers with inner shielding however, deterministic programs hit their limits. Furthermore we investigate the effect of an inhomogeneous material and activity distribution on the results. The calculations are still ongoing. Results will be presented in the final abstract.

Visual Data Analysis for Satellites

NASA Technical Reports Server (NTRS)

Lau, Yee; Bhate, Sachin; Fitzpatrick, Patrick

2008-01-01

The Visual Data Analysis Package is a collection of programs and scripts that facilitate visual analysis of data available from NASA and NOAA satellites, as well as dropsonde, buoy, and conventional in-situ observations. The package features utilities for data extraction, data quality control, statistical analysis, and data visualization. The Hierarchical Data Format (HDF) satellite data extraction routines from NASA's Jet Propulsion Laboratory were customized for specific spatial coverage and file input/output. Statistical analysis includes the calculation of the relative error, the absolute error, and the root mean square error. Other capabilities include curve fitting through the data points to fill in missing data points between satellite passes or where clouds obscure satellite data. For data visualization, the software provides customizable Generic Mapping Tool (GMT) scripts to generate difference maps, scatter plots, line plots, vector plots, histograms, timeseries, and color fill images.

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

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

Packaging Your Training Materials

ERIC Educational Resources Information Center

Espeland, Pamela

1977-01-01

The types of packaging and packaging materials to use for training materials should be determined during the planning of the training programs, according to the packaging market. Five steps to follow in shopping for packaging are presented, along with a list of packaging manufacturers. (MF)

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

PubMed

Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

2015-01-01

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

SEDA: A software package for the Statistical Earthquake Data Analysis

NASA Astrophysics Data System (ADS)

Lombardi, A. M.

2017-03-01

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

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.

PubMed

Bennett, Dominic J; Sutton, Mark D; Turvey, Samuel T

2017-01-07

Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.

SEDA: A software package for the Statistical Earthquake Data Analysis

PubMed Central

Lombardi, A. M.

2017-01-01

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

20 CFR 633.307 - Packages of benefits.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Packages of benefits. 633.307 Section 633.307 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR MIGRANT AND SEASONAL FARMWORKER PROGRAMS Program Design and Administrative Procedures § 633.307 Packages of benefits. (a) Where...

A Pipeline Tool for CCD Image Processing

NASA Astrophysics Data System (ADS)

Bell, Jon F.; Young, Peter J.; Roberts, William H.; Sebo, Kim M.

MSSSO is part of a collaboration developing a wide field imaging CCD mosaic (WFI). As part of this project, we have developed a GUI based pipeline tool that is an integrated part of MSSSO's CICADA data acquisition environment and processes CCD FITS images as they are acquired. The tool is also designed to run as a stand alone program to process previously acquired data. IRAF tasks are used as the central engine, including the new NOAO mscred package for processing multi-extension FITS files. The STScI OPUS pipeline environment may be used to manage data and process scheduling. The Motif GUI was developed using SUN Visual Workshop. C++ classes were written to facilitate launching of IRAF and OPUS tasks. While this first version implements calibration processing up to and including flat field corrections, there is scope to extend it to other processing.

Implementing Earned Value Management in the CxP EVA Systems Project Office

NASA Technical Reports Server (NTRS)

Sorge, Les L.

2009-01-01

Earned Value Management (EVM), like project management, is as much art as it is science to develop an implementation plan for a project. This presentation will cover issues that were overcome and the implementation strategy to deploy Earned Value Management (EVM) within the Constellation Program (CxP), EVA Systems Project Office (ESPO), as well as discuss additional hurdles that currently prevent the organization from optimizing EVM. Each organization and each project within an organization needs to mold an EVM implementation plan around existing processes and tools, while at the same time revising those existing processes and tools as necessary to make them compatible with EVM. The ESPO EVM implementation covers work breakdown structure, organizational breakdown structure, control account, work/planning package development; integrated master schedule development using an integrated master plan; incorporating reporting requirements for existing funding process such as Planning, Programming, Budgeting, and Execution (PPBE) and JSC Internal Task Agreements (ITA); and interfacing with other software tools such as the Systems Applications and Products (SAP) accounting system and the CxP wInsight EVM analysis tool. However, there are always areas for improvement and EVM is no exception. As EVM continues to mature within the NASA CxP, these areas will continue to be worked to resolution to provide the Program Managers, Project Managers, and Control Account Managers the best EVM data possible to make informed decisions.

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

PubMed

Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

2017-01-06

The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements.

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2009-10-23

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

minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information.

PubMed

Meyer, Patrick E; Lafitte, Frédéric; Bontempi, Gianluca

2008-10-29

This paper presents the R/Bioconductor package minet (version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a network where nodes denote genes, edges model statistical dependencies between genes and the weight of an edge quantifies the statistical evidence of a specific (e.g transcriptional) gene-to-gene interaction. Four different entropy estimators are made available in the package minet (empirical, Miller-Madow, Schurmann-Grassberger and shrink) as well as four different inference methods, namely relevance networks, ARACNE, CLR and MRNET. Also, the package integrates accuracy assessment tools, like F-scores, PR-curves and ROC-curves in order to compare the inferred network with a reference one. The package minet provides a series of tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive R Archive Network (CRAN) as well as from the Bioconductor website.

Implementation of interconnect simulation tools in spice

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

A Roadmap to Continuous Integration for ATLAS Software Development

NASA Astrophysics Data System (ADS)

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

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

simBio: a Java package for the development of detailed cell models.

PubMed

Sarai, Nobuaki; Matsuoka, Satoshi; Noma, Akinori

2006-01-01

Quantitative dynamic computer models, which integrate a variety of molecular functions into a cell model, provide a powerful tool to create and test working hypotheses. We have developed a new modeling tool, the simBio package (freely available from ), which can be used for constructing cell models, such as cardiac cells (the Kyoto model from Matsuoka et al., 2003, 2004 a, b, the LRd model from Faber and Rudy, 2000, and the Noble 98 model from Noble et al., 1998), epithelial cells (Strieter et al., 1990) and pancreatic beta cells (Magnus and Keizer, 1998). The simBio package is written in Java, uses XML and can solve ordinary differential equations. In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models. This way of building models, through the combination of various modules, is enabled through the use of object-oriented programming concepts. Thus, simBio is a straightforward system for the creation of a variety of cell models on a common database of functional modules.

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.

A program for the Bayesian Neural Network in the ROOT framework

NASA Astrophysics Data System (ADS)

Zhong, Jiahang; Huang, Run-Sheng; Lee, Shih-Chang

2011-12-01

We present a Bayesian Neural Network algorithm implemented in the TMVA package (Hoecker et al., 2007 [1]), within the ROOT framework (Brun and Rademakers, 1997 [2]). Comparing to the conventional utilization of Neural Network as discriminator, this new implementation has more advantages as a non-parametric regression tool, particularly for fitting probabilities. It provides functionalities including cost function selection, complexity control and uncertainty estimation. An example of such application in High Energy Physics is shown. The algorithm is available with ROOT release later than 5.29. Program summaryProgram title: TMVA-BNN Catalogue identifier: AEJX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: BSD license No. of lines in distributed program, including test data, etc.: 5094 No. of bytes in distributed program, including test data, etc.: 1,320,987 Distribution format: tar.gz Programming language: C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system Operating system: Most UNIX/Linux systems. The application programs were thoroughly tested under Fedora and Scientific Linux CERN. Classification: 11.9 External routines: ROOT package version 5.29 or higher ( http://root.cern.ch) Nature of problem: Non-parametric fitting of multivariate distributions Solution method: An implementation of Neural Network following the Bayesian statistical interpretation. Uses Laplace approximation for the Bayesian marginalizations. Provides the functionalities of automatic complexity control and uncertainty estimation. Running time: Time consumption for the training depends substantially on the size of input sample, the NN topology, the number of training iterations, etc. For the example in this manuscript, about 7 min was used on a PC/Linux with 2.0 GHz processors.

METLIN-PC: An applications-program package for problems of mathematical programming

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

Pshenichnyi, B.N.; Sobolenko, L.A.; Sosnovskii, A.A.

1994-05-01

The METLIN-PC applications-program package (APP) was developed at the V.M. Glushkov Institute of Cybernetics of the Academy of Sciences of Ukraine on IBM PC XT and AT computers. The present version of the package was written in Turbo Pascal and Fortran-77. The METLIN-PC is chiefly designed for the solution of smooth problems of mathematical programming and is a further development of the METLIN prototype, which was created earlier on a BESM-6 computer. The principal property of the previous package is retained - the applications modules employ a single approach based on the linearization method of B.N. Pschenichnyi. Hence the namemore » {open_quotes}METLIN.{close_quotes}« less

Modularization and Packaging of Public Television Programs.

ERIC Educational Resources Information Center

Carey, John; And Others

This report examines the changing relationship between public television programming and program distribution methods, and considers whether there is a need to change the design and packaging of some public television programming to respond to changes in the way the audience receives its programming as interactive cable systems, videocassettes,…

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.

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

Spectral-element Seismic Wave Propagation on CUDA/OpenCL Hardware Accelerators

NASA Astrophysics Data System (ADS)

Peter, D. B.; Videau, B.; Pouget, K.; Komatitsch, D.

2015-12-01

Seismic wave propagation codes are essential tools to investigate a variety of wave phenomena in the Earth. Furthermore, they can now be used for seismic full-waveform inversions in regional- and global-scale adjoint tomography. Although these seismic wave propagation solvers are crucial ingredients to improve the resolution of tomographic images to answer important questions about the nature of Earth's internal processes and subsurface structure, their practical application is often limited due to high computational costs. They thus need high-performance computing (HPC) facilities to improving the current state of knowledge. At present, numerous large HPC systems embed many-core architectures such as graphics processing units (GPUs) to enhance numerical performance. Such hardware accelerators can be programmed using either the CUDA programming environment or the OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted by additional hardware accelerators, like e.g. AMD graphic cards, ARM-based processors as well as Intel Xeon Phi coprocessors. For seismic wave propagation simulations using the open-source spectral-element code package SPECFEM3D_GLOBE, we incorporated an automatic source-to-source code generation tool (BOAST) which allows us to use meta-programming of all computational kernels for forward and adjoint runs. Using our BOAST kernels, we generate optimized source code for both CUDA and OpenCL languages within the source code package. Thus, seismic wave simulations are able now to fully utilize CUDA and OpenCL hardware accelerators. We show benchmarks of forward seismic wave propagation simulations using SPECFEM3D_GLOBE on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

A new method for the prediction of combustion instability

NASA Astrophysics Data System (ADS)

Flanagan, Steven Meville

This dissertation presents a new approach to the prediction of combustion instability in solid rocket motors. Previous attempts at developing computational tools to solve this problem have been largely unsuccessful, showing very poor agreement with experimental results and having little or no predictive capability. This is due primarily to deficiencies in the linear stability theory upon which these efforts have been based. Recent advances in linear instability theory by Flandro have demonstrated the importance of including unsteady rotational effects, previously considered negligible. Previous versions of the theory also neglected corrections to the unsteady flow field of the first order in the mean flow Mach number. This research explores the stability implications of extending the solution to include these corrections. Also, the corrected linear stability theory based upon a rotational unsteady flow field extended to first order in mean flow Mach number has been implemented in two computer programs developed for the Macintosh platform. A quasi one-dimensional version of the program has been developed which is based upon an approximate solution to the cavity acoustics problem. The three-dimensional program applies Greens's Function Discretization (GFD) to the solution for the acoustic mode shapes and frequency. GFD is a recently developed numerical method for finding fully three dimensional solutions for this class of problems. The analysis of complex motor geometries, previously a tedious and time consuming task, has also been greatly simplified through the development of a drawing package designed specifically to facilitate the specification of typical motor geometries. The combination of the drawing package, improved acoustic solutions, and new analysis, results in a tool which is capable of producing more accurate and meaningful predictions than have been possible in the past.

SUTIL: system utilities routines programmer's reference manual

NASA Technical Reports Server (NTRS)

Harper, D.

1976-01-01

A package of FORTRAN callable subroutines which allows efficient communication of data between users and programs is described. Proper utilization of the SUTIL package to reduce program core requirements and expedite program development is emphasized.

9 CFR 592.340 - Supervision of marking and packaging.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Supervision of marking and packaging... § 592.340 Supervision of marking and packaging. (a) Evidence of label approval. Inspection program... product or container thereof except by an inspection program employee or under the supervision of an...

9 CFR 592.340 - Supervision of marking and packaging.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Supervision of marking and packaging... § 592.340 Supervision of marking and packaging. (a) Evidence of label approval. Inspection program... product or container thereof except by an inspection program employee or under the supervision of an...

9 CFR 592.340 - Supervision of marking and packaging.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Supervision of marking and packaging... § 592.340 Supervision of marking and packaging. (a) Evidence of label approval. Inspection program... product or container thereof except by an inspection program employee or under the supervision of an...

9 CFR 592.340 - Supervision of marking and packaging.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Supervision of marking and packaging... § 592.340 Supervision of marking and packaging. (a) Evidence of label approval. Inspection program... product or container thereof except by an inspection program employee or under the supervision of an...

9 CFR 592.340 - Supervision of marking and packaging.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Supervision of marking and packaging... § 592.340 Supervision of marking and packaging. (a) Evidence of label approval. Inspection program... product or container thereof except by an inspection program employee or under the supervision of an...

An integrated tool for loop calculations: AITALC

NASA Astrophysics Data System (ADS)

Lorca, Alejandro; Riemann, Tord

2006-01-01

AITALC, a new tool for automating loop calculations in high energy physics, is described. The package creates Fortran code for two-fermion scattering processes automatically, starting from the generation and analysis of the Feynman graphs. We describe the modules of the tool, the intercommunication between them and illustrate its use with three examples. Program summaryTitle of the program:AITALC version 1.2.1 (9 August 2005) Catalogue identifier:ADWO Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWO Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Computer:PC i386 Operating system:GNU/ LINUX, tested on different distributions SuSE 8.2 to 9.3, Red Hat 7.2, Debian 3.0, Ubuntu 5.04. Also on SOLARIS Programming language used:GNU MAKE, DIANA, FORM, FORTRAN77 Additional programs/libraries used:DIANA 2.35 ( QGRAF 2.0), FORM 3.1, LOOPTOOLS 2.1 ( FF) Memory required to execute with typical data:Up to about 10 MB No. of processors used:1 No. of lines in distributed program, including test data, etc.:40 926 No. of bytes in distributed program, including test data, etc.:371 424 Distribution format:tar gzip file High-speed storage required:from 1.5 to 30 MB, depending on modules present and unfolding of examples Nature of the physical problem:Calculation of differential cross sections for ee annihilation in one-loop approximation. Method of solution:Generation and perturbative analysis of Feynman diagrams with later evaluation of matrix elements and form factors. Restriction of the complexity of the problem:The limit of application is, for the moment, the 2→2 particle reactions in the electro-weak standard model. Typical running time:Few minutes, being highly depending on the complexity of the process and the FORTRAN compiler.

A Geant4 simulation of the depth dose percentage in brain tumors treatments using protons and carbon ions

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

Diaz, José A. M., E-mail: joadiazme@unal.edu.co; Torres, D. A., E-mail: datorresg@unal.edu.co

2016-07-07

The deposited energy and dose distribution of beams of protons and carbon over a head are simulated using the free tool package Geant4 and the data analysis package ROOT-C++. The present work shows a methodology to understand the microscopical process occurring in a session of hadron-therapy using advance simulation tools.

A New Assessment Tool. A Professional Development Kit for Trainers and Assessors Incorporating Language, Literacy and Numeracy Skills into Training Packages.

ERIC Educational Resources Information Center

Goulbourn, Barbara; Alexander, Ann

This kit is designed to help trainers and assessors understand the importance of workplace communication in training packages. Section 1 explains what trainers and assessors need to know about communication skills, and how to use the kit. Section 2 provides an overview of training packages. It describes the endorsed parts of the package, which…

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

Hagberg, Aric; Swart, Pieter; S Chult, Daniel

NetworkX is a Python language package for exploration and analysis of networks and network algorithms. The core package provides data structures for representing many types of networks, or graphs, including simple graphs, directed graphs, and graphs with parallel edges and self loops. The nodes in NetworkX graphs can be any (hashable) Python object and edges can contain arbitrary data; this flexibility mades NetworkX ideal for representing networks found in many different scientific fields. In addition to the basic data structures many graph algorithms are implemented for calculating network properties and structure measures: shortest paths, betweenness centrality, clustering, and degree distributionmore » and many more. NetworkX can read and write various graph formats for eash exchange with existing data, and provides generators for many classic graphs and popular graph models, such as the Erdoes-Renyi, Small World, and Barabasi-Albert models, are included. The ease-of-use and flexibility of the Python programming language together with connection to the SciPy tools make NetworkX a powerful tool for scientific computations. We discuss some of our recent work studying synchronization of coupled oscillators to demonstrate how NetworkX enables research in the field of computational networks.« less

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

PubMed

Hartman, Amber L; Riddle, Sean; McPhillips, Timothy; Ludäscher, Bertram; Eisen, Jonathan A

2010-06-12

For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.

Summary of the Ratfor language, an extended portable dialect called REP, its style and flavor, and details of its implementation on the PDP-10

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

Figen, J.

1981-09-10

Ratfor (RATional FORtran) is a dialect of Fortran that allows structured programming and the use of simple macros. It is the language of the Software Tools package, and is documented in the book Software Tools. It has proved significantly easier than Fortran to read, write, and understand. Although debugging is slightly harder in Ratfor than in Fortran, there is usually less of it to do, since Ratfor lends itself to better program design. Ratfor operates as a preprocessor to any existing Fortran system. It is relatively easy, using Ratfor, to write programs that are portable with little or no changemore » to any environment that supports standard Fortran. REP (Ratfor Extended and Portable) is an extended version of Ratfor. It is fully upward compatible with the Addison-Wesley translator, though there are a few divergences from certain Unix and Software Tools User Group dialects. The principal feature of REP is its fully developed macro facility, a language within a language, capable of doing such things as creating new data types, data structuring, recursive procedures, and much more, portably, and in the spirit of Ratfor, but there are many other lesser though nevertheless important extensions.« less

78 FR 17890 - Energy Efficiency Program for Commercial and Industrial Equipment: Public Meeting and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-25

... Document for Packaged Terminal Air Conditioners and Packaged Terminal Heat Pumps AGENCY: Office of Energy... must identify the framework document for packaged terminal air conditioners and packaged terminal heat... packaged terminal air conditioners and packaged terminal heat pumps. 78 FR 12252. The document provided for...

Picante: R tools for integrating phylogenies and ecology.

PubMed

Kembel, Steven W; Cowan, Peter D; Helmus, Matthew R; Cornwell, William K; Morlon, Helene; Ackerly, David D; Blomberg, Simon P; Webb, Campbell O

2010-06-01

Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).

SMMP v. 3.0—Simulating proteins and protein interactions in Python and Fortran

NASA Astrophysics Data System (ADS)

Meinke, Jan H.; Mohanty, Sandipan; Eisenmenger, Frank; Hansmann, Ulrich H. E.

2008-03-01

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more. Program summaryTitle of program:SMMP Catalogue identifier:ADOJ_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.html Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language used:FORTRAN, Python No. of lines in distributed program, including test data, etc.:52 105 No. of bytes in distributed program, including test data, etc.:599 150 Distribution format:tar.gz Computer:Platform independent Operating system:OS independent RAM:2 Mbytes Classification:3 Does the new version supersede the previous version?:Yes Nature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins. Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles. Reasons for new version:API changes and increased functionality. Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings. Restrictions:The consumed CPU time increases with the size of protein molecule. Running time:Depends on the size of the simulated molecule.

Solar water heater design package

NASA Technical Reports Server (NTRS)

1981-01-01

Package describes commercial domestic-hot-water heater with roof or rack mounted solar collectors. System is adjustable to pre-existing gas or electric hot-water house units. Design package includes drawings, description of automatic control logic, evaluation measurements, possible design variations, list of materials and installation tools, and trouble-shooting guide and manual.

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

Shishlo, Andrei P; Chu, Paul; Pelaia II, Tom

A data plotting package residing in the XAL tools set is presented. This package is based on Java SWING, and therefore it has the same portability as Java itself. The data types for charts, bar-charts, and color-surface plots are described. The algorithms, performance, interactive capabilities, limitations, and the best usage practices of this plotting package are discussed.

Analysis of reference transactions using packaged computer programs.

PubMed

Calabretta, N; Ross, R

1984-01-01

Motivated by a continuing education class attended by the authors on the measurement of reference desk activities, the reference department at Scott Memorial Library initiated a project to gather data on reference desk transactions and to analyze the data by using packaged computer programs. The programs utilized for the project were SPSS (Statistical Package for the Social Sciences) and SAS (Statistical Analysis System). The planning, implementation and development of the project are described.

The INTERGROWTH-21st Project Neurodevelopment Package: A Novel Method for the Multi-Dimensional Assessment of Neurodevelopment in Pre-School Age Children

PubMed Central

Fernandes, Michelle; Stein, Alan; Newton, Charles R.; Cheikh-Ismail, Leila; Kihara, Michael; Wulff, Katharina; de León Quintana, Enrique; Aranzeta, Luis; Soria-Frisch, Aureli; Acedo, Javier; Ibanez, David; Abubakar, Amina; Giuliani, Francesca; Lewis, Tamsin; Kennedy, Stephen; Villar, Jose

2014-01-01

Background The International Fetal and Newborn Growth Consortium for the 21st Century (INTERGROWTH-21st) Project is a population-based, longitudinal study describing early growth and development in an optimally healthy cohort of 4607 mothers and newborns. At 24 months, children are assessed for neurodevelopmental outcomes with the INTERGROWTH-21st Neurodevelopment Package. This paper describes neurodevelopment tools for preschoolers and the systematic approach leading to the development of the Package. Methods An advisory panel shortlisted project-specific criteria (such as multi-dimensional assessments and suitability for international populations) to be fulfilled by a neurodevelopment instrument. A literature review of well-established tools for preschoolers revealed 47 candidates, none of which fulfilled all the project's criteria. A multi-dimensional assessment was, therefore, compiled using a package-based approach by: (i) categorizing desired outcomes into domains, (ii) devising domain-specific criteria for tool selection, and (iii) selecting the most appropriate measure for each domain. Results The Package measures vision (Cardiff tests); cortical auditory processing (auditory evoked potentials to a novelty oddball paradigm); and cognition, language skills, behavior, motor skills and attention (the INTERGROWTH-21st Neurodevelopment Assessment) in 35–45 minutes. Sleep-wake patterns (actigraphy) are also assessed. Tablet-based applications with integrated quality checks and automated, wireless electroencephalography make the Package easy to administer in the field by non-specialist staff. The Package is in use in Brazil, India, Italy, Kenya and the United Kingdom. Conclusions The INTERGROWTH-21st Neurodevelopment Package is a multi-dimensional instrument measuring early child development (ECD). Its developmental approach may be useful to those involved in large-scale ECD research and surveillance efforts. PMID:25423589

Magnetic resonance imaging diffusion tensor tractography: evaluation of anatomic accuracy of different fiber tracking software packages.

PubMed

Feigl, Guenther C; Hiergeist, Wolfgang; Fellner, Claudia; Schebesch, Karl-Michael M; Doenitz, Christian; Finkenzeller, Thomas; Brawanski, Alexander; Schlaier, Juergen

2014-01-01

Diffusion tensor imaging (DTI)-based tractography has become an integral part of preoperative diagnostic imaging in many neurosurgical centers, and other nonsurgical specialties depend increasingly on DTI tractography as a diagnostic tool. The aim of this study was to analyze the anatomic accuracy of visualized white matter fiber pathways using different, readily available DTI tractography software programs. Magnetic resonance imaging scans of the head of 20 healthy volunteers were acquired using a Siemens Symphony TIM 1.5T scanner and a 12-channel head array coil. The standard settings of the scans in this study were 12 diffusion directions and 5-mm slices. The fornices were chosen as an anatomic structure for the comparative fiber tracking. Identical data sets were loaded into nine different fiber tracking packages that used different algorithms. The nine software packages and algorithms used were NeuroQLab (modified tensor deflection [TEND] algorithm), Sörensen DTI task card (modified streamline tracking technique algorithm), Siemens DTI module (modified fourth-order Runge-Kutta algorithm), six different software packages from Trackvis (interpolated streamline algorithm, modified FACT algorithm, second-order Runge-Kutta algorithm, Q-ball [FACT algorithm], tensorline algorithm, Q-ball [second-order Runge-Kutta algorithm]), DTI Query (modified streamline tracking technique algorithm), Medinria (modified TEND algorithm), Brainvoyager (modified TEND algorithm), DTI Studio modified FACT algorithm, and the BrainLab DTI module based on the modified Runge-Kutta algorithm. Three examiners (a neuroradiologist, a magnetic resonance imaging physicist, and a neurosurgeon) served as examiners. They were double-blinded with respect to the test subject and the fiber tracking software used in the presented images. Each examiner evaluated 301 images. The examiners were instructed to evaluate screenshots from the different programs based on two main criteria: (i) anatomic accuracy of the course of the displayed fibers and (ii) number of fibers displayed outside the anatomic boundaries. The mean overall grade for anatomic accuracy was 2.2 (range, 1.1-3.6) with a standard deviation (SD) of 0.9. The mean overall grade for incorrectly displayed fibers was 2.5 (range, 1.6-3.5) with a SD of 0.6. The mean grade of the overall program ranking was 2.3 with a SD of 0.6. The overall mean grade of the program ranked number one (NeuroQLab) was 1.7 (range, 1.5-2.8). The mean overall grade of the program ranked last (BrainLab iPlan Cranial 2.6 DTI Module) was 3.3 (range, 1.7-4). The difference between the mean grades of these two programs was statistically highly significant (P < 0.0001). There was no statistically significant difference between the programs ranked 1-3: NeuroQLab, Sörensen DTI Task Card, and Siemens DTI module. The results of this study show that there is a statistically significant difference in the anatomic accuracy of the tested DTI fiber tracking programs. Although incorrectly displayed fibers could lead to wrong conclusions in the neurosciences field, which relies heavily on this noninvasive imaging technique, incorrectly displayed fibers in neurosurgery could lead to surgical decisions potentially harmful for the patient if used without intraoperative cortical stimulation. DTI fiber tracking presents a valuable noninvasive preoperative imaging tool, which requires further validation after important standardization of the acquisition and processing techniques currently available. Copyright © 2014 Elsevier Inc. All rights reserved.

77 FR 20695 - Tax Counseling for the Elderly (TCE) Program Availability of Application Packages

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-05

... DEPARTMENT OF THE TREASURY Internal Revenue Service Tax Counseling for the Elderly (TCE) Program...: This document provides notice of the availability of Application Packages for the 2013 Tax Counseling... . The deadline for submitting an application package to the IRS for the Tax Counseling for the Elderly...

76 FR 30243 - Tax Counseling for the Elderly (TCE) Program Availability of Application Packages

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

... DEPARTMENT OF THE TREASURY Internal Revenue Service Tax Counseling for the Elderly (TCE) Program...: This document provides notice of the availability of Application Packages for the 2012 Tax Counseling.... The deadline for submitting an application package to the IRS for the 2012 Tax Counseling for the...

75 FR 22437 - Tax Counseling for the Elderly (TCE) Program Availability of Application Packages

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-28

... DEPARTMENT OF THE TREASURY Internal Revenue Service Tax Counseling for the Elderly (TCE) Program...: This document provides notice of the availability of Application Packages for the 2011 Tax Counseling.... The deadline for submitting an application package to the IRS for the 2011 Tax Counseling for the...

Suggested Courseware for the Non-Calculus Physics Student: Projectile Motion, Circular Motion, Rotational Dynamics, and Statics.

ERIC Educational Resources Information Center

Mahoney, Joyce; And Others

1988-01-01

Evaluates 10 courseware packages covering topics for introductory physics. Discusses the price; sub-topics; program type; interaction; possible hardware; time; calculus required; graphics; and comments on each program. Recommends two packages in projectile and circular motion, and three packages in statics and rotational dynamics. (YP)

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

ERIC Educational Resources Information Center

McArthur, David

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

40 CFR 157.27 - Unit packaging.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Unit packaging. 157.27 Section 157.27 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PACKAGING REQUIREMENTS FOR PESTICIDES AND DEVICES Child-Resistant Packaging § 157.27 Unit packaging. Pesticide products...

Interactive Visualization of Complex Seismic Data and Models Using Bokeh

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

Chai, Chengping; Ammon, Charles J.; Maceira, Monica

Visualizing multidimensional data and models becomes more challenging as the volume and resolution of seismic data and models increase. But thanks to the development of powerful and accessible computer systems, a model web browser can be used to visualize complex scientific data and models dynamically. In this paper, we present four examples of seismic model visualization using an open-source Python package Bokeh. One example is a visualization of a surface-wave dispersion data set, another presents a view of three-component seismograms, and two illustrate methods to explore a 3D seismic-velocity model. Unlike other 3D visualization packages, our visualization approach has amore » minimum requirement on users and is relatively easy to develop, provided you have reasonable programming skills. Finally, utilizing familiar web browsing interfaces, the dynamic tools provide us an effective and efficient approach to explore large data sets and models.« less

Programming with BIG data in R: Scaling analytics from one to thousands of nodes

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

Schmidt, Drew; Chen, Wei -Chen; Matheson, Michael A.

Here, we present a tutorial overview showing how one can achieve scalable performance with R. We do so by utilizing several package extensions, including those from the pbdR project. These packages consist of high performance, high-level interfaces to and extensions of MPI, PBLAS, ScaLAPACK, I/O libraries, profiling libraries, and more. While these libraries shine brightest on large distributed platforms, they also work rather well on small clusters and often, surprisingly, even on a laptop with only two cores. Our tutorial begins with recommendations on how to get more performance out of your R code before considering parallel implementations. Because Rmore » is a high-level language, a function can have a deep hierarchy of operations. For big data, this can easily lead to inefficiency. Profiling is an important tool to understand the performance of an R code for both serial and parallel improvements.« less

GeMS: an advanced software package for designing synthetic genes.

PubMed

Jayaraj, Sebastian; Reid, Ralph; Santi, Daniel V

2005-01-01

A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.

Interactive Visualization of Complex Seismic Data and Models Using Bokeh

DOE PAGES

Chai, Chengping; Ammon, Charles J.; Maceira, Monica; ...

2018-02-14

Visualizing multidimensional data and models becomes more challenging as the volume and resolution of seismic data and models increase. But thanks to the development of powerful and accessible computer systems, a model web browser can be used to visualize complex scientific data and models dynamically. In this paper, we present four examples of seismic model visualization using an open-source Python package Bokeh. One example is a visualization of a surface-wave dispersion data set, another presents a view of three-component seismograms, and two illustrate methods to explore a 3D seismic-velocity model. Unlike other 3D visualization packages, our visualization approach has amore » minimum requirement on users and is relatively easy to develop, provided you have reasonable programming skills. Finally, utilizing familiar web browsing interfaces, the dynamic tools provide us an effective and efficient approach to explore large data sets and models.« less

GfaPy: a flexible and extensible software library for handling sequence graphs in Python.

PubMed

Gonnella, Giorgio; Kurtz, Stefan

2017-10-01

GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Here, we present GfaPy, a software package for creating, parsing and editing GFA graphs using the programming language Python. GfaPy supports GFA 1 and GFA 2, using the same interface and allows for interconversion between both formats. The software package provides a simple interface for custom record types, which is an important new feature of GFA 2 (compared to GFA 1). This enables new applications of the format. GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip. gonnella@zbh.uni-hamburg.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

RNA-Seq-Based Transcript Structure Analysis with TrBorderExt.

PubMed

Wang, Yejun; Sun, Ming-An; White, Aaron P

2018-01-01

RNA-Seq has become a routine strategy for genome-wide gene expression comparisons in bacteria. Despite lower resolution in transcript border parsing compared with dRNA-Seq, TSS-EMOTE, Cappable-seq, Term-seq, and others, directional RNA-Seq still illustrates its advantages: low cost, quantification and transcript border analysis with a medium resolution (±10-20 nt). To facilitate mining of directional RNA-Seq datasets especially with respect to transcript structure analysis, we developed a tool, TrBorderExt, which can parse transcript start sites and termination sites accurately in bacteria. A detailed protocol is described in this chapter for how to use the software package step by step to identify bacterial transcript borders from raw RNA-Seq data. The package was developed with Perl and R programming languages, and is accessible freely through the website: http://www.szu-bioinf.org/TrBorderExt .

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

Dr. George L. Mesina; Steven P. Miller

The XMGR5 graphing package [1] for drawing RELAP5 [2] plots is being re-written in Java [3]. Java is a robust programming language that is available at no cost for most computer platforms from Sun Microsystems, Inc. XMGR5 is an extension of an XY plotting tool called ACE/gr extended to plot data from several US Nuclear Regulatory Commission (NRC) applications. It is also the most popular graphing package worldwide for making RELAP5 plots. In Section 1, a short review of XMGR5 is given, followed by a brief overview of Java. In Section 2, shortcomings of both tkXMGR [4] and XMGR5 aremore » discussed and the value of converting to Java is given. Details of the conversion to Java are given in Section 3. The progress to date, some conclusions and future work are given in Section 4. Some screen shots of the Java version are shown.« less

Programming with BIG data in R: Scaling analytics from one to thousands of nodes

DOE PAGES

Schmidt, Drew; Chen, Wei -Chen; Matheson, Michael A.; ...

2016-11-09

Here, we present a tutorial overview showing how one can achieve scalable performance with R. We do so by utilizing several package extensions, including those from the pbdR project. These packages consist of high performance, high-level interfaces to and extensions of MPI, PBLAS, ScaLAPACK, I/O libraries, profiling libraries, and more. While these libraries shine brightest on large distributed platforms, they also work rather well on small clusters and often, surprisingly, even on a laptop with only two cores. Our tutorial begins with recommendations on how to get more performance out of your R code before considering parallel implementations. Because Rmore » is a high-level language, a function can have a deep hierarchy of operations. For big data, this can easily lead to inefficiency. Profiling is an important tool to understand the performance of an R code for both serial and parallel improvements.« less

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)

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

NASA Astrophysics Data System (ADS)

Jaggi, S.

1993-02-01

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

Rapid tooling for functional prototyping of metal mold processes. CRADA final report

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

Zacharia, T.; Ludtka, G.M.; Bjerke, M.A.

1997-12-01

The overall scope of this endeavor was to develop an integrated computer system, running on a network of heterogeneous computers, that would allow the rapid development of tool designs, and then use process models to determine whether the initial tooling would have characteristics which produce the prototype parts. The major thrust of this program for ORNL was the definition of the requirements for the development of the integrated die design system with the functional purpose to link part design, tool design, and component fabrication through a seamless software environment. The principal product would be a system control program that wouldmore » coordinate the various application programs and implement the data transfer so that any networked workstation would be useable. The overall system control architecture was to be required to easily facilitate any changes, upgrades, or replacements of the model from either the manufacturing end or the design criteria standpoint. The initial design of such a program is described in the section labeled ``Control Program Design``. A critical aspect of this research was the design of the system flow chart showing the exact system components and the data to be transferred. All of the major system components would have been configured to ensure data file compatibility and transferability across the Internet. The intent was to use commercially available packages to model the various manufacturing processes for creating the die and die inserts in addition to modeling the processes for which these parts were to be used. In order to meet all of these requirements, investigative research was conducted to determine the system flow features and software components within the various organizations contributing to this project. This research is summarized.« less

Using Kepler for Tool Integration in Microarray Analysis Workflows.

PubMed

Gan, Zhuohui; Stowe, Jennifer C; Altintas, Ilkay; McCulloch, Andrew D; Zambon, Alexander C

Increasing numbers of genomic technologies are leading to massive amounts of genomic data, all of which requires complex analysis. More and more bioinformatics analysis tools are being developed by scientist to simplify these analyses. However, different pipelines have been developed using different software environments. This makes integrations of these diverse bioinformatics tools difficult. Kepler provides an open source environment to integrate these disparate packages. Using Kepler, we integrated several external tools including Bioconductor packages, AltAnalyze, a python-based open source tool, and R-based comparison tool to build an automated workflow to meta-analyze both online and local microarray data. The automated workflow connects the integrated tools seamlessly, delivers data flow between the tools smoothly, and hence improves efficiency and accuracy of complex data analyses. Our workflow exemplifies the usage of Kepler as a scientific workflow platform for bioinformatics pipelines.

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.

SIGPROC: Pulsar Signal Processing Programs

NASA Astrophysics Data System (ADS)

Lorimer, D. R.

2011-07-01

SIGPROC is a package designed to standardize the initial analysis of the many types of fast-sampled pulsar data. Currently recognized machines are the Wide Band Arecibo Pulsar Processor (WAPP), the Penn State Pulsar Machine (PSPM), the Arecibo Observatory Fourier Transform Machine (AOFTM), the Berkeley Pulsar Processors (BPP), the Parkes/Jodrell 1-bit filterbanks (SCAMP) and the filterbank at the Ooty radio telescope (OOTY). The SIGPROC tools should help users look at their data quickly, without the need to write (yet) another routine to read data or worry about big/little endian compatibility (byte swapping is handled automatically).

Computer software tool REALM for sustainable water allocation and management.

PubMed

Perera, B J C; James, B; Kularathna, M D U

2005-12-01

REALM (REsource ALlocation Model) is a generalised computer simulation package that models harvesting and bulk distribution of water resources within a water supply system. It is a modeling tool, which can be applied to develop specific water allocation models. Like other water resource simulation software tools, REALM uses mass-balance accounting at nodes, while the movement of water within carriers is subject to capacity constraints. It uses a fast network linear programming algorithm to optimise the water allocation within the network during each simulation time step, in accordance with user-defined operating rules. This paper describes the main features of REALM and provides potential users with an appreciation of its capabilities. In particular, it describes two case studies covering major urban and rural water supply systems. These case studies illustrate REALM's capabilities in the use of stochastically generated data in water supply planning and management, modelling of environmental flows, and assessing security of supply issues.

BCRA 2.0 R Package

Cancer.gov

BCRA is an R package that projects absolute risk of invasive breast cancer according to NCI’s Breast Cancer Risk Assessment Tool (BCRAT) algorithm for specified race/ethnic groups and age intervals.

9975 SHIPPING PACKAGE LIFE EXTENSION SURVEILLANCE PROGRAM RESULTS SUMMARY

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

Dunn, K.; Daugherty, W.; Hackney, B.

2011-05-27

Results from the 9975 shipping package Storage and Surveillance Program at the Savannah River Site (SRS) are summarized for justification to extend the life of the 9975 packages currently stored in the K-Area Complex (KAC). This justification is established with the stipulation that surveillance activities will continue throughout the extended time to ensure the continued integrity of the 9975 materials of construction and to further understand the currently identified degradation mechanisms. The 10 year storage life justification was developed prior to storage. A subsequent report was later used to validate the qualification of the 9975 shipping packages for 10 yearsmore » in storage. However the qualification for the storage period was provided by the monitoring requirements of the 9975 Storage and Surveillance Program. This report summarizes efforts to determine a new safe storage limit for the 9975 shipping package based on the surveillance data collected since 2005 when the 9975 Storage and Surveillance Program began. The Program has demonstrated that the 9975 package has a robust design that can perform under a variety of conditions. The primary emphasis of the on-going 9975 Storage and Surveillance Program is an aging study of the 9975 Viton{reg_sign} containment vessel O-rings and the Celotex{reg_sign} fiberboard thermal insulation at bounding conditions of radiation, elevated temperatures and/or elevated humidity.« less

Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

USDA-ARS?s Scientific Manuscript database

Poppr is an R package for analysis of population genetic data. It extends the adegenet package and provides several novel tools, particularly with regard to analysis of data from admixed, clonal, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid gene...

49 CFR 173.63 - Packaging exceptions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... vehicle, freight container, or cargo-only aircraft; (2) Off-shore down-hole tool pallet carried on an off... tubing 12 feet long or longer may be packed as follows in which case they are excepted from the packaging... delay charges) may be packed as follows in which case they are excepted from the packaging requirements...

Computer assisted learning (CAL) of oral manifestations of HIV disease.

PubMed

Porter, S R; Telford, A; Chandler, K; Furber, S; Williams, J; Price, S; Scully, C; Triantos, D; Bain, L

1996-09-07

General dental practitioners (GDPs) in the UK may wish additional education on relevant aspects of human immunodeficiency virus (HIV) disease. The aim of the present study was to develop and assess a computer assisted learning package on the oral manifestations of HIV disease of relevance to GDPs. A package was developed using a commercially-available software development tool and assessed by a group of 75 GDPs interested in education and computers. Fifty-four (72%) of the GDPs completed a self-administered questionnaire of their opinions of the package. The majority reported the package to be easy to load and run, that it provided clear instructions and displays, and that it was a more effective educational tool than videotapes, audiotapes, professional journals and textbooks, and of similar benefit as post-graduate courses. The GDPs often commented favourably on the effectiveness of the clinical images and use of questions and answers, although some had criticisms of these and other aspects of the package. As a consequence of this investigation the package has been modified and distributed to GDPs in England and Wales.

9975 SHIPPING PACKAGE LIFE EXTENSION SURVEILLANCE PROGRAM RESULTS SUMMARY

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

Daugherty, W.; Dunn, K.; Hackney, B.

2011-01-06

Results from the 9975 Surveillance Program at the Savannah River Site (SRS) are summarized for justification to extend the life of the 9975 packages currently stored in the K-Area Materials Storage (KAMS) facility from 10 years to 15 years. This justification is established with the stipulation that surveillance activities will continue throughout this extended time to ensure the continued integrity of the 9975 materials of construction and to further understand the currently identified degradation mechanisms. The current 10 year storage life was developed prior to storage. A subsequent report was later used to extend the qualification of the 9975 shippingmore » packages for 2 years for shipping plus 10 years for storage. However the qualification for the storage period was provided by the monitoring requirements of the Storage and Surveillance Program. This report summarizes efforts to determine a new safe storage limit for the 9975 shipping package based on the surveillance data collected since 2005 when the surveillance program began. KAMS is a zero-release facility that depends upon containment by the 9975 to meet design basis storage requirements. Therefore, to confirm the continued integrity of the 9975 packages while stored in KAMS, a 9975 Storage and Surveillance Program was implemented alongside the DOE required Integrated Surveillance Program (ISP) for 3013 plutonium-bearing containers. The 9975 Storage and Surveillance Program performs field surveillance as well as accelerated aging tests to ensure any degradation due to aging, to the extent that could affect packaging performance, is detected in advance of such degradation occurring in the field. The Program has demonstrated that the 9975 package has a robust design that can perform under a variety of conditions. As such the primary emphasis of the on-going 9975 Surveillance Program is an aging study of the 9975 Viton(reg.sign) GLT containment vessel O-rings and the Celotex(reg.sign) fiberboard thermal insulation at bounding conditions of radiation and elevated temperatures. Other materials of construction, however, are also discussed.« less

Grid Stiffened Structure Analysis Tool

NASA Technical Reports Server (NTRS)

1999-01-01

The Grid Stiffened Analysis Tool contract is contract performed by Boeing under NASA purchase order H30249D. The contract calls for a "best effort" study comprised of two tasks: (1) Create documentation for a composite grid-stiffened structure analysis tool, in the form of a Microsoft EXCEL spread sheet, that was developed by originally at Stanford University and later further developed by the Air Force, and (2) Write a program that functions as a NASTRAN pre-processor to generate an FEM code for grid-stiffened structure. In performing this contract, Task 1 was given higher priority because it enables NASA to make efficient use of a unique tool they already have; Task 2 was proposed by Boeing because it also would be beneficial to the analysis of composite grid-stiffened structures, specifically in generating models for preliminary design studies. The contract is now complete, this package includes copies of the user's documentation for Task 1 and a CD ROM & diskette with an electronic copy of the user's documentation and an updated version of the "GRID 99" spreadsheet.

Management and Economic Implications of Bundling and Block Booking of Television and Cable Programming.

ERIC Educational Resources Information Center

Picard, Robert G.

Bundling, a practice which has increased dramatically in the television and cable industries in recent years, occurs when program distributors package groups of movies and episodes of series, and then sell licenses to use these packages to TV stations and cable channels. Typically, such bundled packages include both highly desirable and less…

Reading Programs for Gifted Readers. Learning Package No. 28.

ERIC Educational Resources Information Center

Collins, Norma, Comp.; Smith, Carl, Ed.

Originally developed as part of a project for the Department of Defense Schools (DoDDS) system, this learning package on reading programs for gifted readers is designed for teachers who wish to upgrade or expand their teaching skills on their own. The package includes an overview of the project; a comprehensive search of the ERIC database; a…

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

40 CFR 157.30 - Voluntary use of child-resistant packaging.

Code of Federal Regulations, 2010 CFR

2010-07-01

... packaging. 157.30 Section 157.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PACKAGING REQUIREMENTS FOR PESTICIDES AND DEVICES Child-Resistant Packaging § 157.30 Voluntary use of child-resistant packaging. A registrant whose product is not required to be in child...

Advances in the production of freeform optical surfaces

NASA Astrophysics Data System (ADS)

Tohme, Yazid E.; Luniya, Suneet S.

2007-05-01

Recent market demands for free-form optics have challenged the industry to find new methods and techniques to manufacture free-form optical surfaces with a high level of accuracy and reliability. Production techniques are becoming a mix of multi-axis single point diamond machining centers or deterministic ultra precision grinding centers coupled with capable measurement systems to accomplish the task. It has been determined that a complex software tool is required to seamlessly integrate all aspects of the manufacturing process chain. Advances in computational power and improved performance of computer controlled precision machinery have driven the use of such software programs to measure, visualize, analyze, produce and re-validate the 3D free-form design thus making the process of manufacturing such complex surfaces a viable task. Consolidation of the entire production cycle in a comprehensive software tool that can interact with all systems in design, production and measurement phase will enable manufacturers to solve these complex challenges providing improved product quality, simplified processes, and enhanced performance. The work being presented describes the latest advancements in developing such software package for the entire fabrication process chain for aspheric and free-form shapes. It applies a rational B-spline based kernel to transform an optical design in the form of parametrical definition (optical equation), standard CAD format, or a cloud of points to a central format that drives the simulation. This software tool creates a closed loop for the fabrication process chain. It integrates surface analysis and compensation, tool path generation, and measurement analysis in one package.

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

Kelly, D L

The US Department of Energy (DOE) has been conducting, through several of its operating contractors, an evaluation and testing program to qualify Type A radioactive material packagings per US Department of Transportation (DOT) Specification 7A (DOT-7A) of the Code of Federal Regulations (CFR), Title 49, Part 178 (49 CFR 178). This document summarizes the evaluation and testing performed for all of the packagings successfully qualified in this program. This document supersedes DOE Evaluation Document for DOT-7A Type A Packaging (Edling 1987), originally issued in 1987 by Monsanto Research Corporation Mound Laboratory (MLM), Miamisburg, Ohio, for the Department of Energy, Securitymore » Evaluation Program (I)P-4. Mound Laboratory issued four revisions to the document between November 1988 and December 1989. In September 1989, the program was transferred to Westinghouse Hanford Company (Westinghouse Hanford) in Richland, Washington. One additional revision was issued in March 1990 by Westinghouse Hanford. This revision reflects the earlier material and incorporates a number of changes. Evaluation and testing activities on 1208 three DOT-7A Program Dockets resulted in the qualification of three new packaging configurations, which are incorporated herein and summarized. This document presents approximately 300 different packagings that have been determined to meet the requirements for a DOT-7A, type A packaging per 49 CFR 178.350.« less

Paperless Work Package Application

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

Kilgore, Jr., William R.; Morrell, Jr., Otto K.; Morrison, Dan

2014-07-31

Paperless Work Package (PWP) System is a computer program process that takes information from Asset Suite, provides a platform for other electronic inputs, Processes the inputs into an electronic package that can be downloaded onto an electronic work tablet or laptop computer, provides a platform for electronic inputs into the work tablet, and then transposes those inputs back into Asset Suite and to permanent SRS records. The PWP System will basically eliminate paper requirements from the maintenance work control system. The program electronically relays the instructions given by the planner to work on a piece of equipment which is currentlymore » relayed via a printed work package. The program does not control/approve what is done. The planner will continue to plan the work package, the package will continue to be routed, approved, and scheduled. The supervisor reviews and approves the work to be performed and assigns work to individuals or to a work group. (The supervisor conducts pre job briefings with the workers involved in the job) The Operations Manager (Work Controlling Entity) approves the work package electronically for the work that will be done in his facility prior to work starting. The PWP System will provide the package in an electronic form. All the reviews, approvals, and safety measures taken by people outside the electronic package does not change from the paper driven work packages.« less

A geometry package for generation of input data for a three-dimensional potential-flow program

NASA Technical Reports Server (NTRS)

Halsey, N. D.; Hess, J. L.

1978-01-01

The preparation of geometric data for input to three-dimensional potential flow programs was automated and simplified by a geometry package incorporated into the NASA Langley version of the 3-D lifting potential flow program. Input to the computer program for the geometry package consists of a very sparse set of coordinate data, often with an order of magnitude of fewer points than required for the actual potential flow calculations. Isolated components, such as wings, fuselages, etc. are paneled automatically, using one of several possible element distribution algorithms. Curves of intersection between components are calculated, using a hybrid curve-fit/surface-fit approach. Intersecting components are repaneled so that adjacent elements on either side of the intersection curves line up in a satisfactory manner for the potential-flow calculations. Many cases may be run completely (from input, through the geometry package, and through the flow calculations) without interruption. Use of the package significantly reduces the time and expense involved in making three-dimensional potential flow calculations.

SchemaOnRead: A Package for Schema-on-Read in R

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

North, Michael J.

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info,more » Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.« less

Examining National Public Health Law to Realize the Global Health Security Agenda.

PubMed

Meier, Benjamin Mason; Tureski, Kara; Bockh, Emily; Carr, Derek; Ayala, Ana; Roberts, Anna; Cloud, Lindsay; Wilhelm, Nicolas; Burris, Scott

2017-05-01

Where the Global Health Security Agenda (GHSA) seeks to accelerate progress toward a world safe and secure from public health emergencies, the realization of GHSA 'Action Packages' will require national governments to establish necessary legal frameworks to prevent, detect, and respond to infectious disease. By analyzing the scope and content of existing national legislation in each of the GHSA Action Packages, this comparative cross-national research has developed a framework that disaggregates the legal domains necessary to meet each Action Package target. Based upon these legal domains, this study developed an assessment tool that can identify specific attributes of national legislation. This article applies this tool to assess the legal environment in twenty Sub-Saharan African countries, examining the content of laws across the GHSA Action Packages, analyzing the legal domains necessary to implement each Action Package, and highlighting specific national laws that reflect attributes of each legal domain. © The Author 2017. Published by Oxford University Press; all rights reserved. For Permissions, please email: journals.permissions@oup.com.

A reduction package for cross-dispersed echelle spectrograph data in IDL

NASA Astrophysics Data System (ADS)

Hall, Jeffrey C.; Neff, James E.

1992-12-01

We have written in IDL a data reduction package that performs reduction and extraction of cross-dispersed echelle spectrograph data. The present package includes a complete set of tools for extracting data from any number of spectral orders with arbitrary tilt and curvature. Essential elements include debiasing and flatfielding of the raw CCD image, removal of scattered light background, either nonoptimal or optimal extraction of data, and wavelength calibration and continuum normalization of the extracted orders. A growing set of support routines permits examination of the frame being processed to provide continuing checks on the statistical properties of the data and on the accuracy of the extraction. We will display some sample reductions and discuss the algorithms used. The inherent simplicity and user-friendliness of the IDL interface make this package a useful tool for spectroscopists. We will provide an email distribution list for those interested in receiving the package, and further documentation will be distributed at the meeting.

Tai Chi: moving for better balance -- development of a community-based falls prevention program.

PubMed

Li, Fuzhong; Harmer, Peter; Mack, Karin A; Sleet, David; Fisher, K John; Kohn, Melvin A; Millet, Lisa M; Xu, Junheng; Yang, Tingzhong; Sutton, Beth; Tompkins, Yvaughn

2008-05-01

This study was designed to develop an evidence- and community based falls prevention program -- Tai Chi: Moving for Better Balance. A mixed qualitative and quantitative approach was used to develop a package of materials for program implementation and evaluation. The developmental work was conducted in 2 communities in the Pacific Northwest. Participants included a panel of experts, senior service program managers or activity coordinators, and older adults. Outcome measures involved program feasibility and satisfaction. Through an iterative process, a program package was developed. The package contained an implementation plan and class training materials (ie, instructor's manual, videotape, and user's guidebook). Pilot testing of program materials showed that the content was appropriate for the targeted users (community-living older adults) and providers (local senior service organizations). A feasibility survey indicated interest and support from users and providers for program implementation. A 2-week pilot evaluation showed that the program implementation was feasible and evidenced good class attendance, high participant satisfaction, and interest in continuing Tai Chi. The package of materials developed in this study provides a solid foundation for larger scale implementation and evaluation of the program in community settings.

VRML and Collaborative Environments: New Tools for Networked Visualization

NASA Astrophysics Data System (ADS)

Crutcher, R. M.; Plante, R. L.; Rajlich, P.

We present two new applications that engage the network as a tool for astronomical research and/or education. The first is a VRML server which allows users over the Web to interactively create three-dimensional visualizations of FITS images contained in the NCSA Astronomy Digital Image Library (ADIL). The server's Web interface allows users to select images from the ADIL, fill in processing parameters, and create renderings featuring isosurfaces, slices, contours, and annotations; the often extensive computations are carried out on an NCSA SGI supercomputer server without the user having an individual account on the system. The user can then download the 3D visualizations as VRML files, which may be rotated and manipulated locally on virtually any class of computer. The second application is the ADILBrowser, a part of the NCSA Horizon Image Data Browser Java package. ADILBrowser allows a group of participants to browse images from the ADIL within a collaborative session. The collaborative environment is provided by the NCSA Habanero package which includes text and audio chat tools and a white board. The ADILBrowser is just an example of a collaborative tool that can be built with the Horizon and Habanero packages. The classes provided by these packages can be assembled to create custom collaborative applications that visualize data either from local disk or from anywhere on the network.

Multi-Media Instruction: Vocational Education Research Package.

ERIC Educational Resources Information Center

Evaluation and Training Inst., Los Angeles, CA.

Designed to assist community college administrators and faculty in enhancing vocational education programs and services, this resource package on multi-media instruction contains information on successful program strategies and ideas currently in use in vocational education programs in the California Community Colleges (CCC). Following a brief…

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.

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

Development of the AGREE II, part 2: assessment of validity of items and tools to support application

PubMed Central

Brouwers, Melissa C.; Kho, Michelle E.; Browman, George P.; Burgers, Jako S.; Cluzeau, Françoise; Feder, Gene; Fervers, Béatrice; Graham, Ian D.; Hanna, Steven E.; Makarski, Julie

2010-01-01

Background We established a program of research to improve the development, reporting and evaluation of practice guidelines. We assessed the construct validity of the items and user’s manual in the β version of the AGREE II. Methods We designed guideline excerpts reflecting high-and low-quality guideline content for 21 of the 23 items in the tool. We designed two study packages so that one low-quality and one high-quality version of each item were randomly assigned to each package. We randomly assigned 30 participants to one of the two packages. Participants reviewed and rated the guideline content according to the instructions of the user’s manual and completed a survey assessing the manual. Results In all cases, content designed to be of high quality was rated higher than low-quality content; in 18 of 21 cases, the differences were significant (p < 0.05). The manual was rated by participants as appropriate, easy to use, and helpful in differentiating guidelines of varying quality, with all scores above the mid-point of the seven-point scale. Considerable feedback was offered on how the items and manual of the β-AGREE II could be improved. Interpretation The validity of the items was established and the user’s manual was rated as highly useful by users. We used these results and those of our study presented in part 1 to modify the items and user’s manual. We recommend AGREE II (available at www.agreetrust.org) as the revised standard for guideline development, reporting and evaluation. PMID:20513779

Microcomputer Programs for Educational Statistics: A Review of Popular Programs. TME Report 89.

ERIC Educational Resources Information Center

Stemmer, Paul M.; Berger, Carl F.

This publication acquaints the user with microcomputer statistical packages and offers a method for evaluation based on a set of criteria that can be adapted to the needs of the user. Several popular packages, typical of those available, are reviewed in detail: (1) Abstat, an easy to use command driven package compatible with the IBM PC or the…

Evaluating the Progress of the School Reading Program. Learning Package No. 17.

ERIC Educational Resources Information Center

Nelson, Carol; Smith, Carl, Comp.

Originally developed for the Department of Defense Schools (DoDDS) system, this learning package on evaluating the progress of the school reading program is designed for teachers who wish to upgrade or expand their teaching skills on their own. The package includes a comprehensive search of the ERIC database; a lecture giving an overview on the…

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications.

PubMed

Du, Likai; Lan, Zhenggang

2015-04-14

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Dendroscope: An interactive viewer for large phylogenetic trees

PubMed Central

Huson, Daniel H; Richter, Daniel C; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula

2007-01-01

Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. PMID:18034891

TmoleX--a graphical user interface for TURBOMOLE.

PubMed

Steffen, Claudia; Thomas, Klaus; Huniar, Uwe; Hellweg, Arnim; Rubner, Oliver; Schroer, Alexander

2010-12-01

We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data.

PubMed

Gong, Ting; Szustakowski, Joseph D

2013-04-15

For heterogeneous tissues, measurements of gene expression through mRNA-Seq data are confounded by relative proportions of cell types involved. In this note, we introduce an efficient pipeline: DeconRNASeq, an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It adopts a globally optimized non-negative decomposition algorithm through quadratic programming for estimating the mixing proportions of distinctive tissue types in next-generation sequencing data. We demonstrated the feasibility and validity of DeconRNASeq across a range of mixing levels and sources using mRNA-Seq data mixed in silico at known concentrations. We validated our computational approach for various benchmark data, with high correlation between our predicted cell proportions and the real fractions of tissues. Our study provides a rigorous, quantitative and high-resolution tool as a prerequisite to use mRNA-Seq data. The modularity of package design allows an easy deployment of custom analytical pipelines for data from other high-throughput platforms. DeconRNASeq is written in R, and is freely available at http://bioconductor.org/packages. Supplementary data are available at Bioinformatics online.

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

GDF v2.0, an enhanced version of GDF

NASA Astrophysics Data System (ADS)

Tsoulos, Ioannis G.; Gavrilis, Dimitris; Dermatas, Evangelos

2007-12-01

An improved version of the function estimation program GDF is presented. The main enhancements of the new version include: multi-output function estimation, capability of defining custom functions in the grammar and selection of the error function. The new version has been evaluated on a series of classification and regression datasets, that are widely used for the evaluation of such methods. It is compared to two known neural networks and outperforms them in 5 (out of 10) datasets. Program summaryTitle of program: GDF v2.0 Catalogue identifier: ADXC_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXC_v2_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.: 98 147 No. of bytes in distributed program, including test data, etc.: 2 040 684 Distribution format: tar.gz Programming language: GNU C++ Computer: The program is designed to be portable in all systems running the GNU C++ compiler Operating system: Linux, Solaris, FreeBSD RAM: 200000 bytes Classification: 4.9 Does the new version supersede the previous version?: Yes Nature of problem: The technique of function estimation tries to discover from a series of input data a functional form that best describes them. This can be performed with the use of parametric models, whose parameters can adapt according to the input data. Solution method: Functional forms are being created by genetic programming which are approximations for the symbolic regression problem. Reasons for new version: The GDF package was extended in order to be more flexible and user customizable than the old package. The user can extend the package by defining his own error functions and he can extend the grammar of the package by adding new functions to the function repertoire. Also, the new version can perform function estimation of multi-output functions and it can be used for classification problems. Summary of revisions: The following features have been added to the package GDF: Multi-output function approximation. The package can now approximate any function f:R→R. This feature gives also to the package the capability of performing classification and not only regression. User defined function can be added to the repertoire of the grammar, extending the regression capabilities of the package. This feature is limited to 3 functions, but easily this number can be increased. Capability of selecting the error function. The package offers now to the user apart from the mean square error other error functions such as: mean absolute square error, maximum square error. Also, user defined error functions can be added to the set of error functions. More verbose output. The main program displays more information to the user as well as the default values for the parameters. Also, the package gives to the user the capability to define an output file, where the output of the gdf program for the testing set will be stored after the termination of the process. Additional comments: A technical report describing the revisions, experiments and test runs is packaged with the source code. Running time: Depending on the train data.

Two NextGen Air Safety Tools: An ADS-B Equipped UAV and a Wake Turbulence Estimator

NASA Astrophysics Data System (ADS)

Handley, Ward A.

Two air safety tools are developed in the context of the FAA's NextGen program. The first tool addresses the alarming increase in the frequency of near-collisions between manned and unmanned aircraft by equipping a common hobby class UAV with an ADS-B transponder that broadcasts its position, speed, heading and unique identification number to all local air traffic. The second tool estimates and outputs the location of dangerous wake vortex corridors in real time based on the ADS-B data collected and processed using a custom software package developed for this project. The TRansponder based Position Information System (TRAPIS) consists of data packet decoders, an aircraft database, Graphical User Interface (GUI) and the wake vortex extension application. Output from TRAPIS can be visualized in Google Earth and alleviates the problem of pilots being left to imagine where invisible wake vortex corridors are based solely on intuition or verbal warnings from ATC. The result of these two tools is the increased situational awareness, and hence safety, of human pilots in the National Airspace System (NAS).

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.

Effect of a health education program on reduction of pediculosis in school girls at Amphoe Muang, Khon Kaen Province, Thailand.

PubMed

Yingklang, Manachai; Sengthong, Chatchawan; Haonon, Ornuma; Dangtakot, Rungtiwa; Pinlaor, Porntip; Sota, Chulaporn; Pinlaor, Somchai

2018-01-01

Pediculosis caused by head lice (Pediculus humanus capitis) infestation is still an important health problem in schoolchildren, especially girls, worldwide, including in Thailand. Although pediculicidal agents effectively kill head lice, the re-infestation rate is still high. Thus, prevention is an important strategy for any sustainable control program. We aimed to develop and evaluate the efficacy of a health education program for increasing knowledge, changing attitudes and promoting preventive practices to reduce prevalence of pediculosis among school girls in Amphoe Muang, Khon Kaen, northeastern Thailand. Six schools were selected using multistage simple randomization and were allocated into intervention or control groups. A total of 267 girls was enrolled from these schools. A "knowledge, attitude and practice" (KAP) questionnaire, consent forms and health education materials were constructed and tested by experts and in one pilot school before the main investigation. Baseline prevalence of adult lice and nits was determined. The health education package was given only to the intervention group. The KAP questionnaire was re-evaluated at two months after intervention. At baseline, the prevalence and intensity of head lice infestation, and the KAP scores did not differ significantly between the two groups. After re-evaluation at two months, the KAP score was significantly greater in the intervention group. A significant decrease of the infestation rate from 59% to 44% was observed in the intervention group, whereas infestation increased in the control group (from 56% to 65%). The incidence of new cases in the intervention group (6.14%) was lower than in the control group (12.62%). These findings indicated that the newly-established health education package is an effective tool for increasing KAP and reducing head lice infestation in school girls. Efforts to combat pediculosis in schoolchildren elsewhere may consider including this, or a similar, health education package in their programs.

AN ADA NAMELIST PACKAGE

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

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

NASA X-34 Technology in Motion

NASA Technical Reports Server (NTRS)

Beech, Geoffrey; Chandler, Kristie

1997-01-01

The X-34 technology development program is a joint industry/government project to develop, test, and operate a small, fully-reusable hypersonic flight vehicle. The objective is to demonstrate key technologies and operating concepts applicable to future reusable launch vehicles. Integrated in the vehicle are various systems to assure successful completion of mission objectives, including the Main Propulsion System (MPS). NASA-Marshall Space Flight Center (MSFC) is responsible for developing the X-34's MPS including the design and complete build package for the propulsion system components. The X-34 will be powered by the Fastrac Engine, which is currently in design and development at NASA-MSFC. Fastrac is a single-stage main engine, which burns a mixture of liquid oxygen (LOX) and kerosene(RP-1). The interface between the MPS and Fastrac engine are critical for proper system operation and technologies applicable to future reusable launch vehicles. Deneb's IGRIP software package with the Dynamic analysis option provided a key tool for conducting studies critical to this interface as well as a mechanism to drive the design of the LOX and RP-1 feedlines. Kinematic models were created for the Fastrac Engine and the feedlines for various design concepts. Based on the kinematic simulation within Envision, design and joint limits were verified and system interference controlled. It was also critical to the program to evaluate the effect of dynamic loads visually, providing a verification tool for dynamic analysis and in some cases uncovering areas that had not been considered. Deneb's software put the X-34 technology in motion and has been a key factor in facilitating the strenuous design schedule.

Meta-analyzing dependent correlations: an SPSS macro and an R script.

PubMed

Cheung, Shu Fai; Chan, Darius K-S

2014-06-01

The presence of dependent correlation is a common problem in meta-analysis. Cheung and Chan (2004, 2008) have shown that samplewise-adjusted procedures perform better than the more commonly adopted simple within-sample mean procedures. However, samplewise-adjusted procedures have rarely been applied in meta-analytic reviews, probably due to the lack of suitable ready-to-use programs. In this article, we compare the samplewise-adjusted procedures with existing procedures to handle dependent effect sizes, and present the samplewise-adjusted procedures in a way that will make them more accessible to researchers conducting meta-analysis. We also introduce two tools, an SPSS macro and an R script, that researchers can apply to their meta-analyses; these tools are compatible with existing meta-analysis software packages.

High Performance Computing Modeling Advances Accelerator Science for High-Energy Physics

DOE PAGES

Amundson, James; Macridin, Alexandru; Spentzouris, Panagiotis

2014-07-28

The development and optimization of particle accelerators are essential for advancing our understanding of the properties of matter, energy, space, and time. Particle accelerators are complex devices whose behavior involves many physical effects on multiple scales. Therefore, advanced computational tools utilizing high-performance computing are essential for accurately modeling them. In the past decade, the US Department of Energy's SciDAC program has produced accelerator-modeling tools that have been employed to tackle some of the most difficult accelerator science problems. The authors discuss the Synergia framework and its applications to high-intensity particle accelerator physics. Synergia is an accelerator simulation package capable ofmore » handling the entire spectrum of beam dynamics simulations. Our authors present Synergia's design principles and its performance on HPC platforms.« less

Design and Construction of a Positron Emission Tomography (PET) Unit and Medical Applications with GEANT Detector Simulation Package

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

Karagoz, Muge

1998-01-01

In order to investigate the possibility of the construction of a sample PET coincidence unit in our HEP laboratory, a setup with two face to face PMTs and two 2x8 Csi(Tl) scintillator matrices has been constructed. In this setup, 1-D projections of a pointlike 22 Na positron source at different angles have been measured. Using these projections a 2-D image has been formed. Monte Carlo studies of this setup have been implemented using the detector simulation tool in CERN program library, GEANT. Again with GEANT a sample human body is created to study the effects of proton therapy. Utilization ofmore » the simulation as a pretherapy tool is also investigated.« less

chipPCR: an R package to pre-process raw data of amplification curves.

PubMed

Rödiger, Stefan; Burdukiewicz, Michał; Schierack, Peter

2015-09-01

Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. stefan.roediger@b-tu.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2014-09-29

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

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

PubMed Central

2014-01-01

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

A CAI (Computer-Assisted Instruction) Course on Constructing PLANIT lessons: Development, Content, and Evaluation

DTIC Science & Technology

1980-06-01

courseware package on how to program lessons for an automated system. Since PLANIT (Programming Language for Interactive Teaching) is the student/author...assisted instruction (CAI), how to program PLANIT lessons, and to evaluate the effectiveness of the package for select Army users. The resultant courseware

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…

SARA - SURE/ASSIST RELIABILITY ANALYSIS WORKSTATION (VAX VMS VERSION)

NASA Technical Reports Server (NTRS)

Butler, R. W.

1994-01-01

SARA, the SURE/ASSIST Reliability Analysis Workstation, is a bundle of programs used to solve reliability problems. The mathematical approach chosen to solve a reliability problem may vary with the size and nature of the problem. The Systems Validation Methods group at NASA Langley Research Center has created a set of four software packages that form the basis for a reliability analysis workstation, including three for use in analyzing reconfigurable, fault-tolerant systems and one for analyzing non-reconfigurable systems. The SARA bundle includes the three for reconfigurable, fault-tolerant systems: SURE reliability analysis program (COSMIC program LAR-13789, LAR-14921); the ASSIST specification interface program (LAR-14193, LAR-14923), and PAWS/STEM reliability analysis programs (LAR-14165, LAR-14920). As indicated by the program numbers in parentheses, each of these three packages is also available separately in two machine versions. The fourth package, which is only available separately, is FTC, the Fault Tree Compiler (LAR-14586, LAR-14922). FTC is used to calculate the top-event probability for a fault tree which describes a non-reconfigurable system. PAWS/STEM and SURE are analysis programs which utilize different solution methods, but have a common input language, the SURE language. ASSIST is a preprocessor that generates SURE language from a more abstract definition. ASSIST, SURE, and PAWS/STEM are described briefly in the following paragraphs. For additional details about the individual packages, including pricing, please refer to their respective abstracts. ASSIST, the Abstract Semi-Markov Specification Interface to the SURE Tool program, allows a reliability engineer to describe the failure behavior of a fault-tolerant computer system in an abstract, high-level language. The ASSIST program then automatically generates a corresponding semi-Markov model. A one-page ASSIST-language description may result in a semi-Markov model with thousands of states and transitions. The ASSIST program also includes model-reduction techniques to facilitate efficient modeling of large systems. The semi-Markov model generated by ASSIST is in the format needed for input to SURE and PAWS/STEM. The Semi-Markov Unreliability Range Evaluator, SURE, is an analysis tool for reconfigurable, fault-tolerant systems. SURE provides an efficient means for calculating accurate upper and lower bounds for the death state probabilities for a large class of semi-Markov models, not just those which can be reduced to critical-pair architectures. The calculated bounds are close enough (usually within 5 percent of each other) for use in reliability studies of ultra-reliable computer systems. The SURE bounding theorems have algebraic solutions and are consequently computationally efficient even for large and complex systems. SURE can optionally regard a specified parameter as a variable over a range of values, enabling an automatic sensitivity analysis. SURE output is tabular. The PAWS/STEM package includes two programs for the creation and evaluation of pure Markov models describing the behavior of fault-tolerant reconfigurable computer systems: the Pade Approximation with Scaling (PAWS) and Scaled Taylor Exponential Matrix (STEM) programs. PAWS and STEM produce exact solutions for the probability of system failure and provide a conservative estimate of the number of significant digits in the solution. Markov models of fault-tolerant architectures inevitably lead to numerically stiff differential equations. Both PAWS and STEM have the capability to solve numerically stiff models. These complementary programs use separate methods to determine the matrix exponential in the solution of the model's system of differential equations. In general, PAWS is better suited to evaluate small and dense models. STEM operates at lower precision, but works faster than PAWS for larger models. The programs that comprise the SARA package were originally developed for use on DEC VAX series computers running VMS and were later ported for use on Sun series computers running SunOS. They are written in C-language, Pascal, and FORTRAN 77. An ANSI compliant C compiler is required in order to compile the C portion of the Sun version source code. The Pascal and FORTRAN code can be compiled on Sun computers using Sun Pascal and Sun Fortran. For the VMS version, VAX C, VAX PASCAL, and VAX FORTRAN can be used to recompile the source code. The standard distribution medium for the VMS version of SARA (COS-10041) is a 9-track 1600 BPI magnetic tape in VMSINSTAL format. It is also available on a TK50 tape cartridge in VMSINSTAL format. Executables are included. The standard distribution medium for the Sun version of SARA (COS-10039) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. Both Sun3 and Sun4 executables are included. Electronic copies of the ASSIST user's manual in TeX and PostScript formats are provided on the distribution medium. DEC, VAX, VMS, and TK50 are registered trademarks of Digital Equipment Corporation. Sun, Sun3, Sun4, and SunOS are trademarks of Sun Microsystems, Inc. TeX is a trademark of the American Mathematical Society. PostScript is a registered trademark of Adobe Systems Incorporated.

SARA - SURE/ASSIST RELIABILITY ANALYSIS WORKSTATION (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Butler, R. W.

1994-01-01

SARA, the SURE/ASSIST Reliability Analysis Workstation, is a bundle of programs used to solve reliability problems. The mathematical approach chosen to solve a reliability problem may vary with the size and nature of the problem. The Systems Validation Methods group at NASA Langley Research Center has created a set of four software packages that form the basis for a reliability analysis workstation, including three for use in analyzing reconfigurable, fault-tolerant systems and one for analyzing non-reconfigurable systems. The SARA bundle includes the three for reconfigurable, fault-tolerant systems: SURE reliability analysis program (COSMIC program LAR-13789, LAR-14921); the ASSIST specification interface program (LAR-14193, LAR-14923), and PAWS/STEM reliability analysis programs (LAR-14165, LAR-14920). As indicated by the program numbers in parentheses, each of these three packages is also available separately in two machine versions. The fourth package, which is only available separately, is FTC, the Fault Tree Compiler (LAR-14586, LAR-14922). FTC is used to calculate the top-event probability for a fault tree which describes a non-reconfigurable system. PAWS/STEM and SURE are analysis programs which utilize different solution methods, but have a common input language, the SURE language. ASSIST is a preprocessor that generates SURE language from a more abstract definition. ASSIST, SURE, and PAWS/STEM are described briefly in the following paragraphs. For additional details about the individual packages, including pricing, please refer to their respective abstracts. ASSIST, the Abstract Semi-Markov Specification Interface to the SURE Tool program, allows a reliability engineer to describe the failure behavior of a fault-tolerant computer system in an abstract, high-level language. The ASSIST program then automatically generates a corresponding semi-Markov model. A one-page ASSIST-language description may result in a semi-Markov model with thousands of states and transitions. The ASSIST program also includes model-reduction techniques to facilitate efficient modeling of large systems. The semi-Markov model generated by ASSIST is in the format needed for input to SURE and PAWS/STEM. The Semi-Markov Unreliability Range Evaluator, SURE, is an analysis tool for reconfigurable, fault-tolerant systems. SURE provides an efficient means for calculating accurate upper and lower bounds for the death state probabilities for a large class of semi-Markov models, not just those which can be reduced to critical-pair architectures. The calculated bounds are close enough (usually within 5 percent of each other) for use in reliability studies of ultra-reliable computer systems. The SURE bounding theorems have algebraic solutions and are consequently computationally efficient even for large and complex systems. SURE can optionally regard a specified parameter as a variable over a range of values, enabling an automatic sensitivity analysis. SURE output is tabular. The PAWS/STEM package includes two programs for the creation and evaluation of pure Markov models describing the behavior of fault-tolerant reconfigurable computer systems: the Pade Approximation with Scaling (PAWS) and Scaled Taylor Exponential Matrix (STEM) programs. PAWS and STEM produce exact solutions for the probability of system failure and provide a conservative estimate of the number of significant digits in the solution. Markov models of fault-tolerant architectures inevitably lead to numerically stiff differential equations. Both PAWS and STEM have the capability to solve numerically stiff models. These complementary programs use separate methods to determine the matrix exponential in the solution of the model's system of differential equations. In general, PAWS is better suited to evaluate small and dense models. STEM operates at lower precision, but works faster than PAWS for larger models. The programs that comprise the SARA package were originally developed for use on DEC VAX series computers running VMS and were later ported for use on Sun series computers running SunOS. They are written in C-language, Pascal, and FORTRAN 77. An ANSI compliant C compiler is required in order to compile the C portion of the Sun version source code. The Pascal and FORTRAN code can be compiled on Sun computers using Sun Pascal and Sun Fortran. For the VMS version, VAX C, VAX PASCAL, and VAX FORTRAN can be used to recompile the source code. The standard distribution medium for the VMS version of SARA (COS-10041) is a 9-track 1600 BPI magnetic tape in VMSINSTAL format. It is also available on a TK50 tape cartridge in VMSINSTAL format. Executables are included. The standard distribution medium for the Sun version of SARA (COS-10039) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. Both Sun3 and Sun4 executables are included. Electronic copies of the ASSIST user's manual in TeX and PostScript formats are provided on the distribution medium. DEC, VAX, VMS, and TK50 are registered trademarks of Digital Equipment Corporation. Sun, Sun3, Sun4, and SunOS are trademarks of Sun Microsystems, Inc. TeX is a trademark of the American Mathematical Society. PostScript is a registered trademark of Adobe Systems Incorporated.

Sustainable Library Development Training Package

ERIC Educational Resources Information Center

Peace Corps, 2012

2012-01-01

This Sustainable Library Development Training Package supports Peace Corps' Focus In/Train Up strategy, which was implemented following the 2010 Comprehensive Agency Assessment. Sustainable Library Development is a technical training package in Peace Corps programming within the Education sector. The training package addresses the Volunteer…

9 CFR 381.144 - Packaging materials.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., from the packaging supplier under whose brand name and firm name the material is marketed to the... packaging supplier will be accepted by Program inspectors to establish that the use of material complies.... Official establishments and packaging suppliers providing written guaranties to those official...

9 CFR 381.144 - Packaging materials.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., from the packaging supplier under whose brand name and firm name the material is marketed to the... packaging supplier will be accepted by Program inspectors to establish that the use of material complies.... Official establishments and packaging suppliers providing written guaranties to those official...

9 CFR 381.144 - Packaging materials.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., from the packaging supplier under whose brand name and firm name the material is marketed to the... packaging supplier will be accepted by Program inspectors to establish that the use of material complies.... Official establishments and packaging suppliers providing written guaranties to those official...

Psyplot: Visualizing rectangular and triangular Climate Model Data with Python

NASA Astrophysics Data System (ADS)

Sommer, Philipp

2016-04-01

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

Sensory impacts of food-packaging interactions.

PubMed

Duncan, Susan E; Webster, Janet B

2009-01-01

Sensory changes in food products result from intentional or unintentional interactions with packaging materials and from failure of materials to protect product integrity or quality. Resolving sensory issues related to plastic food packaging involves knowledge provided by sensory scientists, materials scientists, packaging manufacturers, food processors, and consumers. Effective communication among scientists and engineers from different disciplines and industries can help scientists understand package-product interactions. Very limited published literature describes sensory perceptions associated with food-package interactions. This article discusses sensory impacts, with emphasis on oxidation reactions, associated with the interaction of food and materials, including taints, scalping, changes in food quality as a function of packaging, and examples of material innovations for smart packaging that can improve sensory quality of foods and beverages. Sensory evaluation is an important tool for improved package selection and development of new materials.

AN ADA LINEAR ALGEBRA PACKAGE MODELED AFTER HAL/S

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

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

Reliability of High I/O High Density CCGA Interconnect Electronic Packages under Extreme Thermal Environment

NASA Technical Reports Server (NTRS)

Ramesham, Rajeshuni

2012-01-01

This paper provides the experimental test results of advanced CCGA packages tested in extreme temperature thermal environments. Standard optical inspection and x-ray non-destructive inspection tools were used to assess the reliability of high density CCGA packages for deep space extreme temperature missions. Ceramic column grid array (CCGA) packages have been increasing in use based on their advantages such as high interconnect density, very good thermal and electrical performances, compatibility with standard surface-mount packaging assembly processes, and so on. CCGA packages are used in space applications such as in logic and microprocessor functions, telecommunications, payload electronics, and flight avionics. As these packages tend to have less solder joint strain relief than leaded packages or more strain relief over lead-less chip carrier packages, the reliability of CCGA packages is very important for short-term and long-term deep space missions. We have employed high density CCGA 1152 and 1272 daisy chained electronic packages in this preliminary reliability study. Each package is divided into several daisy-chained sections. The physical dimensions of CCGA1152 package is 35 mm x 35 mm with a 34 x 34 array of columns with a 1 mm pitch. The dimension of the CCGA1272 package is 37.5 mm x 37.5 mm with a 36 x 36 array with a 1 mm pitch. The columns are made up of 80% Pb/20%Sn material. CCGA interconnect electronic package printed wiring polyimide boards have been assembled and inspected using non-destructive x-ray imaging techniques. The assembled CCGA boards were subjected to extreme temperature thermal atmospheric cycling to assess their reliability for future deep space missions. The resistance of daisy-chained interconnect sections were monitored continuously during thermal cycling. This paper provides the experimental test results of advanced CCGA packages tested in extreme temperature thermal environments. Standard optical inspection and x-ray non-destructive inspection tools were used to assess the reliability of high density CCGA packages for deep space extreme temperature missions. Keywords: Extreme temperatures, High density CCGA qualification, CCGA reliability, solder joint failures, optical inspection, and x-ray inspection.

"Plain packaging" regulations for tobacco products: the impact of standardizing the color and design of cigarette packs.

PubMed

Hammond, David

2010-01-01

Tobacco packaging and labeling policies have emerged as prominent and cost-effective tobacco control measures. Although packaging policies have primarily focused on health warnings, there is growing recognition of the importance of packaging as a marketing tool for the tobacco industry. The current paper reviews evidence on the potential impact of standardizing the color and design of tobacco packages -so called "plain" packaging. The evidence indicates three primary benefits of plain packaging: increasing the effectiveness of health warnings, reducing false health beliefs about cigarettes, and reducing brand appeal especially among youth and young adults. Overall, the research to date suggests that "plain" packaging regulations would be an effective tobacco control measure, particularly in jurisdictions with comprehensive restrictions on other forms of marketing.

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages.

PubMed

Taminau, Jonatan; Meganck, Stijn; Lazar, Cosmin; Steenhoff, David; Coletta, Alain; Molter, Colin; Duque, Robin; de Schaetzen, Virginie; Weiss Solís, David Y; Bersini, Hugues; Nowé, Ann

2012-12-24

With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck. We present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well. By providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

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.

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

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

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

2011-03-01

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

Advanced Spacesuit Portable Life Support System Packaging Concept Mock-Up Design & Development

NASA Technical Reports Server (NTRS)

O''Connell, Mary K.; Slade, Howard G.; Stinson, Richard G.

1998-01-01

A concentrated development effort was begun at NASA Johnson Space Center to create an advanced Portable Life Support System (PLSS) packaging concept. Ease of maintenance, technological flexibility, low weight, and minimal volume are targeted in the design of future micro-gravity and planetary PLSS configurations. Three main design concepts emerged from conceptual design techniques and were carried forth into detailed design, then full scale mock-up creation. "Foam", "Motherboard", and "LEGOtm" packaging design concepts are described in detail. Results of the evaluation process targeted maintenance, robustness, mass properties, and flexibility as key aspects to a new PLSS packaging configuration. The various design tools used to evolve concepts into high fidelity mock ups revealed that no single tool was all encompassing, several combinations were complimentary, the devil is in the details, and, despite efforts, many lessons were learned only after working with hardware.

chimeraviz: a tool for visualizing chimeric RNA.

PubMed

Lågstad, Stian; Zhao, Sen; Hoff, Andreas M; Johannessen, Bjarne; Lingjærde, Ole Christian; Skotheim, Rolf I

2017-09-15

Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz , a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION. chimeraviz is an R package available via Bioconductor ( https://bioconductor.org/packages/release/bioc/html/chimeraviz.html ) under Artistic-2.0. Source code and support is available at GitHub ( https://github.com/stianlagstad/chimeraviz ). rolf.i.skotheim@rr-research.no. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

[Preference on screening frequency and willingness-to-pay for multiple-cancer packaging screening programs in urban populations in China].

PubMed

Zhu, J; Huang, H Y; Mao, A Y; Sun, Z X; Qiu, W Q; Lei, H K; Dong, P; Huang, J W; Bai, Y N; Sun, X J; Liu, G X; Wang, D B; Liao, X Z; Ren, J S; Guo, L W; Lan, L; Zhou, Q; Song, B B; Liu, Y Q; Du, L B; Zhu, L; Cao, R; Wang, J L; Mai, L; Ren, Y; Zhou, J Y; Sun, X H; Wu, S L; Qi, X; Lou, P A; Cai, B; Li, N; Zhang, K; He, J; Dai, M; Shi, J F

2018-02-10

Objective: From an actual cancer screening service demanders' perspective, we tried to understand the preference on screening frequency and willingness-to-pay for the packaging screening program on common cancers and to evaluate its long-term sustainability in urban populations in China. Methods: From 2012 to 2014, a multi-center cross-sectional survey was conducted among the actual screening participants from 13 provinces covered by the Cancer Screening Program in Urban China (CanSPUC). By face-to-face interview, information regarding to preference to screening frequency, willingness-to-pay for packaging screening program, maximum amount on payment and related reasons for unwillingness were investigated. Results: A total of 31 029 participants were included in this survey, with an average age as (55.2±7.5) years and median annual income per family as 25 000 Chinese Yuan. People's preference to screening frequency varied under different assumptions ( " totally free" and "self-paid" ). When the packaging screening was assumed totally free, 93.9% of residents would prefer to take the screening program every 1 to 3 years. However, the corresponding proportion dropped to 67.3% when assuming a self-paid pattern. 76.7% of the participants had the willingness-to-pay for the packaging screening, but only 11.2% of them would like to pay more than 500 Chinese Yuan (the expenditure of the particular packaging screening were about 1 500 Chinese Yuan). The remaining 23.3% of residents showed no willingness-to-pay, and the main reasons were unaffordable expenditure (71.7%) and feeling'no need'(40.4%). Conclusions: People who participated in the CanSPUC program generally tended to choose high-frequency packaging screening program, indicating the high potential acceptance for scale-up packaging screening, while it needs cautious assessments and rational guidance to the public. Although about seven in ten of the residents were willing to pay, the payment amount was limited, revealing the necessity of strengthening individual's awareness of his or her key role in health self-management, and a reasonable payment proportion should be considered when establishing co-compensation mechanism.

cp-R, an interface the R programming language for clinical laboratory method comparisons.

PubMed

Holmes, Daniel T

2015-02-01

Clinical scientists frequently need to compare two different bioanalytical methods as part of assay validation/monitoring. As a matter necessity, regression methods for quantitative comparison in clinical chemistry, hematology and other clinical laboratory disciplines must allow for error in both the x and y variables. Traditionally the methods popularized by 1) Deming and 2) Passing and Bablok have been recommended. While commercial tools exist, no simple open source tool is available. The purpose of this work was to develop and entirely open-source GUI-driven program for bioanalytical method comparisons capable of performing these regression methods and able to produce highly customized graphical output. The GUI is written in python and PyQt4 with R scripts performing regression and graphical functions. The program can be run from source code or as a pre-compiled binary executable. The software performs three forms of regression and offers weighting where applicable. Confidence bands of the regression are calculated using bootstrapping for Deming and Passing Bablok methods. Users can customize regression plots according to the tools available in R and can produced output in any of: jpg, png, tiff, bmp at any desired resolution or ps and pdf vector formats. Bland Altman plots and some regression diagnostic plots are also generated. Correctness of regression parameter estimates was confirmed against existing R packages. The program allows for rapid and highly customizable graphical output capable of conforming to the publication requirements of any clinical chemistry journal. Quick method comparisons can also be performed and cut and paste into spreadsheet or word processing applications. We present a simple and intuitive open source tool for quantitative method comparison in a clinical laboratory environment. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Stellar and Binary Evolution in Star Clusters

NASA Technical Reports Server (NTRS)

McMillan, Stephen L. W.

2001-01-01

This paper presents a final report on research activities covered on Stellar and Binary Evolution in Star Clusters. Substantial progress was made in the development and dissemination of the "Starlab" software environment. Significant improvements were made to "kira," an N-body simulation program tailored to the study of dense stellar systems such as star clusters and galactic nuclei. Key advances include (1) the inclusion of stellar and binary evolution in a self-consistent manner, (2) proper treatment of the anisotropic Galactic tidal field, (3) numerous technical enhancements in the treatment of binary dynamics and interactions, and (4) full support for the special-purpose GRAPE-4 hardware, boosting the program's performance by a factor of 10-100 over the accelerated version. The data-reduction and analysis tools in Starlab were also substantially expanded. A Starlab Web site (http://www.sns.ias.edu/-starlab) was created and developed. The site contains detailed information on the structure and function of the various tools that comprise the package, as well as download information, "how to" tips and examples of common operations, demonstration programs, animations, etc. All versions of the software are freely distributed to all interested users, along with detailed installation instructions.

Tools and techniques for computational reproducibility.

PubMed

Piccolo, Stephen R; Frampton, Michael B

2016-07-11

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced because of complexities in how software is packaged, installed, and executed-and because of limitations associated with how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges; here we describe seven such strategies. With a broad scientific audience in mind, we describe the strengths and limitations of each approach, as well as the circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.

Interactive Educational Tool for Turbofan and Afterburning Turbojet Engines

NASA Technical Reports Server (NTRS)

Benson, Thomas J.

1997-01-01

A workstation-based, interactive educational computer program has been developed at the NASA Lewis Research Center to aid in the teaching and understanding of turbine engine design and analysis. This tool has recently been extended to model the performance of two-spool turbofans and afterburning turbojets. The program solves for the flow conditions through the engine by using classical one-dimensional thermodynamic analysis found in various propulsion textbooks. Either an approximately thermally perfect or calorically perfect gas can be used in the thermodynamic analysis. Students can vary the design conditions through a graphical user interface; engine performance is calculated immediately. A variety of graphical formats are used to present results, including numerical results, moving bar charts, and student-generated temperature versus entropy (Ts), pressure versus specific volume (pv), and engine performance plots. The package includes user-controlled printed output, restart capability, online help screens, and a browser that displays teacher-prepared lessons in turbomachinery. The program runs on a variety of workstations or a personal computer using the UNIX operating system and X-based graphics. It is being tested at several universities in the midwestern United States; the source and executables are available free from the author.

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

PubMed

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

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

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.

Estimates of Dietary Exposure to Bisphenol A (BPA) from Light Metal Packaging using Food Consumption and Packaging usage Data: A Refined Deterministic Approach and a Fully Probabilistic (FACET) Approach

PubMed Central

Oldring, P.K.T.; Castle, L.; O'Mahony, C.; Dixon, J.

2013-01-01

The FACET tool is a probabilistic model to estimate exposure to chemicals in foodstuffs, originating from flavours, additives and food contact materials. This paper demonstrates the use of the FACET tool to estimate exposure to BPA (bisphenol A) from light metal packaging. For exposure to migrants from food packaging, FACET uses industry-supplied data on the occurrence of substances in the packaging, their concentrations and construction of the packaging, which were combined with data from a market research organisation and food consumption data supplied by national database managers. To illustrate the principles, UK packaging data were used together with consumption data from the UK National Diet and Nutrition Survey (NDNS) dietary survey for 19–64 year olds for a refined deterministic verification. The UK data were chosen mainly because the consumption surveys are detailed, data for UK packaging at a detailed level were available and, arguably, the UK population is composed of high consumers of packaged foodstuffs. Exposures were run for each food category that could give rise to BPA from light metal packaging. Consumer loyalty to a particular type of packaging, commonly referred to as packaging loyalty, was set. The BPA extraction levels used for the 15 types of coating chemistries that could release BPA were in the range of 0.00005–0.012 mg dm−2. The estimates of exposure to BPA using FACET for the total diet were 0.0098 (mean) and 0.0466 (97.5th percentile) mg/person/day, corresponding to 0.00013 (mean) and 0.00059 (97.5th percentile) mg kg−1 body weight day−1 for consumers of foods packed in light metal packaging. This is well below the current EFSA (and other recognised bodies) TDI of 0.05 mg kg−1 body weight day. These probabilistic estimates were compared with estimates using a refined deterministic approach drawing on the same input data. The results from FACET for the mean, 95th and 97.5th percentile exposures to BPA lay between the lowest and the highest estimates from the refined deterministic calculations. Since this should be the case, for a fully probabilistic compared with a deterministic approach, it is concluded that the FACET tool has been verified in this example. A recent EFSA draft opinion on exposure to BPA from different sources showed that canned foods were a major contributor and compared results from various models, including those from FACET. The results from FACET were overall conservative. PMID:24405320

Data Service Provider Cost Estimation Tool

NASA Technical Reports Server (NTRS)

Fontaine, Kathy; Hunolt, Greg; Booth, Arthur L.; Banks, Mel

2011-01-01

The Data Service Provider Cost Estimation Tool (CET) and Comparables Database (CDB) package provides to NASA s Earth Science Enterprise (ESE) the ability to estimate the full range of year-by-year lifecycle cost estimates for the implementation and operation of data service providers required by ESE to support its science and applications programs. The CET can make estimates dealing with staffing costs, supplies, facility costs, network services, hardware and maintenance, commercial off-the-shelf (COTS) software licenses, software development and sustaining engineering, and the changes in costs that result from changes in workload. Data Service Providers may be stand-alone or embedded in flight projects, field campaigns, research or applications projects, or other activities. The CET and CDB package employs a cost-estimation-by-analogy approach. It is based on a new, general data service provider reference model that provides a framework for construction of a database by describing existing data service providers that are analogs (or comparables) to planned, new ESE data service providers. The CET implements the staff effort and cost estimation algorithms that access the CDB and generates the lifecycle cost estimate for a new data services provider. This data creates a common basis for an ESE proposal evaluator for considering projected data service provider costs.

ELAS: A powerful, general purpose image processing package

NASA Technical Reports Server (NTRS)

Walters, David; Rickman, Douglas

1991-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Risk Management of Microelectronics: The NASA Electronic Parts and Packaging (NEPP) Program

NASA Technical Reports Server (NTRS)

LaBel, Kenneth A.; Sampson, Michael J.

2005-01-01

This viewgraph information provides information on how the NASA Electronic Parts and Packaging (NEPP) Program evaluates the reliability of technologies for Electrical, Electronic, and Electromechanical (EEE) parts, and their suitability for spacecraft applications.

Cantera and Cantera Electrolyte Thermodynamics Objects

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

John Hewson, Harry Moffat

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It is a multi-organizational effort to create and formulate high quality 0D and 1D constitutive modeling tools for reactive transport codes.Institutions involved with the effort include Sandia, MIT, Colorado School of Mines, U. Texas, NASA, and Oak Ridge National Labs. Specific to Sandia's contributions, the Cantera Electrolyte Thermo Objects (CETO) packages is comprised of add-on routines for Cantera that handle electrolyte thermochemistry and reactions within the overall Cantera package. Cantera is a C++ Cal Tech code that handles gas phase species transport, reaction,more » and thermodynamics. With this addition, Cantera can be extended to handle problems involving liquid phase reactions and transport in electrolyte systems, and phase equilibrium problemsinvolving concentrated electrolytes and gas/solid phases. A full treatment of molten salt thermodynamics and transport has also been implemented in CETO. The routines themselves consist of .cpp and .h files containing C++ objects that are derived from parent Cantera objects representing thermodynamic functions. They are linked unto the main Cantera libraries when requested by the user. As an addendum to the main thermodynamics objects, several utility applications are provided. The first is multiphase Gibbs free energy minimizer based on the vcs algorithm, called vcs_cantera. This code allows for the calculation of thermodynamic equilibrium in multiple phases at constant temperature and pressure. Note, a similar code capability exists already in Cantera. This version follows the same algorithm, but gas a different code-base starting point, and is used as a research tool for algorithm development. The second program, cttables, prints out tables of thermodynamic and kinetic information for thermodynamic and kinetic objects within Cantera. This program serves as a "Get the numbers out" utility for Cantera, and as such it is very useful as a verification tool. These add-on utilities are encapsulated into a directory structure named cantera_apps, whose installation uses autoconf and also utilizes Cantera's application environment (i.e., they utilize Cantera as a library).« less

WORK INSTRUCTION PROGRAMS FOR THE FOOD SERVICE INDUSTRY.

ERIC Educational Resources Information Center

KONZ, STEPHAN A.; MIDDLETON, RAYMONA

A PROJECT WAS INITIATED TO DEVELOP EFFICIENT WORK METHODS FOR 100 COMMON TASKS IN THE FOOD SERVICE INDUSTRY AND THEN TO PREPARE PROGRAMED LEARNING "PACKAGES" FOR EACH OF THESE TASKS FOR TRAINING POTENTIAL EMPLOYEES AND EMPLOYEES WITH LOWER LEVELS OF EDUCATION TO HOLD USEFUL JOBS. THE CONCEPT OF PROGRAMED LEARNING PACKAGES FOR FOOD SERVICING WAS…

Outreach and Orientation for ESL Students and Bilingual Welding and Automotive Programs. Vocational Education Resource Package.

ERIC Educational Resources Information Center

Evaluation and Training Inst., Los Angeles, CA.

This Vocational Education Resource Package (VERP) was developed to provide materials useful in replicating an exemplary vocational education program for special student populations in the California Community Colleges. This VERP provides information on two programs for limited English proficient students developed at Santa Barbara City College…

75 FR 25319 - Tax Counseling for the Elderly (TCE) Program Availability of Application Packages; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... DEPARTMENT OF THE TREASURY Internal Revenue Service Tax Counseling for the Elderly (TCE) Program...: Correction to a notice. SUMMARY: This document contains a correction to a notice of the Tax Counseling for... application packages for the 2011 Tax Counseling for the Elderly (TCE) Program. FOR FURTHER INFORMATION...

Preparing to Take Advantage of New Programs in the Economic Stimulus Package

ERIC Educational Resources Information Center

Stelow, Shawn

2009-01-01

The proposed federal stimulus package could help to strengthen existing programs with track records of proven performance and strong accountability and administrative systems. This is good news for afterschool programs leaders who can leverage existing relationships and sustainability plans to access new funding opportunities. In these times, a…

An Analysis of U.S. Business Schools' Catalogs, Application Packages, and Program Materials from an International Perspective.

ERIC Educational Resources Information Center

Webb, Marion S.; Mayer, Kenneth R.; Pioche, Virginie

1999-01-01

Catalogs, application packages, and program materials from 106 business schools were analyzed to determine the degree of international coverage in business schools' curricula. Findings indicated a trend to require international functional courses, such as international finance, in the traditional Master in business administration programs and to…

Safety. A Guide for Industrial Cooperative Training Programs. Learning Activity Package. LAP 6.

ERIC Educational Resources Information Center

Duenk, Lester G.; Lear, George

This learning activity package, one of six intended for use in Industrial Cooperative Training Programs, is designed to provide students with information on several general safety topics which would apply in most employment situations. (The industrial cooperative training program provides industrial occupational training experience for high school…

[Application of three control banding tools to occupational health risk assessment of titanium dioxide manufacturing factory].

PubMed

Xu, H D; Zhao, L; Tang, S C; Zhang, J; Kong, F L; Jia, G

2016-12-20

Objective: To explore and validate suitable risk assessment methods for titanium dioxide though applying three risk assessment tools for nanomaterials based on the control banding (CB) approach. Methods: A factory manufacturing titanium dioxide in Jinan city, Shandong province, was assessed using a quantitative exposure method and qualitative risk assessment methods in September, 2014. A condensation particle counter equipment was used to monitor the number concentration of particles at packaging workshop and jet milling workshop. We employed three control banding tools, including CB nanotool, Stoffenmanager nano and the Guidance on working safely with nanomaterials and nanoproducts (GWSNN) to evaluate the two workshops, then compared the evaluation results. Results: The increases of particle concentrations were generated directly by packaging and jet milling processes, the number concentration from (3.52±1.46) ×10(4)/cm(3) to (14.70±8.86) ×10(4)/cm(3) at packaging workshop and from (0.97±0.25) ×10(4)/cm(3) to (1.26±0.35) ×10(4)/cm(3) at milling workshop (both P <0.05) . The number concentrations at packaging workshop were higher than those at jet milling workshop during both manufacturing and break times (both P <0.05) . The results of CB nanotool showed that the risk level of the packaging workshop was classified as high and the risk level of the jet milling workshop was classified asmedium. The results of Stoffenmanager nano showed that the risk level of the packaging workshop was classified as medium and the risk level of the jet milling workshop was classified as low. The results of GWSNN showed that the risk level of packaging workshop was classified as high and the risk level of jet milling workshop was classified as low. Conclusion: The results of evaluation based on the three control banding tools are related and aligned with the results of quantitative monitoring, so they are all suitable to perform occupational health risk assessment on industrial scale production of titanium dioxideto some extent.

Program evaluation of a model to integrate internationally educated health professionals into clinical practice

PubMed Central

2013-01-01

Background The demand for health professionals continues to increase, partially due to the aging population and the high proportion of practitioners nearing retirement. The University of British Columbia (UBC) has developed a program to address this demand, by providing support for internationally trained Physiotherapists in their preparation for taking the National Physiotherapy competency examinations. The aim was to create a program comprised of the educational tools and infrastructure to support internationally educated physiotherapists (IEPs) in their preparation for entry to practice in Canada and, to improve their pass rate on the national competency examination. Methods The program was developed using a logic model and evaluated using program evaluation methodology. Program tools and resources included educational modules and curricular packages which were developed and refined based on feedback from clinical experts, IEPs and clinical physical therapy mentors. An examination bank was created and used to include test-enhanced education. Clinical mentors were recruited and trained to provide clinical and cultural support for participants. Results The IEP program has recruited 124 IEPs, with 69 now integrated into the Canadian physiotherapy workforce, and more IEPs continuing to apply to the program. International graduates who participated in the program had an improved pass rate on the national Physiotherapy Competency Examination (PCE); participation in the program resulted in them having a 28% (95% CI, 2% to 59%) greater possibility of passing the written section than their counterparts who did not take the program. In 2010, 81% of all IEP candidates who completed the UBC program passed the written component, and 82% passed the clinical component. Conclusion The program has proven to be successful and sustainable. This program model could be replicated to support the successful integration of other international health professionals into the workforce. PMID:24119470

RAGG - R EPISODIC AGGREGATION PACKAGE

EPA Science Inventory

The RAGG package is an R implementation of the CMAQ episodic model aggregation method developed by Constella Group and the Environmental Protection Agency. RAGG is a tool to provide climatological seasonal and annual deposition of sulphur and nitrogen for multimedia management. ...

Deriving stellar parameters with the SME software package

NASA Astrophysics Data System (ADS)

Piskunov, N.

2017-09-01

Photometry and spectroscopy are complementary tools for deriving accurate stellar parameters. Here I present one of the popular packages for stellar spectroscopy called SME with the emphasis on the latest developments and error assessment for the derived parameters.

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

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.

IMCS reflight certification requirements and design specifications

NASA Technical Reports Server (NTRS)

1984-01-01

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

Testing forward model against OCO-2 and TANSO-FTS/GOSAT observed spectra in near infrared range

NASA Astrophysics Data System (ADS)

Zadvornykh, Ilya V.; Gribanov, Konstantin G.

2015-11-01

An existing software package FIRE-ARMS (Fine InfraRed Explorer for Atmospheric Remote MeasurementS) was modified by embedding vector radiative transfer model VLIDORT. Thus the program tool includes both thermal (TIR) and near infrared (NIR) regions. We performed forward simulation of near infrared spectra on the top of the atmosphere for outgoing radiation accounting multiple scattering in cloudless atmosphere. Simulated spectra are compared with spectra measured by TANSO-FTS/GOSAT and OCO-2 in the condition of cloudless atmosphere over Western Siberia. NCEP/NCAR reanalysis data were used to complete model atmosphere.

Simulation Environment for Orion Launch Abort System Control Design Studies

NASA Technical Reports Server (NTRS)

McMinn, J. Dana; Jackson, E. Bruce; Christhilf, David M.

2007-01-01

The development and use of an interactive environment to perform control system design and analysis of the proposed Crew Exploration Vehicle Launch Abort System is described. The environment, built using a commercial dynamic systems design package, includes use of an open-source configuration control software tool and a collaborative wiki to coordinate between the simulation developers, control law developers and users. A method for switching between multiple candidate control laws and vehicle configurations is described. Aerodynamic models, especially in a development program, change rapidly, so a means for automating the implementation of new aerodynamic models is described.

Toolkit for testing scientific CCD cameras

NASA Astrophysics Data System (ADS)

Uzycki, Janusz; Mankiewicz, Lech; Molak, Marcin; Wrochna, Grzegorz

2006-03-01

The CCD Toolkit (1) is a software tool for testing CCD cameras which allows to measure important characteristics of a camera like readout noise, total gain, dark current, 'hot' pixels, useful area, etc. The application makes a statistical analysis of images saved in files with FITS format, commonly used in astronomy. A graphical interface is based on the ROOT package, which offers high functionality and flexibility. The program was developed in a way to ensure future compatibility with different operating systems: Windows and Linux. The CCD Toolkit was created for the "Pie of the Sky" project collaboration (2).

Automating approximate Bayesian computation by local linear regression.

PubMed

Thornton, Kevin R

2009-07-07

In several biological contexts, parameter inference often relies on computationally-intensive techniques. "Approximate Bayesian Computation", or ABC, methods based on summary statistics have become increasingly popular. A particular flavor of ABC based on using a linear regression to approximate the posterior distribution of the parameters, conditional on the summary statistics, is computationally appealing, yet no standalone tool exists to automate the procedure. Here, I describe a program to implement the method. The software package ABCreg implements the local linear-regression approach to ABC. The advantages are: 1. The code is standalone, and fully-documented. 2. The program will automatically process multiple data sets, and create unique output files for each (which may be processed immediately in R), facilitating the testing of inference procedures on simulated data, or the analysis of multiple data sets. 3. The program implements two different transformation methods for the regression step. 4. Analysis options are controlled on the command line by the user, and the program is designed to output warnings for cases where the regression fails. 5. The program does not depend on any particular simulation machinery (coalescent, forward-time, etc.), and therefore is a general tool for processing the results from any simulation. 6. The code is open-source, and modular.Examples of applying the software to empirical data from Drosophila melanogaster, and testing the procedure on simulated data, are shown. In practice, the ABCreg simplifies implementing ABC based on local-linear regression.

Validating module network learning algorithms using simulated data.

PubMed

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

2007-05-03

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

Comparing estimates of child mortality reduction modelled in LiST with pregnancy history survey data for a community-based NGO project in Mozambique

PubMed Central

2011-01-01

Background There is a growing body of evidence that integrated packages of community-based interventions, a form of programming often implemented by NGOs, can have substantial child mortality impact. More countries may be able to meet Millennium Development Goal (MDG) 4 targets by leveraging such programming. Analysis of the mortality effect of this type of programming is hampered by the cost and complexity of direct mortality measurement. The Lives Saved Tool (LiST) produces an estimate of mortality reduction by modelling the mortality effect of changes in population coverage of individual child health interventions. However, few studies to date have compared the LiST estimates of mortality reduction with those produced by direct measurement. Methods Using results of a recent review of evidence for community-based child health programming, a search was conducted for NGO child health projects implementing community-based interventions that had independently verified child mortality reduction estimates, as well as population coverage data for modelling in LiST. One child survival project fit inclusion criteria. Subsequent searches of the USAID Development Experience Clearinghouse and Child Survival Grants databases and interviews of staff from NGOs identified no additional projects. Eight coverage indicators, covering all the project’s technical interventions were modelled in LiST, along with indicator values for most other non-project interventions in LiST, mainly from DHS data from 1997 and 2003. Results The project studied was implemented by World Relief from 1999 to 2003 in Gaza Province, Mozambique. An independent evaluation collecting pregnancy history data estimated that under-five mortality declined 37% and infant mortality 48%. Using project-collected coverage data, LiST produced estimates of 39% and 34% decline, respectively. Conclusions LiST gives reasonably accurate estimates of infant and child mortality decline in an area where a package of community-based interventions was implemented. This and other validation exercises support use of LiST as an aid for program planning to tailor packages of community-based interventions to the epidemiological context and for project evaluation. Such targeted planning and assessments will be useful to accelerate progress in reaching MDG4 targets. PMID:21501454

Neo: an object model for handling electrophysiology data in multiple formats

PubMed Central

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L.; Rodgers, Chris C.; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P.

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology. PMID:24600386

Neo: an object model for handling electrophysiology data in multiple formats.

PubMed

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L; Rodgers, Chris C; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named "Neo," suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.

PubMed

Smelter, Andrey; Astra, Morgan; Moseley, Hunter N B

2017-03-17

The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis. To aid in the use of this public resource, we have developed a package called nmrstarlib in the popular open-source programming language Python. The nmrstarlib's implementation is very efficient, both in design and execution. The library has facilities for reading and writing both NMR-STAR version 2.1 and 3.1 formatted files, parsing them into usable Python dictionary- and list-based data structures, making access and manipulation of the experimental data very natural within Python programs (i.e. "saveframe" and "loop" records represented as individual Python dictionary data structures). Another major advantage of this design is that data stored in original NMR-STAR can be easily converted into its equivalent JavaScript Object Notation (JSON) format, a lightweight data interchange format, facilitating data access and manipulation using Python and any other programming language that implements a JSON parser/generator (i.e., all popular programming languages). We have also developed tools to visualize assigned chemical shift values and to convert between NMR-STAR and JSONized NMR-STAR formatted files. Full API Reference Documentation, User Guide and Tutorial with code examples are also available. We have tested this new library on all current BMRB entries: 100% of all entries are parsed without any errors for both NMR-STAR version 2.1 and version 3.1 formatted files. We also compared our software to three currently available Python libraries for parsing NMR-STAR formatted files: PyStarLib, NMRPyStar, and PyNMRSTAR. The nmrstarlib package is a simple, fast, and efficient library for accessing data from the BMRB. The library provides an intuitive dictionary-based interface with which Python programs can read, edit, and write NMR-STAR formatted files and their equivalent JSONized NMR-STAR files. The nmrstarlib package can be used as a library for accessing and manipulating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STAR file format into its equivalent JSON file format and vice versa, and to visualize chemical shift values. Furthermore, the nmrstarlib implementation provides a guide for effectively JSONizing other older scientific formats, improving the FAIRness of data in these formats.

Implementation and use of direct-flow connections in a coupled ground-water and surface-water model

USGS Publications Warehouse

Swain, Eric D.

1994-01-01

The U.S. Geological Survey's MODFLOW finite-difference ground-water flow model has been coupled with three surface-water packages - the MODBRANCH, River, and Stream packages - to simulate surface water and its interaction with ground water. Prior to the development of the coupling packages, the only interaction between these modeling packages was that leakage values could be passed between MODFLOW and the three surface-water packages. To facilitate wider and more flexible uses of the models, a computer program was developed and added to MODFLOW to allow direct flows or stages to be passed between any of the packages and MODFLOW. The flows or stages calculated in one package can be set as boundary discharges or stages to be used in another package. Several modeling packages can be used in the same simulation depending upon the level of sophistication needed in the various reaches being modeled. This computer program is especially useful when any of the River, Stream, or MODBRANCH packages are used to model a river flowing directly into or out of wetlands in direct connection with the aquifer and represented in the model as an aquifer block. A field case study is shown to illustrate an application.

PyCoTools: A Python Toolbox for COPASI.

PubMed

Welsh, Ciaran M; Fullard, Nicola; Proctor, Carole J; Martinez-Guimera, Alvaro; Isfort, Robert J; Bascom, Charles C; Tasseff, Ryan; Przyborski, Stefan A; Shanley, Daryl P

2018-05-22

COPASI is an open source software package for constructing, simulating and analysing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface. PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations. Additional 'composite' tasks which use COPASI tasks as building blocks are available for increasing parameter estimation throughput, performing identifiability analysis and performing model selection. PyCoTools supports exploratory data analysis on parameter estimation data to assist with troubleshooting model calibrations. We demonstrate PyCoTools by posing a model selection problem designed to show case PyCoTools within a realistic scenario. The aim of the model selection problem is to test the feasibility of three alternative hypotheses in explaining experimental data derived from neonatal dermal fibroblasts in response to TGF-β over time. PyCoTools is used to critically analyse the parameter estimations and propose strategies for model improvement. PyCoTools can be downloaded from the Python Package Index (PyPI) using the command 'pip install pycotools' or directly from GitHub (https://github.com/CiaranWelsh/pycotools). Documentation at http://pycotools.readthedocs.io. Supplementary data are available at Bioinformatics.

Does introducing an immunization package of services for migrant children improve the coverage, service quality and understanding? An evidence from an intervention study among 1548 migrant children in eastern China.

PubMed

Hu, Yu; Luo, Shuying; Tang, Xuewen; Lou, Linqiao; Chen, Yaping; Guo, Jing; Zhang, Bing

2015-07-15

An EPI (Expanded Program on Immunization) intervention package was implemented from October 2011 to May 2014 among migrant children in Yiwu, east China. This study aimed to evaluate its impacts on vaccination coverage, maternal understanding of EPI and the local immunization service performance. A pre- and post-test design was used. The EPI intervention package included: (1) extending the EPI service time and increasing the frequency of vaccination service; (2) training program for vaccinators; (3) developing a screening tool to identify vaccination demands among migrant clinic attendants; (4) Social mobilization for immunization. Data were obtained from random sampling investigations, vaccination service statistics and qualitative interviews with vaccinators and mothers of migrant children. The analysis of quantitative data was based on a "before and after" evaluation and qualitative data were analyzed using content analysis. The immunization registration (records kept by immunization clinics) rate increased from 87.4 to 91.9% (P = 0.016) after implementation of the EPI intervention package and the EPI card holding (EPI card kept by caregivers) rate increased from 90.9 to 95.6% (P = 0.003). The coverage of fully immunized increased from 71.5 to 88.6% for migrant children aged 1-4 years (P < 0.001) and increased from 42.2 to 80.5% for migrant children aged 2-4 years (P < 0.001). The correct response rates on valid doses and management of adverse events among vaccinators were over 90% after training. The correct response rates on immunization among mothers of migrant children were 86.8-99.3% after interventions. Our study showed a substantial improvement in vaccination coverage among migrant children in Yiwu after implementation of the EPI intervention package. Further studies are needed to evaluate the cost-effectiveness of the interventions, to identify individual interventions that make the biggest contribution to coverage, and to examine the sustainability of the interventions within the existing vaccination service delivery system in a larger scale settings or in a longer term.

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.

PubMed

Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

2013-07-15

The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ (http://imagej.nih.gov/ij/) for image processing and quantitative analysis and R (http://cran.r-project.org) for statistical processing of measurement results. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization. TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. They are both free and open source, available (http://biophysique.mnhn.fr/tango) for Linux, Microsoft Windows and Macintosh OSX. Distribution is under the GPL v.2 licence. thomas.boudier@snv.jussieu.fr Supplementary data are available at Bioinformatics online.

Evaluating variability and uncertainty separately in microbial quantitative risk assessment using two R packages.

PubMed

Pouillot, Régis; Delignette-Muller, Marie Laure

2010-09-01

Quantitative risk assessment has emerged as a valuable tool to enhance the scientific basis of regulatory decisions in the food safety domain. This article introduces the use of two new computing resources (R packages) specifically developed to help risk assessors in their projects. The first package, "fitdistrplus", gathers tools for choosing and fitting a parametric univariate distribution to a given dataset. The data may be continuous or discrete. Continuous data may be right-, left- or interval-censored as is frequently obtained with analytical methods, with the possibility of various censoring thresholds within the dataset. Bootstrap procedures then allow the assessor to evaluate and model the uncertainty around the parameters and to transfer this information into a quantitative risk assessment model. The second package, "mc2d", helps to build and study two dimensional (or second-order) Monte-Carlo simulations in which the estimation of variability and uncertainty in the risk estimates is separated. This package easily allows the transfer of separated variability and uncertainty along a chain of conditional mathematical and probabilistic models. The usefulness of these packages is illustrated through a risk assessment of hemolytic and uremic syndrome in children linked to the presence of Escherichia coli O157:H7 in ground beef. These R packages are freely available at the Comprehensive R Archive Network (cran.r-project.org). Copyright 2010 Elsevier B.V. All rights reserved.

Promising Practices: Vocational Education Resource Package.

ERIC Educational Resources Information Center

Evaluation and Training Inst., Los Angeles, CA.

Developed to assist community college administrators and faculty in enhancing vocational educational programs and services, this Vocational Education Resource Package profiles four vocational education programs at California community colleges that show promise in serving special population students. First, the Applied Mathematics for Electronics…

Ada Namelist Package

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.

1991-01-01

Ada Namelist Package, developed for Ada programming language, enables calling program to read and write FORTRAN-style namelist files. Features are: handling of any combination of types defined by user; ability to read vectors, matrices, and slices of vectors and matrices; handling of mismatches between variables in namelist file and those in programmed list of namelist variables; and ability to avoid searching entire input file for each variable. Principle benefits derived by user: ability to read and write namelist-readable files, ability to detect most file errors in initialization phase, and organization keeping number of instantiated units to few packages rather than to many subprograms.

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

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Lawson, Charles L.

1990-01-01

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

IMGui-A Desktop GUI Application for Isolation with Migration Analyses.

PubMed

Knoblauch, Jared; Sethuraman, Arun; Hey, Jody

2017-02-01

The Isolation with Migration (IM) programs (e.g., IMa2) have been utilized extensively by evolutionary biologists for model-based inference of demographic parameters including effective population sizes, migration rates, and divergence times. Here, we describe a graphical user interface for the latest IM program. IMGui provides a comprehensive set of tools for performing demographic analyses, tracking progress of runs, and visualizing results. Developed using node. js and the Electron framework, IMGui is an application that runs on any desktop operating system, and is available for download at https://github.com/jaredgk/IMgui-electron-packages. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Environmental Effect on Evolutionary Cyclic Plasticity Material Parameters of 316 Stainless Steel: An Experimental & Material Modeling Approach

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

Mohanty, Subhasish; Soppet, William K.; Majumdar, Saurin

2014-09-20

This report provides an update on an earlier assessment of environmentally assisted fatigue for light water reactor (LWR) materials under extended service conditions. This report is a deliverable under the work package for environmentally assisted fatigue in the Light Water Reactor Sustainability (LWRS) program. The overall objective of this LWRS project is to assess the degradation by environmentally assisted cracking/fatigue of LWR materials such as various alloy base metals and their welds used in reactor coolant system piping. This effort is to support the Department of Energy LWRS program for developing tools to understand the aging/failure mechanism and to predictmore » the remaining life of LWR components for anticipated 60-80 year operation.« less

Correcting systematic bias and instrument measurement drift with mzRefinery

DOE PAGES

Gibbons, Bryson C.; Chambers, Matthew C.; Monroe, Matthew E.; ...

2015-08-04

Systematic bias in mass measurement adversely affects data quality and negates the advantages of high precision instruments. We introduce the mzRefinery tool into the ProteoWizard package for calibration of mass spectrometry data files. Using confident peptide spectrum matches, three different calibration methods are explored and the optimal transform function is chosen. After calibration, systematic bias is removed and the mass measurement errors are centered at zero ppm. Because it is part of the ProteoWizard package, mzRefinery can read and write a wide variety of file formats. In conclusion, we report on availability; the mzRefinery tool is part of msConvert, availablemore » with the ProteoWizard open source package at http://proteowizard.sourceforge.net/« less

Constructing and Modifying Sequence Statistics for relevent Using informR in 𝖱

PubMed Central

Marcum, Christopher Steven; Butts, Carter T.

2015-01-01

The informR package greatly simplifies the analysis of complex event histories in 𝖱 by providing user friendly tools to build sufficient statistics for the relevent package. Historically, building sufficient statistics to model event sequences (of the form a→b) using the egocentric generalization of Butts’ (2008) relational event framework for modeling social action has been cumbersome. The informR package simplifies the construction of the complex list of arrays needed by the rem() model fitting for a variety of cases involving egocentric event data, multiple event types, and/or support constraints. This paper introduces these tools using examples from real data extracted from the American Time Use Survey. PMID:26185488

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.

Packaging- and transportation-related occurrence reports : FY 1996 annual report

DOT National Transportation Integrated Search

1997-02-01

The Oak Ridge National Laboratory (ORNL) Packaging and Transportation Safety Program (PATS) has been charged with the responsibility of retrieving reports and information pertaining to transportation and packaging incidents from the centralized ORPS ...

Development of an Ada package library

NASA Technical Reports Server (NTRS)

Burton, Bruce; Broido, Michael

1986-01-01

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

A data base processor semantics specification package

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1983-01-01

A Semantics Specification Package (DBPSSP) for the Intel Data Base Processor (DBP) is defined. DBPSSP serves as a collection of cross assembly tools that allow the analyst to assemble request blocks on the host computer for passage to the DBP. The assembly tools discussed in this report may be effectively used in conjunction with a DBP compatible data communications protocol to form a query processor, precompiler, or file management system for the database processor. The source modules representing the components of DBPSSP are fully commented and included.

Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh

PubMed Central

Chattopadhyay, Ansuman; Tannery, Nancy Hrinya; Silverman, Deborah A. L.; Bergen, Phillip; Epstein, Barbara A.

2006-01-01

Setting: In summer 2002, the Health Sciences Library System (HSLS) at the University of Pittsburgh initiated an information service in molecular biology and genetics to assist researchers with identifying and utilizing bioinformatics tools. Program Components: This novel information service comprises hands-on training workshops and consultation on the use of bioinformatics tools. The HSLS also provides an electronic portal and networked access to public and commercial molecular biology databases and software packages. Evaluation Mechanisms: Researcher feedback gathered during the first three years of workshops and individual consultation indicate that the information service is meeting user needs. Next Steps/Future Directions: The service's workshop offerings will expand to include emerging bioinformatics topics. A frequently asked questions database is also being developed to reuse advice on complex bioinformatics questions. PMID:16888665

Employing Cognitive Tools within Interactive Multimedia Applications.

ERIC Educational Resources Information Center

Hedberg, John; And Others

This paper describes research into the use of cognitive tools in the classroom using "Exploring the Nardoo", an information landscape designed to support student investigation. Simulations and support tools which allow multimedia reporting are embedded in the package and are supported by several metacognitive tools for the writing…

Visual Data Comm: A Tool for Visualizing Data Communication in the Multi Sector Planner Study

NASA Technical Reports Server (NTRS)

Lee, Hwasoo Eric

2010-01-01

Data comm is a new technology proposed in future air transport system as a potential tool to provide comprehensive data connectivity. It is a key enabler to manage 4D trajectory digitally, potentially resulting in improved flight times and increased throughput. Future concepts with data comm integration have been tested in a number of human-in-the-loop studies but analyzing the results has proven to be particularly challenging because future traffic environment in which data comm is fully enabled has assumed high traffic density, resulting in data set with large amount of information. This paper describes the motivation, design, current and potential future application of Visual Data Comm (VDC), a tool for visualizing data developed in Java using Processing library which is a tool package designed for interactive visualization programming. This paper includes an example of an application of VDC on data pertaining to the most recent Multi Sector Planner study, conducted at NASA s Airspace Operations Laboratory in 2009, in which VDC was used to visualize and interpret data comm activities

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.

Highly scalable parallel processing of extracellular recordings of Multielectrode Arrays.

PubMed

Gehring, Tiago V; Vasilaki, Eleni; Giugliano, Michele

2015-01-01

Technological advances of Multielectrode Arrays (MEAs) used for multisite, parallel electrophysiological recordings, lead to an ever increasing amount of raw data being generated. Arrays with hundreds up to a few thousands of electrodes are slowly seeing widespread use and the expectation is that more sophisticated arrays will become available in the near future. In order to process the large data volumes resulting from MEA recordings there is a pressing need for new software tools able to process many data channels in parallel. Here we present a new tool for processing MEA data recordings that makes use of new programming paradigms and recent technology developments to unleash the power of modern highly parallel hardware, such as multi-core CPUs with vector instruction sets or GPGPUs. Our tool builds on and complements existing MEA data analysis packages. It shows high scalability and can be used to speed up some performance critical pre-processing steps such as data filtering and spike detection, helping to make the analysis of larger data sets tractable.

An Assessment of IMPAC - Integrated Methodology for Propulsion and Airframe Controls

NASA Technical Reports Server (NTRS)

Walker, G. P.; Wagner, E. A.; Bodden, D. S.

1996-01-01

This report documents the work done under a NASA sponsored contract to transition to industry technologies developed under the NASA Lewis Research Center IMPAC (Integrated Methodology for Propulsion and Airframe Control) program. The critical steps in IMPAC are exercised on an example integrated flight/propulsion control design for linear airframe/engine models of a conceptual STOVL (Short Take-Off and Vertical Landing) aircraft, and MATRIXX (TM) executive files to implement each step are developed. The results from the example study are analyzed and lessons learned are listed along with recommendations that will improve the application of each design step. The end product of this research is a set of software requirements for developing a user-friendly control design tool which will automate the steps in the IMPAC methodology. Prototypes for a graphical user interface (GUI) are sketched to specify how the tool will interact with the user, and it is recommended to build the tool around existing computer aided control design software packages.

SSSFD manipulator engineering using statistical experiment design techniques

NASA Technical Reports Server (NTRS)

Barnes, John

1991-01-01

The Satellite Servicer System Flight Demonstration (SSSFD) program is a series of Shuttle flights designed to verify major on-orbit satellite servicing capabilities, such as rendezvous and docking of free flyers, Orbital Replacement Unit (ORU) exchange, and fluid transfer. A major part of this system is the manipulator system that will perform the ORU exchange. The manipulator must possess adequate toolplate dexterity to maneuver a variety of EVA-type tools into position to interface with ORU fasteners, connectors, latches, and handles on the satellite, and to move workpieces and ORUs through 6 degree of freedom (dof) space from the Target Vehicle (TV) to the Support Module (SM) and back. Two cost efficient tools were combined to perform a study of robot manipulator design parameters. These tools are graphical computer simulations and Taguchi Design of Experiment methods. Using a graphics platform, an off-the-shelf robot simulation software package, and an experiment designed with Taguchi's approach, the sensitivities of various manipulator kinematic design parameters to performance characteristics are determined with minimal cost.

A dynamic simulation based water resources education tool.

PubMed

Williams, Alison; Lansey, Kevin; Washburne, James

2009-01-01

Educational tools to assist the public in recognizing impacts of water policy in a realistic context are not generally available. This project developed systems with modeling-based educational decision support simulation tools to satisfy this need. The goal of this model is to teach undergraduate students and the general public about the implications of common water management alternatives so that they can better understand or become involved in water policy and make more knowledgeable personal or community decisions. The model is based on Powersim, a dynamic simulation software package capable of producing web-accessible, intuitive, graphic, user-friendly interfaces. Modules are included to represent residential, agricultural, industrial, and turf uses, as well as non-market values, water quality, reservoir, flow, and climate conditions. Supplementary materials emphasize important concepts and lead learners through the model, culminating in an open-ended water management project. The model is used in a University of Arizona undergraduate class and within the Arizona Master Watershed Stewards Program. Evaluation results demonstrated improved understanding of concepts and system interactions, fulfilling the project's objectives.

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

PubMed

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

2014-03-01

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

VisRseq: R-based visual framework for analysis of sequencing data

PubMed Central

2015-01-01

Background Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. Results We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. Conclusions To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights. PMID:26328469

VisRseq: R-based visual framework for analysis of sequencing data.

PubMed

Younesy, Hamid; Möller, Torsten; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

2015-01-01

Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights.

Army-NASA aircrew/aircraft integration program (A3I) software detailed design document, phase 3

NASA Technical Reports Server (NTRS)

Banda, Carolyn; Chiu, Alex; Helms, Gretchen; Hsieh, Tehming; Lui, Andrew; Murray, Jerry; Shankar, Renuka

1990-01-01

The capabilities and design approach of the MIDAS (Man-machine Integration Design and Analysis System) computer-aided engineering (CAE) workstation under development by the Army-NASA Aircrew/Aircraft Integration Program is detailed. This workstation uses graphic, symbolic, and numeric prototyping tools and human performance models as part of an integrated design/analysis environment for crewstation human engineering. Developed incrementally, the requirements and design for Phase 3 (Dec. 1987 to Jun. 1989) are described. Software tools/models developed or significantly modified during this phase included: an interactive 3-D graphic cockpit design editor; multiple-perspective graphic views to observe simulation scenarios; symbolic methods to model the mission decomposition, equipment functions, pilot tasking and loading, as well as control the simulation; a 3-D dynamic anthropometric model; an intermachine communications package; and a training assessment component. These components were successfully used during Phase 3 to demonstrate the complex interactions and human engineering findings involved with a proposed cockpit communications design change in a simulated AH-64A Apache helicopter/mission that maps to empirical data from a similar study and AH-1 Cobra flight test.

Suggested Courseware for the Non-Calculus Physics Student: Simple Harmonic Motion, Wave Motion, and Sound.

ERIC Educational Resources Information Center

Grable-Wallace, Lisa; And Others

1989-01-01

Evaluates 5 courseware packages covering the topics of simple harmonic motion, 7 packages for wave motion, and 10 packages for sound. Discusses the price range, sub-topics, program type, interaction, time, calculus required, graphics, and comments of each courseware. Selects several packages based on the criteria. (YP)

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.

Solving PDEs with Intrepid

DOE PAGES

Bochev, P.; Edwards, H. C.; Kirby, R. C.; ...

2012-01-01

Intrepid is a Trilinos package for advanced discretizations of Partial Differential Equations (PDEs). The package provides a comprehensive set of tools for local, cell-based construction of a wide range of numerical methods for PDEs. This paper describes the mathematical ideas and software design principles incorporated in the package. We also provide representative examples showcasing the use of Intrepid both in the context of numerical PDEs and the more general context of data analysis.