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

PubMed

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

2016-08-01

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

GIS based model interfacing : incorporating existing software and new techniques into a streamlined interface package

DOT National Transportation Integrated Search

2000-01-01

The ability to visualize data has grown immensely as the speed and functionality of Geographic Information Systems (GIS) have increased. Now, with modeling software and GIS, planners are able to view a prediction of the future traffic demands in thei...

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

NASA Astrophysics Data System (ADS)

Pilz, Tobias; Francke, Till; Bronstert, Axel

2017-08-01

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

Mold heating and cooling microprocessor conversion. Final report

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

Hoffman, D.P.

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

NEWFIRM Software--System Integration Using OPC

NASA Astrophysics Data System (ADS)

Daly, P. N.

2004-07-01

The NOAO Extremely Wide-Field Infra-Red Mosaic (NEWFIRM) camera is being built to satisfy the survey science requirements on the KPNO Mayall and CTIO Blanco 4m telescopes in an era of 8m+ aperture telescopes. Rather than re-invent the wheel, the software system to control the instrument has taken existing software packages and re-used what is appropriate. The result is an end-to-end observation control system using technology components from DRAMA, ORAC, observing tools, GWC, existing in-house motor controllers and new developments like the MONSOON pixel server.

XDesign: an open-source software package for designing X-ray imaging phantoms and experiments.

PubMed

Ching, Daniel J; Gürsoy, Dogˇa

2017-03-01

The development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

DOE PAGES

Ching, Daniel J.; Gursoy, Dogˇa

2017-02-21

Here, the development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

Courseware Authoring and Delivering System for Chinese Language Instruction. Final Report.

ERIC Educational Resources Information Center

Mao, Tang

A study investigated technical methods for simplifying and improving the creation of software for teaching uncommonly taught languages such as Chinese. Research consisted of assessment of existing authoring systems, domestic and overseas, available hardware, peripherals, and software packages that could be integrated into this project. Then some…

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...

Deferred Maintenance.

ERIC Educational Resources Information Center

DeLong, Richard A.

1984-01-01

Unusually hard hit by the 1970s recession, the University of Michigan accumulated more deferred maintenance problems than could be analyzed efficiently either by hand or with existing computer systems. Using an existing microcomputer and a database management software package, the maintenance service developed its own database to support…

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.

A streamlined Python framework for AT-TPC data analysis

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

The LINDSAY Virtual Human Project: An immersive Approach to Anatomy and Physiology

ERIC Educational Resources Information Center

Tworek, Janet K.; Jamniczky, Heather A.; Jacob, Christian; Hallgrímsson, Benedikt; Wright, Bruce

2013-01-01

The increasing number of digital anatomy teaching software packages challenges anatomy educators on how to best integrate these tools for teaching and learning. Realistically, there exists a complex interplay of design, implementation, politics, and learning needs in the development and integration of software for education, each of which may be…

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.

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.

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

PubMed Central

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

2016-01-01

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

Cooperative Work and Sustainable Scientific Software Practices in R

NASA Astrophysics Data System (ADS)

Weber, N.

2013-12-01

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

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.

Computing and software

USGS Publications Warehouse

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

2004-01-01

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

Parallel computation and the Basis system

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

Smith, G.R.

1992-12-16

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

Parallel computation and the basis system

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

Smith, G.R.

1993-05-01

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

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...

VCFR: A package to manipulate and visualize variant call format data in R

USDA-ARS?s Scientific Manuscript database

Software to call single nucleotide polymorphisms or related genetic variants has converged on the variant call format (vcf) as their output format of choice. This has created a need for tools to work with vcf files. While an increasing number of software exists to read vcf data, many of them only ex...

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

PubMed

Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

1997-12-01

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

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

PubMed

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

2017-03-30

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

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

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

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

2009-01-01

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

The interactive electrode localization utility: software for automatic sorting and labeling of intracranial subdural electrodes

PubMed Central

Tang, Wei; Peled, Noam; Vallejo, Deborah I.; Borzello, Mia; Dougherty, Darin D.; Eskandar, Emad N.; Widge, Alik S.; Cash, Sydney S.; Stufflebeam, Steven M.

2018-01-01

Purpose Existing methods for sorting, labeling, registering, and across-subject localization of electrodes in intracranial encephalography (iEEG) may involve laborious work requiring manual inspection of radiological images. Methods We describe a new open-source software package, the interactive electrode localization utility which presents a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images. In addition, we describe a method to automatically sort and label electrodes from subdural grids of known geometry. Results We validated our software against manual inspection methods in twelve subjects undergoing iEEG for medically intractable epilepsy. Our algorithm for sorting and labeling performed correct identification on 96% of the electrodes. Conclusions The sorting and labeling methods we describe offer nearly perfect performance and the software package we have distributed may simplify the process of registering, sorting, labeling, and localizing subdural iEEG grid electrodes by manual inspection. PMID:27915398

Designing a Humane Multimedia Interface for the Visually Impaired.

ERIC Educational Resources Information Center

Ghaoui, Claude; Mann, M.; Ng, Eng Huat

2001-01-01

Promotes the provision of interfaces that allow users to access most of the functionality of existing graphical user interfaces (GUI) using speech. Uses the design of a speech control tool that incorporates speech recognition and synthesis into existing packaged software such as Teletext, the Internet, or a word processor. (Contains 22…

DSISoft—a MATLAB VSP data processing package

NASA Astrophysics Data System (ADS)

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

2002-05-01

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

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

NASA Astrophysics Data System (ADS)

Novakov, Ognian; Sicard, Claude-Henri

1994-12-01

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

Advanced statistical methods for improved data analysis of NASA astrophysics missions

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.

1992-01-01

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

Variations in algorithm implementation among quantitative texture analysis software packages

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Progress in the Development of a Prototype Reuse Enablement System

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

JMorph: Software for performing rapid morphometric measurements on digital images of fossil assemblages

NASA Astrophysics Data System (ADS)

Lelièvre, Peter G.; Grey, Melissa

2017-08-01

Quantitative morphometric analyses of form are widely used in palaeontology, especially for taxonomic and evolutionary research. These analyses can involve several measurements performed on hundreds or even thousands of samples. Performing measurements of size and shape on large assemblages of macro- or microfossil samples is generally infeasible or impossible with traditional instruments such as vernier calipers. Instead, digital image processing software is required to perform measurements via suitable digital images of samples. Many software packages exist for morphometric analyses but there is not much available for the integral stage of data collection, particularly for the measurement of the outlines of samples. Some software exists to automatically detect the outline of a fossil sample from a digital image. However, automatic outline detection methods may perform inadequately when samples have incomplete outlines or images contain poor contrast between the sample and staging background. Hence, a manual digitization approach may be the only option. We are not aware of any software packages that are designed specifically for efficient digital measurement of fossil assemblages with numerous samples, especially for the purposes of manual outline analysis. Throughout several previous studies, we have developed a new software tool, JMorph, that is custom-built for that task. JMorph provides the means to perform many different types of measurements, which we describe in this manuscript. We focus on JMorph's ability to rapidly and accurately digitize the outlines of fossils. JMorph is freely available from the authors.

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.

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

PubMed

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

2015-02-01

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

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

PubMed

Hill, Jon; Davis, Katie E

2014-01-01

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

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

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

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

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

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.

Implementation of Interaction Algorithm to Non-Matching Discrete Interfaces Between Structure and Fluid Mesh

NASA Technical Reports Server (NTRS)

Chen, Shu-Po

1999-01-01

This paper presents software for solving the non-conforming fluid structure interfaces in aeroelastic simulation. It reviews the algorithm of interpolation and integration, highlights the flexibility and the user-friendly feature that allows the user to select the existing structure and fluid package, like NASTRAN and CLF3D, to perform the simulation. The presented software is validated by computing the High Speed Civil Transport model.

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

P-Mart was designed specifically to allow cancer researchers to perform robust statistical processing of publicly available cancer proteomic datasets. To date an online statistical processing suite for proteomics does not exist. The P-Mart software is designed to allow statistical programmers to utilize these algorithms through packages in the R programming language as well as offering a web-based interface using the Azure cloud technology. The Azure cloud technology also allows the release of the software via Docker containers.

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

NASA Technical Reports Server (NTRS)

Cheng, U.

1989-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

PMIX_Ring patch for SLURM

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

Moody, A. T.

2014-04-20

This code adds an implementation of PMIX_Ring to the existing PM12 Library in the SLURM open source software package (Simple Linux Utility for Resource Management). PMIX_Ring executes a particular communication pattern that is used to bootstrap connections between MPI processes in a parallel job.

Design Optimization Toolkit: Users' Manual

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

Aguilo Valentin, Miguel Alejandro

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

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

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

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

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

Improving Building Energy Simulation Programs Through Diagnostic Testing (Fact Sheet)

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

Not Available

2012-02-01

New test procedure evaluates quality and accuracy of energy analysis tools for the residential building retrofit market. Reducing the energy use of existing homes in the United States offers significant energy-saving opportunities, which can be identified through building simulation software tools that calculate optimal packages of efficiency measures. To improve the accuracy of energy analysis for residential buildings, the National Renewable Energy Laboratory's (NREL) Buildings Research team developed the Building Energy Simulation Test for Existing Homes (BESTEST-EX), a method for diagnosing and correcting errors in building energy audit software and calibration procedures. BESTEST-EX consists of building physics and utility billmore » calibration test cases, which software developers can use to compare their tools simulation findings to reference results generated with state-of-the-art simulation tools. Overall, the BESTEST-EX methodology: (1) Tests software predictions of retrofit energy savings in existing homes; (2) Ensures building physics calculations and utility bill calibration procedures perform to a minimum standard; and (3) Quantifies impacts of uncertainties in input audit data and occupant behavior. BESTEST-EX is helping software developers identify and correct bugs in their software, as well as develop and test utility bill calibration procedures.« less

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

PubMed

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

2017-11-16

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

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

PubMed Central

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

2012-01-01

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

ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations.

PubMed

Yesylevskyy, Semen O

2007-01-01

The major challenge in setting up membrane protein simulations is embedding the protein into the pre-equilibrated lipid bilayer. Several techniques were proposed to achieve optimal packing of the lipid molecules around the protein. However, all of them possess serious disadvantages, which limit their applicability and discourage the users of simulation packages from using them. In the present work, we analyzed existing approaches and proposed a new procedure of protein insertion into the lipid bilayer, which is implemented in the ProtSqueeze software. The advantages of ProtSqueeze are as follows: (1) the insertion algorithm is simple, understandable, and controllable; (2) the software can work with virtually any simulation package on virtually any platform; (3) no modification of the source code of the simulation package is needed; (4) the procedure of insertion is as automated as possible; (5) ProtSqueeze is distributed for free under a general public license. In this work, we present the architecture and the algorithm of ProtSqueeze and demonstrate its usage in case studies.

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

NASA Astrophysics Data System (ADS)

Nelson, Andrew

2010-11-01

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

Psynteract: A flexible, cross-platform, open framework for interactive experiments.

PubMed

Henninger, Felix; Kieslich, Pascal J; Hilbig, Benjamin E

2017-10-01

We introduce a novel platform for interactive studies, that is, any form of study in which participants' experiences depend not only on their own responses, but also on those of other participants who complete the same study in parallel, for example a prisoner's dilemma or an ultimatum game. The software thus especially serves the rapidly growing field of strategic interaction research within psychology and behavioral economics. In contrast to all available software packages, our platform does not handle stimulus display and response collection itself. Instead, we provide a mechanism to extend existing experimental software to incorporate interactive functionality. This approach allows us to draw upon the capabilities already available, such as accuracy of temporal measurement, integration with auxiliary hardware such as eye-trackers or (neuro-)physiological apparatus, and recent advances in experimental software, for example capturing response dynamics through mouse-tracking. Through integration with OpenSesame, an open-source graphical experiment builder, studies can be assembled via a drag-and-drop interface requiring little or no further programming skills. In addition, by using the same communication mechanism across software packages, we also enable interoperability between systems. Our source code, which provides support for all major operating systems and several popular experimental packages, can be freely used and distributed under an open source license. The communication protocols underlying its functionality are also well documented and easily adapted to further platforms. Code and documentation are available at https://github.com/psynteract/ .

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

PubMed Central

2014-01-01

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

Introducing Python tools for magnetotellurics: MTpy

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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

PubMed

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

2016-06-01

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

An Integrated Library System from Existing Microcomputer Programs.

ERIC Educational Resources Information Center

Kuntz, Lynda S.

1988-01-01

Demonstrates how three commercial microcomputer software packages--PC-Talk III, Wordstar, and dBase III--were combined to produce an integrated library system at the U.S. Army Concepts Analysis Agency library. The retrospective conversion process is discussed, and the four modules of the system are described: acquisitions/cataloging; online…

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

SADE is a software package for rapidly assembling analytic pipelines to manipulate data. The packages consists of the engine that manages the data and coordinates the movement of data between the tasks performing a function? a set of core libraries consisting of plugins that perform common tasks? and a framework to extend the system supporting the development of new plugins. Currently through configuration files, a pipeline can be defined that maps the routing of data through a series of plugins. Pipelines can be run in a batch mode or can process streaming data? they can be executed from the commandmore » line or run through a Windows background service. There currently exists over a hundred plugins, over fifty pipeline configurations? and the software is now being used by about a half-dozen projects.« less

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

PubMed

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

2017-08-01

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

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

NASA Technical Reports Server (NTRS)

1981-01-01

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

MTpy - Python Tools for Magnetotelluric Data Processing and Analysis

NASA Astrophysics Data System (ADS)

Krieger, Lars; Peacock, Jared; Thiel, Stephan; Inverarity, Kent; Kirkby, Alison; Robertson, Kate; Soeffky, Paul; Didana, Yohannes

2014-05-01

We present the Python package MTpy, which provides functions for the processing, analysis, and handling of magnetotelluric (MT) data sets. MT is a relatively immature and not widely applied geophysical method in comparison to other geophysical techniques such as seismology. As a result, the data processing within the academic MT community is not thoroughly standardised and is often based on a loose collection of software, adapted to the respective local specifications. We have developed MTpy to overcome problems that arise from missing standards, and to provide a simplification of the general handling of MT data. MTpy is written in Python, and the open-source code is freely available from a GitHub repository. The setup follows the modular approach of successful geoscience software packages such as GMT or Obspy. It contains sub-packages and modules for the various tasks within the standard work-flow of MT data processing and interpretation. In order to allow the inclusion of already existing and well established software, MTpy does not only provide pure Python classes and functions, but also wrapping command-line scripts to run standalone tools, e.g. modelling and inversion codes. Our aim is to provide a flexible framework, which is open for future dynamic extensions. MTpy has the potential to promote the standardisation of processing procedures and at same time be a versatile supplement for existing algorithms. Here, we introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing, interpretation, and visualisation utilising MTpy on example data sets collected over different regions of Australia and the USA.

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

DTIC Science & Technology

2012-09-30

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

Evaluation of Magnetospheric Internal Magnetic Field models and Existing Software

DTIC Science & Technology

1990-01-31

than an order of magnitude. The polar maxima are still visible, but they are not as distinct. The SAA is still apparent, but apin it is not as...completely overlap each other either. These plots show polar maxima (the right two panels) and the SAA minimum (the lower right panel). Note, that the...coGRF85 83M Contours Year - 1990.0 Atitude 1.5000 to 40 1221020.0 -225 4. DISCUSSION OF SOFWARE 4.1 INTRODUCION iliree basic software packages were used

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

PsychoPy--Psychophysics software in Python.

PubMed

Peirce, Jonathan W

2007-05-15

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

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

PubMed Central

Vernick, Kenneth D.

2017-01-01

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

PsychoPy—Psychophysics software in Python

PubMed Central

Peirce, Jonathan W.

2007-01-01

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

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

NASA Astrophysics Data System (ADS)

AlHamaydeh, Mohammad; Najib, Mohamad; Alawnah, Sameer

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

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

PubMed

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

2009-04-01

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

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

PubMed

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

2017-12-21

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

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

Hart, William Eugene

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

The Structure of the Library Market for Scientific Journals: The Case of Chemistry.

ERIC Educational Resources Information Center

Bensman, Stephen J.

1996-01-01

An analysis of price and scientific value of chemistry journals concluded that scientific value does not play a role in the pricing of scientific journals and that consequently little relationship exists between scientific value and the prices charged libraries for journals. Describes a software package, Serials Evaluator, being developed at…

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

NDE Software Developed at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Roth, Donald J.; Martin, Richard E.; Rauser, Richard W.; Nichols, Charles; Bonacuse, Peter J.

2014-01-01

NASA Glenn Research Center has developed several important Nondestructive Evaluation (NDE) related software packages for different projects in the last 10 years. Three of the software packages have been created with commercial-grade user interfaces and are available to United States entities for download on the NASA Technology Transfer and Partnership Office server (https://sr.grc.nasa.gov/). This article provides brief overviews of the software packages.

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.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

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.

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.

pyLIMA : an open source microlensing software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne

2017-01-01

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

PATHFINDER: Probing Atmospheric Flows in an Integrated and Distributed Environment

NASA Technical Reports Server (NTRS)

Wilhelmson, R. B.; Wojtowicz, D. P.; Shaw, C.; Hagedorn, J.; Koch, S.

1995-01-01

PATHFINDER is a software effort to create a flexible, modular, collaborative, and distributed environment for studying atmospheric, astrophysical, and other fluid flows in the evolving networked metacomputer environment of the 1990s. It uses existing software, such as HDF (Hierarchical Data Format), DTM (Data Transfer Mechanism), GEMPAK (General Meteorological Package), AVS, SGI Explorer, and Inventor to provide the researcher with the ability to harness the latest in desktop to teraflop computing. Software modules developed during the project are available in the public domain via anonymous FTP from the National Center for Supercomputing Applications (NCSA). The address is ftp.ncsa.uiuc.edu, and the directory is /SGI/PATHFINDER.

MAIL LOG, program summary and specifications

NASA Technical Reports Server (NTRS)

Harris, D. K.

1979-01-01

The summary and specifications to obtain the software package, MAIL LOG, developed for the Scout Project Automatic Data System, SPADS are provided. The MAIL LOG program has four modes of operation: (1) input - putting new records into the data base; (2) revise - changing or modifying existing records in the data base; (3) search - finding special records existing in the data base; and (4) archive - store or put away existing records in the data base. The output includes special printouts of records in the data base and results from the input and search modes.

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.

PubMed

Lun, Aaron T L; Smyth, Gordon K

2015-08-19

Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.

NMRbox: A Resource for Biomolecular NMR Computation.

PubMed

Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

2017-04-25

Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

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.

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

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

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

PubMed

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

2017-03-29

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

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

PubMed

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

2004-01-01

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

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

PubMed Central

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

2004-01-01

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

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.

SpecBit, DecayBit and PrecisionBit: GAMBIT modules for computing mass spectra, particle decay rates and precision observables

NASA Astrophysics Data System (ADS)

Athron, Peter; Balázs, Csaba; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Kvellestad, Anders; McKay, James; Putze, Antje; Rogan, Chris; Scott, Pat; Weniger, Christoph; White, Martin

2018-01-01

We present the GAMBIT modules SpecBit, DecayBit and PrecisionBit. Together they provide a new framework for linking publicly available spectrum generators, decay codes and other precision observable calculations in a physically and statistically consistent manner. This allows users to automatically run various combinations of existing codes as if they are a single package. The modular design allows software packages fulfilling the same role to be exchanged freely at runtime, with the results presented in a common format that can easily be passed to downstream dark matter, collider and flavour codes. These modules constitute an essential part of the broader GAMBIT framework, a major new software package for performing global fits. In this paper we present the observable calculations, data, and likelihood functions implemented in the three modules, as well as the conventions and assumptions used in interfacing them with external codes. We also present 3-BIT-HIT, a command-line utility for computing mass spectra, couplings, decays and precision observables in the MSSM, which shows how the three modules can easily be used independently of GAMBIT.

Don't give an inch!

NASA Astrophysics Data System (ADS)

Geller, Robert J.

The camera ready copy (CRC) procedures for Geophysical Research Letters are now being revised. As one of the new editors, I looked through preliminary versions of the new forms and instructions for authors. Remarkably, all of the units (for example, maximum length = 75 inches or 189.9 cm) are given in both British and metric units, despite the fact that AGU's style guide for authors (Eos, October 11, 1988) states that “all quantities must be in metric units.”When I contacted the AGU staff to ask them to eliminate the anachronistic British units they refused, claiming that “In the word-processing packages with which we are familiar all margins are given in inches. It is inconvenient for folks not to have both measurements if the software they are using for making CRC requires them to give commands in the British system.” They did not, however, cite any examples of a software package that will not also accept metric units, perhaps because none exists. All packages with which I am familiar accept both inches and metric units.

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

PubMed

DeBry, P W

2001-04-01

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

Marrying Two Existing Software Packages into an Efficient Online Tutoring Tool

ERIC Educational Resources Information Center

Byrne, Timothy

2007-01-01

Many teachers today use Learning Management Systems (LMS), several of which are open-source. Specific examples are Claroline and Moodle. However, they are not specifically designed for language learning, and hence not entirely suitable. In this article, I will compare two uses of the Claroline LMS available at Louvain-la-Neuve within the framework…

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…

General Nonlinear Ferroelectric Model v. Beta

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

Dong, Wen; Robbins, Josh

2017-03-14

The purpose of this software is to function as a generalized ferroelectric material model. The material model is designed to work with existing finite element packages by providing updated information on material properties that are nonlinear and dependent on loading history. The two major nonlinear phenomena this model captures are domain-switching and phase transformation. The software itself does not contain potentially sensitive material information and instead provides a framework for different physical phenomena observed within ferroelectric materials. The model is calibrated to a specific ferroelectric material through input parameters provided by the user.

Integrating existing software toolkits into VO system

NASA Astrophysics Data System (ADS)

Cui, Chenzhou; Zhao, Yong-Heng; Wang, Xiaoqian; Sang, Jian; Luo, Ze

2004-09-01

Virtual Observatory (VO) is a collection of interoperating data archives and software tools. Taking advantages of the latest information technologies, it aims to provide a data-intensively online research environment for astronomers all around the world. A large number of high-qualified astronomical software packages and libraries are powerful and easy of use, and have been widely used by astronomers for many years. Integrating those toolkits into the VO system is a necessary and important task for the VO developers. VO architecture greatly depends on Grid and Web services, consequently the general VO integration route is "Java Ready - Grid Ready - VO Ready". In the paper, we discuss the importance of VO integration for existing toolkits and discuss the possible solutions. We introduce two efforts in the field from China-VO project, "gImageMagick" and "Galactic abundance gradients statistical research under grid environment". We also discuss what additional work should be done to convert Grid service to VO service.

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

DTIC Science & Technology

2011-01-01

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

GlobiPack v. 1.0

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

Bartlett, Roscoe

2010-03-31

GlobiPack contains a small collection of optimization globalization algorithms. These algorithms are used by optimization and various nonlinear equation solver algorithms.Used as the line-search procedure with Newton and Quasi-Newton optimization and nonlinear equation solver methods. These are standard published 1-D line search algorithms such as are described in the book Nocedal and Wright Numerical Optimization: 2nd edition, 2006. One set of algorithms were copied and refactored from the existing open-source Trilinos package MOOCHO where the linear search code is used to globalize SQP methods. This software is generic to any mathematical optimization problem where smooth derivatives exist. There is nomore » specific connection or mention whatsoever to any specific application, period. You cannot find more general mathematical software.« less

Astronomical Software Directory Service

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

Quantitative evaluation of software packages for single-molecule localization microscopy.

PubMed

Sage, Daniel; Kirshner, Hagai; Pengo, Thomas; Stuurman, Nico; Min, Junhong; Manley, Suliana; Unser, Michael

2015-08-01

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

Browndye: A Software Package for Brownian Dynamics

PubMed Central

McCammon, J. Andrew

2010-01-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. PMID:21132109

Development of a software package for solid-angle calculations using the Monte Carlo method

NASA Astrophysics Data System (ADS)

Zhang, Jie; Chen, Xiulian; Zhang, Changsheng; Li, Gang; Xu, Jiayun; Sun, Guangai

2014-02-01

Solid-angle calculations play an important role in the absolute calibration of radioactivity measurement systems and in the determination of the activity of radioactive sources, which are often complicated. In the present paper, a software package is developed to provide a convenient tool for solid-angle calculations in nuclear physics. The proposed software calculates solid angles using the Monte Carlo method, in which a new type of variance reduction technique was integrated. The package, developed under the environment of Microsoft Foundation Classes (MFC) in Microsoft Visual C++, has a graphical user interface, in which, the visualization function is integrated in conjunction with OpenGL. One advantage of the proposed software package is that it can calculate the solid angle subtended by a detector with different geometric shapes (e.g., cylinder, square prism, regular triangular prism or regular hexagonal prism) to a point, circular or cylindrical source without any difficulty. The results obtained from the proposed software package were compared with those obtained from previous studies and calculated using Geant4. It shows that the proposed software package can produce accurate solid-angle values with a greater computation speed than Geant4.

The integration of a LANDSAT analysis capability with a geographic information system

NASA Technical Reports Server (NTRS)

Nordstrand, E. A.

1981-01-01

The integration of LANDSAT data was achieved through the development of a flexible, compatible analysis tool and using an existing data base to select the usable data from a LANDSAT analysis. The software package allows manipulation of grid cell data plus the flexibility to allow the user to include FORTRAN statements for special functions. Using this combination of capabilities the user can classify a LANDSAT image and then selectivity merge the results with other data that may exist for the study area.

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

ERIC Educational Resources Information Center

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

2008-01-01

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

International Inventory of Software Packages in the Information Field.

ERIC Educational Resources Information Center

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

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

ATLAS software configuration and build tool optimisation

NASA Astrophysics Data System (ADS)

Rybkin, Grigory; Atlas Collaboration

2014-06-01

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

Glioblastoma Segmentation: Comparison of Three Different Software Packages.

PubMed

Fyllingen, Even Hovig; Stensjøen, Anne Line; Berntsen, Erik Magnus; Solheim, Ole; Reinertsen, Ingerid

2016-01-01

To facilitate a more widespread use of volumetric tumor segmentation in clinical studies, there is an urgent need for reliable, user-friendly segmentation software. The aim of this study was therefore to compare three different software packages for semi-automatic brain tumor segmentation of glioblastoma; namely BrainVoyagerTM QX, ITK-Snap and 3D Slicer, and to make data available for future reference. Pre-operative, contrast enhanced T1-weighted 1.5 or 3 Tesla Magnetic Resonance Imaging (MRI) scans were obtained in 20 consecutive patients who underwent surgery for glioblastoma. MRI scans were segmented twice in each software package by two investigators. Intra-rater, inter-rater and between-software agreement was compared by using differences of means with 95% limits of agreement (LoA), Dice's similarity coefficients (DSC) and Hausdorff distance (HD). Time expenditure of segmentations was measured using a stopwatch. Eighteen tumors were included in the analyses. Inter-rater agreement was highest for BrainVoyager with difference of means of 0.19 mL and 95% LoA from -2.42 mL to 2.81 mL. Between-software agreement and 95% LoA were very similar for the different software packages. Intra-rater, inter-rater and between-software DSC were ≥ 0.93 in all analyses. Time expenditure was approximately 41 min per segmentation in BrainVoyager, and 18 min per segmentation in both 3D Slicer and ITK-Snap. Our main findings were that there is a high agreement within and between the software packages in terms of small intra-rater, inter-rater and between-software differences of means and high Dice's similarity coefficients. Time expenditure was highest for BrainVoyager, but all software packages were relatively time-consuming, which may limit usability in an everyday clinical setting.

Blade Vibration Measurement System

NASA Technical Reports Server (NTRS)

Platt, Michael J.

2014-01-01

The Phase I project successfully demonstrated that an advanced noncontacting stress measurement system (NSMS) could improve classification of blade vibration response in terms of mistuning and closely spaced modes. The Phase II work confirmed the microwave sensor design process, modified the sensor so it is compatible as an upgrade to existing NSMS, and improved and finalized the NSMS software. The result will be stand-alone radar/tip timing radar signal conditioning for current conventional NSMS users (as an upgrade) and new users. The hybrid system will use frequency data and relative mode vibration levels from the radar sensor to provide substantially superior capabilities over current blade-vibration measurement technology. This frequency data, coupled with a reduced number of tip timing probes, will result in a system capable of detecting complex blade vibrations that would confound traditional NSMS systems. The hardware and software package was validated on a compressor rig at Mechanical Solutions, Inc. (MSI). Finally, the hybrid radar/tip timing NSMS software package and associated sensor hardware will be installed for use in the NASA Glenn spin pit test facility.

FRACOR-software toolbox for deterministic mapping of fracture corridors in oil fields on AutoCAD platform

NASA Astrophysics Data System (ADS)

Ozkaya, Sait I.

2018-03-01

Fracture corridors are interconnected large fractures in a narrow sub vertical tabular array, which usually traverse entire reservoir vertically and extended for several hundreds of meters laterally. Fracture corridors with their huge conductivities constitute an important element of many fractured reservoirs. Unlike small diffuse fractures, actual fracture corridors must be mapped deterministically for simulation or field development purposes. Fracture corridors can be identified and quantified definitely with borehole image logs and well testing. However, there are rarely sufficient image logs or well tests, and it is necessary to utilize various fracture corridor indicators with varying degrees of reliability. Integration of data from many different sources, in turn, requires a platform with powerful editing and layering capability. Available commercial reservoir characterization software packages, with layering and editing capabilities, can be cost intensive. CAD packages are far more affordable and may easily acquire the versatility and power of commercial software packages with addition of a small software toolbox. The objective of this communication is to present FRACOR, a software toolbox which enables deterministic 2D fracture corridor mapping and modeling on AutoCAD platform. The FRACOR toolbox is written in AutoLISPand contains several independent routines to import and integrate available fracture corridor data from an oil field, and export results as text files. The resulting fracture corridor maps consists mainly of fracture corridors with different confidence levels from combination of static and dynamic data and exclusion zones where no fracture corridor can exist. The exported text file of fracture corridors from FRACOR can be imported into an upscaling programs to generate fracture grid for dual porosity simulation or used for field development and well planning.

Introducing a New Software for Geodetic Analysis

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Evaluation of copy number variation detection for a SNP array platform

PubMed Central

2014-01-01

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

The Future of Data Reduction at UKIRT

NASA Astrophysics Data System (ADS)

Economou, F.; Bridger, A.; Wright, G. S.; Rees, N. P.; Jenness, T.

The Observatory Reduction and Acquisition Control (ORAC) project is a comprehensive re-implementation of all existing instrument user interfaces and data handling software involved at the United Kingdom Infrared Telescope (UKIRT). This paper addresses the design of the data reduction part of the system. Our main aim is to provide data reduction facilities for the new generation of UKIRT instruments of a similar standard to our current software packages, which have enjoyed success because of their science-driven approach. Additionally we wish to use modern software techniques in order to produce a system that is portable, flexible and extensible so as to have modest maintenance requirements, both in the medium and the longer term.

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

PubMed

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

2014-08-01

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

Development of a Nevada Statewide Database for Safety Analyst Software

DOT National Transportation Integrated Search

2017-02-02

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

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

PubMed

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

2018-01-09

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

Computer Aided Drafting Packages for Secondary Education. Edition 2. PC DOS Compatible Programs. A MicroSIFT Quarterly Report.

ERIC Educational Resources Information Center

Pollard, Jim

This report reviews eight IBM-compatible software packages that are available to secondary schools to teach computer-aided drafting (CAD). Software packages to be considered were selected following reviews of CAD periodicals, computers in education periodicals, advertisements, and recommendations of teachers. The packages were then rated by…

QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.

PubMed

Jung, Sang-Kyu; Aleman-Meza, Boanerges; Riepe, Celeste; Zhong, Weiwei

2014-01-01

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.

Regression methods for spatially correlated data: an example using beetle attacks in a seed orchard

Treesearch

Preisler Haiganoush; Nancy G. Rappaport; David L. Wood

1997-01-01

We present a statistical procedure for studying the simultaneous effects of observed covariates and unmeasured spatial variables on responses of interest. The procedure uses regression type analyses that can be used with existing statistical software packages. An example using the rate of twig beetle attacks on Douglas-fir trees in a seed orchard illustrates the...

Structural dynamics payload loads estimates

NASA Technical Reports Server (NTRS)

Engels, R. C.

1982-01-01

Methods for the prediction of loads on large space structures are discussed. Existing approaches to the problem of loads calculation are surveyed. A full scale version of an alternate numerical integration technique to solve the response part of a load cycle is presented, and a set of short cut versions of the algorithm developed. The implementation of these techniques using the software package developed is discussed.

Vertical bone measurements from cone beam computed tomography images using different software packages.

PubMed

Vasconcelos, Taruska Ventorini; Neves, Frederico Sampaio; Moraes, Lívia Almeida Bueno; Freitas, Deborah Queiroz

2015-01-01

This article aimed at comparing the accuracy of linear measurement tools of different commercial software packages. Eight fully edentulous dry mandibles were selected for this study. Incisor, canine, premolar, first molar and second molar regions were selected. Cone beam computed tomography (CBCT) images were obtained with i-CAT Next Generation. Linear bone measurements were performed by one observer on the cross-sectional images using three different software packages: XoranCat®, OnDemand3D® and KDIS3D®, all able to assess DICOM images. In addition, 25% of the sample was reevaluated for the purpose of reproducibility. The mandibles were sectioned to obtain the gold standard for each region. Intraclass coefficients (ICC) were calculated to examine the agreement between the two periods of evaluation; the one-way analysis of variance performed with the post-hoc Dunnett test was used to compare each of the software-derived measurements with the gold standard. The ICC values were excellent for all software packages. The least difference between the software-derived measurements and the gold standard was obtained with the OnDemand3D and KDIS3D (-0.11 and -0.14 mm, respectively), and the greatest, with the XoranCAT (+0.25 mm). However, there was no statistical significant difference between the measurements obtained with the different software packages and the gold standard (p> 0.05). In conclusion, linear bone measurements were not influenced by the software package used to reconstruct the image from CBCT DICOM data.

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

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

1972-01-01

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

Stackfile Database

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Western aeronautical test range real-time graphics software package MAGIC

NASA Technical Reports Server (NTRS)

Malone, Jacqueline C.; Moore, Archie L.

1988-01-01

The master graphics interactive console (MAGIC) software package used on the Western Aeronautical Test Range (WATR) of the NASA Ames Research Center is described. MAGIC is a resident real-time research tool available to flight researchers-scientists in the NASA mission control centers of the WATR at the Dryden Flight Research Facility at Edwards, California. The hardware configuration and capabilities of the real-time software package are also discussed.

CheMentor Software System by H. A. Peoples

NASA Astrophysics Data System (ADS)

Reid, Brian P.

1997-09-01

CheMentor Software System H. A. Peoples. Computerized Learning Enhancements: http://www.ecis.com/~clehap; email: clehap@ecis.com; 1996 - 1997. CheMentor is a series of software packages for introductory-level chemistry, which includes Practice Items (I), Stoichiometry (I), Calculating Chemical Formulae, and the CheMentor Toolkit. The first three packages provide practice problems for students and various types of help to solve them; the Toolkit includes "calculators" for determining chemical quantities as well as the Practice Items (I) set of problems. The set of software packages is designed so that each individual product acts as a module of a common CheMentor program. As the name CheMentor implies, the software is designed as a "mentor" for students learning introductory chemistry concepts and problems. The typical use of the software would be by individual students (or perhaps small groups) as an adjunct to lectures. CheMentor is a HyperCard application and the modules are HyperCard stacks. The requirements to run the packages include a Macintosh computer with at least 1 MB of RAM, a hard drive with several MB of available space depending upon the packages selected (10 MB were required for all the packages reviewed here), and the Mac operating system 6.0.5 or later.

Playing with Plug-ins

ERIC Educational Resources Information Center

Thompson, Douglas E.

2013-01-01

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

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

PubMed

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

2008-01-01

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

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

PubMed Central

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

2009-01-01

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

Introduction to Software Packages. [Final Report.

ERIC Educational Resources Information Center

Frankel, Sheila, Ed.; And Others

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

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

PubMed

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

2012-08-01

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

Application of remote sensing to state and regional problems. [mississippi

NASA Technical Reports Server (NTRS)

Miller, W. F.; Powers, J. S.; Clark, J. R.; Solomon, J. L.; Williams, S. G. (Principal Investigator)

1981-01-01

The methods and procedures used, accomplishments, current status, and future plans are discussed for each of the following applications of LANDSAT in Mississippi: (1) land use planning in Lowndes County; (2) strip mine inventory and reclamation; (3) white-tailed deer habitat evaluation; (4) remote sensing data analysis support systems; (5) discrimination of unique forest habitats in potential lignite areas; (6) changes in gravel operations; and (7) determining freshwater wetlands for inventory and monitoring. The documentation of all existing software and the integration of the image analysis and data base software into a single package are now considered very high priority items.

Laboratory Connections: Review of Two Commercial Interfacing Packages.

ERIC Educational Resources Information Center

Powers, Michael H.

1989-01-01

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

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

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

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

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

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

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

2012-01-15

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

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

PubMed

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

2017-10-01

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

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

ERIC Educational Resources Information Center

Suen, Che-yin; Pok, Yang-ming

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

Issues in Defining Software Architectures in a GIS Environment

NASA Technical Reports Server (NTRS)

Acosta, Jesus; Alvorado, Lori

1997-01-01

The primary mission of the Pan-American Center for Earth and Environmental Studies (PACES) is to advance the research areas that are relevant to NASA's Mission to Planet Earth program. One of the activities at PACES is the establishment of a repository for geographical, geological and environmental information that covers various regions of Mexico and the southwest region of the U.S. and that is acquired from NASA and other sources through remote sensing, ground studies or paper-based maps. The center will be providing access of this information to other government entities in the U.S. and Mexico, and research groups from universities, national laboratories and industry. Geographical Information Systems(GIS) provide the means to manage, manipulate, analyze and display geographically referenced information that will be managed by PACES. Excellent off-the-shelf software exists for a complete GIS as well as software for storing and managing spatial databases, processing images, networking and viewing maps with layered information. This allows the user flexibility in combining systems to create a GIS or to mix these software packages with custom-built application programs. Software architectural languages provide the ability to specify the computational components and interactions among these components, an important topic in the domain of GIS because of the need to integrate numerous software packages. This paper discusses the characteristics that architectural languages address with respect to the issues relating to the data that must be communicated between software systems and components when systems interact. The paper presents a background on GIS in section 2. Section 3 gives an overview of software architecture and architectural languages. Section 4 suggests issues that may be of concern when defining the software architecture of a GIS. The last section discusses the future research effort and finishes with a summary.

Integrated optomechanical analysis and testing software development at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2013-09-01

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

Technology Assessment Software Package: Final Report.

ERIC Educational Resources Information Center

Hutinger, Patricia L.

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

The Hidden Cost of Buying a Computer.

ERIC Educational Resources Information Center

Johnson, Michael

1983-01-01

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

Software for Managing Personal Files.

ERIC Educational Resources Information Center

Lundeen, Gerald

1989-01-01

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

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering

PubMed Central

Sun, Peng; Speicher, Nora K.; Röttger, Richard; Guo, Jiong; Baumbach, Jan

2014-01-01

Abstract The explosion of the biological data has dramatically reformed today's biological research. The need to integrate and analyze high-dimensional biological data on a large scale is driving the development of novel bioinformatics approaches. Biclustering, also known as ‘simultaneous clustering’ or ‘co-clustering’, has been successfully utilized to discover local patterns in gene expression data and similar biomedical data types. Here, we contribute a new heuristic: ‘Bi-Force’. It is based on the weighted bicluster editing model, to perform biclustering on arbitrary sets of biological entities, given any kind of pairwise similarities. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol in a recent review paper from Eren et al. (2013) (A comparative analysis of biclustering algorithms for gene expressiondata. Brief. Bioinform., 14:279–292.) and compared Bi-Force against eight existing tools: FABIA, QUBIC, Cheng and Church, Plaid, BiMax, Spectral, xMOTIFs and ISA. To this end, a suite of synthetic datasets as well as nine large gene expression datasets from Gene Expression Omnibus were analyzed. All resulting biclusters were subsequently investigated by Gene Ontology enrichment analysis to evaluate their biological relevance. The distinct theoretical foundation of Bi-Force (bicluster editing) is more powerful than strict biclustering. We thus outperformed existing tools with Bi-Force at least when following the evaluation protocols from Eren et al. Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. The software as well as all used datasets are publicly available at http://biclue.mpi-inf.mpg.de. PMID:24682815

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

PubMed

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

2002-11-01

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

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

NASA Astrophysics Data System (ADS)

Gerber, Florian; Mösinger, Kaspar; Furrer, Reinhard

2017-07-01

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

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

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

Not Available

1985-01-01

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

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

PubMed Central

2011-01-01

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

A Study of Visualization for Mathematics Education

NASA Technical Reports Server (NTRS)

Daugherty, Sarah C.

2008-01-01

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

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

NASA Astrophysics Data System (ADS)

Luc̆ić, Vladan

1995-11-01

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

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

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Lawson, Charles L.

1990-01-01

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

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

PubMed Central

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

2011-01-01

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

NDAS Hardware Translation Layer Development

NASA Technical Reports Server (NTRS)

Nazaretian, Ryan N.; Holladay, Wendy T.

2011-01-01

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

Academic Web Authoring Mulitmedia Development and Course Management Tools

ERIC Educational Resources Information Center

Halloran, Margaret E.

2005-01-01

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

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

PubMed

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

2014-10-01

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

Approaches to Linked Open Data at data.oceandrilling.org

NASA Astrophysics Data System (ADS)

Fils, D.

2012-12-01

The data.oceandrilling.org web application applies Linked Open Data (LOD) patterns to expose Deep Sea Drilling Project (DSDP), Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) data. Ocean drilling data is represented in a rich range of data formats: high resolution images, file based data sets and sample based data. This richness of data types has been well met by semantic approaches and will be demonstrated. Data has been extracted from CSV, HTML and RDBMS through custom software and existing packages for loading into a SPARQL 1.1 compliant triple store. Practices have been developed to streamline the maintenance of the RDF graphs and properly expose them using LOD approaches like VoID and HTML embedded structured data. Custom and existing vocabularies are used to allow semantic relations between resources. Use of the W3c draft RDF Data Cube Vocabulary and other approaches for encoding time scales, taxonomic fossil data and other graphs will be shown. A software layer written in Google Go mediates the RDF to web pipeline. The approach used is general and can be applied to other similar environments like node.js or Python Twisted. To facilitate communication user interface software libraries such as D3 and packages such as S2S and LodLive have been used. Additionally OpenSearch API's, structured data in HTML and SPARQL endpoints provide various access methods for applications. The data.oceandrilling.org is not viewed as a web site but as an application that communicate with a range of clients. This approach helps guide the development more along software practices than along web site authoring approaches.

UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences.

PubMed

Du, Pu-Feng; Zhao, Wei; Miao, Yang-Yang; Wei, Le-Yi; Wang, Likun

2017-11-14

With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes. Every time a new sequence representation mode is developed, a new program will be needed. In this paper, we propose the UltraPse as a universal software platform for this problem. The function of the UltraPse is not only to generate various existing sequence representation modes, but also to simplify all future programming works in developing novel representation modes. The extensibility of UltraPse is particularly enhanced. It allows the users to define their own representation mode, their own physicochemical properties, or even their own types of biological sequences. Moreover, UltraPse is also the fastest software of its kind. The source code package, as well as the executables for both Linux and Windows platforms, can be downloaded from the GitHub repository.

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

PubMed

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

2018-06-01

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

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

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

A Characteristics Approach to the Evaluation of Economics Software Packages.

ERIC Educational Resources Information Center

Lumsden, Keith; Scott, Alex

1988-01-01

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

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

ERIC Educational Resources Information Center

Gabaldon, Diana J.

1984-01-01

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

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

ERIC Educational Resources Information Center

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

2017-01-01

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

Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

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

An Overview of Software for Conducting Dimensionality Assessment in Multidimensional Models

ERIC Educational Resources Information Center

Svetina, Dubravka; Levy, Roy

2012-01-01

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

Cognitive Foundry v. 3.0 (OSS)

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

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

2009-11-18

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

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

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

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

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

DTIC Science & Technology

1994-03-15

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

Using an architectural approach to integrate heterogeneous, distributed software components

NASA Technical Reports Server (NTRS)

Callahan, John R.; Purtilo, James M.

1995-01-01

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

Inferring Phylogenetic Networks Using PhyloNet.

PubMed

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

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.

Multidisciplinary Optimization for Aerospace Using Genetic Optimization

NASA Technical Reports Server (NTRS)

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

2007-01-01

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

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

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

The Package-Based Development Process in the Flight Dynamics Division

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

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

PubMed

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

2011-09-10

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

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

PubMed

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

2015-06-01

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

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

PubMed

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

2015-09-04

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

Scalable computing for evolutionary genomics.

PubMed

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

2012-01-01

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

General-Purpose Ada Software Packages

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.

1991-01-01

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

Advance Directives and Do Not Resuscitate Orders

MedlinePlus

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

Nested Cohort - R software package

Cancer.gov

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

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

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

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

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

ERIC Educational Resources Information Center

Weaver, Dave, Ed.

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

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

ERIC Educational Resources Information Center

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

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

On Designing Lightweight Threads for Substrate Software

NASA Technical Reports Server (NTRS)

Haines, Matthew

1997-01-01

Existing user-level thread packages employ a 'black box' design approach, where the implementation of the threads is hidden from the user. While this approach is often sufficient for application-level programmers, it hides critical design decisions that system-level programmers must be able to change in order to provide efficient service for high-level systems. By applying the principles of Open Implementation Analysis and Design, we construct a new user-level threads package that supports common thread abstractions and a well-defined meta-interface for altering the behavior of these abstractions. As a result, system-level programmers will have the advantages of using high-level thread abstractions without having to sacrifice performance, flexibility or portability.

BeadArray Expression Analysis Using Bioconductor

PubMed Central

Ritchie, Matthew E.; Dunning, Mark J.; Smith, Mike L.; Shi, Wei; Lynch, Andy G.

2011-01-01

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered. PMID:22144879

A Digital Control Algorithm for Magnetic Suspension Systems

NASA Technical Reports Server (NTRS)

Britton, Thomas C.

1996-01-01

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

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

NASA Astrophysics Data System (ADS)

Schwind, Michael

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

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

Salama, A.; Mikhail, M.

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

Software Library for Bruker TopSpin NMR Data Files

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

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

Software Review. Macintosh Laboratory Automation: Three Software Packages.

ERIC Educational Resources Information Center

Jezl, Barbara Ann

1990-01-01

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

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

MTpy: A Python toolbox for magnetotellurics

NASA Astrophysics Data System (ADS)

Krieger, Lars; Peacock, Jared R.

2014-11-01

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

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

PubMed

Steyn, Rachelle; Boniaszczuk, John; Geldenhuys, Theodore

2014-01-01

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

ELAS: A powerful, general purpose image processing package

NASA Technical Reports Server (NTRS)

Walters, David; Rickman, Douglas

1991-01-01

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

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

PubMed

West, Brady T

2009-09-01

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

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

PubMed

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

2009-01-01

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

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

PubMed Central

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

2009-01-01

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

Detailed Investigation and Comparison of the XCMS and MZmine 2 Chromatogram Construction and Chromatographic Peak Detection Methods for Preprocessing Mass Spectrometry Metabolomics Data.

PubMed

Myers, Owen D; Sumner, Susan J; Li, Shuzhao; Barnes, Stephen; Du, Xiuxia

2017-09-05

XCMS and MZmine 2 are two widely used software packages for preprocessing untargeted LC/MS metabolomics data. Both construct extracted ion chromatograms (EICs) and detect peaks from the EICs, the first two steps in the data preprocessing workflow. While both packages have performed admirably in peak picking, they also detect a problematic number of false positive EIC peaks and can also fail to detect real EIC peaks. The former and latter translate downstream into spurious and missing compounds and present significant limitations with most existing software packages that preprocess untargeted mass spectrometry metabolomics data. We seek to understand the specific reasons why XCMS and MZmine 2 find the false positive EIC peaks that they do and in what ways they fail to detect real compounds. We investigate differences of EIC construction methods in XCMS and MZmine 2 and find several problems in the XCMS centWave peak detection algorithm which we show are partly responsible for the false positive and false negative compound identifications. In addition, we find a problem with MZmine 2's use of centWave. We hope that a detailed understanding of the XCMS and MZmine 2 algorithms will allow users to work with them more effectively and will also help with future algorithmic development.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

PubMed

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Hysteretic Models Considering Axial-Shear-Flexure Interaction

NASA Astrophysics Data System (ADS)

Ceresa, Paola; Negrisoli, Giorgio

2017-10-01

Most of the existing numerical models implemented in finite element (FE) software, at the current state of the art, are not capable to describe, with enough reliability, the interaction between axial, shear and flexural actions under cyclic loading (e.g. seismic actions), neglecting crucial effects for predicting the nature of the collapse of reinforced concrete (RC) structural elements. Just a few existing 3D volume models or fibre beam models can lead to a quite accurate response, but they are still computationally inefficient for typical applications in earthquake engineering and also characterized by very complex formulation. Thus, discrete models with lumped plasticity hinges may be the preferred choice for modelling the hysteretic behaviour due to cyclic loading conditions, in particular with reference to its implementation in a commercial software package. These considerations lead to this research work focused on the development of a model for RC beam-column elements able to consider degradation effects and interaction between the actions under cyclic loading conditions. In order to develop a model for a general 3D discrete hinge element able to take into account the axial-shear-flexural interaction, it is necessary to provide an implementation which involves a corrector-predictor iterative scheme. Furthermore, a reliable constitutive model based on damage plasticity theory is formulated and implemented for its numerical validation. Aim of this research work is to provide the formulation of a numerical model, which will allow implementation within a FE software package for nonlinear cyclic analysis of RC structural members. The developed model accounts for stiffness degradation effect and stiffness recovery for loading reversal.

Computer Aided Instruction (CAI) for the Shipboard Nontactical ADP Program (SNAP). Interim report

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

Duncan, L.D.; Hammons, C.E.; Hume, R.

Oak Ridge National Laboratory is developing a prototype computer aided instruction package for the Navy Management Systems Support Office. This report discusses the background of the project and the progress to date including a description of the software design, problems encountered, solutions found, and recommendations. The objective of this project is to provide a prototype that will enhance training and can be used as a shipboard refresher and retraining tool. The prototype system will be installed onboard ships where Navy personnel will have ready access to the training. The subsequent testing and evaluation of the prototype could provide the basismore » for a Navy-wide effort to implement computer aided instruction. The work to date has followed a rigorous structured analysis methodology based on the Yourdon/DeMarco techniques. A set of data flow diagrams and a data dictionary are included in the appendices. The problems encountered revolve around requirements to use existing hardware, software, and programmer capabilities for development, implementation, and maintenance of the instructional software. Solutions have been developed which will allow the software to exist in the given environment and still provide advanced features not available in commercial courses.« less

Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

NASA Astrophysics Data System (ADS)

Fisher, Ward

2014-05-01

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

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

PubMed

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

2013-11-01

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

Office Computer Software: A Comprehensive Review of Software Programs.

ERIC Educational Resources Information Center

Secretary, 1992

1992-01-01

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

Cross-Matching of Very Large Catalogs

NASA Astrophysics Data System (ADS)

Martynov, M. V.; Bodryagin, D. V.

Modern astronomical catalogs and sky surveys, that contain billions of objects, belong to the "big data" data class. Existing available services have limited functionality and do not include all required and available catalogs. The software package ACrId (Astronomical Cross Identification) for cross-matching large astronomical catalogs, which uses an sphere pixelation algorithm HEALPix, ReiserFS file system and JSON-type text files for storage, has been developed at the Research Institution "Mykolaiv Astronomical Observatory".

The National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) Software: Version 3 (User’s Manual)

DTIC Science & Technology

2003-01-01

Steven Goodbred, Martin Gurtz, Evan Hornig, Clifford Hupp, Terry Maret , Michael Meador, Bruce Moring, Mark Munn, Karen Murray, James Petersen...Zappia, James Coles, Ian Waite, Thomas Abrahamsen, Elise Giddings, Robert Ourso, Mitch Harris, Terry Maret , Dorene MacCoy, Karen Murray, and...appropriate user manuals or online help: http://www.microsoft.com CAUTION: The installation package will alert you when it tries to replace an existing

ScanImage: flexible software for operating laser scanning microscopes.

PubMed

Pologruto, Thomas A; Sabatini, Bernardo L; Svoboda, Karel

2003-05-17

Laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. Although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. A major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope. We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality. We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.

User Documentation for Multiple Software Releases

NASA Technical Reports Server (NTRS)

Humphrey, R.

1982-01-01

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

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

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Hoadley, Sherwood T.

1998-01-01

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

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

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

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

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

2011-01-25

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2013 CFR

2013-10-01

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2014 CFR

2014-10-01

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2012 CFR

2012-10-01

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

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

Environmental databases and other computerized information tools

NASA Technical Reports Server (NTRS)

Clark-Ingram, Marceia

1995-01-01

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

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools.

PubMed

O'Callaghan, Sean; De Souza, David P; Isaac, Andrew; Wang, Qiao; Hodkinson, Luke; Olshansky, Moshe; Erwin, Tim; Appelbe, Bill; Tull, Dedreia L; Roessner, Ute; Bacic, Antony; McConville, Malcolm J; Likić, Vladimir A

2012-05-30

Gas chromatography-mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data tightly integrate data processing methods with graphical user interface facilitating interactive data processing. While interactive processing remains critically important in GC-MS applications, high-throughput studies increasingly dictate the need for command line tools, suitable for scripting of high-throughput, customized processing pipelines. PyMS comprises a library of functions for processing of instrument GC-MS data developed in Python. PyMS currently provides a complete set of GC-MS processing functions, including reading of standard data formats (ANDI- MS/NetCDF and JCAMP-DX), noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment by dynamic programming. A novel common ion single quantitation algorithm allows automated, accurate quantitation of GC-MS electron impact (EI) fragmentation spectra when a large number of experiments are being analyzed. PyMS implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI), allowing processing to scale on multiple CPUs in distributed computing environments. A set of specifically designed experiments was performed in-house and used to comparatively evaluate the performance of PyMS and three widely used software packages for GC-MS data processing (AMDIS, AnalyzerPro, and XCMS). PyMS is a novel software package for the processing of raw GC-MS data, particularly suitable for scripting of customized processing pipelines and for data processing in batch mode. PyMS provides limited graphical capabilities and can be used both for routine data processing and interactive/exploratory data analysis. In real-life GC-MS data processing scenarios PyMS performs as well or better than leading software packages. We demonstrate data processing scenarios simple to implement in PyMS, yet difficult to achieve with many conventional GC-MS data processing software. Automated sample processing and quantitation with PyMS can provide substantial time savings compared to more traditional interactive software systems that tightly integrate data processing with the graphical user interface.

Reviews.

ERIC Educational Resources Information Center

Radcliffe, George; And Others

1988-01-01

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

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

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

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

2012-10-19

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

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

NASA Technical Reports Server (NTRS)

Wolf, Stephen W. D.

1988-01-01

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

IPO: a tool for automated optimization of XCMS parameters.

PubMed

Libiseller, Gunnar; Dvorzak, Michaela; Kleb, Ulrike; Gander, Edgar; Eisenberg, Tobias; Madeo, Frank; Neumann, Steffen; Trausinger, Gert; Sinner, Frank; Pieber, Thomas; Magnes, Christoph

2015-04-16

Untargeted metabolomics generates a huge amount of data. Software packages for automated data processing are crucial to successfully process these data. A variety of such software packages exist, but the outcome of data processing strongly depends on algorithm parameter settings. If they are not carefully chosen, suboptimal parameter settings can easily lead to biased results. Therefore, parameter settings also require optimization. Several parameter optimization approaches have already been proposed, but a software package for parameter optimization which is free of intricate experimental labeling steps, fast and widely applicable is still missing. We implemented the software package IPO ('Isotopologue Parameter Optimization') which is fast and free of labeling steps, and applicable to data from different kinds of samples and data from different methods of liquid chromatography - high resolution mass spectrometry and data from different instruments. IPO optimizes XCMS peak picking parameters by using natural, stable (13)C isotopic peaks to calculate a peak picking score. Retention time correction is optimized by minimizing relative retention time differences within peak groups. Grouping parameters are optimized by maximizing the number of peak groups that show one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiments, and the resulting scores are evaluated using response surface models. IPO was tested on three different data sets, each consisting of a training set and test set. IPO resulted in an increase of reliable groups (146% - 361%), a decrease of non-reliable groups (3% - 8%) and a decrease of the retention time deviation to one third. IPO was successfully applied to data derived from liquid chromatography coupled to high resolution mass spectrometry from three studies with different sample types and different chromatographic methods and devices. We were also able to show the potential of IPO to increase the reliability of metabolomics data. The source code is implemented in R, tested on Linux and Windows and it is freely available for download at https://github.com/glibiseller/IPO . The training sets and test sets can be downloaded from https://health.joanneum.at/IPO .

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

USGS Publications Warehouse

Ellefsen, Karl J.

2017-06-27

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2011 CFR

2011-10-01

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

Scout 2008 Version 1.0 User Guide

EPA Science Inventory

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

INTERFACING SAS TO ORACLE IN THE UNIX ENVIRONMENT

EPA Science Inventory

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

Optimisation of cascaded Yb fiber amplifier chains using numerical-modelling

NASA Astrophysics Data System (ADS)

He, F.; Price, J. H.; Vu, K. T.; Malinowski, A.; Sahu, J. K.; Richardson, D. J.

2006-12-01

We show that it is possible to adapt existing software packages developed originally for modeling telecommunication devices and systems to reliably predict and optimize the performance of high-power Ytterbium-doped fiber amplifier and laser systems. The ready availability of a flexible, user-friendly design tool should be of considerable practical interest to scientists and engineers working with this important new laser technology since Ytterbium amplifier and amplifier cascades are often difficult to optimize experimentally due to the three-level nature of the Ytterbium laser transition. As examples of the utility and accuracy of the software, as well as the complexity of the systems and amplifier properties that can be successfully modeled, we present a comparison of experimental and theoretical results for individual core and cladding pumped amplifiers, and also for an ultra-short pulse four-stage amplifier system optimized both to provide a broad gain bandwidth and to minimize nonlinear effects. We also show how high energy 100 ns pulses with complex user definable temporal profiles can be created in a gain-saturated amplifier by suitable pre-shaping of the low-energy input pulses. Furthermore, with appropriate modifications the same software package can be applied to fiber amplifiers based on other rare-earth elements and glass hosts.

Envision: An interactive system for the management and visualization of large geophysical data sets

NASA Technical Reports Server (NTRS)

Searight, K. R.; Wojtowicz, D. P.; Walsh, J. E.; Pathi, S.; Bowman, K. P.; Wilhelmson, R. B.

1995-01-01

Envision is a software project at the University of Illinois and Texas A&M, funded by NASA's Applied Information Systems Research Project. It provides researchers in the geophysical sciences convenient ways to manage, browse, and visualize large observed or model data sets. Envision integrates data management, analysis, and visualization of geophysical data in an interactive environment. It employs commonly used standards in data formats, operating systems, networking, and graphics. It also attempts, wherever possible, to integrate with existing scientific visualization and analysis software. Envision has an easy-to-use graphical interface, distributed process components, and an extensible design. It is a public domain package, freely available to the scientific community.

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

DTIC Science & Technology

2014-04-30

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

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

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

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

PIV Data Validation Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

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

Formation of Minor Phases in a Nickel-Based Disk Superalloy

NASA Technical Reports Server (NTRS)

Gabb, T. P.; Garg, A.; Miller, D. R.; Sudbrack, C. K.; Hull, D. R.; Johnson, D.; Rogers, R. B.; Gayda, J.; Semiatin, S. L.

2012-01-01

The minor phases of powder metallurgy disk superalloy LSHR were studied. Samples were consistently heat treated at three different temperatures for long times to approximate equilibrium. Additional heat treatments were also performed for shorter times, to then assess non-equilibrium conditions. Minor phases including MC carbides, M23C6 carbides, M3B2 borides, and sigma were identified. Their transformation temperatures, lattice parameters, compositions, average sizes and total area fractions were determined, and compared to estimates of an existing phase prediction software package. Parameters measured at equilibrium sometimes agreed reasonably well with software model estimates, with potential for further improvements. Results for shorter times representing non-equilibrium indicated significant potential for further extension of the software to such conditions, which are more commonly observed during heat treatments and service at high temperatures for disk applications.

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

PubMed

Vasilyev, K N

2013-01-01

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

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

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

PubMed

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

2014-01-01

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

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

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

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering.

PubMed

Sun, Peng; Speicher, Nora K; Röttger, Richard; Guo, Jiong; Baumbach, Jan

2014-05-01

The explosion of the biological data has dramatically reformed today's biological research. The need to integrate and analyze high-dimensional biological data on a large scale is driving the development of novel bioinformatics approaches. Biclustering, also known as 'simultaneous clustering' or 'co-clustering', has been successfully utilized to discover local patterns in gene expression data and similar biomedical data types. Here, we contribute a new heuristic: 'Bi-Force'. It is based on the weighted bicluster editing model, to perform biclustering on arbitrary sets of biological entities, given any kind of pairwise similarities. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol in a recent review paper from Eren et al. (2013) (A comparative analysis of biclustering algorithms for gene expressiondata. Brief. Bioinform., 14:279-292.) and compared Bi-Force against eight existing tools: FABIA, QUBIC, Cheng and Church, Plaid, BiMax, Spectral, xMOTIFs and ISA. To this end, a suite of synthetic datasets as well as nine large gene expression datasets from Gene Expression Omnibus were analyzed. All resulting biclusters were subsequently investigated by Gene Ontology enrichment analysis to evaluate their biological relevance. The distinct theoretical foundation of Bi-Force (bicluster editing) is more powerful than strict biclustering. We thus outperformed existing tools with Bi-Force at least when following the evaluation protocols from Eren et al. Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. The software as well as all used datasets are publicly available at http://biclue.mpi-inf.mpg.de. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Scientific Software - the role of best practices and recommendations

NASA Astrophysics Data System (ADS)

Fritzsch, Bernadette; Bernstein, Erik; Castell, Wolfgang zu; Diesmann, Markus; Haas, Holger; Hammitzsch, Martin; Konrad, Uwe; Lähnemann, David; McHardy, Alice; Pampel, Heinz; Scheliga, Kaja; Schreiber, Andreas; Steglich, Dirk

2017-04-01

In Geosciences - like in most other communities - scientific work strongly depends on software. For big data analysis, existing (closed or open source) program packages are often mixed with newly developed codes. Different versions of software components and varying configurations can influence the result of data analysis. This often makes reproducibility of results and reuse of codes very difficult. Policies for publication and documentation of used and newly developed software, along with best practices, can help tackle this problem. Within the Helmholtz Association a Task Group "Access to and Re-use of scientific software" was implemented by the Open Science Working Group in 2016. The aim of the Task Group is to foster the discussion about scientific software in the Open Science context and to formulate recommendations for the production and publication of scientific software, ensuring open access to it. As a first step, a workshop gathered interested scientists from institutions across Germany. The workshop brought together various existing initiatives from different scientific communities to analyse current problems, share established best practices and come up with possible solutions. The subjects in the working groups covered a broad range of themes, including technical infrastructures, standards and quality assurance, citation of software and reproducibility. Initial recommendations are presented and discussed in the talk. They are the foundation for further discussions in the Helmholtz Association and the Priority Initiative "Digital Information" of the Alliance of Science Organisations in Germany. The talk aims to inform about the activities and to link with other initiatives on the national or international level.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Orbit determination for ISRO satellite missions

NASA Astrophysics Data System (ADS)

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

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

Prototyping with Data Dictionaries for Requirements Analysis.

DTIC Science & Technology

1985-03-01

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

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

NASA Technical Reports Server (NTRS)

Doig, G. A.

1980-01-01

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

The Shock and Vibration Digest. Volume 17, Number 4

DTIC Science & Technology

1985-04-01

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

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

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

Grama, Ananth

2013-12-18

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

Developing a Virtual Physics World

ERIC Educational Resources Information Center

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

2012-01-01

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

Teaching Science and Mathematics Subjects Using the Excel Spreadsheet Package

ERIC Educational Resources Information Center

Ibrahim, Dogan

2009-01-01

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

Description of the IV + V System Software Package.

ERIC Educational Resources Information Center

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

1984-01-01

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

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

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

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

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

PubMed

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

2017-12-01

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

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.

Human Motion Tracking and Glove-Based User Interfaces for Virtual Environments in ANVIL

NASA Technical Reports Server (NTRS)

Dumas, Joseph D., II

2002-01-01

The Army/NASA Virtual Innovations Laboratory (ANVIL) at Marshall Space Flight Center (MSFC) provides an environment where engineers and other personnel can investigate novel applications of computer simulation and Virtual Reality (VR) technologies. Among the many hardware and software resources in ANVIL are several high-performance Silicon Graphics computer systems and a number of commercial software packages, such as Division MockUp by Parametric Technology Corporation (PTC) and Jack by Unigraphics Solutions, Inc. These hardware and software platforms are used in conjunction with various VR peripheral I/O (input / output) devices, CAD (computer aided design) models, etc. to support the objectives of the MSFC Engineering Systems Department/Systems Engineering Support Group (ED42) by studying engineering designs, chiefly from the standpoint of human factors and ergonomics. One of the more time-consuming tasks facing ANVIL personnel involves the testing and evaluation of peripheral I/O devices and the integration of new devices with existing hardware and software platforms. Another important challenge is the development of innovative user interfaces to allow efficient, intuitive interaction between simulation users and the virtual environments they are investigating. As part of his Summer Faculty Fellowship, the author was tasked with verifying the operation of some recently acquired peripheral interface devices and developing new, easy-to-use interfaces that could be used with existing VR hardware and software to better support ANVIL projects.

PyPedal, an open source software package for pedigree analysis

USDA-ARS?s Scientific Manuscript database

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

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

ERIC Educational Resources Information Center

Engelhardt, Larry

2012-01-01

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

A Software Development Approach for Computer Assisted Language Learning

ERIC Educational Resources Information Center

Cushion, Steve

2005-01-01

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

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

ERIC Educational Resources Information Center

Li, Jian; Lomax, Richard G.

2011-01-01

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

A Multi-User Microcomputer System for Small Libraries.

ERIC Educational Resources Information Center

Leggate, Peter

1988-01-01

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

Microcomputer Software Programs for Vocational Education.

ERIC Educational Resources Information Center

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

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

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

ERIC Educational Resources Information Center

Happer, Stephanie K.

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

Computerised data reduction.

PubMed

Datson, D J; Carter, N G

1988-10-01

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

Propensity Score Analysis in R: A Software Review

ERIC Educational Resources Information Center

Keller, Bryan; Tipton, Elizabeth

2016-01-01

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

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.

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

Advanced fingerprint verification software

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Salvus: A flexible open-source package for waveform modelling and inversion from laboratory to global scales

NASA Astrophysics Data System (ADS)

Afanasiev, M.; Boehm, C.; van Driel, M.; Krischer, L.; May, D.; Rietmann, M.; Fichtner, A.

2016-12-01

Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Based on a high order finite (spectral) element discretization, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and discuss some of the extensible design points.

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

PubMed

Thomas, Philipp; Matuschek, Hannes; Grima, Ramon

2012-01-01

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

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

PubMed Central

Grima, Ramon

2012-01-01

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

Salvus: A flexible high-performance and open-source package for waveform modelling and inversion from laboratory to global scales

NASA Astrophysics Data System (ADS)

Afanasiev, Michael; Boehm, Christian; van Driel, Martin; Krischer, Lion; May, Dave; Rietmann, Max; Fichtner, Andreas

2017-04-01

Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Currently based on an abstract implementation of high order finite (spectral) elements, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. viscoelastic, coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ template mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and discuss some of the extensible design points.

Development and use of mathematical models and software frameworks for integrated analysis of agricultural systems and associated water use impacts

USGS Publications Warehouse

Fowler, K. R.; Jenkins, E.W.; Parno, M.; Chrispell, J.C.; Colón, A. I.; Hanson, Randall T.

2016-01-01

The development of appropriate water management strategies requires, in part, a methodology for quantifying and evaluating the impact of water policy decisions on regional stakeholders. In this work, we describe the framework we are developing to enhance the body of resources available to policy makers, farmers, and other community members in their e orts to understand, quantify, and assess the often competing objectives water consumers have with respect to usage. The foundation for the framework is the construction of a simulation-based optimization software tool using two existing software packages. In particular, we couple a robust optimization software suite (DAKOTA) with the USGS MF-OWHM water management simulation tool to provide a flexible software environment that will enable the evaluation of one or multiple (possibly competing) user-defined (or stakeholder) objectives. We introduce the individual software components and outline the communication strategy we defined for the coupled development. We present numerical results for case studies related to crop portfolio management with several defined objectives. The objectives are not optimally satisfied for any single user class, demonstrating the capability of the software tool to aid in the evaluation of a variety of competing interests.

Report: Scientific Software.

ERIC Educational Resources Information Center

Borman, Stuart A.

1985-01-01

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

SeisCode: A seismological software repository for discovery and collaboration

NASA Astrophysics Data System (ADS)

Trabant, C.; Reyes, C. G.; Clark, A.; Karstens, R.

2012-12-01

SeisCode is a community repository for software used in seismological and related fields. The repository is intended to increase discoverability of such software and to provide a long-term home for software projects. Other places exist where seismological software may be found, but none meet the requirements necessary for an always current, easy to search, well documented, and citable resource for projects. Organizations such as IRIS, ORFEUS, and the USGS have websites with lists of available or contributed seismological software. Since the authors themselves do often not maintain these lists, the documentation often consists of a sentence or paragraph, and the available software may be outdated. Repositories such as GoogleCode and SourceForge, which are directly maintained by the authors, provide version control and issue tracking but do not provide a unified way of locating geophysical software scattered in and among countless unrelated projects. Additionally, projects are hosted at language-specific sites such as Mathworks and PyPI, in FTP directories, and in websites strewn across the Web. Search engines are only partially effective discovery tools, as the desired software is often hidden deep within the results. SeisCode provides software authors a place to present their software, codes, scripts, tutorials, and examples to the seismological community. Authors can choose their own level of involvement. At one end of the spectrum, the author might simply create a web page that points to an existing site. At the other extreme, an author may choose to leverage the many tools provided by SeisCode, such as a source code management tool with integrated issue tracking, forums, news feeds, downloads, wikis, and more. For software development projects with multiple authors, SeisCode can also be used as a central site for collaboration. SeisCode provides the community with an easy way to discover software, while providing authors a way to build a community around their software packages. IRIS invites the seismological community to browse and to submit projects to https://seiscode.iris.washington.edu/

Open Marketplace for Simulation Software on the Basis of a Web Platform

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-02-01

The focus in development of a new generation of middleware shifts from the global grid systems to building convenient and efficient web platforms for remote access to individual computing resources. Further line of their development, suggested in this work, is related not only with the quantitative increase in their number and with the expansion of scientific, engineering, and manufacturing areas in which they are used, but also with improved technology for remote deployment of application software on the resources interacting with the web platforms. Currently, the services for providers of application software in the context of scientific-oriented web platforms is not developed enough. The proposed in this work new web platforms of application software market should have all the features of the existing web platforms for submissions of jobs to remote resources plus the provision of specific web services for interaction on market principles between the providers and consumers of application packages. The suggested approach will be approved on the example of simulation applications in the field of nonlinear optics.

Numerical simulation of deformation and failure processes of a complex technical object under impact loading

NASA Astrophysics Data System (ADS)

Kraus, E. I.; Shabalin, I. I.; Shabalin, T. I.

2018-04-01

The main points of development of numerical tools for simulation of deformation and failure of complex technical objects under nonstationary conditions of extreme loading are presented. The possibility of extending the dynamic method for construction of difference grids to the 3D case is shown. A 3D realization of discrete-continuum approach to the deformation and failure of complex technical objects is carried out. The efficiency of the existing software package for 3D modelling is shown.

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

Teaching NMR spectra analysis with nmr.cheminfo.org.

PubMed

Patiny, Luc; Bolaños, Alejandro; Castillo, Andrés M; Bernal, Andrés; Wist, Julien

2018-06-01

Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems. Copyright © 2018 John Wiley & Sons, Ltd.

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

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

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

2016-11-02

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

Space vehicle onboard command encoder

NASA Technical Reports Server (NTRS)

1975-01-01

A flexible onboard encoder system was designed for the space shuttle. The following areas were covered: (1) implementation of the encoder design into hardware to demonstrate the various encoding algorithms/code formats, (2) modulation techniques in a single hardware package to maintain comparable reliability and link integrity of the existing link systems and to integrate the various techniques into a single design using current technology. The primary function of the command encoder is to accept input commands, generated either locally onboard the space shuttle or remotely from the ground, format and encode the commands in accordance with the payload input requirements and appropriately modulate a subcarrier for transmission by the baseband RF modulator. The following information was provided: command encoder system design, brassboard hardware design, test set hardware and system packaging, and software.

Evolution of the Space Shuttle Primary Avionics Software and Avionics for Shuttle Derived Launch Vehicles

NASA Technical Reports Server (NTRS)

Ferguson, Roscoe C.

2011-01-01

As a result of recommendation from the Augustine Panel, the direction for Human Space Flight has been altered from the original plan referred to as Constellation. NASA s Human Exploration Framework Team (HEFT) proposes the use of a Shuttle Derived Heavy Lift Launch Vehicle (SDLV) and an Orion derived spacecraft (salvaged from Constellation) to support a new flexible direction for space exploration. The SDLV must be developed within an environment of a constrained budget and a preferred fast development schedule. Thus, it has been proposed to utilize existing assets from the Shuttle Program to speed development at a lower cost. These existing assets should not only include structures such as external tanks or solid rockets, but also the Flight Software which has traditionally been a "long pole" in new development efforts. The avionics and software for the Space Shuttle was primarily developed in the 70 s and considered state of the art for that time. As one may argue that the existing avionics and flight software may be too outdated to support the new SDLV effort, this is a fallacy if they can be evolved over time into a "modern avionics" platform. The technology may be outdated, but the avionics concepts and flight software algorithms are not. The reuse of existing avionics and software also allows for the reuse of development, verification, and operations facilities. The keyword is evolve in that these assets can support the fast development of such a vehicle, but then be gradually evolved over time towards more modern platforms as budget and schedule permits. The "gold" of the flight software is the "control loop" algorithms of the vehicle. This is the Guidance, Navigation, and Control (GNC) software algorithms. This software is typically the most expensive to develop, test, and verify. Thus, the approach is to preserve the GNC flight software, while first evolving the supporting software (such as Command and Data Handling, Caution and Warning, Telemetry, etc.). This can be accomplished by gradually removing the "support software" from the legacy flight software leaving only the GNC algorithms. The "support software" could be re-developed for modern platforms, while leaving the GNC algorithms to execute on technology compatible with the legacy system. It is also possible to package the GNC algorithms into an emulated version of the original computer (via Field Programmable Gate Arrays or FPGAs), thus becoming a "GNC on a Chip" solution where it could live forever to be embedded in modern avionics platforms.

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Use of symbolic computation in robotics education

NASA Technical Reports Server (NTRS)

Vira, Naren; Tunstel, Edward

1992-01-01

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

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

PubMed

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

2015-10-15

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

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

PubMed Central

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

2015-01-01

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

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

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

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

Extreme Ultraviolet Imaging Telescope (EIT)

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

A User-Friendly Software Package for HIFU Simulation

NASA Astrophysics Data System (ADS)

Soneson, Joshua E.

2009-04-01

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

OCEAN-PC and a distributed network for ocean data

NASA Technical Reports Server (NTRS)

Mclain, Douglas R.

1992-01-01

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

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.

MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

PubMed

Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

2017-08-15

Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. 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

Software package for modeling spin-orbit motion in storage rings

NASA Astrophysics Data System (ADS)

Zyuzin, D. V.

2015-12-01

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

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

PubMed

Fuglsang, Anders; Schütz, Helmut; Labes, Detlew

2015-03-01

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

Painting a picture across the landscape with ModelMap

Treesearch

Brian Cooke; Elizabeth Freeman; Gretchen Moisen; Tracey Frescino

2017-01-01

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

"FluSpec": A Simulated Experiment in Fluorescence Spectroscopy

ERIC Educational Resources Information Center

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

2014-01-01

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

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

ERIC Educational Resources Information Center

Yavuz, Guler; Hambleton, Ronald K.

2017-01-01

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

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

ERIC Educational Resources Information Center

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

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

Virginia Transit Performance Evaluation Package (VATPEP).

DOT National Transportation Integrated Search

1987-01-01

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

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

NASA Technical Reports Server (NTRS)

Jumper, Judith K.

1994-01-01

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

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

PubMed

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

2009-11-01

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

Space-Shuttle Emulator Software

NASA Technical Reports Server (NTRS)

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

Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-09-01

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

Back to the future: An online OSCE Management Information System for nursing OSCEs.

PubMed

Meskell, Pauline; Burke, Eimear; Kropmans, Thomas J B; Byrne, Evelyn; Setyonugroho, Winny; Kennedy, Kieran M

2015-11-01

The Objective Structured Clinical Examination (OSCE) is an established tool in the repertoire of clinical assessment methods in nurse education. The use of OSCEs facilitates the assessment of psychomotor skills as well as knowledge and attitudes. Identified benefits of OSCE assessment include development of students' confidence in their clinical skills and preparation for clinical practice. However, a number of challenges exist with the traditional paper methodology, including documentation errors and inadequate student feedback. To explore electronic OSCE delivery and evaluate the benefits of using an electronic OSCE management system. To explore assessors' perceptions of and attitudes to the computer based package. This study was conducted using electronic software in the management of a four station OSCE assessment with a cohort of first year undergraduate nursing students delivered over two consecutive years (n=203) in one higher education institution in Ireland. A quantitative descriptive survey methodology was used to obtain the views of the assessors on the process and outcome of using the software. OSCE documentation was converted to electronic format. Assessors were trained in the use of the OSCE management software package and laptops were procured to facilitate electronic management of the OSCE assessment. Following the OSCE assessment, assessors were invited to evaluate the experience. Electronic software facilitated the storage and analysis of overall group and individual results thereby offering considerable time savings. Submission of electronic forms was allowed only when fully completed thus removing the potential for missing data. The feedback facility allowed the student to receive timely evaluation on their performance and to benchmark their performance against the class. Assessors' satisfaction with the software was high. Analysis of assessment results can highlight issues around internal consistency being moderate and examiners variability. Regression analysis increases fairness of result calculations. Copyright © 2015. Published by Elsevier Ltd.

Fullrmc, a rigid body Reverse Monte Carlo modeling package enabled with machine learning and artificial intelligence.

PubMed

Aoun, Bachir

2016-05-05

A new Reverse Monte Carlo (RMC) package "fullrmc" for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group. © 2016 Wiley Periodicals, Inc.

DoE Phase II SBIR: Spectrally-Assisted Vehicle Tracking

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

Villeneuve, Pierre V.

2013-02-28

The goal of this Phase II SBIR is to develop a prototype software package to demonstrate spectrally-aided vehicle tracking performance. The primary application is to demonstrate improved target vehicle tracking performance in complex environments where traditional spatial tracker systems may show reduced performance. Example scenarios in Figure 1 include a) the target vehicle obscured by a large structure for an extended period of time, or b), the target engaging in extreme maneuvers amongst other civilian vehicles. The target information derived from spatial processing is unable to differentiate between the green versus the red vehicle. Spectral signature exploitation enables comparison ofmore » new candidate targets with existing track signatures. The ambiguity in this confusing scenario is resolved by folding spectral analysis results into each target nomination and association processes. Figure 3 shows a number of example spectral signatures from a variety of natural and man-made materials. The work performed over the two-year effort was divided into three general areas: algorithm refinement, software prototype development, and prototype performance demonstration. The tasks performed under this Phase II to accomplish the program goals were as follows: 1. Acquire relevant vehicle target datasets to support prototype. 2. Refine algorithms for target spectral feature exploitation. 3. Implement a prototype multi-hypothesis target tracking software package. 4. Demonstrate and quantify tracking performance using relevant data.« less

Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

DOE PAGES

Aoun, Bachir

2016-01-22

Here, a new Reverse Monte Carlo (RMC) package ‘fullrmc’ for atomic or rigid body and molecular, amorphous or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython ,C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with amore » set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modelling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. Also fullrmc provides a unique way with almost no additional computational cost to recur a group’s selection, allowing the system to go out of local minimas by refining a group’s position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.« less

Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

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

Aoun, Bachir

Here, a new Reverse Monte Carlo (RMC) package ‘fullrmc’ for atomic or rigid body and molecular, amorphous or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython ,C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with amore » set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modelling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. Also fullrmc provides a unique way with almost no additional computational cost to recur a group’s selection, allowing the system to go out of local minimas by refining a group’s position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.« less

Design Considerations of a Virtual Laboratory for Advanced X-ray Sources

NASA Astrophysics Data System (ADS)

Luginsland, J. W.; Frese, M. H.; Frese, S. D.; Watrous, J. J.; Heileman, G. L.

2004-11-01

The field of scientific computation has greatly advanced in the last few years, resulting in the ability to perform complex computer simulations that can predict the performance of real-world experiments in a number of fields of study. Among the forces driving this new computational capability is the advent of parallel algorithms, allowing calculations in three-dimensional space with realistic time scales. Electromagnetic radiation sources driven by high-voltage, high-current electron beams offer an area to further push the state-of-the-art in high fidelity, first-principles simulation tools. The physics of these x-ray sources combine kinetic plasma physics (electron beams) with dense fluid-like plasma physics (anode plasmas) and x-ray generation (bremsstrahlung). There are a number of mature techniques and software packages for dealing with the individual aspects of these sources, such as Particle-In-Cell (PIC), Magneto-Hydrodynamics (MHD), and radiation transport codes. The current effort is focused on developing an object-oriented software environment using the Rational© Unified Process and the Unified Modeling Language (UML) to provide a framework where multiple 3D parallel physics packages, such as a PIC code (ICEPIC), a MHD code (MACH), and a x-ray transport code (ITS) can co-exist in a system-of-systems approach to modeling advanced x-ray sources. Initial software design and assessments of the various physics algorithms' fidelity will be presented.

Towards a mature measurement environment: Creating a software engineering research environment

NASA Technical Reports Server (NTRS)

Basili, Victor R.

1990-01-01

Software engineering researchers are building tools, defining methods, and models; however, there are problems with the nature and style of the research. The research is typically bottom-up, done in isolation so the pieces cannot be easily logically or physically integrated. A great deal of the research is essentially the packaging of a particular piece of technology with little indication of how the work would be integrated with other prices of research. The research is not aimed at solving the real problems of software engineering, i.e., the development and maintenance of quality systems in a productive manner. The research results are not evaluated or analyzed via experimentation or refined and tailored to the application environment. Thus, it cannot be easily transferred into practice. Because of these limitations we have not been able to understand the components of the discipline as a coherent whole and the relationships between various models of the process and product. What is needed is a top down experimental, evolutionary framework in which research can be focused, logically and physically integrated to produce quality software productively, and evaluated and tailored to the application environment. This implies the need for experimentation, which in turn implies the need for a laboratory that is associated with the artifact we are studying. This laboratory can only exist in an environment where software is being built, i.e., as part of a real software development and maintenance organization. Thus, we propose that Software Engineering Laboratory (SEL) type activities exist in all organizations to support software engineering research. We describe the SEL from a researcher's point of view, and discuss the corporate and government benefits of the SEL. The discussion focuses on the benefits to the research community.

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

USGS Publications Warehouse

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

2006-01-01

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

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

PubMed

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

2016-12-23

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

A LEAN approach toward automated analysis and data processing of polymers using proton NMR spectroscopy.

PubMed

de Brouwer, Hans; Stegeman, Gerrit

2011-02-01

To maximize utilization of expensive laboratory instruments and to make most effective use of skilled human resources, the entire chain of data processing, calculation, and reporting that is needed to transform raw NMR data into meaningful results was automated. The LEAN process improvement tools were used to identify non-value-added steps in the existing process. These steps were eliminated using an in-house developed software package, which allowed us to meet the key requirement of improving quality and reliability compared with the existing process while freeing up valuable human resources and increasing productivity. Reliability and quality were improved by the consistent data treatment as performed by the software and the uniform administration of results. Automating a single NMR spectrophotometer led to a reduction in operator time of 35%, doubling of the annual sample throughput from 1400 to 2800, and reducing the turn around time from 6 days to less than 2. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

PubMed

Burdick, David B; Cavnor, Chris C; Handcock, Jeremy; Killcoyne, Sarah; Lin, Jake; Marzolf, Bruz; Ramsey, Stephen A; Rovira, Hector; Bressler, Ryan; Shmulevich, Ilya; Boyle, John

2010-07-14

High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

PubMed Central

2010-01-01

Background High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Results Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. Conclusion The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services. PMID:20630057

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

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

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

1991-07-01

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

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

PubMed

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

2015-06-01

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

Flight simulation software at NASA Dryden Flight Research Center

NASA Technical Reports Server (NTRS)

Norlin, Ken A.

1995-01-01

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

The Ettention software package.

PubMed

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

2016-02-01

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

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

PubMed

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

2017-06-05

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

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

NASA Astrophysics Data System (ADS)

Pandey, Palak; Kunte, Pravin D.

2016-10-01

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

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools

PubMed Central

2012-01-01

Background Gas chromatography–mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data tightly integrate data processing methods with graphical user interface facilitating interactive data processing. While interactive processing remains critically important in GC-MS applications, high-throughput studies increasingly dictate the need for command line tools, suitable for scripting of high-throughput, customized processing pipelines. Results PyMS comprises a library of functions for processing of instrument GC-MS data developed in Python. PyMS currently provides a complete set of GC-MS processing functions, including reading of standard data formats (ANDI- MS/NetCDF and JCAMP-DX), noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment by dynamic programming. A novel common ion single quantitation algorithm allows automated, accurate quantitation of GC-MS electron impact (EI) fragmentation spectra when a large number of experiments are being analyzed. PyMS implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI), allowing processing to scale on multiple CPUs in distributed computing environments. A set of specifically designed experiments was performed in-house and used to comparatively evaluate the performance of PyMS and three widely used software packages for GC-MS data processing (AMDIS, AnalyzerPro, and XCMS). Conclusions PyMS is a novel software package for the processing of raw GC-MS data, particularly suitable for scripting of customized processing pipelines and for data processing in batch mode. PyMS provides limited graphical capabilities and can be used both for routine data processing and interactive/exploratory data analysis. In real-life GC-MS data processing scenarios PyMS performs as well or better than leading software packages. We demonstrate data processing scenarios simple to implement in PyMS, yet difficult to achieve with many conventional GC-MS data processing software. Automated sample processing and quantitation with PyMS can provide substantial time savings compared to more traditional interactive software systems that tightly integrate data processing with the graphical user interface. PMID:22647087

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

NASA Technical Reports Server (NTRS)

Schlosser, E. H.

1980-01-01

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

Identifying patient safety problems associated with information technology in general practice: an analysis of incident reports.

PubMed

Magrabi, Farah; Liaw, Siaw Teng; Arachi, Diana; Runciman, William; Coiera, Enrico; Kidd, Michael R

2016-11-01

To identify the categories of problems with information technology (IT), which affect patient safety in general practice. General practitioners (GPs) reported incidents online or by telephone between May 2012 and November 2013. Incidents were reviewed against an existing classification for problems associated with IT and the clinical process impacted. 87 GPs across Australia. Types of problems, consequences and clinical processes. GPs reported 90 incidents involving IT which had an observable impact on the delivery of care, including actual patient harm as well as near miss events. Practice systems and medications were the most affected clinical processes. Problems with IT disrupted clinical workflow, wasted time and caused frustration. Issues with user interfaces, routine updates to software packages and drug databases, and the migration of records from one package to another generated clinical errors that were unique to IT; some could affect many patients at once. Human factors issues gave rise to some errors that have always existed with paper records but are more likely to occur and cause harm with IT. Such errors were linked to slips in concentration, multitasking, distractions and interruptions. Problems with patient identification and hybrid records generated errors that were in principle no different to paper records. Problems associated with IT include perennial risks with paper records, but additional disruptions in workflow and hazards for patients unique to IT, occasionally affecting multiple patients. Surveillance for such hazards may have general utility, but particularly in the context of migrating historical records to new systems and software updates to existing systems. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

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

PubMed

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

2013-12-24

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

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

ERIC Educational Resources Information Center

McConkie, George W.; And Others

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

Overview of Current Activities in Combustion Instability

DTIC Science & Technology

2015-10-02

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

Sigma 2 Graphic Display Software Program Description

NASA Technical Reports Server (NTRS)

Johnson, B. T.

1973-01-01

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

Mail LOG: Program operating instructions

NASA Technical Reports Server (NTRS)

Harris, D. K.

1979-01-01

The operating instructions for the software package, MAIL LOG, developed for the Scout Project Automatic Data System, SPADS, are provided. The program is written in FORTRAN for the PRIME 300 computer system. The MAIL LOG program has the following four modes of operation: (1) INPUT - putting new records into the data base (2) REVISE - changing or modifying existing records in the data base (3) SEARCH - finding special records existing in the data base (4) ARCHIVE - store or put away existing records in the data base. The output includes special printouts of records in the data base and results from the INPUT and SEARCH modes. The MAIL LOG data base consists of three main subfiles: Incoming and outgoing mail correspondence; Design Information Releases and Releases and Reports; and Drawings and Engineering orders.

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

ERIC Educational Resources Information Center

Snell, Meggan; Yatsenko, Olga

2002-01-01

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

Object-oriented design of medical imaging software.

PubMed

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

1994-01-01

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

Optimization of large matrix calculations for execution on the Cray X-MP vector supercomputer

NASA Technical Reports Server (NTRS)

Hornfeck, William A.

1988-01-01

A considerable volume of large computational computer codes were developed for NASA over the past twenty-five years. This code represents algorithms developed for machines of earlier generation. With the emergence of the vector supercomputer as a viable, commercially available machine, an opportunity exists to evaluate optimization strategies to improve the efficiency of existing software. This result is primarily due to architectural differences in the latest generation of large-scale machines and the earlier, mostly uniprocessor, machines. A sofware package being used by NASA to perform computations on large matrices is described, and a strategy for conversion to the Cray X-MP vector supercomputer is also described.

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.

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

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

Open Source Software to Control Bioflo Bioreactors

PubMed Central

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

2014-01-01

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

scoringRules - A software package for probabilistic model evaluation

NASA Astrophysics Data System (ADS)

Lerch, Sebastian; Jordan, Alexander; Krüger, Fabian

2016-04-01

Models in the geosciences are generally surrounded by uncertainty, and being able to quantify this uncertainty is key to good decision making. Accordingly, probabilistic forecasts in the form of predictive distributions have become popular over the last decades. With the proliferation of probabilistic models arises the need for decision theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way. Various scoring rules have been developed over the past decades to address this demand. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. As such, they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This poster presents the software package scoringRules for the statistical programming language R, which contains functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. Two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, Bayesian forecasts produced via Markov Chain Monte Carlo take this form. Thereby, the scoringRules package provides a framework for generalized model evaluation that both includes Bayesian as well as classical parametric models. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices.

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

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

Not Available

1984-03-01

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

IntraFace

PubMed Central

De la Torre, Fernando; Chu, Wen-Sheng; Xiong, Xuehan; Vicente, Francisco; Ding, Xiaoyu; Cohn, Jeffrey

2016-01-01

Within the last 20 years, there has been an increasing interest in the computer vision community in automated facial image analysis algorithms. This has been driven by applications in animation, market research, autonomous-driving, surveillance, and facial editing among others. To date, there exist several commercial packages for specific facial image analysis tasks such as facial expression recognition, facial attribute analysis or face tracking. However, free and easy-to-use software that incorporates all these functionalities is unavailable. This paper presents IntraFace (IF), a publicly-available software package for automated facial feature tracking, head pose estimation, facial attribute recognition, and facial expression analysis from video. In addition, IFincludes a newly develop technique for unsupervised synchrony detection to discover correlated facial behavior between two or more persons, a relatively unexplored problem in facial image analysis. In tests, IF achieved state-of-the-art results for emotion expression and action unit detection in three databases, FERA, CK+ and RU-FACS; measured audience reaction to a talk given by one of the authors; and discovered synchrony for smiling in videos of parent-infant interaction. IF is free of charge for academic use at http://www.humansensing.cs.cmu.edu/intraface/. PMID:27346987

Using VCL as an Aspect-Oriented Approach to Requirements Modelling

NASA Astrophysics Data System (ADS)

Amálio, Nuno; Kelsen, Pierre; Ma, Qin; Glodt, Christian

Software systems are becoming larger and more complex. By tackling the modularisation of crosscutting concerns, aspect orientation draws attention to modularity as a means to address the problems of scalability, complexity and evolution in software systems development. Aspect-oriented modelling (AOM) applies aspect-orientation to the construction of models. Most existing AOM approaches are designed without a formal semantics, and use multi-view partial descriptions of behaviour. This paper presents an AOM approach based on the Visual Contract Language (VCL): a visual language for abstract and precise modelling, designed with a formal semantics, and comprising a novel approach to visual behavioural modelling based on design by contract where behavioural descriptions are total. By applying VCL to a large case study of a car-crash crisis management system, the paper demonstrates how modularity of VCL's constructs, at different levels of granularity, help to tackle complexity. In particular, it shows how VCL's package construct and its associated composition mechanisms are key in supporting separation of concerns, coarse-grained problem decomposition and aspect-orientation. The case study's modelling solution has a clear and well-defined modular structure; the backbone of this structure is a collection of packages encapsulating local solutions to concerns.

IntraFace.

PubMed

De la Torre, Fernando; Chu, Wen-Sheng; Xiong, Xuehan; Vicente, Francisco; Ding, Xiaoyu; Cohn, Jeffrey

2015-05-01

Within the last 20 years, there has been an increasing interest in the computer vision community in automated facial image analysis algorithms. This has been driven by applications in animation, market research, autonomous-driving, surveillance, and facial editing among others. To date, there exist several commercial packages for specific facial image analysis tasks such as facial expression recognition, facial attribute analysis or face tracking. However, free and easy-to-use software that incorporates all these functionalities is unavailable. This paper presents IntraFace (IF), a publicly-available software package for automated facial feature tracking, head pose estimation, facial attribute recognition, and facial expression analysis from video. In addition, IFincludes a newly develop technique for unsupervised synchrony detection to discover correlated facial behavior between two or more persons, a relatively unexplored problem in facial image analysis. In tests, IF achieved state-of-the-art results for emotion expression and action unit detection in three databases, FERA, CK+ and RU-FACS; measured audience reaction to a talk given by one of the authors; and discovered synchrony for smiling in videos of parent-infant interaction. IF is free of charge for academic use at http://www.humansensing.cs.cmu.edu/intraface/.

MCTBI: a web server for predicting metal ion effects in RNA structures.

PubMed

Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

2017-08-01

Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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.

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.

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

PubMed

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

2014-07-30

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

Autonomous microexplosives subsurface tracing system final report.

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

Engler, Bruce Phillip; Nogan, John; Melof, Brian Matthew

The objective of the autonomous micro-explosive subsurface tracing system is to image the location and geometry of hydraulically induced fractures in subsurface petroleum reservoirs. This system is based on the insertion of a swarm of autonomous micro-explosive packages during the fracturing process, with subsequent triggering of the energetic material to create an array of micro-seismic sources that can be detected and analyzed using existing seismic receiver arrays and analysis software. The project included investigations of energetic mixtures, triggering systems, package size and shape, and seismic output. Given the current absence of any technology capable of such high resolution mapping ofmore » subsurface structures, this technology has the potential for major impact on petroleum industry, which spends approximately $1 billion dollar per year on hydraulic fracturing operations in the United States alone.« less

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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.

Automated data collection in single particle electron microscopy

PubMed Central

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

2016-01-01

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

Defense AT and L. Volume 42, Number 1

DTIC Science & Technology

2013-02-01

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

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

ERIC Educational Resources Information Center

Gagne, Phill; Furlow, Carolyn; Ross, Terris

2009-01-01

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

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

ERIC Educational Resources Information Center

Weaver, Dave

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

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

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

Isobe, G.W.

1985-10-01

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

Sampling and sensitivity analyses tools (SaSAT) for computational modelling

PubMed Central

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

2008-01-01

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

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

PubMed

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

2016-08-01

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

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

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

PubMed

Stoet, Gijsbert

2010-11-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Software package for modeling spin–orbit motion in storage rings

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

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

2015-12-15

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

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

ERIC Educational Resources Information Center

Levy, Roy

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Advanced Software Development Workstation Project

NASA Technical Reports Server (NTRS)

Lee, Daniel

1989-01-01

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

IBM Watson Analytics: Automating Visualization, Descriptive, and Predictive Statistics

PubMed Central

2016-01-01

Background We live in an era of explosive data generation that will continue to grow and involve all industries. One of the results of this explosion is the need for newer and more efficient data analytics procedures. Traditionally, data analytics required a substantial background in statistics and computer science. In 2015, International Business Machines Corporation (IBM) released the IBM Watson Analytics (IBMWA) software that delivered advanced statistical procedures based on the Statistical Package for the Social Sciences (SPSS). The latest entry of Watson Analytics into the field of analytical software products provides users with enhanced functions that are not available in many existing programs. For example, Watson Analytics automatically analyzes datasets, examines data quality, and determines the optimal statistical approach. Users can request exploratory, predictive, and visual analytics. Using natural language processing (NLP), users are able to submit additional questions for analyses in a quick response format. This analytical package is available free to academic institutions (faculty and students) that plan to use the tools for noncommercial purposes. Objective To report the features of IBMWA and discuss how this software subjectively and objectively compares to other data mining programs. Methods The salient features of the IBMWA program were examined and compared with other common analytical platforms, using validated health datasets. Results Using a validated dataset, IBMWA delivered similar predictions compared with several commercial and open source data mining software applications. The visual analytics generated by IBMWA were similar to results from programs such as Microsoft Excel and Tableau Software. In addition, assistance with data preprocessing and data exploration was an inherent component of the IBMWA application. Sensitivity and specificity were not included in the IBMWA predictive analytics results, nor were odds ratios, confidence intervals, or a confusion matrix. Conclusions IBMWA is a new alternative for data analytics software that automates descriptive, predictive, and visual analytics. This program is very user-friendly but requires data preprocessing, statistical conceptual understanding, and domain expertise. PMID:27729304

IBM Watson Analytics: Automating Visualization, Descriptive, and Predictive Statistics.

PubMed

Hoyt, Robert Eugene; Snider, Dallas; Thompson, Carla; Mantravadi, Sarita

2016-10-11

We live in an era of explosive data generation that will continue to grow and involve all industries. One of the results of this explosion is the need for newer and more efficient data analytics procedures. Traditionally, data analytics required a substantial background in statistics and computer science. In 2015, International Business Machines Corporation (IBM) released the IBM Watson Analytics (IBMWA) software that delivered advanced statistical procedures based on the Statistical Package for the Social Sciences (SPSS). The latest entry of Watson Analytics into the field of analytical software products provides users with enhanced functions that are not available in many existing programs. For example, Watson Analytics automatically analyzes datasets, examines data quality, and determines the optimal statistical approach. Users can request exploratory, predictive, and visual analytics. Using natural language processing (NLP), users are able to submit additional questions for analyses in a quick response format. This analytical package is available free to academic institutions (faculty and students) that plan to use the tools for noncommercial purposes. To report the features of IBMWA and discuss how this software subjectively and objectively compares to other data mining programs. The salient features of the IBMWA program were examined and compared with other common analytical platforms, using validated health datasets. Using a validated dataset, IBMWA delivered similar predictions compared with several commercial and open source data mining software applications. The visual analytics generated by IBMWA were similar to results from programs such as Microsoft Excel and Tableau Software. In addition, assistance with data preprocessing and data exploration was an inherent component of the IBMWA application. Sensitivity and specificity were not included in the IBMWA predictive analytics results, nor were odds ratios, confidence intervals, or a confusion matrix. IBMWA is a new alternative for data analytics software that automates descriptive, predictive, and visual analytics. This program is very user-friendly but requires data preprocessing, statistical conceptual understanding, and domain expertise.

Linear programming computational experience with onyx

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

Atrek, E.

1994-12-31

ONYX is a linear programming software package based on an efficient variation of the gradient projection method. When fully configured, it is intended for application to industrial size problems. While the computational experience is limited at the time of this abstract, the technique is found to be robust and competitive with existing methodology in terms of both accuracy and speed. An overview of the approach is presented together with a description of program capabilities, followed by a discussion of up-to-date computational experience with the program. Conclusions include advantages of the approach and envisioned future developments.

STEMsalabim: A high-performance computing cluster friendly code for scanning transmission electron microscopy image simulations of thin specimens.

PubMed

Oelerich, Jan Oliver; Duschek, Lennart; Belz, Jürgen; Beyer, Andreas; Baranovskii, Sergei D; Volz, Kerstin

2017-06-01

We present a new multislice code for the computer simulation of scanning transmission electron microscope (STEM) images based on the frozen lattice approximation. Unlike existing software packages, the code is optimized to perform well on highly parallelized computing clusters, combining distributed and shared memory architectures. This enables efficient calculation of large lateral scanning areas of the specimen within the frozen lattice approximation and fine-grained sweeps of parameter space. Copyright © 2017 Elsevier B.V. All rights reserved.

The STARLINK software collection

NASA Astrophysics Data System (ADS)

Penny, A. J.; Wallace, P. T.; Sherman, J. C.; Terret, D. L.

1993-12-01

A demonstration will be given of some recent Starlink software. STARLINK is: a network of computers used by UK astronomers; a collection of programs for the calibration and analysis of astronomical data; a team of people giving hardware, software and administrative support. The Starlink Project has been in operation since 1980 to provide UK astronomers with interactive image processing and data reduction facilities. There are now Starlink computer systems at 25 UK locations, serving about 1500 registered users. The Starlink software collection now has about 25 major packages covering a wide range of astronomical data reduction and analysis techniques, as well as many smaller programs and utilities. At the core of most of the packages is a common `software environment', which provides many of the functions which applications need and offers standardized methods of structuring and accessing data. The software environment simplifies programming and support, and makes it easy to use different packages for different stages of the data reduction. Users see a consistent style, and can mix applications without hitting problems of differing data formats. The Project group coordinates the writing and distribution of this software collection, which is Unix based. Outside the UK, Starlink is used at a large number of places, which range from installations at major UK telescopes, which are Starlink-compatible and managed like Starlink sites, to individuals who run only small parts of the Starlink software collection.

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

DTIC Science & Technology

1993-05-01

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

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets

PubMed Central

2010-01-01

Background The development of DNA microarrays has facilitated the generation of hundreds of thousands of transcriptomic datasets. The use of a common reference microarray design allows existing transcriptomic data to be readily compared and re-analysed in the light of new data, and the combination of this design with large datasets is ideal for 'systems'-level analyses. One issue is that these datasets are typically collected over many years and may be heterogeneous in nature, containing different microarray file formats and gene array layouts, dye-swaps, and showing varying scales of log2- ratios of expression between microarrays. Excellent software exists for the normalisation and analysis of microarray data but many data have yet to be analysed as existing methods struggle with heterogeneous datasets; options include normalising microarrays on an individual or experimental group basis. Our solution was to develop the Batch Anti-Banana Algorithm in R (BABAR) algorithm and software package which uses cyclic loess to normalise across the complete dataset. We have already used BABAR to analyse the function of Salmonella genes involved in the process of infection of mammalian cells. Results The only input required by BABAR is unprocessed GenePix or BlueFuse microarray data files. BABAR provides a combination of 'within' and 'between' microarray normalisation steps and diagnostic boxplots. When applied to a real heterogeneous dataset, BABAR normalised the dataset to produce a comparable scaling between the microarrays, with the microarray data in excellent agreement with RT-PCR analysis. When applied to a real non-heterogeneous dataset and a simulated dataset, BABAR's performance in identifying differentially expressed genes showed some benefits over standard techniques. Conclusions BABAR is an easy-to-use software tool, simplifying the simultaneous normalisation of heterogeneous two-colour common reference design cDNA microarray-based transcriptomic datasets. We show BABAR transforms real and simulated datasets to allow for the correct interpretation of these data, and is the ideal tool to facilitate the identification of differentially expressed genes or network inference analysis from transcriptomic datasets. PMID:20128918

The GRIDView Visualization Package

NASA Astrophysics Data System (ADS)

Kent, B. R.

2011-07-01

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

Lean Development with the Morpheus Simulation Software

NASA Technical Reports Server (NTRS)

Brogley, Aaron C.

2013-01-01

The Morpheus project is an autonomous robotic testbed currently in development at NASA's Johnson Space Center (JSC) with support from other centers. Its primary objectives are to test new 'green' fuel propulsion systems and to demonstrate the capability of the Autonomous Lander Hazard Avoidance Technology (ALHAT) sensor, provided by the Jet Propulsion Laboratory (JPL) on a lunar landing trajectory. If successful, these technologies and lessons learned from the Morpheus testing cycle may be incorporated into a landing descent vehicle used on the moon, an asteroid, or Mars. In an effort to reduce development costs and cycle time, the project employs lean development engineering practices in its development of flight and simulation software. The Morpheus simulation makes use of existing software packages where possible to reduce the development time. The development and testing of flight software occurs primarily through the frequent test operation of the vehicle and incrementally increasing the scope of the test. With rapid development cycles, risk of loss of the vehicle and loss of the mission are possible, but efficient progress in development would not be possible without that risk.

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

NASA Astrophysics Data System (ADS)

Sardina, V.

2012-12-01

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

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

Code of Federal Regulations, 2014 CFR

2014-04-01

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

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

PubMed

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

2015-10-20

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

Community-driven computational biology with Debian Linux.

PubMed

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

2010-12-21

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

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2017-03-01

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

Evaluation of RDBMS packages for use in astronomy

NASA Technical Reports Server (NTRS)

Page, C. G.; Davenhall, A. C.

1992-01-01

Tabular data sets arise in many areas of astronomical data analysis, from raw data (such as photon event lists) to final results (such as source catalogs). The Starlink catalog access and reporting package, SCAR, was originally developed to handle IRAS data and it has been the principal relational DBMS in the Starlink software collection for several years. But SCAR has many limitations and is VMS-specific, while Starlink is in transition from VMS to Unix. Rather than attempt a major re-write of SCAR for Unix, it seemed more sensible to see whether any existing database packages are suitable for general astronomical use. The authors first drew up a list of desirable properties for such a system and then used these criteria to evaluate a number of packages, both free ones and those commercially available. It is already clear that most commercial DBMS packages are not very well suited to the requirements; for example, most cannot carry out efficiently even fairly basic operations such as joining two catalogs on an approximate match of celestial positions. This paper reports the results of the evaluation exercise and notes the problems in using a standard DBMS package to process scientific data. In parallel with this the authors have started to develop a simple database engine that can handle tabular data in a range of common formats including simple direct-access files (such as SCAR and Exosat DBMS tables) and FITS tables (both ASCII and binary).

Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling.

PubMed

Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver

2015-08-01

Reliable detection of peptides in LC-MS data is a key algorithmic step in the analysis of quantitative proteomics experiments. While highly abundant peptides can be detected reliably by most modern software tools, there is much less agreement on medium and low-intensity peptides in a sample. The choice of software tools can have a big impact on the quantification of proteins, especially for proteins that appear in lower concentrations. However, in many experiments, it is precisely this region of less abundant but substantially regulated proteins that holds the biggest potential for discoveries. This is particularly true for discovery proteomics in the pharmacological sector with a specific interest in key regulatory proteins. In this viewpoint article, we discuss how the development of novel software algorithms allows us to study this region of the proteome with increased confidence. Reliable results are one of many aspects to be considered when deciding on a bioinformatics software platform. Deployment into existing IT infrastructures, compatibility with other software packages, scalability, automation, flexibility, and support need to be considered and are briefly addressed in this viewpoint article. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

EPA Science Inventory

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

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

DTIC Science & Technology

1988-03-01

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

Review and analysis of dense linear system solver package for distributed memory machines

NASA Technical Reports Server (NTRS)

Narang, H. N.

1993-01-01

A dense linear system solver package recently developed at the University of Texas at Austin for distributed memory machine (e.g. Intel Paragon) has been reviewed and analyzed. The package contains about 45 software routines, some written in FORTRAN, and some in C-language, and forms the basis for parallel/distributed solutions of systems of linear equations encountered in many problems of scientific and engineering nature. The package, being studied by the Computer Applications Branch of the Analysis and Computation Division, may provide a significant computational resource for NASA scientists and engineers in parallel/distributed computing. Since the package is new and not well tested or documented, many of its underlying concepts and implementations were unclear; our task was to review, analyze, and critique the package as a step in the process that will enable scientists and engineers to apply it to the solution of their problems. All routines in the package were reviewed and analyzed. Underlying theory or concepts which exist in the form of published papers or technical reports, or memos, were either obtained from the author, or from the scientific literature; and general algorithms, explanations, examples, and critiques have been provided to explain the workings of these programs. Wherever the things were still unclear, communications were made with the developer (author), either by telephone or by electronic mail, to understand the workings of the routines. Whenever possible, tests were made to verify the concepts and logic employed in their implementations. A detailed report is being separately documented to explain the workings of these routines.

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

PubMed

McCarthy, Davis J; Campbell, Kieran R; Lun, Aaron T L; Wills, Quin F

2017-04-15

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater . davis@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

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

PubMed

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

2014-12-01

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

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

NASA Astrophysics Data System (ADS)

Chen, Lujie

2013-06-01

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

A Coupled Simulation Architecture for Agent-Based/Geohydrological Modelling

NASA Astrophysics Data System (ADS)

Jaxa-Rozen, M.

2016-12-01

The quantitative modelling of social-ecological systems can provide useful insights into the interplay between social and environmental processes, and their impact on emergent system dynamics. However, such models should acknowledge the complexity and uncertainty of both of the underlying subsystems. For instance, the agent-based models which are increasingly popular for groundwater management studies can be made more useful by directly accounting for the hydrological processes which drive environmental outcomes. Conversely, conventional environmental models can benefit from an agent-based depiction of the feedbacks and heuristics which influence the decisions of groundwater users. From this perspective, this work describes a Python-based software architecture which couples the popular NetLogo agent-based platform with the MODFLOW/SEAWAT geohydrological modelling environment. This approach enables users to implement agent-based models in NetLogo's user-friendly platform, while benefiting from the full capabilities of MODFLOW/SEAWAT packages or reusing existing geohydrological models. The software architecture is based on the pyNetLogo connector, which provides an interface between the NetLogo agent-based modelling software and the Python programming language. This functionality is then extended and combined with Python's object-oriented features, to design a simulation architecture which couples NetLogo with MODFLOW/SEAWAT through the FloPy library (Bakker et al., 2016). The Python programming language also provides access to a range of external packages which can be used for testing and analysing the coupled models, which is illustrated for an application of Aquifer Thermal Energy Storage (ATES).

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

PubMed

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

2014-09-01

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

MOSAIC: Software for creating mosaics from collections of images

NASA Technical Reports Server (NTRS)

Varosi, F.; Gezari, D. Y.

1992-01-01

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

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

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

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

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. K.

FTOOLS, a highly modular collection of over 110 utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Science Archive Research Center) at NASA's Goddard Space Flight Center. Each utility performs a single simple task such as presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual utilities can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. The collection of utilities provides both generic processing and analysis utilities and utilities specific to high energy astrophysics data sets used for the ASCA, ROSAT, GRO, and XTE missions. A core set of FTOOLS providing support for generic FITS data processing, FITS image analysis and timing analysis can easily be split out of the full software package for users not needing the high energy astrophysics mission utilities. The FTOOLS software package is designed to be both compatible with IRAF and completely stand alone in a UNIX or VMS environment. The user interface is controlled by standard IRAF parameter files. The package is self documenting through the IRAF help facility and a stand alone help task. Software is written in ANSI C and \\fortran to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

Courseware Review.

ERIC Educational Resources Information Center

Risley, John, Ed.

1988-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1984-01-01

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

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.

CACTI: free, open-source software for the sequential coding of behavioral interactions.

PubMed

Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

Universal programming interface with concurrent access

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

Alferov, Oleg

2004-10-07

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

Error correction and diversity analysis of population mixtures determined by NGS

PubMed Central

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

2014-01-01

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

Attributes and Behaviors of Performance-Centered Systems.

ERIC Educational Resources Information Center

Gery, Gloria

1995-01-01

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

WGCNA: an R package for weighted correlation network analysis.

PubMed

Langfelder, Peter; Horvath, Steve

2008-12-29

Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA.

WGCNA: an R package for weighted correlation network analysis

PubMed Central

Langfelder, Peter; Horvath, Steve

2008-01-01

Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at . PMID:19114008

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

PubMed

Yavorska, Olena O; Burgess, Stephen

2017-12-01

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

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

PubMed

Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J; Beerli, Peter; Holder, Mark T; Lewis, Paul O; Huelsenbeck, John P; Ronquist, Fredrik; Swofford, David L; Cummings, Michael P; Rambaut, Andrew; Suchard, Marc A

2012-01-01

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

PubMed Central

Eklund, Anders; Dufort, Paul; Villani, Mattias; LaConte, Stephen

2014-01-01

Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful graphics processing units (GPUs) to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further, dramatic speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github (https://github.com/wanderine/BROCCOLI/). PMID:24672471

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

PubMed Central

Ayres, Daniel L.; Darling, Aaron; Zwickl, Derrick J.; Beerli, Peter; Holder, Mark T.; Lewis, Paul O.; Huelsenbeck, John P.; Ronquist, Fredrik; Swofford, David L.; Cummings, Michael P.; Rambaut, Andrew; Suchard, Marc A.

2012-01-01

Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. PMID:21963610

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

PubMed Central

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

2013-01-01

The development of a complex system depends on the self-coordinated action of a large number of agents, often determining unexpected global behavior. The case of software evolution has great practical importance: knowledge of what is to be considered atypical can guide developers in recognizing and reacting to abnormal behavior. Although the initial framework of a theory of software exists, the current theoretical achievements do not fully capture existing quantitative data or predict future trends. Here we show that two elementary laws describe the evolution of package sizes in a Linux-based operating system: first, relative changes in size follow a random walk with non-Gaussian jumps; second, each size change is bounded by a limit that is dependent on the starting size, an intriguing behavior that we call “soft bound.” Our approach is based on data analysis and on a simple theoretical model, which is able to reproduce empirical details without relying on any adjustable parameter and generates definite predictions. The same analysis allows us to formulate and support the hypothesis that a similar mechanism is shaping the distribution of mammalian body sizes, via size-dependent constraints during cladogenesis. Whereas generally accepted approaches struggle to reproduce the large-mass shoulder displayed by the distribution of extant mammalian species, this is a natural consequence of the softly bounded nature of the process. Additionally, the hypothesis that this model is valid has the relevant implication that, contrary to a common assumption, mammalian masses are still evolving, albeit very slowly. PMID:24324175

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

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

MANN, F.M.

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

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

DTIC Science & Technology

1992-03-03

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

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

DTIC Science & Technology

1992-03-03

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

Advanced Simulation in Undergraduate Pilot Training: Automatic Instructional System

DTIC Science & Technology

1975-10-01

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

'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/

Find Pairs: The Module for Protein Quantification of the PeakQuant Software Suite

PubMed Central

Eisenacher, Martin; Kohl, Michael; Wiese, Sebastian; Hebeler, Romano; Meyer, Helmut E.

2012-01-01

Abstract Accurate quantification of proteins is one of the major tasks in current proteomics research. To address this issue, a wide range of stable isotope labeling techniques have been developed, allowing one to quantitatively study thousands of proteins by means of mass spectrometry. In this article, the FindPairs module of the PeakQuant software suite is detailed. It facilitates the automatic determination of protein abundance ratios based on the automated analysis of stable isotope-coded mass spectrometric data. Furthermore, it implements statistical methods to determine outliers due to biological as well as technical variance of proteome data obtained in replicate experiments. This provides an important means to evaluate the significance in obtained protein expression data. For demonstrating the high applicability of FindPairs, we focused on the quantitative analysis of proteome data acquired in 14N/15N labeling experiments. We further provide a comprehensive overview of the features of the FindPairs software, and compare these with existing quantification packages. The software presented here supports a wide range of proteomics applications, allowing one to quantitatively assess data derived from different stable isotope labeling approaches, such as 14N/15N labeling, SILAC, and iTRAQ. The software is publicly available at http://www.medizinisches-proteom-center.de/software and free for academic use. PMID:22909347

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

PubMed

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

2017-12-14

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

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.

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

ERIC Educational Resources Information Center

Lovell, Ashley C., Comp.

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

Sustaining Software-Intensive Systems

DTIC Science & Technology

2006-05-01

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

Nuclear Data Online Services at Peking University

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

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

2005-05-24

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

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

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

2005-05-01

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

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.

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

DOE PAGES

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

2016-11-07

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

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

PubMed

Becker, Alexander D; Grenfell, Bryan T

2017-01-01

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

Aspects on Transfer of Aided - Design Files

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations.

PubMed

Samoylova, Liubov; Buzmakov, Alexey; Chubar, Oleg; Sinn, Harald

2016-08-01

This article describes the WavePropaGator ( WPG ) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop ( SRW ) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

Supporting 64-bit global indices in Epetra and other Trilinos packages :

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

Jhurani, Chetan; Austin, Travis M.; Heroux, Michael Allen

The Trilinos Project is an effort to facilitate the design, development, integration and ongoing support of mathematical software libraries within an object-oriented framework. It is intended for large-scale, complex multiphysics engineering and scientific applications [2, 4, 3]. Epetra is one of its basic packages. It provides serial and parallel linear algebra capabilities. Before Trilinos version 11.0, released in 2012, Epetra used the C++ int data-type for storing global and local indices for degrees of freedom (DOFs). Since int is typically 32-bit, this limited the largest problem size to be smaller than approximately two billion DOFs. This was true even ifmore » a distributed memory machine could handle larger problems. We have added optional support for C++ long long data-type, which is at least 64-bit wide, for global indices. To save memory, maintain the speed of memory-bound operations, and reduce further changes to the code, the local indices are still 32-bit. We document the changes required to achieve this feature and how the new functionality can be used. We also report on the lessons learned in modifying a mature and popular package from various perspectives design goals, backward compatibility, engineering decisions, C++ language features, effects on existing users and other packages, and build integration.« less

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

PubMed

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

2015-07-15

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

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

PubMed

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

2018-06-07

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

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.

PubMed

McDonald, Thomas O; Michor, Franziska

2017-07-15

SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own. SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ). Supplementary data are available at Bioinformatics online. michor@jimmy.harvard.edu. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Space life support engineering program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1992-01-01

A comprehensive study to develop software to simulate the dynamic operation of water reclamation systems in long-term closed-loop life support systems is being carried out as part of an overall program for the design of systems for a moon station or a Mars voyage. This project is being done in parallel with a similar effort in the Department of Chemistry to develop durable accurate low-cost sensors for monitoring of trace chemical and biological species in recycled water supplies. Aspen-Plus software is being used on a group of high-performance work stations to develop the steady state descriptions for a number of existing technologies. Following completion, a dynamic simulation package will be developed for determining the response of such systems to changes in the metabolic needs of the crew and to upsets in system hardware performance.

LEWICE 2.2 Capabilities and Thermal Validation

NASA Technical Reports Server (NTRS)

Wright, William B.

2002-01-01

A computational model of bleed air anti-icing and electrothermal de-icing have been added to the LEWICE 2.0 software by integrating the capabilities of two previous programs, ANTICE and LEWICE/ Thermal. This combined model has been released as LEWICE version 2.2. Several advancements have also been added to the previous capabilities of each module. This report will present the capabilities of the software package and provide results for both bleed air and electrothermal cases. A comprehensive validation effort has also been performed to compare the predictions to an existing electrothermal database. A quantitative comparison shows that for deicing cases, the average difference is 9.4 F (26%) compared to 3 F for the experimental data while for evaporative cases the average difference is 2 F (32%) compared to an experimental error of 4 F.

Development of Continuum-Atomistic Approach for Modeling Metal Irradiation by Heavy Ions

NASA Astrophysics Data System (ADS)

Batgerel, Balt; Dimova, Stefka; Puzynin, Igor; Puzynina, Taisia; Hristov, Ivan; Hristova, Radoslava; Tukhliev, Zafar; Sharipov, Zarif

2018-02-01

Over the last several decades active research in the field of materials irradiation by high-energy heavy ions has been worked out. The experiments in this area are labor-consuming and expensive. Therefore the improvement of the existing mathematical models and the development of new ones based on the experimental data of interaction of high-energy heavy ions with materials are of interest. Presently, two approaches are used for studying these processes: a thermal spike model and molecular dynamics methods. The combination of these two approaches - the continuous-atomistic model - will give the opportunity to investigate more thoroughly the processes of irradiation of materials by high-energy heavy ions. To solve the equations of the continuous-atomistic model, a software package was developed and the block of molecular dynamics software was tested on the heterogeneous cluster HybriLIT.

Microscopy image segmentation tool: Robust image data analysis

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

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

Increasing Accessibility by Pooling Digital Resources

ERIC Educational Resources Information Center

Cushion, Steve

2004-01-01

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

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

ERIC Educational Resources Information Center

Evermann, Joerg

2010-01-01

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

LANZ: Software solving the large sparse symmetric generalized eigenproblem

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1990-01-01

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

MIBPB: a software package for electrostatic analysis.

PubMed

Chen, Duan; Chen, Zhan; Chen, Changjun; Geng, Weihua; Wei, Guo-Wei

2011-03-01

The Poisson-Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This article presents a matched interface and boundary (MIB)-based PBE software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that it is the first interface technique-based PBE solver that rigorously enforces the solution and flux continuity conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities, the MIB scheme makes the MIBPB by far the only existing PBE solver that is able to deliver the second-order convergence, that is, the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet-to-Neumann mapping technique that builds a Green's function approach to analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions at meshes as coarse as 1 Å--whereas it usually takes other traditional PB solvers 0.25 Å to reach similar level of reliability. This work further accelerates the rate of convergence of linear equation systems resulting from the MIBPB by using the Krylov subspace (KS) techniques. Condition numbers of the MIBPB matrices are significantly reduced by using appropriate KS solver and preconditioner combinations. Both linear and nonlinear PBE solvers in the MIBPB package are tested by protein-solvent solvation energy calculations and analysis of salt effects on protein-protein binding energies, respectively. Copyright © 2010 Wiley Periodicals, Inc.

MIBPB: A software package for electrostatic analysis

PubMed Central

Chen, Duan; Chen, Zhan; Chen, Changjun; Geng, Weihua; Wei, Guo-Wei

2010-01-01

The Poisson-Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This paper presents a matched interface and boundary (MIB) based PBE software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that it is the first interface technique based PBE solver that rigorously enforces the solution and flux continuity conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces which may possess troublesome geometrical singularities, the MIB scheme makes the MIBPB by far the only existing PBE solver that is able to deliver the second order convergence, i.e., the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet-to-Neumann mapping (DNM) technique, that builds a Green's function approach to analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions at meshes as coarse as 1Å — while it usually takes other traditional PB solvers 0.25Å to reach similar level of reliability. The present work further accelerates the rate of convergence of linear equation systems resulting from the MIBPB by utilizing the Krylov subspace (KS) techniques. Condition numbers of the MIBPB matrices are significantly reduced by using appropriate Krylov subspace solver and preconditioner combinations. Both linear and nonlinear PBE solvers in the MIBPB package are tested by protein-solvent solvation energy calculations and analysis of salt effects on protein-protein binding energies, respectively. PMID:20845420

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

ERIC Educational Resources Information Center

Khan, A. H.; And Others

1996-01-01

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

Modelling robotic systems with DADS

NASA Technical Reports Server (NTRS)

Churchill, L. W.; Sharf, I.

1993-01-01

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

Aviation Design Software

NASA Technical Reports Server (NTRS)

1997-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

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

Huang, Renke; Jin, Shuangshuang; Chen, Yousu

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

KiT: a MATLAB package for kinetochore tracking.

PubMed

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

2016-06-15

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

MPTinR: analysis of multinomial processing tree models in R.

PubMed

Singmann, Henrik; Kellen, David

2013-06-01

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

Reviews.

ERIC Educational Resources Information Center

Science Teacher, 1988

1988-01-01

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

Volumetric neuroimage analysis extensions for the MIPAV software package.

PubMed

Bazin, Pierre-Louis; Cuzzocreo, Jennifer L; Yassa, Michael A; Gandler, William; McAuliffe, Matthew J; Bassett, Susan S; Pham, Dzung L

2007-09-15

We describe a new collection of publicly available software tools for performing quantitative neuroimage analysis. The tools perform semi-automatic brain extraction, tissue classification, Talairach alignment, and atlas-based measurements within a user-friendly graphical environment. They are implemented as plug-ins for MIPAV, a freely available medical image processing software package from the National Institutes of Health. Because the plug-ins and MIPAV are implemented in Java, both can be utilized on nearly any operating system platform. In addition to the software plug-ins, we have also released a digital version of the Talairach atlas that can be used to perform regional volumetric analyses. Several studies are conducted applying the new tools to simulated and real neuroimaging data sets.

[Microcomputer control of a LED stimulus display device].

PubMed

Ohmoto, S; Kikuchi, T; Kumada, T

1987-02-01

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

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

PubMed

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

2012-09-01

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

LHCb Build and Deployment Infrastructure for run 2

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.

2015-12-01

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

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

NASA Astrophysics Data System (ADS)

Goldsmith, Jack G.

1997-10-01

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

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

NASA Technical Reports Server (NTRS)

Soeder, J. F.

1985-01-01

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

Long-term Preservation of Data Analysis Capabilities

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Using WNTR to Model Water Distribution System Resilience ...

EPA Pesticide Factsheets

The Water Network Tool for Resilience (WNTR) is a new open source Python package developed by the U.S. Environmental Protection Agency and Sandia National Laboratories to model and evaluate resilience of water distribution systems. WNTR can be used to simulate a wide range of disruptive events, including earthquakes, contamination incidents, floods, climate change, and fires. The software includes the EPANET solver as well as a WNTR solver with the ability to model pressure-driven demand hydraulics, pipe breaks, component degradation and failure, changes to supply and demand, and cascading failure. Damage to individual components in the network (i.e. pipes, tanks) can be selected probabilistically using fragility curves. WNTR can also simulate different types of resilience-enhancing actions, including scheduled pipe repair or replacement, water conservation efforts, addition of back-up power, and use of contamination warning systems. The software can be used to estimate potential damage in a network, evaluate preparedness, prioritize repair strategies, and identify worse case scenarios. As a Python package, WNTR takes advantage of many existing python capabilities, including parallel processing of scenarios and graphics capabilities. This presentation will outline the modeling components in WNTR, demonstrate their use, give the audience information on how to get started using the code, and invite others to participate in this open source project. This pres

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.

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

PubMed Central

Kumar, Shailesh; Vo, Angie Duy; Qin, Fujun; Li, Hui

2016-01-01

RNA-Seq made possible the global identification of fusion transcripts, i.e. “chimeric RNAs”. Even though various software packages have been developed to serve this purpose, they behave differently in different datasets provided by different developers. It is important for both users, and developers to have an unbiased assessment of the performance of existing fusion detection tools. Toward this goal, we compared the performance of 12 well-known fusion detection software packages. We evaluated the sensitivity, false discovery rate, computing time, and memory usage of these tools in four different datasets (positive, negative, mixed, and test). We conclude that some tools are better than others in terms of sensitivity, positive prediction value, time consumption and memory usage. We also observed small overlaps of the fusions detected by different tools in the real dataset (test dataset). This could be due to false discoveries by various tools, but could also be due to the reason that none of the tools are inclusive. We have found that the performance of the tools depends on the quality, read length, and number of reads of the RNA-Seq data. We recommend that users choose the proper tools for their purpose based on the properties of their RNA-Seq data. PMID:26862001

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

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

PubMed Central

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

2016-01-01

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

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

Science.gov Websites

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

Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning

PubMed Central

Officer, Rick; Clarke, Maurice; Reid, David G.; Brophy, Deirdre

2017-01-01

Boosted Regression Trees. Excellent for data-poor spatial management but hard to use Marine resource managers and scientists often advocate spatial approaches to manage data-poor species. Existing spatial prediction and management techniques are either insufficiently robust, struggle with sparse input data, or make suboptimal use of multiple explanatory variables. Boosted Regression Trees feature excellent performance and are well suited to modelling the distribution of data-limited species, but are extremely complicated and time-consuming to learn and use, hindering access for a wide potential user base and therefore limiting uptake and usage. BRTs automated and simplified for accessible general use with rich feature set We have built a software suite in R which integrates pre-existing functions with new tailor-made functions to automate the processing and predictive mapping of species abundance data: by automating and greatly simplifying Boosted Regression Tree spatial modelling, the gbm.auto R package suite makes this powerful statistical modelling technique more accessible to potential users in the ecological and modelling communities. The package and its documentation allow the user to generate maps of predicted abundance, visualise the representativeness of those abundance maps and to plot the relative influence of explanatory variables and their relationship to the response variables. Databases of the processed model objects and a report explaining all the steps taken within the model are also generated. The package includes a previously unavailable Decision Support Tool which combines estimated escapement biomass (the percentage of an exploited population which must be retained each year to conserve it) with the predicted abundance maps to generate maps showing the location and size of habitat that should be protected to conserve the target stocks (candidate MPAs), based on stakeholder priorities, such as the minimisation of fishing effort displacement. Gbm.auto for management in various settings By bridging the gap between advanced statistical methods for species distribution modelling and conservation science, management and policy, these tools can allow improved spatial abundance predictions, and therefore better management, decision-making, and conservation. Although this package was built to support spatial management of a data-limited marine elasmobranch fishery, it should be equally applicable to spatial abundance modelling, area protection, and stakeholder engagement in various scenarios. PMID:29216310

FTOOLS: A general package of software to manipulate FITS files

NASA Astrophysics Data System (ADS)

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

1999-12-01

FTOOLS, a highly modular collection of utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Research Archive Center) at NASA's Goddard Space Flight Center. The FTOOLS package contains many utility programs which perform modular tasks on any FITS image or table, as well as higher-level analysis programs designed specifically for data from current and past high energy astrophysics missions. The utility programs for FITS tables are especially rich and powerful, and provide functions for presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual FTOOLS programs can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. FTOOLS development began in 1991 and has produced the main set of data analysis software for the current ASCA and RXTE space missions and for other archival sets of X-ray and gamma-ray data. The FTOOLS software package is supported on most UNIX platforms and on Windows machines. The user interface is controlled by standard parameter files that are very similar to those used by IRAF. The package is self documenting through a stand alone help task called fhelp. Software is written in ANSI C and FORTRAN to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

A Freeware Path to Neutron Computed Tomography

NASA Astrophysics Data System (ADS)

Schillinger, Burkhard; Craft, Aaron E.

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

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

PubMed Central

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

2017-01-01

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

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

Grime, G. W.

2013-07-01

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

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

NASA Technical Reports Server (NTRS)

Thompson, David S.; Soni, Bharat K.

2000-01-01

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

PINT, A Modern Software Package for Pulsar Timing

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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

PubMed Central

2015-01-01

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

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

PubMed

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

2014-09-22

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

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

PubMed

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

2017-04-01

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