Composite Linear Models | Division of Cancer Prevention

Cancer.gov

By Stuart G. Baker The composite linear models software is a matrix approach to compute maximum likelihood estimates and asymptotic standard errors for models for incomplete multinomial data. It implements the method described in Baker SG. Composite linear models for incomplete multinomial data. Statistics in Medicine 1994;13:609-622. The software includes a library of thirty

Thermal Tracker: The Secret Lives of Bats and Birds Revealed

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

None

Offshore wind developers and stakeholders can accelerate the sustainable, widespread deployment of offshore wind using a new open-source software program, called ThermalTracker. Researchers can now collect the data they need to better understand the potential effects of offshore wind turbines on bird and bat populations. This plug and play software can be used with any standard desktop computer, thermal camera, and statistical software to identify species and behaviors of animals in offshore locations.

Statistical analysis of arsenic contamination in drinking water in a city of Iran and its modeling using GIS.

PubMed

Sadeghi, Fatemeh; Nasseri, Simin; Mosaferi, Mohammad; Nabizadeh, Ramin; Yunesian, Masud; Mesdaghinia, Alireza

2017-05-01

In this research, probable arsenic contamination in drinking water in the city of Ardabil was studied in 163 samples during four seasons. In each season, sampling was carried out randomly in the study area. Results were analyzed statistically applying SPSS 19 software, and the data was also modeled by Arc GIS 10.1 software. The maximum permissible arsenic concentration in drinking water defined by the World Health Organization and Iranian national standard is 10 μg/L. Statistical analysis showed 75, 88, 47, and 69% of samples in autumn, winter, spring, and summer, respectively, had concentrations higher than the national standard. The mean concentrations of arsenic in autumn, winter, spring, and summer were 19.89, 15.9, 10.87, and 14.6 μg/L, respectively, and the overall average in all samples through the year was 15.32 μg/L. Although GIS outputs indicated that the concentration distribution profiles changed in four consecutive seasons, variance analysis of the results showed that statistically there is no significant difference in arsenic levels in four seasons.

Probabilistic Graphical Model Representation in Phylogenetics

PubMed Central

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

S2O - A software tool for integrating research data from general purpose statistic software into electronic data capture systems.

PubMed

Bruland, Philipp; Dugas, Martin

2017-01-07

Data capture for clinical registries or pilot studies is often performed in spreadsheet-based applications like Microsoft Excel or IBM SPSS. Usually, data is transferred into statistic software, such as SAS, R or IBM SPSS Statistics, for analyses afterwards. Spreadsheet-based solutions suffer from several drawbacks: It is generally not possible to ensure a sufficient right and role management; it is not traced who has changed data when and why. Therefore, such systems are not able to comply with regulatory requirements for electronic data capture in clinical trials. In contrast, Electronic Data Capture (EDC) software enables a reliable, secure and auditable collection of data. In this regard, most EDC vendors support the CDISC ODM standard to define, communicate and archive clinical trial meta- and patient data. Advantages of EDC systems are support for multi-user and multicenter clinical trials as well as auditable data. Migration from spreadsheet based data collection to EDC systems is labor-intensive and time-consuming at present. Hence, the objectives of this research work are to develop a mapping model and implement a converter between the IBM SPSS and CDISC ODM standard and to evaluate this approach regarding syntactic and semantic correctness. A mapping model between IBM SPSS and CDISC ODM data structures was developed. SPSS variables and patient values can be mapped and converted into ODM. Statistical and display attributes from SPSS are not corresponding to any ODM elements; study related ODM elements are not available in SPSS. The S2O converting tool was implemented as command-line-tool using the SPSS internal Java plugin. Syntactic and semantic correctness was validated with different ODM tools and reverse transformation from ODM into SPSS format. Clinical data values were also successfully transformed into the ODM structure. Transformation between the spreadsheet format IBM SPSS and the ODM standard for definition and exchange of trial data is feasible. S2O facilitates migration from Excel- or SPSS-based data collections towards reliable EDC systems. Thereby, advantages of EDC systems like reliable software architecture for secure and traceable data collection and particularly compliance with regulatory requirements are achievable.

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.

The Infeasibility of Quantifying the Reliability of Life-Critical Real-Time Software

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Finelli, George B.

1991-01-01

This paper affirms that the quantification of life-critical software reliability is infeasible using statistical methods whether applied to standard software or fault-tolerant software. The classical methods of estimating reliability are shown to lead to exhorbitant amounts of testing when applied to life-critical software. Reliability growth models are examined and also shown to be incapable of overcoming the need for excessive amounts of testing. The key assumption of software fault tolerance separately programmed versions fail independently is shown to be problematic. This assumption cannot be justified by experimentation in the ultrareliability region and subjective arguments in its favor are not sufficiently strong to justify it as an axiom. Also, the implications of the recent multiversion software experiments support this affirmation.

Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1981-01-01

A parametric software cost estimation model prepared for Deep Space Network (DSN) Data Systems implementation tasks is presented. The resource estimation model incorporates principles and data from a number of existing models. The model calibrates task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit DSN software life cycle statistics. The estimation model output scales a standard DSN Work Breakdown Structure skeleton, which is then input into a PERT/CPM system, producing a detailed schedule and resource budget for the project being planned.

Integrating Formal Methods and Testing 2002

NASA Technical Reports Server (NTRS)

Cukic, Bojan

2002-01-01

Traditionally, qualitative program verification methodologies and program testing are studied in separate research communities. None of them alone is powerful and practical enough to provide sufficient confidence in ultra-high reliability assessment when used exclusively. Significant advances can be made by accounting not only tho formal verification and program testing. but also the impact of many other standard V&V techniques, in a unified software reliability assessment framework. The first year of this research resulted in the statistical framework that, given the assumptions on the success of the qualitative V&V and QA procedures, significantly reduces the amount of testing needed to confidently assess reliability at so-called high and ultra-high levels (10-4 or higher). The coming years shall address the methodologies to realistically estimate the impacts of various V&V techniques to system reliability and include the impact of operational risk to reliability assessment. Combine formal correctness verification, process and product metrics, and other standard qualitative software assurance methods with statistical testing with the aim of gaining higher confidence in software reliability assessment for high-assurance applications. B) Quantify the impact of these methods on software reliability. C) Demonstrate that accounting for the effectiveness of these methods reduces the number of tests needed to attain certain confidence level. D) Quantify and justify the reliability estimate for systems developed using various methods.

An SAS Macro for Implementing the Modified Bollen-Stine Bootstrap for Missing Data: Implementing the Bootstrap Using Existing Structural Equation Modeling Software

ERIC Educational Resources Information Center

Enders, Craig K.

2005-01-01

The Bollen-Stine bootstrap can be used to correct for standard error and fit statistic bias that occurs in structural equation modeling (SEM) applications due to nonnormal data. The purpose of this article is to demonstrate the use of a custom SAS macro program that can be used to implement the Bollen-Stine bootstrap with existing SEM software.…

AXAF FITS standard for ray trace interchange

NASA Astrophysics Data System (ADS)

Hsieh, Paul F.

1993-07-01

A standard data format for the archival and transport of x-ray events generated by ray trace models is described. Upon review and acceptance by the Advanced X-ray Astrophysics Facility (AXAF) Software Systems Working Group (SSWG), this standard shall become the official AXAF data format for ray trace events. The Flexible Image Transport System (FITS) is well suited for the purposes of the standard and was selected to be the basis of the standard. FITS is both flexible and efficient and is also widely used within the astronomical community for storage and transfer of data. In addition, software to read and write FITS format files are widely available. In selecting quantities to be included within the ray trace standard, the AXAF Mission Support team, Science Instruments team, and the other contractor teams were surveyed. From the results of this survey, the following requirements were established: (1) for the scientific needs, each photon should have associated with it: position, direction, energy, and statistical weight; the standard must also accommodate path length (relative phase), and polarization. (2) a unique photon identifier is necessary for bookkeeping purposes; (3) a log of individuals, organizations, and software packages that have modified the data must be maintained in order to create an audit trail; (4) a mechanism for extensions to the basic kernel should be provided; and (5) the ray trace standard should integrate with future AXAF data product standards.

AXAF FITS standard for ray trace interchange

NASA Technical Reports Server (NTRS)

Hsieh, Paul F.

1993-01-01

A standard data format for the archival and transport of x-ray events generated by ray trace models is described. Upon review and acceptance by the Advanced X-ray Astrophysics Facility (AXAF) Software Systems Working Group (SSWG), this standard shall become the official AXAF data format for ray trace events. The Flexible Image Transport System (FITS) is well suited for the purposes of the standard and was selected to be the basis of the standard. FITS is both flexible and efficient and is also widely used within the astronomical community for storage and transfer of data. In addition, software to read and write FITS format files are widely available. In selecting quantities to be included within the ray trace standard, the AXAF Mission Support team, Science Instruments team, and the other contractor teams were surveyed. From the results of this survey, the following requirements were established: (1) for the scientific needs, each photon should have associated with it: position, direction, energy, and statistical weight; the standard must also accommodate path length (relative phase), and polarization. (2) a unique photon identifier is necessary for bookkeeping purposes; (3) a log of individuals, organizations, and software packages that have modified the data must be maintained in order to create an audit trail; (4) a mechanism for extensions to the basic kernel should be provided; and (5) the ray trace standard should integrate with future AXAF data product standards.

ToxMiner Software Interface for Visualizing and Analyzing ToxCast Data

EPA Science Inventory

The ToxCast dataset represents a collection of assays and endpoints that will require both standard statistical approaches as well as customized data analysis workflows. To analyze this unique dataset, we have developed an integrated database with Javabased interface called ToxMi...

Software cost/resource modeling: Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. J.

1980-01-01

A parametric software cost estimation model prepared for JPL deep space network (DSN) data systems implementation tasks is presented. The resource estimation model incorporates principles and data from a number of existing models, such as those of the General Research Corporation, Doty Associates, IBM (Walston-Felix), Rome Air Force Development Center, University of Maryland, and Rayleigh-Norden-Putnam. The model calibrates task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit JPL software lifecycle statistics. The estimation model output scales a standard DSN work breakdown structure skeleton, which is then input to a PERT/CPM system, producing a detailed schedule and resource budget for the project being planned.

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

NASA Astrophysics Data System (ADS)

Ramkilowan, A.; Griffith, D. J.

2017-10-01

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

Structure of Student Time Management Scale (STMS)

ERIC Educational Resources Information Center

Balamurugan, M.

2013-01-01

With the aim of constructing a Student Time Management Scale (STMS), the initial version was administered and data were collected from 523 standard eleventh students. (Mean age = 15.64). The data obtained were subjected to Reliability and Factor analysis using PASW Statistical software version 18. From 42 items 14 were dropped, resulting in the…

A new SAS program for behavioral analysis of Electrical Penetration Graph (EPG) data

USDA-ARS?s Scientific Manuscript database

A new program is introduced that uses SAS software to duplicate output of descriptive statistics from the Sarria Excel workbook for EPG waveform analysis. Not only are publishable means and standard errors or deviations output, the user also is guided through four relatively simple sub-programs for ...

Evaluation of vocal acoustic and efficiency analysis parameters in medical students and academic teachers with use of iris and diagnoscope specialist software.

PubMed

Zielińska-Bliźniewska, Hanna; Sułkowski, Wiesław J; Pietkiewicz, Piotr; Miłoński, Jarosław; Mazurek, Agnieszka; Olszewski, Jurek

2012-06-01

The aim of this study was to compare the parameters of vocal acoustic and vocal efficiency analyses in medical students and academic teachers with use of the IRIS and DiagnoScope Specialist software and to evaluate their usefulness in prevention and certification of occupational disease. The study group comprised 40 women, including students and employees of the Military Medical Faculty, Medical University of Łodź. After informed consent had been obtained from the participant women, the primary medical history was taken, videolaryngoscopic and stroboscopic examinations were performed and diagnostic vocal acoustic analysis was carried out with the use of the IRIS and Diagno-Scope Specialist software. Based on the results of the performed measurements, the statistical analysis evidenced the compatibility between two software programs, IRIS and DiagnoScope Specialist, with the only exception of the F4 formant. The mean values of vocal acoustic parameters in medical students and academic teachers, obtained by means of the IRIS software, can be used as standards for the female population not yet developed by the producer. When using the DiagnoScope Specialist software, some mean values were higher and some lower than the standards specified by the producer. The study evidenced the compatibility between two measurement software programs, IRIS and DiagnoScope Specialist, except for the F4 formant. It should be noted that the later has advantage over the former since the standard values of vocal acoustic parameters have been worked out by the producer. Moreover, they only slightly departed from the values obtained in our study and may be useful in diagnostics of occupational voice disorders.

Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

PubMed

Ramus, Claire; Hovasse, Agnès; Marcellin, Marlène; Hesse, Anne-Marie; Mouton-Barbosa, Emmanuelle; Bouyssié, David; Vaca, Sebastian; Carapito, Christine; Chaoui, Karima; Bruley, Christophe; Garin, Jérôme; Cianférani, Sarah; Ferro, Myriam; Van Dorssaeler, Alain; Burlet-Schiltz, Odile; Schaeffer, Christine; Couté, Yohann; Gonzalez de Peredo, Anne

2016-01-30

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods. Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, for detection of variant proteins with different absolute expression levels and fold change values. The dataset presented here can be useful for tuning software tool parameters, and also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Introducing 3D U-statistic method for separating anomaly from background in exploration geochemical data with associated software development

NASA Astrophysics Data System (ADS)

Ghannadpour, Seyyed Saeed; Hezarkhani, Ardeshir

2016-03-01

The U-statistic method is one of the most important structural methods to separate the anomaly from the background. It considers the location of samples and carries out the statistical analysis of the data without judging from a geochemical point of view and tries to separate subpopulations and determine anomalous areas. In the present study, to use U-statistic method in three-dimensional (3D) condition, U-statistic is applied on the grade of two ideal test examples, by considering sample Z values (elevation). So far, this is the first time that this method has been applied on a 3D condition. To evaluate the performance of 3D U-statistic method and in order to compare U-statistic with one non-structural method, the method of threshold assessment based on median and standard deviation (MSD method) is applied on the two example tests. Results show that the samples indicated by U-statistic method as anomalous are more regular and involve less dispersion than those indicated by the MSD method. So that, according to the location of anomalous samples, denser areas of them can be determined as promising zones. Moreover, results show that at a threshold of U = 0, the total error of misclassification for U-statistic method is much smaller than the total error of criteria of bar {x}+n× s. Finally, 3D model of two test examples for separating anomaly from background using 3D U-statistic method is provided. The source code for a software program, which was developed in the MATLAB programming language in order to perform the calculations of the 3D U-spatial statistic method, is additionally provided. This software is compatible with all the geochemical varieties and can be used in similar exploration projects.

A statistical data analysis and plotting program for cloud microphysics experiments

NASA Technical Reports Server (NTRS)

Jordan, A. J.

1981-01-01

The analysis software developed for atmospheric cloud microphysics experiments conducted in the laboratory as well as aboard a KC-135 aircraft is described. A group of four programs was developed and implemented on a Hewlett Packard 1000 series F minicomputer running under HP's RTE-IVB operating system. The programs control and read data from a MEMODYNE Model 3765-8BV cassette recorder, format the data on the Hewlett Packard disk subsystem, and generate statistical data (mean, variance, standard deviation) and voltage and engineering unit plots on a user selected plotting device. The programs are written in HP FORTRAN IV and HP ASSEMBLY Language with the graphics software using the HP 1000 Graphics. The supported plotting devices are the HP 2647A graphics terminal, the HP 9872B four color pen plotter, and the HP 2608A matrix line printer.

NASA space station software standards issues

NASA Technical Reports Server (NTRS)

Tice, G. D., Jr.

1985-01-01

The selection and application of software standards present the NASA Space Station Program with the opportunity to serve as a pacesetter for the United States software in the area of software standards. The strengths and weaknesses of each of the NASA defined software standards issues are summerized and discussed. Several significant standards issues are offered for NASA consideration. A challenge is presented for the NASA Space Station Program to serve as a pacesetter for the U.S. Software Industry through: (1) Management commitment to software standards; (2) Overall program participation in software standards; and (3) Employment of the best available technology to support software standards

The Future of Statistical Software. Proceedings of a Forum--Panel on Guidelines for Statistical Software (Washington, D.C., February 22, 1991).

ERIC Educational Resources Information Center

National Academy of Sciences - National Research Council, Washington, DC.

The Panel on Guidelines for Statistical Software was organized in 1990 to document, assess, and prioritize problem areas regarding quality and reliability of statistical software; present prototype guidelines in high priority areas; and make recommendations for further research and discussion. This document provides the following papers presented…

Semi-automatic computerized approach to radiological quantification in rheumatoid arthritis

NASA Astrophysics Data System (ADS)

Steiner, Wolfgang; Schoeffmann, Sylvia; Prommegger, Andrea; Boegl, Karl; Klinger, Thomas; Peloschek, Philipp; Kainberger, Franz

2004-04-01

Rheumatoid Arthritis (RA) is a common systemic disease predominantly involving the joints. Precise diagnosis and follow-up therapy requires objective quantification. For this purpose, radiological analyses using standardized scoring systems are considered to be the most appropriate method. The aim of our study is to develop a semi-automatic image analysis software, especially applicable for scoring of joints in rheumatic disorders. The X-Ray RheumaCoach software delivers various scoring systems (Larsen-Score and Ratingen-Rau-Score) which can be applied by the scorer. In addition to the qualitative assessment of joints performed by the radiologist, a semi-automatic image analysis for joint detection and measurements of bone diameters and swollen tissue supports the image assessment process. More than 3000 radiographs from hands and feet of more than 200 RA patients were collected, analyzed, and statistically evaluated. Radiographs were quantified using conventional paper-based Larsen score and the X-Ray RheumaCoach software. The use of the software shortened the scoring time by about 25 percent and reduced the rate of erroneous scorings in all our studies. Compared to paper-based scoring methods, the X-Ray RheumaCoach software offers several advantages: (i) Structured data analysis and input that minimizes variance by standardization, (ii) faster and more precise calculation of sum scores and indices, (iii) permanent data storing and fast access to the software"s database, (iv) the possibility of cross-calculation to other scores, (v) semi-automatic assessment of images, and (vii) reliable documentation of results in the form of graphical printouts.

Statistical modeling of software reliability

NASA Technical Reports Server (NTRS)

Miller, Douglas R.

1992-01-01

This working paper discusses the statistical simulation part of a controlled software development experiment being conducted under the direction of the System Validation Methods Branch, Information Systems Division, NASA Langley Research Center. The experiment uses guidance and control software (GCS) aboard a fictitious planetary landing spacecraft: real-time control software operating on a transient mission. Software execution is simulated to study the statistical aspects of reliability and other failure characteristics of the software during development, testing, and random usage. Quantification of software reliability is a major goal. Various reliability concepts are discussed. Experiments are described for performing simulations and collecting appropriate simulated software performance and failure data. This data is then used to make statistical inferences about the quality of the software development and verification processes as well as inferences about the reliability of software versions and reliability growth under random testing and debugging.

How reliable is computerized assessment of readability?

PubMed

Mailloux, S L; Johnson, M E; Fisher, D G; Pettibone, T J

1995-01-01

To assess the consistency and comparability of readability software programs, four software programs (Corporate Voice, Grammatix IV, Microsoft Word for Windows, and RightWriter) were compared. Standard materials included 28 pieces of printed educational materials on human immunodeficiency virus/acquired immunodeficiency syndrome distributed nationally and the Gettysburg Address. Statistical analyses for the educational materials revealed that each of the three formulas assessed (Flesch-Kincaid, Flesch Reading Ease, and Gunning Fog Index) provided significantly different grade equivalent scores and that the Microsoft Word program provided significantly lower grade levels and was more inconsistent in the scores provided. For the Gettysburg Address, considerable variation was revealed among formulas, with the discrepancy being up to two grade levels. When averaging across formulas, there was a variation of 1.3 grade levels between the four software programs. Given the variation between formulas and programs, implications for decisions based on results of these software programs are provided.

DNA Commission of the International Society for Forensic Genetics: Recommendations on the validation of software programs performing biostatistical calculations for forensic genetics applications.

PubMed

Coble, M D; Buckleton, J; Butler, J M; Egeland, T; Fimmers, R; Gill, P; Gusmão, L; Guttman, B; Krawczak, M; Morling, N; Parson, W; Pinto, N; Schneider, P M; Sherry, S T; Willuweit, S; Prinz, M

2016-11-01

The use of biostatistical software programs to assist in data interpretation and calculate likelihood ratios is essential to forensic geneticists and part of the daily case work flow for both kinship and DNA identification laboratories. Previous recommendations issued by the DNA Commission of the International Society for Forensic Genetics (ISFG) covered the application of bio-statistical evaluations for STR typing results in identification and kinship cases, and this is now being expanded to provide best practices regarding validation and verification of the software required for these calculations. With larger multiplexes, more complex mixtures, and increasing requests for extended family testing, laboratories are relying more than ever on specific software solutions and sufficient validation, training and extensive documentation are of upmost importance. Here, we present recommendations for the minimum requirements to validate bio-statistical software to be used in forensic genetics. We distinguish between developmental validation and the responsibilities of the software developer or provider, and the internal validation studies to be performed by the end user. Recommendations for the software provider address, for example, the documentation of the underlying models used by the software, validation data expectations, version control, implementation and training support, as well as continuity and user notifications. For the internal validations the recommendations include: creating a validation plan, requirements for the range of samples to be tested, Standard Operating Procedure development, and internal laboratory training and education. To ensure that all laboratories have access to a wide range of samples for validation and training purposes the ISFG DNA commission encourages collaborative studies and public repositories of STR typing results. Published by Elsevier Ireland Ltd.

A simple linear regression method for quantitative trait loci linkage analysis with censored observations.

PubMed

Anderson, Carl A; McRae, Allan F; Visscher, Peter M

2006-07-01

Standard quantitative trait loci (QTL) mapping techniques commonly assume that the trait is both fully observed and normally distributed. When considering survival or age-at-onset traits these assumptions are often incorrect. Methods have been developed to map QTL for survival traits; however, they are both computationally intensive and not available in standard genome analysis software packages. We propose a grouped linear regression method for the analysis of continuous survival data. Using simulation we compare this method to both the Cox and Weibull proportional hazards models and a standard linear regression method that ignores censoring. The grouped linear regression method is of equivalent power to both the Cox and Weibull proportional hazards methods and is significantly better than the standard linear regression method when censored observations are present. The method is also robust to the proportion of censored individuals and the underlying distribution of the trait. On the basis of linear regression methodology, the grouped linear regression model is computationally simple and fast and can be implemented readily in freely available statistical software.

Trace element reference values in tissues from inhabitants of the EU. XII. Development of BioReVa program for statistical treatment.

PubMed

Iversen, B S; Sabbioni, E; Fortaner, S; Pietra, R; Nicolotti, A

2003-01-20

Statistical data treatment is a key point in the assessment of trace element reference values being the conclusive stage of a comprehensive and organized evaluation process of metal concentration in human body fluids. The EURO TERVIHT project (Trace Elements Reference Values in Human Tissues) was started for evaluating, checking and suggesting harmonized procedures for the establishment of trace element reference intervals in body fluids and tissues. Unfortunately, different statistical approaches are being used in this research field making data comparison difficult and in some cases impossible. Although international organizations such as International Federation of Clinical Chemistry (IFCC) or International Union of Pure and Applied Chemistry (IUPAC) have issued recommended guidelines for reference values assessment, including the statistical data treatment, a unique format and a standardized data layout is still missing. The aim of the present study is to present a software (BioReVa) running under Microsoft Windows platform suitable for calculating the reference intervals of trace elements in body matrices. The main scope for creating an ease-of-use application was to control the data distribution, to establish the reference intervals according to the accepted recommendation, on the base of the simple statistic, to get a standard presentation of experimental data and to have an application to which further need could be integrated in future. BioReVa calculates the IFCC reference intervals as well as the coverage intervals recommended by IUPAC as a supplement to the IFCC intervals. Examples of reference values and reference intervals calculated with BioReVa software concern Pb and Se in blood; Cd, In and Cr in urine, Hg and Mo in hair of different general European populations. University of Michigan

Learning Outcomes in a Laboratory Environment vs. Classroom for Statistics Instruction: An Alternative Approach Using Statistical Software

ERIC Educational Resources Information Center

McCulloch, Ryan Sterling

2017-01-01

The role of any statistics course is to increase the understanding and comprehension of statistical concepts and those goals can be achieved via both theoretical instruction and statistical software training. However, many introductory courses either forego advanced software usage, or leave its use to the student as a peripheral activity. The…

Comparison of Absolute Apparent Diffusion Coefficient (ADC) Values in ADC Maps Generated Across Different Postprocessing Software: Reproducibility in Endometrial Carcinoma.

PubMed

Ghosh, Adarsh; Singh, Tulika; Singla, Veenu; Bagga, Rashmi; Khandelwal, Niranjan

2017-12-01

Apparent diffusion coefficient (ADC) maps are usually generated by builtin software provided by the MRI scanner vendors; however, various open-source postprocessing software packages are available for image manipulation and parametric map generation. The purpose of this study is to establish the reproducibility of absolute ADC values obtained using different postprocessing software programs. DW images with three b values were obtained with a 1.5-T MRI scanner, and the trace images were obtained. ADC maps were automatically generated by the in-line software provided by the vendor during image generation and were also separately generated on postprocessing software. These ADC maps were compared on the basis of ROIs using paired t test, Bland-Altman plot, mountain plot, and Passing-Bablok regression plot. There was a statistically significant difference in the mean ADC values obtained from the different postprocessing software programs when the same baseline trace DW images were used for the ADC map generation. For using ADC values as a quantitative cutoff for histologic characterization of tissues, standardization of the postprocessing algorithm is essential across processing software packages, especially in view of the implementation of vendor-neutral archiving.

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Incorporating Code-Based Software in an Introductory Statistics Course

ERIC Educational Resources Information Center

Doehler, Kirsten; Taylor, Laura

2015-01-01

This article is based on the experiences of two statistics professors who have taught students to write and effectively utilize code-based software in a college-level introductory statistics course. Advantages of using software and code-based software in this context are discussed. Suggestions are made on how to ease students into using code with…

Statistical assessment of crosstalk enrichment between gene groups in biological networks.

PubMed

McCormack, Theodore; Frings, Oliver; Alexeyenko, Andrey; Sonnhammer, Erik L L

2013-01-01

Analyzing groups of functionally coupled genes or proteins in the context of global interaction networks has become an important aspect of bioinformatic investigations. Assessing the statistical significance of crosstalk enrichment between or within groups of genes can be a valuable tool for functional annotation of experimental gene sets. Here we present CrossTalkZ, a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. We demonstrate that the standard z-score is generally an appropriate and unbiased statistic. We further evaluate the ability of four different methods to reliably recover crosstalk within known biological pathways. We conclude that the methods preserving the second-order topological network properties perform best. Finally, we show how CrossTalkZ can be used to annotate experimental gene sets using known pathway annotations and that its performance at this task is superior to gene enrichment analysis (GEA). CrossTalkZ (available at http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/) is implemented in C++, easy to use, fast, accepts various input file formats, and produces a number of statistics. These include z-score, p-value, false discovery rate, and a test of normality for the null distributions.

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer.

PubMed

Bigler, Don C; Aksu, Yaman; Miller, David J; Yang, Qing X

2009-08-01

This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

Software Used to Generate Cancer Statistics - SEER Cancer Statistics

Cancer.gov

Videos that highlight topics and trends in cancer statistics and definitions of statistical terms. Also software tools for analyzing and reporting cancer statistics, which are used to compile SEER's annual reports.

Laharz_py: GIS tools for automated mapping of lahar inundation hazard zones

USGS Publications Warehouse

Schilling, Steve P.

2014-01-01

Laharz_py is written in the Python programming language as a suite of tools for use in ArcMap Geographic Information System (GIS). Primarily, Laharz_py is a computational model that uses statistical descriptions of areas inundated by past mass-flow events to forecast areas likely to be inundated by hypothetical future events. The forecasts use physically motivated and statistically calibrated power-law equations that each has a form A = cV2/3, relating mass-flow volume (V) to planimetric or cross-sectional areas (A) inundated by an average flow as it descends a given drainage. Calibration of the equations utilizes logarithmic transformation and linear regression to determine the best-fit values of c. The software uses values of V, an algorithm for idenitifying mass-flow source locations, and digital elevation models of topography to portray forecast hazard zones for lahars, debris flows, or rock avalanches on maps. Laharz_py offers two methods to construct areas of potential inundation for lahars: (1) Selection of a range of plausible V values results in a set of nested hazard zones showing areas likely to be inundated by a range of hypothetical flows; and (2) The user selects a single volume and a confidence interval for the prediction. In either case, Laharz_py calculates the mean expected A and B value from each user-selected value of V. However, for the second case, a single value of V yields two additional results representing the upper and lower values of the confidence interval of prediction. Calculation of these two bounding predictions require the statistically calibrated prediction equations, a user-specified level of confidence, and t-distribution statistics to calculate the standard error of regression, standard error of the mean, and standard error of prediction. The portrayal of results from these two methods on maps compares the range of inundation areas due to prediction uncertainties with uncertainties in selection of V values. The Open-File Report document contains an explanation of how to install and use the software. The Laharz_py software includes an example data set for Mount Rainier, Washington. The second part of the documentation describes how to use all of the Laharz_py tools in an example dataset at Mount Rainier, Washington.

Statistical modelling of software reliability

NASA Technical Reports Server (NTRS)

Miller, Douglas R.

1991-01-01

During the six-month period from 1 April 1991 to 30 September 1991 the following research papers in statistical modeling of software reliability appeared: (1) A Nonparametric Software Reliability Growth Model; (2) On the Use and the Performance of Software Reliability Growth Models; (3) Research and Development Issues in Software Reliability Engineering; (4) Special Issues on Software; and (5) Software Reliability and Safety.

Comparative evaluation of the accuracy of linear measurements between cone beam computed tomography and 3D microtomography.

PubMed

Mangione, Francesca; Meleo, Deborah; Talocco, Marco; Pecci, Raffaella; Pacifici, Luciano; Bedini, Rossella

2013-01-01

The aim of this study was to evaluate the influence of artifacts on the accuracy of linear measurements estimated with a common cone beam computed tomography (CBCT) system used in dental clinical practice, by comparing it with microCT system as standard reference. Ten bovine bone cylindrical samples containing one implant each, able to provide both points of reference and image quality degradation, have been scanned by CBCT and microCT systems. Thanks to the software of the two systems, for each cylindrical sample, two diameters taken at different levels, by using implants different points as references, have been measured. Results have been analyzed by ANOVA and a significant statistically difference has been found. Due to the obtained results, in this work it is possible to say that the measurements made with the two different instruments are still not statistically comparable, although in some samples were obtained similar performances and therefore not statistically significant. With the improvement of the hardware and software of CBCT systems, in the near future the two instruments will be able to provide similar performances.

Software Formal Inspections Standard

NASA Technical Reports Server (NTRS)

1993-01-01

This Software Formal Inspections Standard (hereinafter referred to as Standard) is applicable to NASA software. This Standard defines the requirements that shall be fulfilled by the software formal inspections process whenever this process is specified for NASA software. The objective of this Standard is to define the requirements for a process that inspects software products to detect and eliminate defects as early as possible in the software life cycle. The process also provides for the collection and analysis of inspection data to improve the inspection process as well as the quality of the software.

A new mathematical approach for the estimation of the AUC and its variability under different experimental designs in preclinical studies.

PubMed

Navarro-Fontestad, Carmen; González-Álvarez, Isabel; Fernández-Teruel, Carlos; Bermejo, Marival; Casabó, Vicente Germán

2012-01-01

The aim of the present work was to develop a new mathematical method for estimating the area under the curve (AUC) and its variability that could be applied in different preclinical experimental designs and amenable to be implemented in standard calculation worksheets. In order to assess the usefulness of the new approach, different experimental scenarios were studied and the results were compared with those obtained with commonly used software: WinNonlin® and Phoenix WinNonlin®. The results do not show statistical differences among the AUC values obtained by both procedures, but the new method appears to be a better estimator of the AUC standard error, measured as the coverage of 95% confidence interval. In this way, the new proposed method demonstrates to be as useful as WinNonlin® software when it was applicable. Copyright © 2011 John Wiley & Sons, Ltd.

Mathematical and Statistical Software Index. Final Report.

ERIC Educational Resources Information Center

Black, Doris E., Comp.

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

Tolerancing aspheres based on manufacturing statistics

NASA Astrophysics Data System (ADS)

Wickenhagen, S.; Möhl, A.; Fuchs, U.

2017-11-01

A standard way of tolerancing optical elements or systems is to perform a Monte Carlo based analysis within a common optical design software package. Although, different weightings and distributions are assumed they are all counting on statistics, which usually means several hundreds or thousands of systems for reliable results. Thus, employing these methods for small batch sizes is unreliable, especially when aspheric surfaces are involved. The huge database of asphericon was used to investigate the correlation between the given tolerance values and measured data sets. The resulting probability distributions of these measured data were analyzed aiming for a robust optical tolerancing process.

Statistical analysis of water-quality data containing multiple detection limits II: S-language software for nonparametric distribution modeling and hypothesis testing

USGS Publications Warehouse

Lee, L.; Helsel, D.

2007-01-01

Analysis of low concentrations of trace contaminants in environmental media often results in left-censored data that are below some limit of analytical precision. Interpretation of values becomes complicated when there are multiple detection limits in the data-perhaps as a result of changing analytical precision over time. Parametric and semi-parametric methods, such as maximum likelihood estimation and robust regression on order statistics, can be employed to model distributions of multiply censored data and provide estimates of summary statistics. However, these methods are based on assumptions about the underlying distribution of data. Nonparametric methods provide an alternative that does not require such assumptions. A standard nonparametric method for estimating summary statistics of multiply-censored data is the Kaplan-Meier (K-M) method. This method has seen widespread usage in the medical sciences within a general framework termed "survival analysis" where it is employed with right-censored time-to-failure data. However, K-M methods are equally valid for the left-censored data common in the geosciences. Our S-language software provides an analytical framework based on K-M methods that is tailored to the needs of the earth and environmental sciences community. This includes routines for the generation of empirical cumulative distribution functions, prediction or exceedance probabilities, and related confidence limits computation. Additionally, our software contains K-M-based routines for nonparametric hypothesis testing among an unlimited number of grouping variables. A primary characteristic of K-M methods is that they do not perform extrapolation and interpolation. Thus, these routines cannot be used to model statistics beyond the observed data range or when linear interpolation is desired. For such applications, the aforementioned parametric and semi-parametric methods must be used.

IMPLEMENTATION AND VALIDATION OF STATISTICAL TESTS IN RESEARCH'S SOFTWARE HELPING DATA COLLECTION AND PROTOCOLS ANALYSIS IN SURGERY.

PubMed

Kuretzki, Carlos Henrique; Campos, Antônio Carlos Ligocki; Malafaia, Osvaldo; Soares, Sandramara Scandelari Kusano de Paula; Tenório, Sérgio Bernardo; Timi, Jorge Rufino Ribas

2016-03-01

The use of information technology is often applied in healthcare. With regard to scientific research, the SINPE(c) - Integrated Electronic Protocols was created as a tool to support researchers, offering clinical data standardization. By the time, SINPE(c) lacked statistical tests obtained by automatic analysis. Add to SINPE(c) features for automatic realization of the main statistical methods used in medicine . The study was divided into four topics: check the interest of users towards the implementation of the tests; search the frequency of their use in health care; carry out the implementation; and validate the results with researchers and their protocols. It was applied in a group of users of this software in their thesis in the strict sensu master and doctorate degrees in one postgraduate program in surgery. To assess the reliability of the statistics was compared the data obtained both automatically by SINPE(c) as manually held by a professional in statistics with experience with this type of study. There was concern for the use of automatic statistical tests, with good acceptance. The chi-square, Mann-Whitney, Fisher and t-Student were considered as tests frequently used by participants in medical studies. These methods have been implemented and thereafter approved as expected. The incorporation of the automatic SINPE (c) Statistical Analysis was shown to be reliable and equal to the manually done, validating its use as a research tool for medical research.

Development of spatial data guidelines and standards: spatial data set documentation to support hydrologic analysis in the U.S. Geological Survey

USGS Publications Warehouse

Fulton, James L.

1992-01-01

Spatial data analysis has become an integral component in many surface and sub-surface hydrologic investigations within the U.S. Geological Survey (USGS). Currently, one of the largest costs in applying spatial data analysis is the cost of developing the needed spatial data. Therefore, guidelines and standards are required for the development of spatial data in order to allow for data sharing and reuse; this eliminates costly redevelopment. In order to attain this goal, the USGS is expanding efforts to identify guidelines and standards for the development of spatial data for hydrologic analysis. Because of the variety of project and database needs, the USGS has concentrated on developing standards for documenting spatial sets to aid in the assessment of data set quality and compatibility of different data sets. An interim data set documentation standard (1990) has been developed that provides a mechanism for associating a wide variety of information with a data set, including data about source material, data automation and editing procedures used, projection parameters, data statistics, descriptions of features and feature attributes, information on organizational contacts lists of operations performed on the data, and free-form comments and notes about the data, made at various times in the evolution of the data set. The interim data set documentation standard has been automated using a commercial geographic information system (GIS) and data set documentation software developed by the USGS. Where possible, USGS developed software is used to enter data into the data set documentation file automatically. The GIS software closely associates a data set with its data set documentation file; the documentation file is retained with the data set whenever it is modified, copied, or transferred to another computer system. The Water Resources Division of the USGS is continuing to develop spatial data and data processing standards, with emphasis on standards needed to support hydrologic analysis, hydrologic data processing, and publication of hydrologic thermatic maps. There is a need for the GIS vendor community to develop data set documentation tools similar to those developed by the USGS, or to incorporate USGS developed tools in their software.

Analyzing huge pathology images with open source software.

PubMed

Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

2013-06-06

Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272.

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272 PMID:23829479

A framework for incorporating DTI Atlas Builder registration into Tract-Based Spatial Statistics and a simulated comparison to standard TBSS.

PubMed

Leming, Matthew; Steiner, Rachel; Styner, Martin

2016-02-27

Tract-based spatial statistics (TBSS) 6 is a software pipeline widely employed in comparative analysis of the white matter integrity from diffusion tensor imaging (DTI) datasets. In this study, we seek to evaluate the relationship between different methods of atlas registration for use with TBSS and different measurements of DTI (fractional anisotropy, FA, axial diffusivity, AD, radial diffusivity, RD, and medial diffusivity, MD). To do so, we have developed a novel tool that builds on existing diffusion atlas building software, integrating it into an adapted version of TBSS called DAB-TBSS (DTI Atlas Builder-Tract-Based Spatial Statistics) by using the advanced registration offered in DTI Atlas Builder 7 . To compare the effectiveness of these two versions of TBSS, we also propose a framework for simulating population differences for diffusion tensor imaging data, providing a more substantive means of empirically comparing DTI group analysis programs such as TBSS. In this study, we used 33 diffusion tensor imaging datasets and simulated group-wise changes in this data by increasing, in three different simulations, the principal eigenvalue (directly altering AD), the second and third eigenvalues (RD), and all three eigenvalues (MD) in the genu, the right uncinate fasciculus, and the left IFO. Additionally, we assessed the benefits of comparing the tensors directly using a functional analysis of diffusion tensor tract statistics (FADTTS 10 ). Our results indicate comparable levels of FA-based detection between DAB-TBSS and TBSS, with standard TBSS registration reporting a higher rate of false positives in other measurements of DTI. Within the simulated changes investigated here, this study suggests that the use of DTI Atlas Builder's registration enhances TBSS group-based studies.

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

PubMed

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

2018-05-01

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

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.

Software phantom with realistic speckle modeling for validation of image analysis methods in echocardiography

NASA Astrophysics Data System (ADS)

Law, Yuen C.; Tenbrinck, Daniel; Jiang, Xiaoyi; Kuhlen, Torsten

2014-03-01

Computer-assisted processing and interpretation of medical ultrasound images is one of the most challenging tasks within image analysis. Physical phenomena in ultrasonographic images, e.g., the characteristic speckle noise and shadowing effects, make the majority of standard methods from image analysis non optimal. Furthermore, validation of adapted computer vision methods proves to be difficult due to missing ground truth information. There is no widely accepted software phantom in the community and existing software phantoms are not exible enough to support the use of specific speckle models for different tissue types, e.g., muscle and fat tissue. In this work we propose an anatomical software phantom with a realistic speckle pattern simulation to _ll this gap and provide a exible tool for validation purposes in medical ultrasound image analysis. We discuss the generation of speckle patterns and perform statistical analysis of the simulated textures to obtain quantitative measures of the realism and accuracy regarding the resulting textures.

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

An overview of the mathematical and statistical analysis component of RICIS

NASA Technical Reports Server (NTRS)

Hallum, Cecil R.

1987-01-01

Mathematical and statistical analysis components of RICIS (Research Institute for Computing and Information Systems) can be used in the following problem areas: (1) quantification and measurement of software reliability; (2) assessment of changes in software reliability over time (reliability growth); (3) analysis of software-failure data; and (4) decision logic for whether to continue or stop testing software. Other areas of interest to NASA/JSC where mathematical and statistical analysis can be successfully employed include: math modeling of physical systems, simulation, statistical data reduction, evaluation methods, optimization, algorithm development, and mathematical methods in signal processing.

Power estimation using simulations for air pollution time-series studies

PubMed Central

2012-01-01

Background Estimation of power to assess associations of interest can be challenging for time-series studies of the acute health effects of air pollution because there are two dimensions of sample size (time-series length and daily outcome counts), and because these studies often use generalized linear models to control for complex patterns of covariation between pollutants and time trends, meteorology and possibly other pollutants. In general, statistical software packages for power estimation rely on simplifying assumptions that may not adequately capture this complexity. Here we examine the impact of various factors affecting power using simulations, with comparison of power estimates obtained from simulations with those obtained using statistical software. Methods Power was estimated for various analyses within a time-series study of air pollution and emergency department visits using simulations for specified scenarios. Mean daily emergency department visit counts, model parameter value estimates and daily values for air pollution and meteorological variables from actual data (8/1/98 to 7/31/99 in Atlanta) were used to generate simulated daily outcome counts with specified temporal associations with air pollutants and randomly generated error based on a Poisson distribution. Power was estimated by conducting analyses of the association between simulated daily outcome counts and air pollution in 2000 data sets for each scenario. Power estimates from simulations and statistical software (G*Power and PASS) were compared. Results In the simulation results, increasing time-series length and average daily outcome counts both increased power to a similar extent. Our results also illustrate the low power that can result from using outcomes with low daily counts or short time series, and the reduction in power that can accompany use of multipollutant models. Power estimates obtained using standard statistical software were very similar to those from the simulations when properly implemented; implementation, however, was not straightforward. Conclusions These analyses demonstrate the similar impact on power of increasing time-series length versus increasing daily outcome counts, which has not previously been reported. Implementation of power software for these studies is discussed and guidance is provided. PMID:22995599

Power estimation using simulations for air pollution time-series studies.

PubMed

Winquist, Andrea; Klein, Mitchel; Tolbert, Paige; Sarnat, Stefanie Ebelt

2012-09-20

Estimation of power to assess associations of interest can be challenging for time-series studies of the acute health effects of air pollution because there are two dimensions of sample size (time-series length and daily outcome counts), and because these studies often use generalized linear models to control for complex patterns of covariation between pollutants and time trends, meteorology and possibly other pollutants. In general, statistical software packages for power estimation rely on simplifying assumptions that may not adequately capture this complexity. Here we examine the impact of various factors affecting power using simulations, with comparison of power estimates obtained from simulations with those obtained using statistical software. Power was estimated for various analyses within a time-series study of air pollution and emergency department visits using simulations for specified scenarios. Mean daily emergency department visit counts, model parameter value estimates and daily values for air pollution and meteorological variables from actual data (8/1/98 to 7/31/99 in Atlanta) were used to generate simulated daily outcome counts with specified temporal associations with air pollutants and randomly generated error based on a Poisson distribution. Power was estimated by conducting analyses of the association between simulated daily outcome counts and air pollution in 2000 data sets for each scenario. Power estimates from simulations and statistical software (G*Power and PASS) were compared. In the simulation results, increasing time-series length and average daily outcome counts both increased power to a similar extent. Our results also illustrate the low power that can result from using outcomes with low daily counts or short time series, and the reduction in power that can accompany use of multipollutant models. Power estimates obtained using standard statistical software were very similar to those from the simulations when properly implemented; implementation, however, was not straightforward. These analyses demonstrate the similar impact on power of increasing time-series length versus increasing daily outcome counts, which has not previously been reported. Implementation of power software for these studies is discussed and guidance is provided.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1993-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X DataSlice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1992-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X Data Slice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

Computer and Software Use in Teaching the Beginning Statistics Course.

ERIC Educational Resources Information Center

Bartz, Albert E.; Sabolik, Marisa A.

2001-01-01

Surveys the extent of computer usage in the beginning statistics course and the variety of statistics software used. Finds that 69% of the psychology departments used computers in beginning statistics courses and 90% used computer-assisted data analysis in statistics or other courses. (CMK)

A Windows application for computing standardized mortality ratios and standardized incidence ratios in cohort studies based on calculation of exact person-years at risk.

PubMed

Geiss, Karla; Meyer, Martin

2013-09-01

Standardized mortality ratios and standardized incidence ratios are widely used in cohort studies to compare mortality or incidence in a study population to that in the general population on a age-time-specific basis, but their computation is not included in standard statistical software packages. Here we present a user-friendly Microsoft Windows program for computing standardized mortality ratios and standardized incidence ratios based on calculation of exact person-years at risk stratified by sex, age and calendar time. The program offers flexible import of different file formats for input data and easy handling of general population reference rate tables, such as mortality or incidence tables exported from cancer registry databases. The application of the program is illustrated with two examples using empirical data from the Bavarian Cancer Registry. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics

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

Karpievitch, Yuliya; Stanley, Jeffrey R.; Taverner, Thomas

2009-08-15

Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level. Results: We present a statistical model that carefully accounts for informative missingness in peak intensities and allows unbiased, model-based, protein-level estimation and inference. The model is applicable to both label-based and label-free quantitation experiments. We also provide automated, model-based, algorithms for filtering of proteins and peptides as well as imputation of missing values. Two LC/MS datasets are used to illustrate themore » methods. In simulation studies, our methods are shown to achieve substantially more discoveries than standard alternatives. Availability: The software has been made available in the opensource proteomics platform DAnTE (http://omics.pnl.gov/software/). Contact: adabney@stat.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online.« less

Permutation-based inference for the AUC: A unified approach for continuous and discontinuous data.

PubMed

Pauly, Markus; Asendorf, Thomas; Konietschke, Frank

2016-11-01

We investigate rank-based studentized permutation methods for the nonparametric Behrens-Fisher problem, that is, inference methods for the area under the ROC curve. We hereby prove that the studentized permutation distribution of the Brunner-Munzel rank statistic is asymptotically standard normal, even under the alternative. Thus, incidentally providing the hitherto missing theoretical foundation for the Neubert and Brunner studentized permutation test. In particular, we do not only show its consistency, but also that confidence intervals for the underlying treatment effects can be computed by inverting this permutation test. In addition, we derive permutation-based range-preserving confidence intervals. Extensive simulation studies show that the permutation-based confidence intervals appear to maintain the preassigned coverage probability quite accurately (even for rather small sample sizes). For a convenient application of the proposed methods, a freely available software package for the statistical software R has been developed. A real data example illustrates the application. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sharing brain mapping statistical results with the neuroimaging data model

PubMed Central

Maumet, Camille; Auer, Tibor; Bowring, Alexander; Chen, Gang; Das, Samir; Flandin, Guillaume; Ghosh, Satrajit; Glatard, Tristan; Gorgolewski, Krzysztof J.; Helmer, Karl G.; Jenkinson, Mark; Keator, David B.; Nichols, B. Nolan; Poline, Jean-Baptiste; Reynolds, Richard; Sochat, Vanessa; Turner, Jessica; Nichols, Thomas E.

2016-01-01

Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publically available at: http://nidm.nidash.org/specs/nidm-results.html. PMID:27922621

Statistical methods and computing for big data.

PubMed

Wang, Chun; Chen, Ming-Hui; Schifano, Elizabeth; Wu, Jing; Yan, Jun

2016-01-01

Big data are data on a massive scale in terms of volume, intensity, and complexity that exceed the capacity of standard analytic tools. They present opportunities as well as challenges to statisticians. The role of computational statisticians in scientific discovery from big data analyses has been under-recognized even by peer statisticians. This article summarizes recent methodological and software developments in statistics that address the big data challenges. Methodologies are grouped into three classes: subsampling-based, divide and conquer, and online updating for stream data. As a new contribution, the online updating approach is extended to variable selection with commonly used criteria, and their performances are assessed in a simulation study with stream data. Software packages are summarized with focuses on the open source R and R packages, covering recent tools that help break the barriers of computer memory and computing power. Some of the tools are illustrated in a case study with a logistic regression for the chance of airline delay.

Statistical methods and computing for big data

PubMed Central

Wang, Chun; Chen, Ming-Hui; Schifano, Elizabeth; Wu, Jing

2016-01-01

Big data are data on a massive scale in terms of volume, intensity, and complexity that exceed the capacity of standard analytic tools. They present opportunities as well as challenges to statisticians. The role of computational statisticians in scientific discovery from big data analyses has been under-recognized even by peer statisticians. This article summarizes recent methodological and software developments in statistics that address the big data challenges. Methodologies are grouped into three classes: subsampling-based, divide and conquer, and online updating for stream data. As a new contribution, the online updating approach is extended to variable selection with commonly used criteria, and their performances are assessed in a simulation study with stream data. Software packages are summarized with focuses on the open source R and R packages, covering recent tools that help break the barriers of computer memory and computing power. Some of the tools are illustrated in a case study with a logistic regression for the chance of airline delay. PMID:27695593

Business Statistics Education: Content and Software in Undergraduate Business Statistics Courses.

ERIC Educational Resources Information Center

Tabatabai, Manouchehr; Gamble, Ralph

1997-01-01

Survey responses from 204 of 500 business schools identified most often topics in business statistics I and II courses. The most popular software at both levels was Minitab. Most schools required both statistics I and II. (SK)

A general framework for parametric survival analysis.

PubMed

Crowther, Michael J; Lambert, Paul C

2014-12-30

Parametric survival models are being increasingly used as an alternative to the Cox model in biomedical research. Through direct modelling of the baseline hazard function, we can gain greater understanding of the risk profile of patients over time, obtaining absolute measures of risk. Commonly used parametric survival models, such as the Weibull, make restrictive assumptions of the baseline hazard function, such as monotonicity, which is often violated in clinical datasets. In this article, we extend the general framework of parametric survival models proposed by Crowther and Lambert (Journal of Statistical Software 53:12, 2013), to incorporate relative survival, and robust and cluster robust standard errors. We describe the general framework through three applications to clinical datasets, in particular, illustrating the use of restricted cubic splines, modelled on the log hazard scale, to provide a highly flexible survival modelling framework. Through the use of restricted cubic splines, we can derive the cumulative hazard function analytically beyond the boundary knots, resulting in a combined analytic/numerical approach, which substantially improves the estimation process compared with only using numerical integration. User-friendly Stata software is provided, which significantly extends parametric survival models available in standard software. Copyright © 2014 John Wiley & Sons, Ltd.

SOCR: Statistics Online Computational Resource

PubMed Central

Dinov, Ivo D.

2011-01-01

The need for hands-on computer laboratory experience in undergraduate and graduate statistics education has been firmly established in the past decade. As a result a number of attempts have been undertaken to develop novel approaches for problem-driven statistical thinking, data analysis and result interpretation. In this paper we describe an integrated educational web-based framework for: interactive distribution modeling, virtual online probability experimentation, statistical data analysis, visualization and integration. Following years of experience in statistical teaching at all college levels using established licensed statistical software packages, like STATA, S-PLUS, R, SPSS, SAS, Systat, etc., we have attempted to engineer a new statistics education environment, the Statistics Online Computational Resource (SOCR). This resource performs many of the standard types of statistical analysis, much like other classical tools. In addition, it is designed in a plug-in object-oriented architecture and is completely platform independent, web-based, interactive, extensible and secure. Over the past 4 years we have tested, fine-tuned and reanalyzed the SOCR framework in many of our undergraduate and graduate probability and statistics courses and have evidence that SOCR resources build student’s intuition and enhance their learning. PMID:21451741

Advanced techniques and technology for efficient data storage, access, and transfer

NASA Technical Reports Server (NTRS)

Rice, Robert F.; Miller, Warner

1991-01-01

Advanced techniques for efficiently representing most forms of data are being implemented in practical hardware and software form through the joint efforts of three NASA centers. These techniques adapt to local statistical variations to continually provide near optimum code efficiency when representing data without error. Demonstrated in several earlier space applications, these techniques are the basis of initial NASA data compression standards specifications. Since the techniques clearly apply to most NASA science data, NASA invested in the development of both hardware and software implementations for general use. This investment includes high-speed single-chip very large scale integration (VLSI) coding and decoding modules as well as machine-transferrable software routines. The hardware chips were tested in the laboratory at data rates as high as 700 Mbits/s. A coding module's definition includes a predictive preprocessing stage and a powerful adaptive coding stage. The function of the preprocessor is to optimally process incoming data into a standard form data source that the second stage can handle.The built-in preprocessor of the VLSI coder chips is ideal for high-speed sampled data applications such as imaging and high-quality audio, but additionally, the second stage adaptive coder can be used separately with any source that can be externally preprocessed into the 'standard form'. This generic functionality assures that the applicability of these techniques and their recent high-speed implementations should be equally broad outside of NASA.

What Software to Use in the Teaching of Mathematical Subjects?

ERIC Educational Resources Information Center

Berežný, Štefan

2015-01-01

We can consider two basic views, when using mathematical software in the teaching of mathematical subjects. First: How to learn to use specific software for the specific tasks, e. g., software Statistica for the subjects of Applied statistics, probability and mathematical statistics, or financial mathematics. Second: How to learn to use the…

Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

PubMed

Spjuth, Ola; Willighagen, Egon L; Guha, Rajarshi; Eklund, Martin; Wikberg, Jarl Es

2010-06-30

QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but also allows for analyzing the effect descriptors have on the statistical model's performance. The presented Bioclipse plugins equip scientists with graphical tools that make QSAR-ML easily accessible for the community.

Towards interoperable and reproducible QSAR analyses: Exchange of datasets

PubMed Central

2010-01-01

Background QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. Results We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Conclusions Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but also allows for analyzing the effect descriptors have on the statistical model's performance. The presented Bioclipse plugins equip scientists with graphical tools that make QSAR-ML easily accessible for the community. PMID:20591161

Making statistical inferences about software reliability

NASA Technical Reports Server (NTRS)

Miller, Douglas R.

1988-01-01

Failure times of software undergoing random debugging can be modelled as order statistics of independent but nonidentically distributed exponential random variables. Using this model inferences can be made about current reliability and, if debugging continues, future reliability. This model also shows the difficulty inherent in statistical verification of very highly reliable software such as that used by digital avionics in commercial aircraft.

Planning the Unplanned Experiment: Assessing the Efficacy of Standards for Safety Critical Software

NASA Technical Reports Server (NTRS)

Graydon, Patrick J.; Holloway, C. Michael

2015-01-01

We need well-founded means of determining whether software is t for use in safety-critical applications. While software in industries such as aviation has an excellent safety record, the fact that software aws have contributed to deaths illustrates the need for justi ably high con dence in software. It is often argued that software is t for safety-critical use because it conforms to a standard for software in safety-critical systems. But little is known about whether such standards `work.' Reliance upon a standard without knowing whether it works is an experiment; without collecting data to assess the standard, this experiment is unplanned. This paper reports on a workshop intended to explore how standards could practicably be assessed. Planning the Unplanned Experiment: Assessing the Ecacy of Standards for Safety Critical Software (AESSCS) was held on 13 May 2014 in conjunction with the European Dependable Computing Conference (EDCC). We summarize and elaborate on the workshop's discussion of the topic, including both the presented positions and the dialogue that ensued.

Towards a Clinical Trial Protocol to Evaluate Health Information Systems: Evaluation of a Computerized System for Monitoring Tuberculosis from a Patient Perspective in Brazil.

PubMed

Crepaldi, Nathalia Yukie; de Lima, Inacia Bezerra; Vicentine, Fernanda Bergamini; Rodrigues, Lídia Maria Lourençon; Sanches, Tiago Lara Michelin; Ruffino-Netto, Antonio; Alves, Domingos; Rijo, Rui Pedro Charters Lopes

2018-05-08

Assessment of health information systems consider different aspects of the system itself. They focus or on the professional who will use the software or on its usability or on the software engineering metrics or on financial and managerial issues. The existent approaches are very resources consuming, disconnected, and not standardized. As the software becomes more critical in the health organizations and in patients, becoming used as a medical device or a medicine, there is an urgency to identify tools and methods that can be applied in the development process. The present work is one of the steps of a broader study to identify standardized protocols to evaluate the health information systems as medicines and medical devices are evaluated by clinical trials. The goal of the present work was to evaluate the effect of the introduction of an information system for monitoring tuberculosis treatment (SISTB) in a Brazilian municipality from the patients' perspective. The Patient Satisfaction Questionnaire and the Hospital Consumer Assessment of Healthcare Providers and Systems were answered by the patients before and after the SISTB introduction, for comparison. Patients from an outpatient clinic, formed the control group, that is, at this site was not implanted the SISTB. Descriptive statistics and mixed effects model were used for data analysis. Eighty-eight interviews were conducted in the study. The questionnaire's results presented better averages after the system introduction but were not considered statistically significant. Therefore, it was not possible to associate system implantation with improved patient satisfaction. The HIS evaluation need be complete, the technical and managerial evaluation, the safety, the impact on the professionals and direct and/or indirect impact on patients are important. Developing the right tools and methods that can evaluate the software in its entirety, from the beginning of the development cycle with a normalized scale, are needed.

Statistical software applications used in health services research: analysis of published studies in the U.S

PubMed Central

2011-01-01

Background This study aims to identify the statistical software applications most commonly employed for data analysis in health services research (HSR) studies in the U.S. The study also examines the extent to which information describing the specific analytical software utilized is provided in published articles reporting on HSR studies. Methods Data were extracted from a sample of 1,139 articles (including 877 original research articles) published between 2007 and 2009 in three U.S. HSR journals, that were considered to be representative of the field based upon a set of selection criteria. Descriptive analyses were conducted to categorize patterns in statistical software usage in those articles. The data were stratified by calendar year to detect trends in software use over time. Results Only 61.0% of original research articles in prominent U.S. HSR journals identified the particular type of statistical software application used for data analysis. Stata and SAS were overwhelmingly the most commonly used software applications employed (in 46.0% and 42.6% of articles respectively). However, SAS use grew considerably during the study period compared to other applications. Stratification of the data revealed that the type of statistical software used varied considerably by whether authors were from the U.S. or from other countries. Conclusions The findings highlight a need for HSR investigators to identify more consistently the specific analytical software used in their studies. Knowing that information can be important, because different software packages might produce varying results, owing to differences in the software's underlying estimation methods. PMID:21977990

[Comparison among various software for LMS growth curve fitting methods].

PubMed

Han, Lin; Wu, Wenhong; Wei, Qiuxia

2015-03-01

To explore the methods to realize the growth curve fitting of coefficients of skewness-median-coefficient of variation (LMS) using different software, and to optimize growth curve statistical method for grass-root child and adolescent staffs. Regular physical examination data of head circumference for normal infants aging 3, 6, 9 and 12 months in Baotou City were analyzed. Statistical software such as SAS, R, STATA and SPSS were used to fit the LMS growth curve and the results were evaluated upon the user 's convenience, study circle, user interface, results display forms, software update and maintenance and so on. Growth curve fitting results showed the same calculation outcome and each of statistical software had its own advantages and disadvantages. With all the evaluation aspects in consideration, R software excelled others in LMS growth curve fitting. R software have the advantage over other software in grass roots child and adolescent staff.

Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data.

PubMed

Tekwe, Carmen D; Carroll, Raymond J; Dabney, Alan R

2012-08-01

Protein abundance in quantitative proteomics is often based on observed spectral features derived from liquid chromatography mass spectrometry (LC-MS) or LC-MS/MS experiments. Peak intensities are largely non-normal in distribution. Furthermore, LC-MS-based proteomics data frequently have large proportions of missing peak intensities due to censoring mechanisms on low-abundance spectral features. Recognizing that the observed peak intensities detected with the LC-MS method are all positive, skewed and often left-censored, we propose using survival methodology to carry out differential expression analysis of proteins. Various standard statistical techniques including non-parametric tests such as the Kolmogorov-Smirnov and Wilcoxon-Mann-Whitney rank sum tests, and the parametric survival model and accelerated failure time-model with log-normal, log-logistic and Weibull distributions were used to detect any differentially expressed proteins. The statistical operating characteristics of each method are explored using both real and simulated datasets. Survival methods generally have greater statistical power than standard differential expression methods when the proportion of missing protein level data is 5% or more. In particular, the AFT models we consider consistently achieve greater statistical power than standard testing procedures, with the discrepancy widening with increasing missingness in the proportions. The testing procedures discussed in this article can all be performed using readily available software such as R. The R codes are provided as supplemental materials. ctekwe@stat.tamu.edu.

Development and Validation of a Portable Hearing Self-Testing System Based on a Notebook Personal Computer.

PubMed

Liu, Yan; Yang, Dong; Xiong, Fen; Yu, Lan; Ji, Fei; Wang, Qiu-Ju

2015-09-01

Hearing loss affects more than 27 million people in mainland China. It would be helpful to develop a portable and self-testing audiometer for the timely detection of hearing loss so that the optimal clinical therapeutic schedule can be determined. The objective of this study was to develop a software-based hearing self-testing system. The software-based self-testing system consisted of a notebook computer, an external sound card, and a pair of 10-Ω insert earphones. The system could be used to test the hearing thresholds by individuals themselves in an interactive manner using software. The reliability and validity of the system at octave frequencies of 0.25 Hz to 8.0 kHz were analyzed in three series of experiments. Thirty-seven normal-hearing particpants (74 ears) were enrolled in experiment 1. Forty individuals (80 ears) with sensorineural hearing loss (SNHL) participated in experiment 2. Thirteen normal-hearing participants (26 ears) and 37 participants (74 ears) with SNHL were enrolled in experiment 3. Each participant was enrolled in only one of the three experiments. In all experiments, pure-tone audiometry in a sound insulation room (standard test) was regarded as the gold standard. SPSS for Windows, version 17.0, was used for statistical analysis. The paired t-test was used to compare the hearing thresholds between the standard test and software-based self-testing (self-test) in experiments 1 and 2. In experiment 3 (main study), one-way analysis of variance and post hoc comparisons were used to compare the hearing thresholds among the standard test and two rounds of the self-test. Linear correlation analysis was carried out for the self-tests performed twice. The concordance was analyzed between the standard test and the self-test using the kappa method. p < 0.05 was considered statistically significant. Experiments 1 and 2: The hearing thresholds determined by the two methods were not significantly different at frequencies of 250, 500, or 8000 Hz (p > 0.05) but were significantly different at frequencies of 1000, 2000, and 4000 Hz (p < 0.05), except for 1000 Hz in the right ear in experiment 2. Experiment 3: The hearing thresholds determined by the standard test and self-tests repeated twice were not significantly different at any frequency (p > 0.05). The overall sensitivity of the self-test method was 97.6%, and the specificity was 98.3%. The sensitivity was 97.6% and the specificity was 97% for the patients with SNHL. The self-test had significant concordance with the standard test (kappa value = 0.848, p < 0.001). This portable hearing self-testing system based on a notebook personal computer is a reliable and sensitive method for hearing threshold assessment and monitoring. American Academy of Audiology.

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…

Observing Arctic Sea Ice from Bow to Screen: Introducing Ice Watch, the Data Network of Near Real-Time and Historic Observations from the Arctic Shipborne Sea Ice Standardization Tool (ASSIST)

NASA Astrophysics Data System (ADS)

Orlich, A.; Hutchings, J. K.; Green, T. M.

2013-12-01

The Ice Watch Program is an open source forum to access in situ Arctic sea ice conditions. It provides the research community and additional stakeholders a convenient resource to monitor sea ice and its role in understanding the Arctic as a system by implementing a standardized observation protocol and hosting a multi-service data portal. International vessels use the Arctic Shipborne Sea Ice Standardization Tool (ASSIST) software to report near-real time sea ice conditions while underway. Essential observations of total ice concentration, distribution of multi-year ice and other ice types, as well as their respective stage of melt are reported. These current and historic sea ice conditions are visualized on interactive maps and in a variety of statistical analyses, and with all data sets available to download for further investigation. The summer of 2012 was the debut of the ASSIST software and the Ice Watch campaign, with research vessels from six nations reporting from a wide spatio-temporal scale spanning from the Beaufort Sea, across the North Pole and Arctic Basin, the coast of Greenland and into the Kara and Barents Seas during mid-season melt and into the first stages of freeze-up. The 2013 summer field season sustained the observation and data archiving record, with participation from some of the same cruises as well as other geographic and seasonal realms covered by new users. These results are presented to illustrate the evolution of the program, increased participation and critical statistics of ice regime change and record of melt and freeze processes revealed by the data. As an ongoing effort, Ice Watch/ASSIST aims to standardize observations of Arctic-specific sea ice features and conditions while utilizing nomenclature and coding based on the World Meteorological Organization (WMO) standards and the Antarctic Sea Ice and Processes & Climate (ASPeCt) protocol. Instigated by members of the CliC Sea Ice Working Group, the program has evolved with coordination from the International Arctic Research Center, software development by the Geographic Information Network of Alaska, and funding support from the Japanese Aerospace Exploration Agency (JAXA), the Japan Agency for Marine-Earth Science & Technology (JAMSTEC), and the National Science Foundation (NSF).

Statistical methods used in the public health literature and implications for training of public health professionals

PubMed Central

Hayat, Matthew J.; Powell, Amanda; Johnson, Tessa; Cadwell, Betsy L.

2017-01-01

Statistical literacy and knowledge is needed to read and understand the public health literature. The purpose of this study was to quantify basic and advanced statistical methods used in public health research. We randomly sampled 216 published articles from seven top tier general public health journals. Studies were reviewed by two readers and a standardized data collection form completed for each article. Data were analyzed with descriptive statistics and frequency distributions. Results were summarized for statistical methods used in the literature, including descriptive and inferential statistics, modeling, advanced statistical techniques, and statistical software used. Approximately 81.9% of articles reported an observational study design and 93.1% of articles were substantively focused. Descriptive statistics in table or graphical form were reported in more than 95% of the articles, and statistical inference reported in more than 76% of the studies reviewed. These results reveal the types of statistical methods currently used in the public health literature. Although this study did not obtain information on what should be taught, information on statistical methods being used is useful for curriculum development in graduate health sciences education, as well as making informed decisions about continuing education for public health professionals. PMID:28591190

Statistical methods used in the public health literature and implications for training of public health professionals.

PubMed

Hayat, Matthew J; Powell, Amanda; Johnson, Tessa; Cadwell, Betsy L

2017-01-01

Statistical literacy and knowledge is needed to read and understand the public health literature. The purpose of this study was to quantify basic and advanced statistical methods used in public health research. We randomly sampled 216 published articles from seven top tier general public health journals. Studies were reviewed by two readers and a standardized data collection form completed for each article. Data were analyzed with descriptive statistics and frequency distributions. Results were summarized for statistical methods used in the literature, including descriptive and inferential statistics, modeling, advanced statistical techniques, and statistical software used. Approximately 81.9% of articles reported an observational study design and 93.1% of articles were substantively focused. Descriptive statistics in table or graphical form were reported in more than 95% of the articles, and statistical inference reported in more than 76% of the studies reviewed. These results reveal the types of statistical methods currently used in the public health literature. Although this study did not obtain information on what should be taught, information on statistical methods being used is useful for curriculum development in graduate health sciences education, as well as making informed decisions about continuing education for public health professionals.

NASA Software Documentation Standard

NASA Technical Reports Server (NTRS)

1991-01-01

The NASA Software Documentation Standard (hereinafter referred to as "Standard") is designed to support the documentation of all software developed for NASA; its goal is to provide a framework and model for recording the essential information needed throughout the development life cycle and maintenance of a software system. The NASA Software Documentation Standard can be applied to the documentation of all NASA software. The Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. The basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

A rule-based software test data generator

NASA Technical Reports Server (NTRS)

Deason, William H.; Brown, David B.; Chang, Kai-Hsiung; Cross, James H., II

1991-01-01

Rule-based software test data generation is proposed as an alternative to either path/predicate analysis or random data generation. A prototype rule-based test data generator for Ada programs is constructed and compared to a random test data generator. Four Ada procedures are used in the comparison. Approximately 2000 rule-based test cases and 100,000 randomly generated test cases are automatically generated and executed. The success of the two methods is compared using standard coverage metrics. Simple statistical tests showing that even the primitive rule-based test data generation prototype is significantly better than random data generation are performed. This result demonstrates that rule-based test data generation is feasible and shows great promise in assisting test engineers, especially when the rule base is developed further.

The FORTRAN static source code analyzer program (SAP) user's guide, revision 1

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Eslinger, S.

1982-01-01

The FORTRAN Static Source Code Analyzer Program (SAP) User's Guide (Revision 1) is presented. SAP is a software tool designed to assist Software Engineering Laboratory (SEL) personnel in conducting studies of FORTRAN programs. SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. This document is a revision of the previous SAP user's guide, Computer Sciences Corporation document CSC/TM-78/6045. SAP Revision 1 is the result of program modifications to provide several new reports, additional complexity analysis, and recognition of all statements described in the FORTRAN 77 standard. This document provides instructions for operating SAP and contains information useful in interpreting SAP output.

NASA software documentation standard software engineering program

NASA Technical Reports Server (NTRS)

1991-01-01

The NASA Software Documentation Standard (hereinafter referred to as Standard) can be applied to the documentation of all NASA software. This Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. This basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

MO-PIS-Exhibit Hall-01: Tools for TG-142 Linac Imaging QA I

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

Clements, M; Wiesmeyer, M

2014-06-15

Partners in Solutions is an exciting new program in which AAPM partners with our vendors to present practical “hands-on” information about the equipment and software systems that we use in our clinics. The therapy topic this year is solutions for TG-142 recommendations for linear accelerator imaging QA. Note that the sessions are being held in a special purpose room built on the Exhibit Hall Floor, to encourage further interaction with the vendors. Automated Imaging QA for TG-142 with RIT Presentation Time: 2:45 – 3:15 PM This presentation will discuss software tools for automated imaging QA and phantom analysis for TG-142.more » All modalities used in radiation oncology will be discussed, including CBCT, planar kV imaging, planar MV imaging, and imaging and treatment coordinate coincidence. Vendor supplied phantoms as well as a variety of third-party phantoms will be shown, along with appropriate analyses, proper phantom setup procedures and scanning settings, and a discussion of image quality metrics. Tools for process automation will be discussed which include: RIT Cognition (machine learning for phantom image identification), RIT Cerberus (automated file system monitoring and searching), and RunQueueC (batch processing of multiple images). In addition to phantom analysis, tools for statistical tracking, trending, and reporting will be discussed. This discussion will include an introduction to statistical process control, a valuable tool in analyzing data and determining appropriate tolerances. An Introduction to TG-142 Imaging QA Using Standard Imaging Products Presentation Time: 3:15 – 3:45 PM Medical Physicists want to understand the logic behind TG-142 Imaging QA. What is often missing is a firm understanding of the connections between the EPID and OBI phantom imaging, the software “algorithms” that calculate the QA metrics, the establishment of baselines, and the analysis and interpretation of the results. The goal of our brief presentation will be to establish and solidify these connections. Our talk will be motivated by the Standard Imaging, Inc. phantom and software solutions. We will present and explain each of the image quality metrics in TG-142 in terms of the theory, mathematics, and algorithms used to implement them in the Standard Imaging PIPSpro software. In the process, we will identify the regions of phantom images that are analyzed by each algorithm. We then will discuss the process of the creation of baselines and typical ranges of acceptable values for each imaging quality metric.« less

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

PubMed

Choi, Hyungwon; Kim, Sinae; Fermin, Damian; Tsou, Chih-Chiang; Nesvizhskii, Alexey I

2015-11-03

We introduce QPROT, a statistical framework and computational tool for differential protein expression analysis using protein intensity data. QPROT is an extension of the QSPEC suite, originally developed for spectral count data, adapted for the analysis using continuously measured protein-level intensity data. QPROT offers a new intensity normalization procedure and model-based differential expression analysis, both of which account for missing data. Determination of differential expression of each protein is based on the standardized Z-statistic based on the posterior distribution of the log fold change parameter, guided by the false discovery rate estimated by a well-known Empirical Bayes method. We evaluated the classification performance of QPROT using the quantification calibration data from the clinical proteomic technology assessment for cancer (CPTAC) study and a recently published Escherichia coli benchmark dataset, with evaluation of FDR accuracy in the latter. QPROT is a statistical framework with computational software tool for comparative quantitative proteomics analysis. It features various extensions of QSPEC method originally built for spectral count data analysis, including probabilistic treatment of missing values in protein intensity data. With the increasing popularity of label-free quantitative proteomics data, the proposed method and accompanying software suite will be immediately useful for many proteomics laboratories. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Database for the collection and analysis of clinical data and images of neoplasms of the sinonasal tract.

PubMed

Trimarchi, Matteo; Lund, Valerie J; Nicolai, Piero; Pini, Massimiliano; Senna, Massimo; Howard, David J

2004-04-01

The Neoplasms of the Sinonasal Tract software package (NSNT v 1.0) implements a complete visual database for patients with sinonasal neoplasia, facilitating standardization of data and statistical analysis. The software, which is compatible with the Macintosh and Windows platforms, provides multiuser application with a dedicated server (on Windows NT or 2000 or Macintosh OS 9 or X and a network of clients) together with web access, if required. The system hardware consists of an Apple Power Macintosh G4500 MHz computer with PCI bus, 256 Mb of RAM plus 60 Gb hard disk, or any IBM-compatible computer with a Pentium 2 processor. Image acquisition may be performed with different frame-grabber cards for analog or digital video input of different standards (PAL, SECAM, or NTSC) and levels of quality (VHS, S-VHS, Betacam, Mini DV, DV). The visual database is based on 4th Dimension by 4D Inc, and video compression is made in real-time MPEG format. Six sections have been developed: demographics, symptoms, extent of disease, radiology, treatment, and follow-up. Acquisition of data includes computed tomography and magnetic resonance imaging, histology, and endoscopy images, allowing sequential comparison. Statistical analysis integral to the program provides Kaplan-Meier survival curves. The development of a dedicated, user-friendly database for sinonasal neoplasia facilitates a multicenter network and has obvious clinical and research benefits.

Space station software reliability analysis based on failures observed during testing at the multisystem integration facility

NASA Technical Reports Server (NTRS)

Tamayo, Tak Chai

1987-01-01

Quality of software not only is vital to the successful operation of the space station, it is also an important factor in establishing testing requirements, time needed for software verification and integration as well as launching schedules for the space station. Defense of management decisions can be greatly strengthened by combining engineering judgments with statistical analysis. Unlike hardware, software has the characteristics of no wearout and costly redundancies, thus making traditional statistical analysis not suitable in evaluating reliability of software. A statistical model was developed to provide a representation of the number as well as types of failures occur during software testing and verification. From this model, quantitative measure of software reliability based on failure history during testing are derived. Criteria to terminate testing based on reliability objectives and methods to estimate the expected number of fixings required are also presented.

Quick Overview Scout 2008 Version 1.0

EPA Science Inventory

The Scout 2008 version 1.0 statistical software package has been updated from past DOS and Windows versions to provide classical and robust univariate and multivariate graphical and statistical methods that are not typically available in commercial or freeware statistical softwar...

The analysis of the statistical and historical information gathered during the development of the Shuttle Orbiter Primary Flight Software

NASA Technical Reports Server (NTRS)

Simmons, D. B.; Marchbanks, M. P., Jr.; Quick, M. J.

1982-01-01

The results of an effort to thoroughly and objectively analyze the statistical and historical information gathered during the development of the Shuttle Orbiter Primary Flight Software are given. The particular areas of interest include cost of the software, reliability of the software, requirements for the software and how the requirements changed during development of the system. Data related to the current version of the software system produced some interesting results. Suggestions are made for the saving of additional data which will allow additional investigation.

Spectral CT with metal artifacts reduction software for improvement of tumor visibility in the vicinity of gold fiducial markers.

PubMed

Brook, Olga R; Gourtsoyianni, Sofia; Brook, Alexander; Mahadevan, Anand; Wilcox, Carol; Raptopoulos, Vassilios

2012-06-01

To evaluate spectral computed tomography (CT) with metal artifacts reduction software (MARS) for reduction of metal artifacts associated with gold fiducial seeds. Thirteen consecutive patients with 37 fiducial seeds implanted for radiation therapy of abdominal lesions were included in this HIPAA-compliant, institutional review board-approved prospective study. Six patients were women (46%) and seven were men (54%). The mean age was 61.1 years (median, 58 years; range, 29-78 years). Spectral imaging was used for arterial phase CT. Images were reconstructed with and without MARS in axial, coronal, and sagittal planes. Two radiologists independently reviewed reconstructions and selected the best image, graded the visibility of the tumor, and assessed the amount of artifacts in all planes. A linear-weighted κ statistic and Wilcoxon signed-rank test were used to assess interobserver variability. Histogram analysis with the Kolmogorov-Smirnov test was used for objective evaluation of artifacts reduction. Fiducial seeds were placed in pancreas (n = 5), liver (n = 7), periportal lymph nodes (n = 1), and gallbladder bed (n = 1). MARS-reconstructed images received a better grade than those with standard reconstruction in 60% and 65% of patients by the first and second radiologist, respectively. Tumor visibility was graded higher with standard versus MARS reconstruction (grade, 3.7 ± 1.0 vs 2.8 ± 1.1; P = .001). Reduction of blooming was noted on MARS-reconstructed images (P = .01). Amount of artifacts, for both any and near field, was significantly smaller on sagittal and coronal MARS-reconstructed images than on standard reconstructions (P < .001 for all comparisons). Far-field artifacts were more prominent on axial MARS-reconstructed images than on standard reconstructions (P < .01). Linear-weighted κ statistic showed moderate to perfect agreement between radiologists. CT number distribution was narrower with MARS than with standard reconstruction in 35 of 37 patients (P < .001). Spectral CT with use of MARS improved tumor visibility in the vicinity of gold fiducial seeds.

BrightStat.com: free statistics online.

PubMed

Stricker, Daniel

2008-10-01

Powerful software for statistical analysis is expensive. Here I present BrightStat, a statistical software running on the Internet which is free of charge. BrightStat's goals, its main capabilities and functionalities are outlined. Three different sample runs, a Friedman test, a chi-square test, and a step-wise multiple regression are presented. The results obtained by BrightStat are compared with results computed by SPSS, one of the global leader in providing statistical software, and VassarStats, a collection of scripts for data analysis running on the Internet. Elementary statistics is an inherent part of academic education and BrightStat is an alternative to commercial products.

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses.

PubMed

Desai, Trunil S; Srivastava, Shireesh

2018-01-01

13 C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13 C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13 C-MFA software that works in various operating systems will enable more researchers to perform 13 C-MFA and to further modify and develop the package.

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses

PubMed Central

Desai, Trunil S.

2018-01-01

13C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13C-MFA software that works in various operating systems will enable more researchers to perform 13C-MFA and to further modify and develop the package. PMID:29736347

Software assurance standard

NASA Technical Reports Server (NTRS)

1992-01-01

This standard specifies the software assurance program for the provider of software. It also delineates the assurance activities for the provider and the assurance data that are to be furnished by the provider to the acquirer. In any software development effort, the provider is the entity or individual that actually designs, develops, and implements the software product, while the acquirer is the entity or individual who specifies the requirements and accepts the resulting products. This standard specifies at a high level an overall software assurance program for software developed for and by NASA. Assurance includes the disciplines of quality assurance, quality engineering, verification and validation, nonconformance reporting and corrective action, safety assurance, and security assurance. The application of these disciplines during a software development life cycle is called software assurance. Subsequent lower-level standards will specify the specific processes within these disciplines.

Software technology insertion: A study of success factors

NASA Technical Reports Server (NTRS)

Lydon, Tom

1990-01-01

Managing software development in large organizations has become increasingly difficult due to increasing technical complexity, stricter government standards, a shortage of experienced software engineers, competitive pressure for improved productivity and quality, the need to co-develop hardware and software together, and the rapid changes in both hardware and software technology. The 'software factory' approach to software development minimizes risks while maximizing productivity and quality through standardization, automation, and training. However, in practice, this approach is relatively inflexible when adopting new software technologies. The methods that a large multi-project software engineering organization can use to increase the likelihood of successful software technology insertion (STI), especially in a standardized engineering environment, are described.

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

DOE PAGES

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-03

Here, we compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchangemore » (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium.« less

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom.

PubMed

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-07

We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

Metric analysis and data validation across FORTRAN projects

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Selby, Richard W., Jr.; Phillips, Tsai-Yun

1983-01-01

The desire to predict the effort in developing or explaining the quality of software has led to the proposal of several metrics. As a step toward validating these metrics, the Software Engineering Laboratory (SEL) has analyzed the software science metrics, cyclomatic complexity, and various standard program measures for their relation to effort (including design through acceptance testing), development errors (both discrete and weighted according to the amount of time to locate and fix), and one another. The data investigated are collected from a project FORTRAN environment and examined across several projects at once, within individual projects and by reporting accuracy checks demonstrating the need to validate a database. When the data comes from individual programmers or certain validated projects, the metrics' correlations with actual effort seem to be strongest. For modules developed entirely by individual programmers, the validity ratios induce a statistically significant ordering of several of the metrics' correlations. When comparing the strongest correlations, neither software science's E metric cyclomatic complexity not source lines of code appears to relate convincingly better with effort than the others.

Analyzing a Mature Software Inspection Process Using Statistical Process Control (SPC)

NASA Technical Reports Server (NTRS)

Barnard, Julie; Carleton, Anita; Stamper, Darrell E. (Technical Monitor)

1999-01-01

This paper presents a cooperative effort where the Software Engineering Institute and the Space Shuttle Onboard Software Project could experiment applying Statistical Process Control (SPC) analysis to inspection activities. The topics include: 1) SPC Collaboration Overview; 2) SPC Collaboration Approach and Results; and 3) Lessons Learned.

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.

Advances in Statistical Methods for Substance Abuse Prevention Research

PubMed Central

MacKinnon, David P.; Lockwood, Chondra M.

2010-01-01

The paper describes advances in statistical methods for prevention research with a particular focus on substance abuse prevention. Standard analysis methods are extended to the typical research designs and characteristics of the data collected in prevention research. Prevention research often includes longitudinal measurement, clustering of data in units such as schools or clinics, missing data, and categorical as well as continuous outcome variables. Statistical methods to handle these features of prevention data are outlined. Developments in mediation, moderation, and implementation analysis allow for the extraction of more detailed information from a prevention study. Advancements in the interpretation of prevention research results include more widespread calculation of effect size and statistical power, the use of confidence intervals as well as hypothesis testing, detailed causal analysis of research findings, and meta-analysis. The increased availability of statistical software has contributed greatly to the use of new methods in prevention research. It is likely that the Internet will continue to stimulate the development and application of new methods. PMID:12940467

[Sem: a suitable statistical software adaptated for research in oncology].

PubMed

Kwiatkowski, F; Girard, M; Hacene, K; Berlie, J

2000-10-01

Many softwares have been adapted for medical use; they rarely enable conveniently both data management and statistics. A recent cooperative work ended up in a new software, Sem (Statistics Epidemiology Medicine), which allows data management of trials and, as well, statistical treatments on them. Very convenient, it can be used by non professional in statistics (biologists, doctors, researchers, data managers), since usually (excepted with multivariate models), the software performs by itself the most adequate test, after what complementary tests can be requested if needed. Sem data base manager (DBM) is not compatible with usual DBM: this constitutes a first protection against loss of privacy. Other shields (passwords, cryptage...) strengthen data security, all the more necessary today since Sem can be run on computers nets. Data organization enables multiplicity: forms can be duplicated by patient. Dates are treated in a special but transparent manner (sorting, date and delay calculations...). Sem communicates with common desktop softwares, often with a simple copy/paste. So, statistics can be easily performed on data stored in external calculation sheets, and slides by pasting graphs with a single mouse click (survival curves...). Already used over fifty places in different hospitals for daily work, this product, combining data management and statistics, appears to be a convenient and innovative solution.

Knowledge and utilization of computer-software for statistics among Nigerian dentists.

PubMed

Chukwuneke, F N; Anyanechi, C E; Obiakor, A O; Amobi, O; Onyejiaka, N; Alamba, I

2013-01-01

The use of computer soft ware for generation of statistic analysis has transformed health information and data to simplest form in the areas of access, storage, retrieval and analysis in the field of research. This survey therefore was carried out to assess the level of knowledge and utilization of computer software for statistical analysis among dental researchers in eastern Nigeria. Questionnaires on the use of computer software for statistical analysis were randomly distributed to 65 practicing dental surgeons of above 5 years experience in the tertiary academic hospitals in eastern Nigeria. The focus was on: years of clinical experience; research work experience; knowledge and application of computer generated software for data processing and stastistical analysis. Sixty-two (62/65; 95.4%) of these questionnaires were returned anonymously, which were used in our data analysis. Twenty-nine (29/62; 46.8%) respondents fall within those with 5-10 years of clinical experience out of which none has completed the specialist training programme. Practitioners with above 10 years clinical experiences were 33 (33/62; 53.2%) out of which 15 (15/33; 45.5%) are specialists representing 24.2% (15/62) of the total number of respondents. All the 15 specialists are actively involved in research activities and only five (5/15; 33.3%) can utilize software statistical analysis unaided. This study has i dentified poor utilization of computer software for statistic analysis among dental researchers in eastern Nigeria. This is strongly associated with lack of exposure on the use of these software early enough especially during the undergraduate training. This call for introduction of computer training programme in dental curriculum to enable practitioners develops the attitude of using computer software for their research.

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.

[Application of Stata software to test heterogeneity in meta-analysis method].

PubMed

Wang, Dan; Mou, Zhen-yun; Zhai, Jun-xia; Zong, Hong-xia; Zhao, Xiao-dong

2008-07-01

To introduce the application of Stata software to heterogeneity test in meta-analysis. A data set was set up according to the example in the study, and the corresponding commands of the methods in Stata 9 software were applied to test the example. The methods used were Q-test and I2 statistic attached to the fixed effect model forest plot, H statistic and Galbraith plot. The existence of the heterogeneity among studies could be detected by Q-test and H statistic and the degree of the heterogeneity could be detected by I2 statistic. The outliers which were the sources of the heterogeneity could be spotted from the Galbraith plot. Heterogeneity test in meta-analysis can be completed by the four methods in Stata software simply and quickly. H and I2 statistics are more robust, and the outliers of the heterogeneity can be clearly seen in the Galbraith plot among the four methods.

Bayesian inference for psychology. Part II: Example applications with JASP.

PubMed

Wagenmakers, Eric-Jan; Love, Jonathon; Marsman, Maarten; Jamil, Tahira; Ly, Alexander; Verhagen, Josine; Selker, Ravi; Gronau, Quentin F; Dropmann, Damian; Boutin, Bruno; Meerhoff, Frans; Knight, Patrick; Raj, Akash; van Kesteren, Erik-Jan; van Doorn, Johnny; Šmíra, Martin; Epskamp, Sacha; Etz, Alexander; Matzke, Dora; de Jong, Tim; van den Bergh, Don; Sarafoglou, Alexandra; Steingroever, Helen; Derks, Koen; Rouder, Jeffrey N; Morey, Richard D

2018-02-01

Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP ( http://www.jasp-stats.org ), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder's BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away.

A method for estimation of bias and variability of continuous gas monitor data: application to carbon monoxide monitor accuracy.

PubMed

Shulman, Stanley A; Smith, Jerome P

2002-01-01

A method is presented for the evaluation of the bias, variability, and accuracy of gas monitors. This method is based on using the parameters for the fitted response curves of the monitors. Thereby, variability between calibrations, between dates within each calibration period, and between different units can be evaluated at several different standard concentrations. By combining variability information with bias information, accuracy can be assessed. An example using carbon monoxide monitor data is provided. Although the most general statistical software required for these tasks is not available on a spreadsheet, when the same number of dates in a calibration period are evaluated for each monitor unit, the calculations can be done on a spreadsheet. An example of such calculations, together with the formulas needed for their implementation, is provided. In addition, the methods can be extended by use of appropriate statistical models and software to evaluate monitor trends within calibration periods, as well as consider the effects of other variables, such as humidity and temperature, on monitor variability and bias.

Standardized development of computer software. Part 2: Standards

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1978-01-01

This monograph contains standards for software development and engineering. The book sets forth rules for design, specification, coding, testing, documentation, and quality assurance audits of software; it also contains detailed outlines for the documentation to be produced.

Integrating Statistical Visualization Research into the Political Science Classroom

ERIC Educational Resources Information Center

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

2011-01-01

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

The National Streamflow Statistics Program: A Computer Program for Estimating Streamflow Statistics for Ungaged Sites

USGS Publications Warehouse

Ries(compiler), Kernell G.; With sections by Atkins, J. B.; Hummel, P.R.; Gray, Matthew J.; Dusenbury, R.; Jennings, M.E.; Kirby, W.H.; Riggs, H.C.; Sauer, V.B.; Thomas, W.O.

2007-01-01

The National Streamflow Statistics (NSS) Program is a computer program that should be useful to engineers, hydrologists, and others for planning, management, and design applications. NSS compiles all current U.S. Geological Survey (USGS) regional regression equations for estimating streamflow statistics at ungaged sites in an easy-to-use interface that operates on computers with Microsoft Windows operating systems. NSS expands on the functionality of the USGS National Flood Frequency Program, and replaces it. The regression equations included in NSS are used to transfer streamflow statistics from gaged to ungaged sites through the use of watershed and climatic characteristics as explanatory or predictor variables. Generally, the equations were developed on a statewide or metropolitan-area basis as part of cooperative study programs. Equations are available for estimating rural and urban flood-frequency statistics, such as the 1 00-year flood, for every state, for Puerto Rico, and for the island of Tutuila, American Samoa. Equations are available for estimating other statistics, such as the mean annual flow, monthly mean flows, flow-duration percentiles, and low-flow frequencies (such as the 7-day, 0-year low flow) for less than half of the states. All equations available for estimating streamflow statistics other than flood-frequency statistics assume rural (non-regulated, non-urbanized) conditions. The NSS output provides indicators of the accuracy of the estimated streamflow statistics. The indicators may include any combination of the standard error of estimate, the standard error of prediction, the equivalent years of record, or 90 percent prediction intervals, depending on what was provided by the authors of the equations. The program includes several other features that can be used only for flood-frequency estimation. These include the ability to generate flood-frequency plots, and plots of typical flood hydrographs for selected recurrence intervals, estimates of the probable maximum flood, extrapolation of the 500-year flood when an equation for estimating it is not available, and weighting techniques to improve flood-frequency estimates for gaging stations and ungaged sites on gaged streams. This report describes the regionalization techniques used to develop the equations in NSS and provides guidance on the applicability and limitations of the techniques. The report also includes a users manual and a summary of equations available for estimating basin lagtime, which is needed by the program to generate flood hydrographs. The NSS software and accompanying database, and the documentation for the regression equations included in NSS, are available on the Web at http://water.usgs.gov/software/.

[Development of a software standardizing optical density with operation settings related to several limitations].

PubMed

Tu, Xiao-Ming; Zhang, Zuo-Heng; Wan, Cheng; Zheng, Yu; Xu, Jin-Mei; Zhang, Yuan-Yuan; Luo, Jian-Ping; Wu, Hai-Wei

2012-12-01

To develop a software that can be used to standardize optical density to normalize the procedures and results of standardization in order to effectively solve several problems generated during standardization of in-direct ELISA results. The software was designed based on the I-STOD method with operation settings to solve the problems that one might encounter during the standardization. Matlab GUI was used as a tool for the development. The software was tested with the results of the detection of sera of persons from schistosomiasis japonica endemic areas. I-STOD V1.0 (WINDOWS XP/WIN 7, 0.5 GB) was successfully developed to standardize optical density. A serial of serum samples from schistosomiasis japonica endemic areas were used to examine the operational effects of I-STOD V1.0 software. The results indicated that the software successfully overcame several problems including reliability of standard curve, applicable scope of samples and determination of dilution for samples outside the scope, so that I-STOD was performed more conveniently and the results of standardization were more consistent. I-STOD V1.0 is a professional software based on I-STOD. It can be easily operated and can effectively standardize the testing results of in-direct ELISA.

JPL Space Telecommunications Radio System Operating Environment

NASA Technical Reports Server (NTRS)

Lux, James P.; Lang, Minh; Peters, Kenneth J.; Taylor, Gregory H.; Duncan, Courtney B.; Orozco, David S.; Stern, Ryan A.; Ahten, Earl R.; Girard, Mike

2013-01-01

A flight-qualified implementation of a Software Defined Radio (SDR) Operating Environment for the JPL-SDR built for the CoNNeCT Project has been developed. It is compliant with the NASA Space Telecommunications Radio System (STRS) Architecture Standard, and provides the software infrastructure for STRS compliant waveform applications. This software provides a standards-compliant abstracted view of the JPL-SDR hardware platform. It uses industry standard POSIX interfaces for most functions, as well as exposing the STRS API (Application Programming In terface) required by the standard. This software includes a standardized interface for IP components instantiated within a Xilinx FPGA (Field Programmable Gate Array). The software provides a standardized abstracted interface to platform resources such as data converters, file system, etc., which can be used by STRS standards conformant waveform applications. It provides a generic SDR operating environment with a much smaller resource footprint than similar products such as SCA (Software Communications Architecture) compliant implementations, or the DoD Joint Tactical Radio Systems (JTRS).

Study designs, use of statistical tests, and statistical analysis software choice in 2015: Results from two Pakistani monthly Medline indexed journals.

PubMed

Shaikh, Masood Ali

2017-09-01

Assessment of research articles in terms of study designs used, statistical tests applied and the use of statistical analysis programmes help determine research activity profile and trends in the country. In this descriptive study, all original articles published by Journal of Pakistan Medical Association (JPMA) and Journal of the College of Physicians and Surgeons Pakistan (JCPSP), in the year 2015 were reviewed in terms of study designs used, application of statistical tests, and the use of statistical analysis programmes. JPMA and JCPSP published 192 and 128 original articles, respectively, in the year 2015. Results of this study indicate that cross-sectional study design, bivariate inferential statistical analysis entailing comparison between two variables/groups, and use of statistical software programme SPSS to be the most common study design, inferential statistical analysis, and statistical analysis software programmes, respectively. These results echo previously published assessment of these two journals for the year 2014.

Building Energy Monitoring and Analysis

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

Hong, Tianzhen; Feng, Wei; Lu, Alison

This project aimed to develop a standard methodology for building energy data definition, collection, presentation, and analysis; apply the developed methods to a standardized energy monitoring platform, including hardware and software, to collect and analyze building energy use data; and compile offline statistical data and online real-time data in both countries for fully understanding the current status of building energy use. This helps decode the driving forces behind the discrepancy of building energy use between the two countries; identify gaps and deficiencies of current building energy monitoring, data collection, and analysis; and create knowledge and tools to collect and analyzemore » good building energy data to provide valuable and actionable information for key stakeholders.« less

[Comparision of Different Methods of Area Measurement in Irregular Scar].

PubMed

Ran, D; Li, W J; Sun, Q G; Li, J Q; Xia, Q

2016-10-01

To determine a measurement standard of irregular scar area by comparing the advantages and disadvantages of different measurement methods in measuring same irregular scar area. Irregular scar area was scanned by digital scanning and measured by coordinate reading method, AutoCAD pixel method, Photoshop lasso pixel method, Photoshop magic bar filled pixel method and Foxit PDF reading software, and some aspects of these methods such as measurement time, repeatability, whether could be recorded and whether could be traced were compared and analyzed. There was no significant difference in the scar areas by the measurement methods above. However, there was statistical difference in the measurement time and repeatability by one or multi performers and only Foxit PDF reading software could be traced back. The methods above can be used for measuring scar area, but each one has its advantages and disadvantages. It is necessary to develop new measurement software for forensic identification. Copyright© by the Editorial Department of Journal of Forensic Medicine

The Elements of an Effective Software Development Plan - Software Development Process Guidebook

DTIC Science & Technology

2011-11-11

standards and practices required for all XMPL software development. This SDP implements the <corporate> Standard Software Process (SSP). as tailored...Developing and integrating reusable software products • Approach to managing COTS/Reuse software implementation • COTS/Reuse software selection...final selection and submit to change board for approval MAINTENANCE Monitor current products for obsolescence or end of support Track new

Asthma in Adults Fact Sheet

MedlinePlus

... American Lung Association Epidemiology and Statistics Unit using SPSS software. Center for Disease Control and Prevention. Behavioral ... American Lung Association Epidemiology and Statistics Unit using SPSS software. Centers for Disease Control and Prevention. National ...

Implementation errors in the GingerALE Software: Description and recommendations.

PubMed

Eickhoff, Simon B; Laird, Angela R; Fox, P Mickle; Lancaster, Jack L; Fox, Peter T

2017-01-01

Neuroscience imaging is a burgeoning, highly sophisticated field the growth of which has been fostered by grant-funded, freely distributed software libraries that perform voxel-wise analyses in anatomically standardized three-dimensional space on multi-subject, whole-brain, primary datasets. Despite the ongoing advances made using these non-commercial computational tools, the replicability of individual studies is an acknowledged limitation. Coordinate-based meta-analysis offers a practical solution to this limitation and, consequently, plays an important role in filtering and consolidating the enormous corpus of functional and structural neuroimaging results reported in the peer-reviewed literature. In both primary data and meta-analytic neuroimaging analyses, correction for multiple comparisons is a complex but critical step for ensuring statistical rigor. Reports of errors in multiple-comparison corrections in primary-data analyses have recently appeared. Here, we report two such errors in GingerALE, a widely used, US National Institutes of Health (NIH)-funded, freely distributed software package for coordinate-based meta-analysis. These errors have given rise to published reports with more liberal statistical inferences than were specified by the authors. The intent of this technical report is threefold. First, we inform authors who used GingerALE of these errors so that they can take appropriate actions including re-analyses and corrective publications. Second, we seek to exemplify and promote an open approach to error management. Third, we discuss the implications of these and similar errors in a scientific environment dependent on third-party software. Hum Brain Mapp 38:7-11, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Space Telecommunications Radio System (STRS) Architecture Standard. Release 1.02.1

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Kacpura, Thomas J.; Handler, Louis M.; Hall, C. Steve; Mortensen, Dale J.; Johnson, Sandra K.; Briones, Janette C.; Nappier, Jennifer M.; Downey, Joseph A.; Lux, James P.

2012-01-01

This document contains the NASA architecture standard for software defined radios used in space- and ground-based platforms to enable commonality among radio developments to enhance capability and services while reducing mission and programmatic risk. Transceivers (or transponders) with functionality primarily defined in software (e.g., firmware) have the ability to change their functional behavior through software alone. This radio architecture standard offers value by employing common waveform software interfaces, method of instantiation, operation, and testing among different compliant hardware and software products. These common interfaces within the architecture abstract application software from the underlying hardware to enable technology insertion independently at either the software or hardware layer.

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.

PubMed

Davis, Sean; Meltzer, Paul S

2007-07-15

Microarray technology has become a standard molecular biology tool. Experimental data have been generated on a huge number of organisms, tissue types, treatment conditions and disease states. The Gene Expression Omnibus (Barrett et al., 2005), developed by the National Center for Bioinformatics (NCBI) at the National Institutes of Health is a repository of nearly 140,000 gene expression experiments. The BioConductor project (Gentleman et al., 2004) is an open-source and open-development software project built in the R statistical programming environment (R Development core Team, 2005) for the analysis and comprehension of genomic data. The tools contained in the BioConductor project represent many state-of-the-art methods for the analysis of microarray and genomics data. We have developed a software tool that allows access to the wealth of information within GEO directly from BioConductor, eliminating many the formatting and parsing problems that have made such analyses labor-intensive in the past. The software, called GEOquery, effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools. Facilitating analyses and meta-analyses of microarray data will increase the efficiency with which biologically important conclusions can be drawn from published genomic data. GEOquery is available as part of the BioConductor project.

Software Development Standard Processes (SDSP)

NASA Technical Reports Server (NTRS)

Lavin, Milton L.; Wang, James J.; Morillo, Ronald; Mayer, John T.; Jamshidian, Barzia; Shimizu, Kenneth J.; Wilkinson, Belinda M.; Hihn, Jairus M.; Borgen, Rosana B.; Meyer, Kenneth N.;

Software engineering standards and practices

NASA Technical Reports Server (NTRS)

Durachka, R. W.

1981-01-01

Guidelines are presented for the preparation of a software development plan. The various phases of a software development project are discussed throughout its life cycle including a general description of the software engineering standards and practices to be followed during each phase.

Software Defined Radio Standard Architecture and its Application to NASA Space Missions

NASA Technical Reports Server (NTRS)

Andro, Monty; Reinhart, Richard C.

2006-01-01

A software defined radio (SDR) architecture used in space-based platforms proposes to standardize certain aspects of radio development such as interface definitions, functional control and execution, and application software and firmware development. NASA has charted a team to develop an open software defined radio hardware and software architecture to support NASA missions and determine the viability of an Agency-wide Standard. A draft concept of the proposed standard has been released and discussed among organizations in the SDR community. Appropriate leveraging of the JTRS SCA, OMG's SWRadio Architecture and other aspects are considered. A standard radio architecture offers potential value by employing common waveform software instantiation, operation, testing and software maintenance. While software defined radios offer greater flexibility, they also poses challenges to the radio development for the space environment in terms of size, mass and power consumption and available technology. An SDR architecture for space must recognize and address the constraints of space flight hardware, and systems along with flight heritage and culture. NASA is actively participating in the development of technology and standards related to software defined radios. As NASA considers a standard radio architecture for space communications, input and coordination from government agencies, the industry, academia, and standards bodies is key to a successful architecture. The unique aspects of space require thorough investigation of relevant terrestrial technologies properly adapted to space. The talk will describe NASA's current effort to investigate SDR applications to space missions and a brief overview of a candidate architecture under consideration for space based platforms.

AstroBus On-Board Software

NASA Astrophysics Data System (ADS)

Biscarros, D.; Cantenot, C.; Séronie-Vivien, J.; Schmidt, G.

AstroBus on-board software is a customisable software for ERC32 based avionics implementing standard ESA Packet Utilization Standard functions. Its architecture based on generic design templates and relying on a library providing standard PUS TC, TM and event services enhances its reusability on various programs. Finally, AstroBus on-board software development and validation environment is based on last generation tools providing an optimised customisation environment.

48 CFR 227.7203-5 - Government rights.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Software and Computer Software Documentation 227.7203-5 Government rights. The standard license rights in computer software that a licensor grants to the Government are unlimited rights, government purpose rights, or restricted rights. The standard license in computer software documentation conveys unlimited...

48 CFR 227.7203-5 - Government rights.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Software and Computer Software Documentation 227.7203-5 Government rights. The standard license rights in computer software that a licensor grants to the Government are unlimited rights, government purpose rights, or restricted rights. The standard license in computer software documentation conveys unlimited...

48 CFR 227.7203-5 - Government rights.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Software and Computer Software Documentation 227.7203-5 Government rights. The standard license rights in computer software that a licensor grants to the Government are unlimited rights, government purpose rights, or restricted rights. The standard license in computer software documentation conveys unlimited...

48 CFR 227.7203-5 - Government rights.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Software and Computer Software Documentation 227.7203-5 Government rights. The standard license rights in computer software that a licensor grants to the Government are unlimited rights, government purpose rights, or restricted rights. The standard license in computer software documentation conveys unlimited...

48 CFR 227.7203-5 - Government rights.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Software and Computer Software Documentation 227.7203-5 Government rights. The standard license rights in computer software that a licensor grants to the Government are unlimited rights, government purpose rights, or restricted rights. The standard license in computer software documentation conveys unlimited...

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)

VOIP for Telerehabilitation: A Risk Analysis for Privacy, Security and HIPAA Compliance: Part II

PubMed Central

Watzlaf, Valerie J.M.; Moeini, Sohrab; Matusow, Laura; Firouzan, Patti

2011-01-01

In a previous publication the authors developed a privacy and security checklist to evaluate Voice over Internet Protocol (VoIP) videoconferencing software used between patients and therapists to provide telerehabilitation (TR) therapy. In this paper, the privacy and security checklist that was previously developed is used to perform a risk analysis of the top ten VoIP videoconferencing software to determine if their policies provide answers to the privacy and security checklist. Sixty percent of the companies claimed they do not listen into video-therapy calls unless maintenance is needed. Only 50% of the companies assessed use some form of encryption, and some did not specify what type of encryption was used. Seventy percent of the companies assessed did not specify any form of auditing on their servers. Statistically significant differences across company websites were found for sharing information outside of the country (p=0.010), encryption (p=0.006), and security evaluation (p=0.005). Healthcare providers considering use of VoIP software for TR services may consider using this privacy and security checklist before deciding to incorporate a VoIP software system for TR. Other videoconferencing software that is specific for TR with strong encryption, good access controls, and hardware that meets privacy and security standards should be considered for use with TR. PMID:25945177

VOIP for Telerehabilitation: A Risk Analysis for Privacy, Security and HIPAA Compliance: Part II.

PubMed

Watzlaf, Valerie J M; Moeini, Sohrab; Matusow, Laura; Firouzan, Patti

2011-01-01

In a previous publication the authors developed a privacy and security checklist to evaluate Voice over Internet Protocol (VoIP) videoconferencing software used between patients and therapists to provide telerehabilitation (TR) therapy. In this paper, the privacy and security checklist that was previously developed is used to perform a risk analysis of the top ten VoIP videoconferencing software to determine if their policies provide answers to the privacy and security checklist. Sixty percent of the companies claimed they do not listen into video-therapy calls unless maintenance is needed. Only 50% of the companies assessed use some form of encryption, and some did not specify what type of encryption was used. Seventy percent of the companies assessed did not specify any form of auditing on their servers. Statistically significant differences across company websites were found for sharing information outside of the country (p=0.010), encryption (p=0.006), and security evaluation (p=0.005). Healthcare providers considering use of VoIP software for TR services may consider using this privacy and security checklist before deciding to incorporate a VoIP software system for TR. Other videoconferencing software that is specific for TR with strong encryption, good access controls, and hardware that meets privacy and security standards should be considered for use with TR.

NASA's SDR Standard: Space Telecommunications Radio System

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Johnson, Sandra K.

2007-01-01

A software defined radio (SDR) architecture used in space-based platforms proposes to standardize certain aspects of radio development such as interface definitions, functional control and execution, and application software and firmware development. NASA has charted a team to develop an open software defined radio hardware and software architecture to support NASA missions and determine the viability of an Agency-wide Standard. A draft concept of the proposed standard has been released and discussed among organizations in the SDR community. Appropriate leveraging of the JTRS SCA, OMG s SWRadio Architecture and other aspects are considered. A standard radio architecture offers potential value by employing common waveform software instantiation, operation, testing and software maintenance. While software defined radios offer greater flexibility, they also poses challenges to the radio development for the space environment in terms of size, mass and power consumption and available technology. An SDR architecture for space must recognize and address the constraints of space flight hardware, and systems along with flight heritage and culture. NASA is actively participating in the development of technology and standards related to software defined radios. As NASA considers a standard radio architecture for space communications, input and coordination from government agencies, the industry, academia, and standards bodies is key to a successful architecture. The unique aspects of space require thorough investigation of relevant terrestrial technologies properly adapted to space. The talk will describe NASA s current effort to investigate SDR applications to space missions and a brief overview of a candidate architecture under consideration for space based platforms.

SPSS macros to compare any two fitted values from a regression model.

PubMed

Weaver, Bruce; Dubois, Sacha

2012-12-01

In regression models with first-order terms only, the coefficient for a given variable is typically interpreted as the change in the fitted value of Y for a one-unit increase in that variable, with all other variables held constant. Therefore, each regression coefficient represents the difference between two fitted values of Y. But the coefficients represent only a fraction of the possible fitted value comparisons that might be of interest to researchers. For many fitted value comparisons that are not captured by any of the regression coefficients, common statistical software packages do not provide the standard errors needed to compute confidence intervals or carry out statistical tests-particularly in more complex models that include interactions, polynomial terms, or regression splines. We describe two SPSS macros that implement a matrix algebra method for comparing any two fitted values from a regression model. The !OLScomp and !MLEcomp macros are for use with models fitted via ordinary least squares and maximum likelihood estimation, respectively. The output from the macros includes the standard error of the difference between the two fitted values, a 95% confidence interval for the difference, and a corresponding statistical test with its p-value.

Software for Statistical Analysis of Weibull Distributions with Application to Gear Fatigue Data: User Manual with Verification

NASA Technical Reports Server (NTRS)

Krantz, Timothy L.

2002-01-01

The Weibull distribution has been widely adopted for the statistical description and inference of fatigue data. This document provides user instructions, examples, and verification for software to analyze gear fatigue test data. The software was developed presuming the data are adequately modeled using a two-parameter Weibull distribution. The calculations are based on likelihood methods, and the approach taken is valid for data that include type 1 censoring. The software was verified by reproducing results published by others.

Software for Statistical Analysis of Weibull Distributions with Application to Gear Fatigue Data: User Manual with Verification

NASA Technical Reports Server (NTRS)

Kranz, Timothy L.

2002-01-01

The Weibull distribution has been widely adopted for the statistical description and inference of fatigue data. This document provides user instructions, examples, and verification for software to analyze gear fatigue test data. The software was developed presuming the data are adequately modeled using a two-parameter Weibull distribution. The calculations are based on likelihood methods, and the approach taken is valid for data that include type I censoring. The software was verified by reproducing results published by others.

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.

The GenABEL Project for statistical genomics.

PubMed

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

A new method to address verification bias in studies of clinical screening tests: cervical cancer screening assays as an example.

PubMed

Xue, Xiaonan; Kim, Mimi Y; Castle, Philip E; Strickler, Howard D

2014-03-01

Studies to evaluate clinical screening tests often face the problem that the "gold standard" diagnostic approach is costly and/or invasive. It is therefore common to verify only a subset of negative screening tests using the gold standard method. However, undersampling the screen negatives can lead to substantial overestimation of the sensitivity and underestimation of the specificity of the diagnostic test. Our objective was to develop a simple and accurate statistical method to address this "verification bias." We developed a weighted generalized estimating equation approach to estimate, in a single model, the accuracy (eg, sensitivity/specificity) of multiple assays and simultaneously compare results between assays while addressing verification bias. This approach can be implemented using standard statistical software. Simulations were conducted to assess the proposed method. An example is provided using a cervical cancer screening trial that compared the accuracy of human papillomavirus and Pap tests, with histologic data as the gold standard. The proposed approach performed well in estimating and comparing the accuracy of multiple assays in the presence of verification bias. The proposed approach is an easy to apply and accurate method for addressing verification bias in studies of multiple screening methods. Copyright © 2014 Elsevier Inc. All rights reserved.

Diversification and Challenges of Software Engineering Standards

NASA Technical Reports Server (NTRS)

Poon, Peter T.

1994-01-01

The author poses certain questions in this paper: 'In the future, should there be just one software engineering standards set? If so, how can we work towards that goal? What are the challenges of internationalizing standards?' Based on the author's personal view, the statement of his position is as follows: 'There should NOT be just one set of software engineering standards in the future. At the same time, there should NOT be the proliferation of standards, and the number of sets of standards should be kept to a minimum.It is important to understand the diversification of the areas which are spanned by the software engineering standards.' The author goes on to describe the diversification of processes, the diversification in the national and international character of standards organizations, the diversification of the professional organizations producing standards, the diversification of the types of businesses and industries, and the challenges of internationalizing standards.

Interactive Web Graphs with Fewer Restrictions

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

Space Station Software Recommendations

NASA Technical Reports Server (NTRS)

Voigt, S. (Editor)

1985-01-01

Four panels of invited experts and NASA representatives focused on the following topics: software management, software development environment, languages, and software standards. Each panel deliberated in private, held two open sessions with audience participation, and developed recommendations for the NASA Space Station Program. The major thrusts of the recommendations were as follows: (1) The software management plan should establish policies, responsibilities, and decision points for software acquisition; (2) NASA should furnish a uniform modular software support environment and require its use for all space station software acquired (or developed); (3) The language Ada should be selected for space station software, and NASA should begin to address issues related to the effective use of Ada; and (4) The space station software standards should be selected (based upon existing standards where possible), and an organization should be identified to promulgate and enforce them. These and related recommendations are described in detail in the conference proceedings.

Factors Influencing the Behavioural Intention to Use Statistical Software: The Perspective of the Slovenian Students of Social Sciences

ERIC Educational Resources Information Center

Brezavšcek, Alenka; Šparl, Petra; Žnidaršic, Anja

2017-01-01

The aim of the paper is to investigate the main factors influencing the adoption and continuous utilization of statistical software among university social sciences students in Slovenia. Based on the Technology Acceptance Model (TAM), a conceptual model was derived where five external variables were taken into account: statistical software…

Planning the Unplanned Experiment: Towards Assessing the Efficacy of Standards for Safety-Critical Software

NASA Technical Reports Server (NTRS)

Graydon, Patrick J.; Holloway, C. M.

2015-01-01

Safe use of software in safety-critical applications requires well-founded means of determining whether software is fit for such use. While software in industries such as aviation has a good safety record, little is known about whether standards for software in safety-critical applications 'work' (or even what that means). It is often (implicitly) argued that software is fit for safety-critical use because it conforms to an appropriate standard. Without knowing whether a standard works, such reliance is an experiment; without carefully collecting assessment data, that experiment is unplanned. To help plan the experiment, we organized a workshop to develop practical ideas for assessing software safety standards. In this paper, we relate and elaborate on the workshop discussion, which revealed subtle but important study design considerations and practical barriers to collecting appropriate historical data and recruiting appropriate experimental subjects. We discuss assessing standards as written and as applied, several candidate definitions for what it means for a standard to 'work,' and key assessment strategies and study techniques and the pros and cons of each. Finally, we conclude with thoughts about the kinds of research that will be required and how academia, industry, and regulators might collaborate to overcome the noted barriers.

Dealing with missing standard deviation and mean values in meta-analysis of continuous outcomes: a systematic review.

PubMed

Weir, Christopher J; Butcher, Isabella; Assi, Valentina; Lewis, Stephanie C; Murray, Gordon D; Langhorne, Peter; Brady, Marian C

2018-03-07

Rigorous, informative meta-analyses rely on availability of appropriate summary statistics or individual participant data. For continuous outcomes, especially those with naturally skewed distributions, summary information on the mean or variability often goes unreported. While full reporting of original trial data is the ideal, we sought to identify methods for handling unreported mean or variability summary statistics in meta-analysis. We undertook two systematic literature reviews to identify methodological approaches used to deal with missing mean or variability summary statistics. Five electronic databases were searched, in addition to the Cochrane Colloquium abstract books and the Cochrane Statistics Methods Group mailing list archive. We also conducted cited reference searching and emailed topic experts to identify recent methodological developments. Details recorded included the description of the method, the information required to implement the method, any underlying assumptions and whether the method could be readily applied in standard statistical software. We provided a summary description of the methods identified, illustrating selected methods in example meta-analysis scenarios. For missing standard deviations (SDs), following screening of 503 articles, fifteen methods were identified in addition to those reported in a previous review. These included Bayesian hierarchical modelling at the meta-analysis level; summary statistic level imputation based on observed SD values from other trials in the meta-analysis; a practical approximation based on the range; and algebraic estimation of the SD based on other summary statistics. Following screening of 1124 articles for methods estimating the mean, one approximate Bayesian computation approach and three papers based on alternative summary statistics were identified. Illustrative meta-analyses showed that when replacing a missing SD the approximation using the range minimised loss of precision and generally performed better than omitting trials. When estimating missing means, a formula using the median, lower quartile and upper quartile performed best in preserving the precision of the meta-analysis findings, although in some scenarios, omitting trials gave superior results. Methods based on summary statistics (minimum, maximum, lower quartile, upper quartile, median) reported in the literature facilitate more comprehensive inclusion of randomised controlled trials with missing mean or variability summary statistics within meta-analyses.

Open Architecture Standard for NASA's Software-Defined Space Telecommunications Radio Systems

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Johnson, Sandra K.; Kacpura, Thomas J.; Hall, Charles S.; Smith, Carl R.; Liebetreu, John

2008-01-01

NASA is developing an architecture standard for software-defined radios used in space- and ground-based platforms to enable commonality among radio developments to enhance capability and services while reducing mission and programmatic risk. Transceivers (or transponders) with functionality primarily defined in software (e.g., firmware) have the ability to change their functional behavior through software alone. This radio architecture standard offers value by employing common waveform software interfaces, method of instantiation, operation, and testing among different compliant hardware and software products. These common interfaces within the architecture abstract application software from the underlying hardware to enable technology insertion independently at either the software or hardware layer. This paper presents the initial Space Telecommunications Radio System (STRS) Architecture for NASA missions to provide the desired software abstraction and flexibility while minimizing the resources necessary to support the architecture.

Program Helps Standardize Documentation Of Software

NASA Technical Reports Server (NTRS)

Howe, G.

1994-01-01

Intelligent Documentation Management System, IDMS, computer program developed to assist project managers in implementing information system documentation standard known as NASA-STD-2100-91, NASA STD, COS-10300, of NASA's Software Management and Assurance Program. Standard consists of data-item descriptions or templates, each of which governs particular component of software documentation. IDMS helps program manager in tailoring documentation standard to project. Written in C language.

Environmental statistics with S-Plus

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

Millard, S.P.; Neerchal, N.K.

1999-12-01

The combination of easy-to-use software with easy access to a description of the statistical methods (definitions, concepts, etc.) makes this book an excellent resource. One of the major features of this book is the inclusion of general information on environmental statistical methods and examples of how to implement these methods using the statistical software package S-Plus and the add-in modules Environmental-Stats for S-Plus, S+SpatialStats, and S-Plus for ArcView.

Modular Software for Spacecraft Navigation Using the Global Positioning System (GPS)

NASA Technical Reports Server (NTRS)

Truong, S. H.; Hartman, K. R.; Weidow, D. A.; Berry, D. L.; Oza, D. H.; Long, A. C.; Joyce, E.; Steger, W. L.

1996-01-01

The Goddard Space Flight Center Flight Dynamics and Mission Operations Divisions have jointly investigated the feasibility of engineering modular Global Positioning SYSTEM (GPS) navigation software to support both real time flight and ground postprocessing configurations. The goals of this effort are to define standard GPS data interfaces and to engineer standard, reusable navigation software components that can be used to build a broad range of GPS navigation support applications. The paper discusses the GPS modular software (GMOD) system and operations concepts, major requirements, candidate software architecture, feasibility assessment and recommended software interface standards. In additon, ongoing efforts to broaden the scope of the initial study and to develop modular software to support autonomous navigation using GPS are addressed,

Space Telecommunications Radio Architecture (STRS)

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.

2006-01-01

A software defined radio (SDR) architecture used in space-based platforms proposes to standardize certain aspects of radio development such as interface definitions, functional control and execution, and application software and firmware development. NASA has charted a team to develop an open software defined radio hardware and software architecture to support NASA missions and determine the viability of an Agency-wide Standard. A draft concept of the proposed standard has been released and discussed among organizations in the SDR community. Appropriate leveraging of the JTRS SCA, OMG's SWRadio Architecture and other aspects are considered. A standard radio architecture offers potential value by employing common waveform software instantiation, operation, testing and software maintenance. While software defined radios offer greater flexibility, they also poses challenges to the radio development for the space environment in terms of size, mass and power consumption and available technology. An SDR architecture for space must recognize and address the constraints of space flight hardware, and systems along with flight heritage and culture. NASA is actively participating in the development of technology and standards related to software defined radios. As NASA considers a standard radio architecture for space communications, input and coordination from government agencies, the industry, academia, and standards bodies is key to a successful architecture. The unique aspects of space require thorough investigation of relevant terrestrial technologies properly adapted to space. The talk will describe NASA s current effort to investigate SDR applications to space missions and a brief overview of a candidate architecture under consideration for space based platforms.

Space Telecommunications Radio Architecture (STRS): Technical Overview

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.

2006-01-01

A software defined radio (SDR) architecture used in space-based platforms proposes to standardize certain aspects of radio development such as interface definitions, functional control and execution, and application software and firmware development. NASA has charted a team to develop an open software defined radio hardware and software architecture to support NASA missions and determine the viability of an Agency-wide Standard. A draft concept of the proposed standard has been released and discussed among organizations in the SDR community. Appropriate leveraging of the JTRS SCA, OMG s SWRadio Architecture and other aspects are considered. A standard radio architecture offers potential value by employing common waveform software instantiation, operation, testing and software maintenance. While software defined radios offer greater flexibility, they also poses challenges to the radio development for the space environment in terms of size, mass and power consumption and available technology. An SDR architecture for space must recognize and address the constraints of space flight hardware, and systems along with flight heritage and culture. NASA is actively participating in the development of technology and standards related to software defined radios. As NASA considers a standard radio architecture for space communications, input and coordination from government agencies, the industry, academia, and standards bodies is key to a successful architecture. The unique aspects of space require thorough investigation of relevant terrestrial technologies properly adapted to space. The talk will describe NASA's current effort to investigate SDR applications to space missions and a brief overview of a candidate architecture under consideration for space based platforms.

Standard practices for the implementation of computer software

NASA Technical Reports Server (NTRS)

Irvine, A. P. (Editor)

1978-01-01

A standard approach to the development of computer program is provided that covers the file cycle of software development from the planning and requirements phase through the software acceptance testing phase. All documents necessary to provide the required visibility into the software life cycle process are discussed in detail.

78 FR 47014 - Configuration Management Plans for Digital Computer Software Used in Safety Systems of Nuclear...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... Software Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear Regulatory Commission. ACTION... Computer Software Used in Safety Systems of Nuclear Power Plants.'' This RG endorses, with clarifications... Electrical and Electronic Engineers (IEEE) Standard 828-2005, ``IEEE Standard for Software Configuration...

Standardization: Hardware and Software Standardization Can Reduce Costs and Save Time

ERIC Educational Resources Information Center

Brooks-Young, Susan

2005-01-01

Sadly, technical support doesn't come cheap. One money-saving strategy that's gained popularity among school technicians is equipment and software standardization. When it works, standardization can be very effective. However, standardization has its drawbacks. This article discusses the advantages and disadvantages of standardization.

Statistical Software Engineering

DTIC Science & Technology

1998-04-13

multiversion software subject to coincident errors. IEEE Trans. Software Eng. SE-11:1511-1517. Eckhardt, D.E., A.K Caglayan, J.C. Knight, L.D. Lee, D.F...J.C. and N.G. Leveson. 1986. Experimental evaluation of the assumption of independence in multiversion software. IEEE Trans. Software

Prediction of Regulation Reserve Requirements in California ISO Control Area based on BAAL Standard

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

Etingov, Pavel V.; Makarov, Yuri V.; Samaan, Nader A.

This paper presents new methodologies developed at Pacific Northwest National Laboratory (PNNL) to estimate regulation capacity requirements in the California ISO control area. Two approaches have been developed: (1) an approach based on statistical analysis of actual historical area control error (ACE) and regulation data, and (2) an approach based on balancing authority ACE limit control performance standard. The approaches predict regulation reserve requirements on a day-ahead basis including upward and downward requirements, for each operating hour of a day. California ISO data has been used to test the performance of the proposed algorithms. Results show that software tool allowsmore » saving up to 30% on the regulation procurements cost .« less

PyEvolve: a toolkit for statistical modelling of molecular evolution.

PubMed

Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Cath; Wakefield, Matthew J; Isaev, Alexander; Huttley, Gavin A

2004-01-05

Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

Exponential order statistic models of software reliability growth

NASA Technical Reports Server (NTRS)

Miller, D. R.

1985-01-01

Failure times of a software reliabilty growth process are modeled as order statistics of independent, nonidentically distributed exponential random variables. The Jelinsky-Moranda, Goel-Okumoto, Littlewood, Musa-Okumoto Logarithmic, and Power Law models are all special cases of Exponential Order Statistic Models, but there are many additional examples also. Various characterizations, properties and examples of this class of models are developed and presented.

Automated system for the on-line monitoring of powder blending processes using near-infrared spectroscopy. Part I. System development and control.

PubMed

Hailey, P A; Doherty, P; Tapsell, P; Oliver, T; Aldridge, P K

1996-03-01

An automated system for the on-line monitoring of powder blending processes is described. The system employs near-infrared (NIR) spectroscopy using fibre-optics and a graphical user interface (GUI) developed in the LabVIEW environment. The complete supervisory control and data analysis (SCADA) software controls blender and spectrophotometer operation and performs statistical spectral data analysis in real time. A data analysis routine using standard deviation is described to demonstrate an approach to the real-time determination of blend homogeneity.

Statistical Software and Artificial Intelligence: A Watershed in Applications Programming.

ERIC Educational Resources Information Center

Pickett, John C.

1984-01-01

AUTOBJ and AUTOBOX are revolutionary software programs which contain the first application of artificial intelligence to statistical procedures used in analysis of time series data. The artificial intelligence included in the programs and program features are discussed. (JN)

Development of parallel line analysis criteria for recombinant adenovirus potency assay and definition of a unit of potency.

PubMed

Ogawa, Yasushi; Fawaz, Farah; Reyes, Candice; Lai, Julie; Pungor, Erno

2007-01-01

Parameter settings of a parallel line analysis procedure were defined by applying statistical analysis procedures to the absorbance data from a cell-based potency bioassay for a recombinant adenovirus, Adenovirus 5 Fibroblast Growth Factor-4 (Ad5FGF-4). The parallel line analysis was performed with a commercially available software, PLA 1.2. The software performs Dixon outlier test on replicates of the absorbance data, performs linear regression analysis to define linear region of the absorbance data, and tests parallelism between the linear regions of standard and sample. Width of Fiducial limit, expressed as a percent of the measured potency, was developed as a criterion for rejection of the assay data and to significantly improve the reliability of the assay results. With the linear range-finding criteria of the software set to a minimum of 5 consecutive dilutions and best statistical outcome, and in combination with the Fiducial limit width acceptance criterion of <135%, 13% of the assay results were rejected. With these criteria applied, the assay was found to be linear over the range of 0.25 to 4 relative potency units, defined as the potency of the sample normalized to the potency of Ad5FGF-4 standard containing 6 x 10(6) adenovirus particles/mL. The overall precision of the assay was estimated to be 52%. Without the application of Fiducial limit width criterion, the assay results were not linear over the range, and an overall precision of 76% was calculated from the data. An absolute unit of potency for the assay was defined by using the parallel line analysis procedure as the amount of Ad5FGF-4 that results in an absorbance value that is 121% of the average absorbance readings of the wells containing cells not infected with the adenovirus.

Contracting for Computer Software in Standardized Computer Languages

PubMed Central

Brannigan, Vincent M.; Dayhoff, Ruth E.

1982-01-01

The interaction between standardized computer languages and contracts for programs which use these languages is important to the buyer or seller of software. The rationale for standardization, the problems in standardizing computer languages, and the difficulties of determining whether the product conforms to the standard are issues which must be understood. The contract law processes of delivery, acceptance testing, acceptance, rejection, and revocation of acceptance are applicable to the contracting process for standard language software. Appropriate contract language is suggested for requiring strict compliance with a standard, and an overview of remedies is given for failure to comply.

The GenABEL Project for statistical genomics

PubMed Central

Karssen, Lennart C.; van Duijn, Cornelia M.; Aulchenko, Yurii S.

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

Rapid processing of PET list-mode data for efficient uncertainty estimation and data analysis

NASA Astrophysics Data System (ADS)

Markiewicz, P. J.; Thielemans, K.; Schott, J. M.; Atkinson, D.; Arridge, S. R.; Hutton, B. F.; Ourselin, S.

2016-07-01

In this technical note we propose a rapid and scalable software solution for the processing of PET list-mode data, which allows the efficient integration of list mode data processing into the workflow of image reconstruction and analysis. All processing is performed on the graphics processing unit (GPU), making use of streamed and concurrent kernel execution together with data transfers between disk and CPU memory as well as CPU and GPU memory. This approach leads to fast generation of multiple bootstrap realisations, and when combined with fast image reconstruction and analysis, it enables assessment of uncertainties of any image statistic and of any component of the image generation process (e.g. random correction, image processing) within reasonable time frames (e.g. within five minutes per realisation). This is of particular value when handling complex chains of image generation and processing. The software outputs the following: (1) estimate of expected random event data for noise reduction; (2) dynamic prompt and random sinograms of span-1 and span-11 and (3) variance estimates based on multiple bootstrap realisations of (1) and (2) assuming reasonable count levels for acceptable accuracy. In addition, the software produces statistics and visualisations for immediate quality control and crude motion detection, such as: (1) count rate curves; (2) centre of mass plots of the radiodistribution for motion detection; (3) video of dynamic projection views for fast visual list-mode skimming and inspection; (4) full normalisation factor sinograms. To demonstrate the software, we present an example of the above processing for fast uncertainty estimation of regional SUVR (standard uptake value ratio) calculation for a single PET scan of 18F-florbetapir using the Siemens Biograph mMR scanner.

Can dead man tooth do tell tales? Tooth prints in forensic identification

PubMed Central

Christopher, Vineetha; Murthy, Sarvani; Ashwinirani, S. R.; Prasad, Kulkarni; Girish, Suragimath; Vinit, Shashikanth Patil

2017-01-01

Background: We know that teeth trouble us a lot when we are alive, but they last longer for thousands of years even after we are dead. Teeth being the strongest and resistant structure are the most significant tool in forensic investigations. Patterns of enamel rod end on the tooth surface are known as tooth prints. Aim: This study is aimed to know whether these tooth prints can become a forensic tool in personal identification such as finger prints. A study has been targeted toward the same. Settings and Design: In the present in-vivo study, acetate peel technique has been used to obtain the replica of enamel rod end patterns. Materials and Methods: Tooth prints of upper first premolars were recorded from 80 individuals after acid etching using cellulose acetate strips. Then, digital images of the tooth prints obtained at two different intervals were subjected to biometric conversion using Verifinger standard software development kit version 6.5 software followed by the use of Automated Fingerprint Identification System (AFIS) software for comparison of the tooth prints. Similarly, each individual's finger prints were also recorded and were subjected to the same software. Statistical Analysis: Further, recordings of AFIS scores obtained from images were statistically analyzed using Cronbach's test. Results: We observed that comparing two tooth prints taken from an individual at two intervals exhibited similarity in many cases, with wavy pattern tooth print being the predominant type. However, the same prints showed dissimilarity when compared with other individuals. We also found that most of the individuals with whorl pattern finger print showed wavy pattern tooth print and few loop type fingerprints showed linear pattern of tooth prints. Conclusions: Further more experiments on both tooth prints and finger prints are required in establishing an individual's identity. PMID:28584483

NASA Software Safety Standard

NASA Technical Reports Server (NTRS)

Rosenberg, Linda

1997-01-01

If software is a critical element in a safety critical system, it is imperative to implement a systematic approach to software safety as an integral part of the overall system safety programs. The NASA-STD-8719.13A, "NASA Software Safety Standard", describes the activities necessary to ensure that safety is designed into software that is acquired or developed by NASA, and that safety is maintained throughout the software life cycle. A PDF version, is available on the WWW from Lewis. A Guidebook that will assist in the implementation of the requirements in the Safety Standard is under development at the Lewis Research Center (LeRC). After completion, it will also be available on the WWW from Lewis.

NASA's Software Safety Standard

NASA Technical Reports Server (NTRS)

Ramsay, Christopher M.

2007-01-01

NASA relies more and more on software to control, monitor, and verify its safety critical systems, facilities and operations. Since the 1960's there has hardly been a spacecraft launched that does not have a computer on board that will provide command and control services. There have been recent incidents where software has played a role in high-profile mission failures and hazardous incidents. For example, the Mars Orbiter, Mars Polar Lander, the DART (Demonstration of Autonomous Rendezvous Technology), and MER (Mars Exploration Rover) Spirit anomalies were all caused or contributed to by software. The Mission Control Centers for the Shuttle, ISS, and unmanned programs are highly dependant on software for data displays, analysis, and mission planning. Despite this growing dependence on software control and monitoring, there has been little to no consistent application of software safety practices and methodology to NASA's projects with safety critical software. Meanwhile, academia and private industry have been stepping forward with procedures and standards for safety critical systems and software, for example Dr. Nancy Leveson's book Safeware: System Safety and Computers. The NASA Software Safety Standard, originally published in 1997, was widely ignored due to its complexity and poor organization. It also focused on concepts rather than definite procedural requirements organized around a software project lifecycle. Led by NASA Headquarters Office of Safety and Mission Assurance, the NASA Software Safety Standard has recently undergone a significant update. This new standard provides the procedures and guidelines for evaluating a project for safety criticality and then lays out the minimum project lifecycle requirements to assure the software is created, operated, and maintained in the safest possible manner. This update of the standard clearly delineates the minimum set of software safety requirements for a project without detailing the implementation for those requirements. This allows the projects leeway to meet these requirements in many forms that best suit a particular project's needs and safety risk. In other words, it tells the project what to do, not how to do it. This update also incorporated advances in the state of the practice of software safety from academia and private industry. It addresses some of the more common issues now facing software developers in the NASA environment such as the use of Commercial-Off-the-Shelf Software (COTS), Modified OTS (MOTS), Government OTS (GOTS), and reused software. A team from across NASA developed the update and it has had both NASA-wide internal reviews by software engineering, quality, safety, and project management. It has also had expert external review. This presentation and paper will discuss the new NASA Software Safety Standard, its organization, and key features. It will start with a brief discussion of some NASA mission failures and incidents that had software as one of their root causes. It will then give a brief overview of the NASA Software Safety Process. This will include an overview of the key personnel responsibilities and functions that must be performed for safety-critical software.

NASA's Software Safety Standard

NASA Technical Reports Server (NTRS)

Ramsay, Christopher M.

2005-01-01

NASA (National Aeronautics and Space Administration) relies more and more on software to control, monitor, and verify its safety critical systems, facilities and operations. Since the 1960's there has hardly been a spacecraft (manned or unmanned) launched that did not have a computer on board that provided vital command and control services. Despite this growing dependence on software control and monitoring, there has been no consistent application of software safety practices and methodology to NASA's projects with safety critical software. Led by the NASA Headquarters Office of Safety and Mission Assurance, the NASA Software Safety Standard (STD-18l9.13B) has recently undergone a significant update in an attempt to provide that consistency. This paper will discuss the key features of the new NASA Software Safety Standard. It will start with a brief history of the use and development of software in safety critical applications at NASA. It will then give a brief overview of the NASA Software Working Group and the approach it took to revise the software engineering process across the Agency.

Software Formal Inspections Guidebook

NASA Technical Reports Server (NTRS)

1993-01-01

The Software Formal Inspections Guidebook is designed to support the inspection process of software developed by and for NASA. This document provides information on how to implement a recommended and proven method for conducting formal inspections of NASA software. This Guidebook is a companion document to NASA Standard 2202-93, Software Formal Inspections Standard, approved April 1993, which provides the rules, procedures, and specific requirements for conducting software formal inspections. Application of the Formal Inspections Standard is optional to NASA program or project management. In cases where program or project management decide to use the formal inspections method, this Guidebook provides additional information on how to establish and implement the process. The goal of the formal inspections process as documented in the above-mentioned Standard and this Guidebook is to provide a framework and model for an inspection process that will enable the detection and elimination of defects as early as possible in the software life cycle. An ancillary aspect of the formal inspection process incorporates the collection and analysis of inspection data to effect continual improvement in the inspection process and the quality of the software subjected to the process.

Certification Processes for Safety-Critical and Mission-Critical Aerospace Software

NASA Technical Reports Server (NTRS)

Nelson, Stacy

2003-01-01

This document is a quick reference guide with an overview of the processes required to certify safety-critical and mission-critical flight software at selected NASA centers and the FAA. Researchers and software developers can use this guide to jumpstart their understanding of how to get new or enhanced software onboard an aircraft or spacecraft. The introduction contains aerospace industry definitions of safety and safety-critical software, as well as, the current rationale for certification of safety-critical software. The Standards for Safety-Critical Aerospace Software section lists and describes current standards including NASA standards and RTCA DO-178B. The Mission-Critical versus Safety-Critical software section explains the difference between two important classes of software: safety-critical software involving the potential for loss of life due to software failure and mission-critical software involving the potential for aborting a mission due to software failure. The DO-178B Safety-critical Certification Requirements section describes special processes and methods required to obtain a safety-critical certification for aerospace software flying on vehicles under auspices of the FAA. The final two sections give an overview of the certification process used at Dryden Flight Research Center and the approval process at the Jet Propulsion Lab (JPL).

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Creation of a virtual cutaneous tissue bank

NASA Astrophysics Data System (ADS)

LaFramboise, William A.; Shah, Sujal; Hoy, R. W.; Letbetter, D.; Petrosko, P.; Vennare, R.; Johnson, Peter C.

2000-04-01

Cellular and non-cellular constituents of skin contain fundamental morphometric features and structural patterns that correlate with tissue function. High resolution digital image acquisitions performed using an automated system and proprietary software to assemble adjacent images and create a contiguous, lossless, digital representation of individual microscope slide specimens. Serial extraction, evaluation and statistical analysis of cutaneous feature is performed utilizing an automated analysis system, to derive normal cutaneous parameters comprising essential structural skin components. Automated digital cutaneous analysis allows for fast extraction of microanatomic dat with accuracy approximating manual measurement. The process provides rapid assessment of feature both within individual specimens and across sample populations. The images, component data, and statistical analysis comprise a bioinformatics database to serve as an architectural blueprint for skin tissue engineering and as a diagnostic standard of comparison for pathologic specimens.

PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

NASA Astrophysics Data System (ADS)

Frigori, Rafael B.

2017-06-01

PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on Aβ25-33 fragments and their cross-seeding with IAPP20-29 isoforms. Excellent parallel scaling is observed, even under numerically difficult first-order like phase transitions, which are properly described by the built-in fully reconfigurable force fields. Still, the package is free and open source, this shall motivate users to readily adapt it to specific purposes.

Integrated data management for clinical studies: automatic transformation of data models with semantic annotations for principal investigators, data managers and statisticians.

PubMed

Dugas, Martin; Dugas-Breit, Susanne

2014-01-01

Design, execution and analysis of clinical studies involves several stakeholders with different professional backgrounds. Typically, principle investigators are familiar with standard office tools, data managers apply electronic data capture (EDC) systems and statisticians work with statistics software. Case report forms (CRFs) specify the data model of study subjects, evolve over time and consist of hundreds to thousands of data items per study. To avoid erroneous manual transformation work, a converting tool for different representations of study data models was designed. It can convert between office format, EDC and statistics format. In addition, it supports semantic annotations, which enable precise definitions for data items. A reference implementation is available as open source package ODMconverter at http://cran.r-project.org.

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

PubMed

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

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

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

PubMed Central

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

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

An empirical evaluation of software quality assurance practices and challenges in a developing country: a comparison of Nigeria and Turkey.

PubMed

Sowunmi, Olaperi Yeside; Misra, Sanjay; Fernandez-Sanz, Luis; Crawford, Broderick; Soto, Ricardo

2016-01-01

The importance of quality assurance in the software development process cannot be overemphasized because its adoption results in high reliability and easy maintenance of the software system and other software products. Software quality assurance includes different activities such as quality control, quality management, quality standards, quality planning, process standardization and improvement amongst others. The aim of this work is to further investigate the software quality assurance practices of practitioners in Nigeria. While our previous work covered areas on quality planning, adherence to standardized processes and the inherent challenges, this work has been extended to include quality control, software process improvement and international quality standard organization membership. It also makes comparison based on a similar study carried out in Turkey. The goal is to generate more robust findings that can properly support decision making by the software community. The qualitative research approach, specifically, the use of questionnaire research instruments was applied to acquire data from software practitioners. In addition to the previous results, it was observed that quality assurance practices are quite neglected and this can be the cause of low patronage. Moreover, software practitioners are neither aware of international standards organizations or the required process improvement techniques; as such their claimed standards are not aligned to those of accredited bodies, and are only limited to their local experience and knowledge, which makes it questionable. The comparison with Turkey also yielded similar findings, making the results typical of developing countries. The research instrument used was tested for internal consistency using the Cronbach's alpha, and it was proved reliable. For the software industry in developing countries to grow strong and be a viable source of external revenue, software assurance practices have to be taken seriously because its effect is evident in the final product. Moreover, quality frameworks and tools which require minimum time and cost are highly needed in these countries.

Supporting the Use of CERT (registered trademark) Secure Coding Standards in DoD Acquisitions

DTIC Science & Technology

2012-07-01

Capability Maturity Model IntegrationSM (CMMI®) [Davis 2009]. SM Team Software Process, TSP, and Capability Maturity Model Integration are service...STP Software Test Plan TEP Test and Evaluation Plan TSP Team Software Process V & V verification and validation CMU/SEI-2012-TN-016 | 47...Supporting the Use of CERT® Secure Coding Standards in DoD Acquisitions Tim Morrow ( Software Engineering Institute) Robert Seacord ( Software

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

Utilization of Solar Dynamics Observatory space weather digital image data for comparative analysis with application to Baryon Oscillation Spectroscopic Survey

NASA Astrophysics Data System (ADS)

Shekoyan, V.; Dehipawala, S.; Liu, Ernest; Tulsee, Vivek; Armendariz, R.; Tremberger, G.; Holden, T.; Marchese, P.; Cheung, T.

2012-10-01

Digital solar image data is available to users with access to standard, mass-market software. Many scientific projects utilize the Flexible Image Transport System (FITS) format, which requires specialized software typically used in astrophysical research. Data in the FITS format includes photometric and spatial calibration information, which may not be useful to researchers working with self-calibrated, comparative approaches. This project examines the advantages of using mass-market software with readily downloadable image data from the Solar Dynamics Observatory for comparative analysis over with the use of specialized software capable of reading data in the FITS format. Comparative analyses of brightness statistics that describe the solar disk in the study of magnetic energy using algorithms included in mass-market software have been shown to give results similar to analyses using FITS data. The entanglement of magnetic energy associated with solar eruptions, as well as the development of such eruptions, has been characterized successfully using mass-market software. The proposed algorithm would help to establish a publicly accessible, computing network that could assist in exploratory studies of all FITS data. The advances in computer, cell phone and tablet technology could incorporate such an approach readily for the enhancement of high school and first-year college space weather education on a global scale. Application to ground based data such as that contained in the Baryon Oscillation Spectroscopic Survey is discussed.

Air Traffic Control Improvement Using Prioritized CSMA

NASA Technical Reports Server (NTRS)

Robinson, Daryl C.

2001-01-01

Version 7 simulations of the industry-standard network simulation software "OPNET" are presented of two applications of the Aeronautical Telecommunications Network (ATN), Controller Pilot Data Link Communications (CPDLC) and Automatic Dependent Surveillance-Broadcast mode (ADS-B), over VHF Data Link mode 2 (VDL-2). Communication is modeled for air traffic between just three cities. All aircraft are assumed to have the same equipage. The simulation involves Air Traffic Control (ATC) ground stations and 105 aircraft taking off, flying realistic free-flight trajectories, and landing in a 24-hr period. All communication is modeled as unreliable. Collision-less, prioritized carrier sense multiple access (CSMA) is successfully tested. The statistics presented include latency, queue length, and packet loss. This research may show that a communications system simpler than the currently accepted standard envisioned may not only suffice, but also surpass performance of the standard at a lower cost of deployment.

Implementation of a data management software system for SSME test history data

NASA Technical Reports Server (NTRS)

Abernethy, Kenneth

1986-01-01

The implementation of a software system for managing Space Shuttle Main Engine (SSME) test/flight historical data is presented. The software system uses the database management system RIM7 for primary data storage and routine data management, but includes several FORTRAN programs, described here, which provide customized access to the RIM7 database. The consolidation, modification, and transfer of data from the database THIST, to the RIM7 database THISRM is discussed. The RIM7 utility modules for generating some standard reports from THISRM and performing some routine updating and maintenance are briefly described. The FORTRAN accessing programs described include programs for initial loading of large data sets into the database, capturing data from files for database inclusion, and producing specialized statistical reports which cannot be provided by the RIM7 report generator utility. An expert system tutorial, constructed using the expert system shell product INSIGHT2, is described. Finally, a potential expert system, which would analyze data in the database, is outlined. This system could use INSIGHT2 as well and would take advantage of RIM7's compatibility with the microcomputer database system RBase 5000.

Detailed analysis of complex single molecule FRET data with the software MASH

NASA Astrophysics Data System (ADS)

Hadzic, Mélodie C. A. S.; Kowerko, Danny; Börner, Richard; Zelger-Paulus, Susann; Sigel, Roland K. O.

2016-04-01

The processing and analysis of surface-immobilized single molecule FRET (Förster resonance energy transfer) data follows systematic steps (e.g. single molecule localization, clearance of different sources of noise, selection of the conformational and kinetic model, etc.) that require a solid knowledge in optics, photophysics, signal processing and statistics. The present proceeding aims at standardizing and facilitating procedures for single molecule detection by guiding the reader through an optimization protocol for a particular experimental data set. Relevant features were determined from single molecule movies (SMM) imaging Cy3- and Cy5-labeled Sc.ai5γ group II intron molecules synthetically recreated, to test the performances of four different detection algorithms. Up to 120 different parameterizations per method were routinely evaluated to finally establish an optimum detection procedure. The present protocol is adaptable to any movie displaying surface-immobilized molecules, and can be easily reproduced with our home-written software MASH (multifunctional analysis software for heterogeneous data) and script routines (both available in the download section of www.chem.uzh.ch/rna).

BRIDG: a domain information model for translational and clinical protocol-driven research.

PubMed

Becnel, Lauren B; Hastak, Smita; Ver Hoef, Wendy; Milius, Robert P; Slack, MaryAnn; Wold, Diane; Glickman, Michael L; Brodsky, Boris; Jaffe, Charles; Kush, Rebecca; Helton, Edward

2017-09-01

It is critical to integrate and analyze data from biological, translational, and clinical studies with data from health systems; however, electronic artifacts are stored in thousands of disparate systems that are often unable to readily exchange data. To facilitate meaningful data exchange, a model that presents a common understanding of biomedical research concepts and their relationships with health care semantics is required. The Biomedical Research Integrated Domain Group (BRIDG) domain information model fulfills this need. Software systems created from BRIDG have shared meaning "baked in," enabling interoperability among disparate systems. For nearly 10 years, the Clinical Data Standards Interchange Consortium, the National Cancer Institute, the US Food and Drug Administration, and Health Level 7 International have been key stakeholders in developing BRIDG. BRIDG is an open-source Unified Modeling Language-class model developed through use cases and harmonization with other models. With its 4+ releases, BRIDG includes clinical and now translational research concepts in its Common, Protocol Representation, Study Conduct, Adverse Events, Regulatory, Statistical Analysis, Experiment, Biospecimen, and Molecular Biology subdomains. The model is a Clinical Data Standards Interchange Consortium, Health Level 7 International, and International Standards Organization standard that has been utilized in national and international standards-based software development projects. It will continue to mature and evolve in the areas of clinical imaging, pathology, ontology, and vocabulary support. BRIDG 4.1.1 and prior releases are freely available at https://bridgmodel.nci.nih.gov . © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A Probabilistic Software System Attribute Acceptance Paradigm for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2005-01-01

Standard software requirement formats are written from top-down perspectives only, that is, from an ideal notion of a client s needs. Despite the exactness of the standard format, software and system errors in designed systems have abounded. Bad and inadequate requirements have resulted in cost overruns, schedule slips and lost profitability. Commercial off-the-shelf (COTS) software components are even more troublesome than designed systems because they are often provided as is and subsequently delivered with unsubstantiated validation of described capabilities. For COTS software, there needs to be a way to express the client s software needs in a consistent and formal manner using software system attributes derived from software quality standards. Additionally, the format needs to be amenable to software evaluation processes that integrate observable evidence garnered from historical data. This paper presents a paradigm that effectively bridges the gap between what a client desires (top-down) and what has been demonstrated (bottom-up) for COTS software evaluation. The paradigm addresses the specification of needs before the software evaluation is performed and can be used to increase the shared understanding between clients and software evaluators about what is required and what is technically possible.

Development of the quality assessment model of EHR software in family medicine practices: research based on user satisfaction.

PubMed

Kralj, Damir; Kern, Josipa; Tonkovic, Stanko; Koncar, Miroslav

2015-09-09

Family medicine practices (FMPs) make the basis for the Croatian health care system. Use of electronic health record (EHR) software is mandatory and it plays an important role in running these practices, but important functional features still remain uneven and largely left to the will of the software developers. The objective of this study was to develop a novel and comprehensive model for functional evaluation of the EHR software in FMPs, based on current world standards, models and projects, as well as on actual user satisfaction and requirements. Based on previous theoretical and experimental research in this area, we made the initial framework model consisting of six basic categories as a base for online survey questionnaire. Family doctors assessed perceived software quality by using a five-point Likert-type scale. Using exploratory factor analysis and appropriate statistical methods over the collected data, the final optimal structure of the novel model was formed. Special attention was focused on the validity and quality of the novel model. The online survey collected a total of 384 cases. The obtained results indicate both the quality of the assessed software and the quality in use of the novel model. The intense ergonomic orientation of the novel measurement model was particularly emphasised. The resulting novel model is multiple validated, comprehensive and universal. It could be used to assess the user-perceived quality of almost all forms of the ambulatory EHR software and therefore useful to all stakeholders in this area of the health care informatisation.

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

PubMed

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

2014-01-01

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

Preliminary clinical evaluation of automated analysis of the sublingual microcirculation in the assessment of patients with septic shock: Comparison of automated versus semi-automated software.

PubMed

Sharawy, Nivin; Mukhtar, Ahmed; Islam, Sufia; Mahrous, Reham; Mohamed, Hassan; Ali, Mohamed; Hakeem, Amr A; Hossny, Osama; Refaa, Amera; Saka, Ahmed; Cerny, Vladimir; Whynot, Sara; George, Ronald B; Lehmann, Christian

2017-01-01

The outcome of patients in septic shock has been shown to be related to changes within the microcirculation. Modern imaging technologies are available to generate high resolution video recordings of the microcirculation in humans. However, evaluation of the microcirculation is not yet implemented in the routine clinical monitoring of critically ill patients. This is mainly due to large amount of time and user interaction required by the current video analysis software. The aim of this study was to validate a newly developed automated method (CCTools®) for microcirculatory analysis of sublingual capillary perfusion in septic patients in comparison to standard semi-automated software (AVA3®). 204 videos from 47 patients were recorded using incident dark field (IDF) imaging. Total vessel density (TVD), proportion of perfused vessels (PPV), perfused vessel density (PVD), microvascular flow index (MFI) and heterogeneity index (HI) were measured using AVA3® and CCTools®. Significant differences between the numeric results obtained by the two different software packages were observed. The values for TVD, PVD and MFI were statistically related though. The automated software technique successes to show septic shock induced microcirculation alterations in near real time. However, we found wide degrees of agreement between AVA3® and CCTools® values due to several technical factors that should be considered in the future studies.

GCS programmer's manual

NASA Technical Reports Server (NTRS)

Lowman, Douglas S.; Withers, B. Edward; Shagnea, Anita M.; Dent, Leslie A.; Hayhurst, Kelly J.

1990-01-01

A variety of instructions to be used in the development of implementations of software for the Guidance and Control Software (GCS) project is described. This document fulfills the Radio Technical Commission for Aeronautics RTCA/DO-178A guidelines, 'Software Considerations in Airborne Systems and Equipment Certification' requirements for document No. 4, which specifies the information necessary for understanding and programming the host computer, and document No. 12, which specifies the software design and implementation standards that are applicable to the software development and testing process. Information on the following subjects is contained: activity recording, communication protocol, coding standards, change management, error handling, design standards, problem reporting, module testing logs, documentation formats, accuracy requirements, and programmer responsibilities.

Quality and standardization of telecommunication switching system software

NASA Astrophysics Data System (ADS)

Ranko, K.; Hivensaio, J.; Myllykangas, A.

1981-12-01

The purpose of this paper has been to illustrate quality and standardization of switching system software from the authors point of view with the aim of developing standardization in the user environment.

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.

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

NASA Technical Reports Server (NTRS)

Stefanski, Philip L.

2015-01-01

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

ANOPP programming and documentation standards document

NASA Technical Reports Server (NTRS)

1976-01-01

Standards defining the requirements for preparing software for the Aircraft Noise Prediction Program (ANOPP) were given. It is the intent of these standards to provide definition, design, coding, and documentation criteria for the achievement of a unity among ANOPP products. These standards apply to all of ANOPP's standard software system. The standards encompass philosophy as well as techniques and conventions.

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.

MRMPROBS suite for metabolomics using large-scale MRM assays.

PubMed

Tsugawa, Hiroshi; Kanazawa, Mitsuhiro; Ogiwara, Atsushi; Arita, Masanori

2014-08-15

We developed new software environment for the metabolome analysis of large-scale multiple reaction monitoring (MRM) assays. It supports the data format of four major mass spectrometer vendors and mzML common data format. This program provides a process pipeline from the raw-format import to high-dimensional statistical analyses. The novel aspect is graphical user interface-based visualization to perform peak quantification, to interpolate missing values and to normalize peaks interactively based on quality control samples. Together with the software platform, the MRM standard library of 301 metabolites with 775 transitions is also available, which contributes to the reliable peak identification by using retention time and ion abundances. MRMPROBS is available for Windows OS under the creative-commons by-attribution license at http://prime.psc.riken.jp. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evaluating statistical consistency in the ocean model component of the Community Earth System Model (pyCECT v2.0)

NASA Astrophysics Data System (ADS)

Baker, Allison H.; Hu, Yong; Hammerling, Dorit M.; Tseng, Yu-heng; Xu, Haiying; Huang, Xiaomeng; Bryan, Frank O.; Yang, Guangwen

2016-07-01

The Parallel Ocean Program (POP), the ocean model component of the Community Earth System Model (CESM), is widely used in climate research. Most current work in CESM-POP focuses on improving the model's efficiency or accuracy, such as improving numerical methods, advancing parameterization, porting to new architectures, or increasing parallelism. Since ocean dynamics are chaotic in nature, achieving bit-for-bit (BFB) identical results in ocean solutions cannot be guaranteed for even tiny code modifications, and determining whether modifications are admissible (i.e., statistically consistent with the original results) is non-trivial. In recent work, an ensemble-based statistical approach was shown to work well for software verification (i.e., quality assurance) on atmospheric model data. The general idea of the ensemble-based statistical consistency testing is to use a qualitative measurement of the variability of the ensemble of simulations as a metric with which to compare future simulations and make a determination of statistical distinguishability. The capability to determine consistency without BFB results boosts model confidence and provides the flexibility needed, for example, for more aggressive code optimizations and the use of heterogeneous execution environments. Since ocean and atmosphere models have differing characteristics in term of dynamics, spatial variability, and timescales, we present a new statistical method to evaluate ocean model simulation data that requires the evaluation of ensemble means and deviations in a spatial manner. In particular, the statistical distribution from an ensemble of CESM-POP simulations is used to determine the standard score of any new model solution at each grid point. Then the percentage of points that have scores greater than a specified threshold indicates whether the new model simulation is statistically distinguishable from the ensemble simulations. Both ensemble size and composition are important. Our experiments indicate that the new POP ensemble consistency test (POP-ECT) tool is capable of distinguishing cases that should be statistically consistent with the ensemble and those that should not, as well as providing a simple, subjective and systematic way to detect errors in CESM-POP due to the hardware or software stack, positively contributing to quality assurance for the CESM-POP code.

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment

PubMed Central

Pasaniuc, Bogdan; Zaitlen, Noah; Shi, Huwenbo; Bhatia, Gaurav; Gusev, Alexander; Pickrell, Joseph; Hirschhorn, Joel; Strachan, David P.; Patterson, Nick; Price, Alkes L.

2014-01-01

Motivation: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. Results: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1–5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case–control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of χ2 association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses. Availability and implementation: Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/. Contact: bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu Supplementary information: Supplementary materials are available at Bioinformatics online. PMID:24990607

Estimating multilevel logistic regression models when the number of clusters is low: a comparison of different statistical software procedures.

PubMed

Austin, Peter C

2010-04-22

Multilevel logistic regression models are increasingly being used to analyze clustered data in medical, public health, epidemiological, and educational research. Procedures for estimating the parameters of such models are available in many statistical software packages. There is currently little evidence on the minimum number of clusters necessary to reliably fit multilevel regression models. We conducted a Monte Carlo study to compare the performance of different statistical software procedures for estimating multilevel logistic regression models when the number of clusters was low. We examined procedures available in BUGS, HLM, R, SAS, and Stata. We found that there were qualitative differences in the performance of different software procedures for estimating multilevel logistic models when the number of clusters was low. Among the likelihood-based procedures, estimation methods based on adaptive Gauss-Hermite approximations to the likelihood (glmer in R and xtlogit in Stata) or adaptive Gaussian quadrature (Proc NLMIXED in SAS) tended to have superior performance for estimating variance components when the number of clusters was small, compared to software procedures based on penalized quasi-likelihood. However, only Bayesian estimation with BUGS allowed for accurate estimation of variance components when there were fewer than 10 clusters. For all statistical software procedures, estimation of variance components tended to be poor when there were only five subjects per cluster, regardless of the number of clusters.

Clinical research in a hospital--from the lone rider to teamwork.

PubMed

Hannisdal, E

1996-01-01

Clinical research of high international standard is very demanding and requires clinical data of high quality, software, hardware and competence in research design and statistical treatment of data. Most busy clinicians have little time allocated for clinical research and this increases the need for a potent infrastructure. This paper describes how the Norwegian Radium Hospital, a specialized cancer hospital, has reorganized the clinical research process. This includes a new department, the Clinical Research Office, which serves the formal framework, a central Diagnosis Registry, clinical databases and multicentre studies. The department assists about 120 users, mainly clinicians. Installation of a network software package with over 10 programs has strongly provided an internal standardization, reduced the costs and saved clinicians a great deal of time. The hospital is building up about 40 diagnosis-specific clinical databases with up to 200 variables registered. These databases are shared by the treatment group and seem to be important tools for quality assurance. We conclude that the clinical research process benefits from a firm infrastructure facilitating teamwork through extensive use of modern information technology. We are now ready for the next phase, which is to work for a better external technical framework for cooperation with other institutions throughout the world.

Head circumference as a useful surrogate for intracranial volume in older adults.

PubMed

Hshieh, Tammy T; Fox, Meaghan L; Kosar, Cyrus M; Cavallari, Michele; Guttmann, Charles R G; Alsop, David; Marcantonio, Edward R; Schmitt, Eva M; Jones, Richard N; Inouye, Sharon K

2016-01-01

Intracranial volume (ICV) has been proposed as a measure of maximum lifetime brain size. Accurate ICV measures require neuroimaging which is not always feasible for epidemiologic investigations. We examined head circumference as a useful surrogate for ICV in older adults. 99 older adults underwent Magnetic Resonance Imaging (MRI). ICV was measured by Statistical Parametric Mapping 8 (SPM8) software or Functional MRI of the Brain Software Library (FSL) extraction with manual editing, typically considered the gold standard. Head circumferences were determined using standardized tape measurement. We examined estimated correlation coefficients between head circumference and the two MRI-based ICV measurements. Head circumference and ICV by SPM8 were moderately correlated (overall r = 0.73, men r = 0.67, women r = 0.63). Head circumference and ICV by FSL were also moderately correlated (overall r = 0.69, men r = 0.63, women r = 0.49). Head circumference measurement was strongly correlated with MRI-derived ICV. Our study presents a simple method to approximate ICV among older patients, which may prove useful as a surrogate for cognitive reserve in large scale epidemiologic studies of cognitive outcomes. This study also suggests the stability of head circumference correlation with ICV throughout the lifespan.

The use of autologous concentrated growth factors to promote syndesmosis fusion in the Agility total ankle replacement. A preliminary study.

PubMed

Coetzee, J Chris; Pomeroy, Gregory C; Watts, J David; Barrow, Craig

2005-10-01

The Agility (DePuy, Warsaw, Indiana) total ankle replacement has been in use since 1984. One of the most common complications continues to be delayed union or nonunions of the distal tibiofibular syndesmosis. In the reported studies on the Agility ankle the delayed union and nonunion rate can be as high as 38%. Since 1999, 114 Agility total ankle replacements were done at two centers in the United States without the use of autologous concentrated growth factors. Since July of 2001, 66 Agility ankles were implanted with Symphony (DePuy, Warsaw, Indiana) augmented bone grafting. The standard operative technique was followed in all the patients. Prospective data was collected on all patients. The standard ankle radiographs were taken preoperatively and postoperative at 8 weeks, 12 weeks, 16 weeks, 6 months, and yearly. CT scans were obtained at 6 months if fusion at the syndesmosis was questionable. The Graphpad Instat software (Graphpad Software Inc., San Diego, CA) was used for statistical analysis. The two-tailed unpaired t-test was used, and the value <0.05 was considered significant. There was no statistical difference in the demographic data for the two groups. In 114 ankle replacements without autologous concentrated growth factors 70 fused at 8 weeks (61%), 14 fused at 12 weeks (12%), 13 fused at 6 months (12%). There were 17 nonunions (15%); delayed unions (3 to 6 months) and nonunions, therefore, equaled 27%. The syndesmosis fused in 50 of the 66 ankle replacements (76%) that had autologous concentrated growth fractures at 8 weeks (76%); 12 fused at 3 months (18%), 2 fused at 6 months (3%), 2 had nonunions (3%). Delayed unions (3 to 6 months) and nonunions equaled 6%. There was a statistically significant improvement in the 8- and 12-week fusion rates, and a statistically significant reduction in delayed unions and nonunions. Autologous concentrated growth factors appear to make a significant positive difference in the syndesmosis union rate in total ankle replacements.

Quality assurance software inspections at NASA Ames: Metrics for feedback and modification

NASA Technical Reports Server (NTRS)

Wenneson, G.

1985-01-01

Software inspections are a set of formal technical review procedures held at selected key points during software development in order to find defects in software documents--is described in terms of history, participants, tools, procedures, statistics, and database analysis.

Space Station Software Issues

NASA Technical Reports Server (NTRS)

Voigt, S. (Editor); Beskenis, S. (Editor)

1985-01-01

Issues in the development of software for the Space Station are discussed. Software acquisition and management, software development environment, standards, information system support for software developers, and a future software advisory board are addressed.

Space and Missile Systems Center Standard: Software Development

DTIC Science & Technology

2015-01-16

maintenance , or any other activity or combination of activities resulting in products . Within this standard, requirements to “develop,” “define...integration, reuse, reengineering, maintenance , or any other activity that results in products ). The term “developer” encompasses all software team...activities that results in software products . Software development includes new development, modification, reuse, reengineering, maintenance , and any other

Software Certification - Coding, Code, and Coders

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Holzmann, Gerard J.

2011-01-01

We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

Quantitative Measures for Software Independent Verification and Validation

NASA Technical Reports Server (NTRS)

Lee, Alice

1996-01-01

As software is maintained or reused, it undergoes an evolution which tends to increase the overall complexity of the code. To understand the effects of this, we brought in statistics experts and leading researchers in software complexity, reliability, and their interrelationships. These experts' project has resulted in our ability to statistically correlate specific code complexity attributes, in orthogonal domains, to errors found over time in the HAL/S flight software which flies in the Space Shuttle. Although only a prototype-tools experiment, the result of this research appears to be extendable to all other NASA software, given appropriate data similar to that logged for the Shuttle onboard software. Our research has demonstrated that a more complete domain coverage can be mathematically demonstrated with the approach we have applied, thereby ensuring full insight into the cause-and-effects relationship between the complexity of a software system and the fault density of that system. By applying the operational profile we can characterize the dynamic effects of software path complexity under this same approach We now have the ability to measure specific attributes which have been statistically demonstrated to correlate to increased error probability, and to know which actions to take, for each complexity domain. Shuttle software verifiers can now monitor the changes in the software complexity, assess the added or decreased risk of software faults in modified code, and determine necessary corrections. The reports, tool documentation, user's guides, and new approach that have resulted from this research effort represent advances in the state of the art of software quality and reliability assurance. Details describing how to apply this technique to other NASA code are contained in this document.

Software Safety Risk in Legacy Safety-Critical Computer Systems

NASA Technical Reports Server (NTRS)

Hill, Janice L.; Baggs, Rhoda

2007-01-01

Safety Standards contain technical and process-oriented safety requirements. Technical requirements are those such as "must work" and "must not work" functions in the system. Process-Oriented requirements are software engineering and safety management process requirements. Address the system perspective and some cover just software in the system > NASA-STD-8719.13B Software Safety Standard is the current standard of interest. NASA programs/projects will have their own set of safety requirements derived from the standard. Safety Cases: a) Documented demonstration that a system complies with the specified safety requirements. b) Evidence is gathered on the integrity of the system and put forward as an argued case. [Gardener (ed.)] c) Problems occur when trying to meet safety standards, and thus make retrospective safety cases, in legacy safety-critical computer systems.

Proportions of maxillary anterior teeth relative to each other and to golden standard in tabriz dental faculty students.

PubMed

Parnia, Fereydoun; Hafezeqoran, Ali; Mahboub, Farhang; Moslehifard, Elnaz; Koodaryan, Rodabeh; Moteyagheni, Rosa; Saleh Saber, Fariba

2010-01-01

Various methods are used to measure the size and form of the teeth, including the golden pro-portion, and the width-to-length ratio of central teeth, referred to as the golden standard. The aim of this study was to eval-uate the occurrence of golden standard values and golden proportion in the anterior teeth. Photographs of 100 dentistry students (50 males and 50 females) were taken under standard conditions. The visible widths and lengths of maxillary right and left incisors were calculated and the ratios were compared with golden standard. Data was analyzed using SPSS 14 software. Review of the results of the means showed statistically significant differences between the width ratio of right lateral teeth to the central teeth width with golden proportion (P<0.001). Likewise, the difference was significant for the left side, too (P<0.001). Test results of mean differences showed that the mean difference between proportion of right laterals to centrals with golden proportion was significant (P<0.001). The difference was significant for the left side, too (P<0.001). As a result, there is no golden proportion among maxillary incisors. The review of results of mean differences for single samples showed that the mean differences between the proportion of width-to-length of left and right central teeth was statistically significant by golden standard (P<0.001). Therefore, considering the width-to-length proportion of maxillary central teeth, no golden standard exists. In the evaluation of the width-to-width and width-to-length proportions of maxillary incisors no golden proportions and standards were detected, respectively.

Processing of meteorological data with ultrasonic thermoanemometers

NASA Astrophysics Data System (ADS)

Telminov, A. E.; Bogushevich, A. Ya.; Korolkov, V. A.; Botygin, I. A.

2017-11-01

The article describes a software system intended for supporting scientific researches of the atmosphere during the processing of data gathered by multi-level ultrasonic complexes for automated monitoring of meteorological and turbulent parameters in the ground layer of the atmosphere. The system allows to process files containing data sets of temperature instantaneous values, three orthogonal components of wind speed, humidity and pressure. The processing task execution is done in multiple stages. During the first stage, the system executes researcher's query for meteorological parameters. At the second stage, the system computes series of standard statistical meteorological field properties, such as averages, dispersion, standard deviation, asymmetry coefficients, excess, correlation etc. The third stage is necessary to prepare for computing the parameters of atmospheric turbulence. The computation results are displayed to user and stored at hard drive.

The IEEE Software Engineering Standards Process

PubMed Central

Buckley, Fletcher J.

1984-01-01

Software Engineering has emerged as a field in recent years, and those involved increasingly recognize the need for standards. As a result, members of the Institute of Electrical and Electronics Engineers (IEEE) formed a subcommittee to develop these standards. This paper discusses the ongoing standards development, and associated efforts.

Visually directed vs. software-based targeted biopsy compared to transperineal template mapping biopsy in the detection of clinically significant prostate cancer.

PubMed

Valerio, Massimo; McCartan, Neil; Freeman, Alex; Punwani, Shonit; Emberton, Mark; Ahmed, Hashim U

2015-10-01

Targeted biopsy based on cognitive or software magnetic resonance imaging (MRI) to transrectal ultrasound registration seems to increase the detection rate of clinically significant prostate cancer as compared with standard biopsy. However, these strategies have not been directly compared against an accurate test yet. The aim of this study was to obtain pilot data on the diagnostic ability of visually directed targeted biopsy vs. software-based targeted biopsy, considering transperineal template mapping (TPM) biopsy as the reference test. Prospective paired cohort study included 50 consecutive men undergoing TPM with one or more visible targets detected on preoperative multiparametric MRI. Targets were contoured on the Biojet software. Patients initially underwent software-based targeted biopsies, then visually directed targeted biopsies, and finally systematic TPM. The detection rate of clinically significant disease (Gleason score ≥3+4 and/or maximum cancer core length ≥4mm) of one strategy against another was compared by 3×3 contingency tables. Secondary analyses were performed using a less stringent threshold of significance (Gleason score ≥4+3 and/or maximum cancer core length ≥6mm). Median age was 68 (interquartile range: 63-73); median prostate-specific antigen level was 7.9ng/mL (6.4-10.2). A total of 79 targets were detected with a mean of 1.6 targets per patient. Of these, 27 (34%), 28 (35%), and 24 (31%) were scored 3, 4, and 5, respectively. At a patient level, the detection rate was 32 (64%), 34 (68%), and 38 (76%) for visually directed targeted, software-based biopsy, and TPM, respectively. Combining the 2 targeted strategies would have led to detection rate of 39 (78%). At a patient level and at a target level, software-based targeted biopsy found more clinically significant diseases than did visually directed targeted biopsy, although this was not statistically significant (22% vs. 14%, P = 0.48; 51.9% vs. 44.3%, P = 0.24). Secondary analysis showed similar results. Based on these findings, a paired cohort study enrolling at least 257 men would verify whether this difference is statistically significant. The diagnostic ability of software-based targeted biopsy and visually directed targeted biopsy seems almost comparable, although utility and efficiency both seem to be slightly in favor of the software-based strategy. Ongoing trials are sufficiently powered to prove or disprove these findings. Copyright © 2015 Elsevier Inc. All rights reserved.

Software Quality Evaluation Models Applicable in Health Information and Communications Technologies. A Review of the Literature.

PubMed

Villamor Ordozgoiti, Alberto; Delgado Hito, Pilar; Guix Comellas, Eva María; Fernandez Sanchez, Carlos Manuel; Garcia Hernandez, Milagros; Lluch Canut, Teresa

2016-01-01

Information and Communications Technologies in healthcare has increased the need to consider quality criteria through standardised processes. The aim of this study was to analyse the software quality evaluation models applicable to healthcare from the perspective of ICT-purchasers. Through a systematic literature review with the keywords software, product, quality, evaluation and health, we selected and analysed 20 original research papers published from 2005-2016 in health science and technology databases. The results showed four main topics: non-ISO models, software quality evaluation models based on ISO/IEC standards, studies analysing software quality evaluation models, and studies analysing ISO standards for software quality evaluation. The models provide cost-efficiency criteria for specific software, and improve use outcomes. The ISO/IEC25000 standard is shown as the most suitable for evaluating the quality of ICTs for healthcare use from the perspective of institutional acquisition.

Analysis of repeated measurement data in the clinical trials

PubMed Central

Singh, Vineeta; Rana, Rakesh Kumar; Singhal, Richa

2013-01-01

Statistics is an integral part of Clinical Trials. Elements of statistics span Clinical Trial design, data monitoring, analyses and reporting. A solid understanding of statistical concepts by clinicians improves the comprehension and the resulting quality of Clinical Trials. In biomedical research it has been seen that researcher frequently use t-test and ANOVA to compare means between the groups of interest irrespective of the nature of the data. In Clinical Trials we record the data on the patients more than two times. In such a situation using the standard ANOVA procedures is not appropriate as it does not consider dependencies between observations within subjects in the analysis. To deal with such types of study data Repeated Measure ANOVA should be used. In this article the application of One-way Repeated Measure ANOVA has been demonstrated by using the software SPSS (Statistical Package for Social Sciences) Version 15.0 on the data collected at four time points 0 day, 15th day, 30th day, and 45th day of multicentre clinical trial conducted on Pandu Roga (~Iron Deficiency Anemia) with an Ayurvedic formulation Dhatrilauha. PMID:23930038

Standard Populations (Millions) for Age-Adjustment - SEER Population Datasets

Cancer.gov

Download files containing standard population data for use in statististical software. The files contain the same data distributed with SEER*Stat software. You can also view the standard populations, either 19 age groups or single ages.

Enhancing requirements engineering for patient registry software systems with evidence-based components.

PubMed

Lindoerfer, Doris; Mansmann, Ulrich

2017-07-01

Patient registries are instrumental for medical research. Often their structures are complex and their implementations use composite software systems to meet the wide spectrum of challenges. Commercial and open-source systems are available for registry implementation, but many research groups develop their own systems. Methodological approaches in the selection of software as well as the construction of proprietary systems are needed. We propose an evidence-based checklist, summarizing essential items for patient registry software systems (CIPROS), to accelerate the requirements engineering process. Requirements engineering activities for software systems follow traditional software requirements elicitation methods, general software requirements specification (SRS) templates, and standards. We performed a multistep procedure to develop a specific evidence-based CIPROS checklist: (1) A systematic literature review to build a comprehensive collection of technical concepts, (2) a qualitative content analysis to define a catalogue of relevant criteria, and (3) a checklist to construct a minimal appraisal standard. CIPROS is based on 64 publications and covers twelve sections with a total of 72 items. CIPROS also defines software requirements. Comparing CIPROS with traditional software requirements elicitation methods, SRS templates and standards show a broad consensus but differences in issues regarding registry-specific aspects. Using an evidence-based approach to requirements engineering for registry software adds aspects to the traditional methods and accelerates the software engineering process for registry software. The method we used to construct CIPROS serves as a potential template for creating evidence-based checklists in other fields. The CIPROS list supports developers in assessing requirements for existing systems and formulating requirements for their own systems, while strengthening the reporting of patient registry software system descriptions. It may be a first step to create standards for patient registry software system assessments. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

CAD/CAE Integration Enhanced by New CAD Services Standard

NASA Technical Reports Server (NTRS)

Claus, Russell W.

2002-01-01

A Government-industry team led by the NASA Glenn Research Center has developed a computer interface standard for accessing data from computer-aided design (CAD) systems. The Object Management Group, an international computer standards organization, has adopted this CAD services standard. The new standard allows software (e.g., computer-aided engineering (CAE) and computer-aided manufacturing software to access multiple CAD systems through one programming interface. The interface is built on top of a distributed computing system called the Common Object Request Broker Architecture (CORBA). CORBA allows the CAD services software to operate in a distributed, heterogeneous computing environment.

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

PubMed

Mägi, Reedik; Morris, Andrew P

2010-05-28

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

A UNIFIED FRAMEWORK FOR VARIANCE COMPONENT ESTIMATION WITH SUMMARY STATISTICS IN GENOME-WIDE ASSOCIATION STUDIES.

PubMed

Zhou, Xiang

2017-12-01

Linear mixed models (LMMs) are among the most commonly used tools for genetic association studies. However, the standard method for estimating variance components in LMMs-the restricted maximum likelihood estimation method (REML)-suffers from several important drawbacks: REML requires individual-level genotypes and phenotypes from all samples in the study, is computationally slow, and produces downward-biased estimates in case control studies. To remedy these drawbacks, we present an alternative framework for variance component estimation, which we refer to as MQS. MQS is based on the method of moments (MoM) and the minimal norm quadratic unbiased estimation (MINQUE) criterion, and brings two seemingly unrelated methods-the renowned Haseman-Elston (HE) regression and the recent LD score regression (LDSC)-into the same unified statistical framework. With this new framework, we provide an alternative but mathematically equivalent form of HE that allows for the use of summary statistics. We provide an exact estimation form of LDSC to yield unbiased and statistically more efficient estimates. A key feature of our method is its ability to pair marginal z -scores computed using all samples with SNP correlation information computed using a small random subset of individuals (or individuals from a proper reference panel), while capable of producing estimates that can be almost as accurate as if both quantities are computed using the full data. As a result, our method produces unbiased and statistically efficient estimates, and makes use of summary statistics, while it is computationally efficient for large data sets. Using simulations and applications to 37 phenotypes from 8 real data sets, we illustrate the benefits of our method for estimating and partitioning SNP heritability in population studies as well as for heritability estimation in family studies. Our method is implemented in the GEMMA software package, freely available at www.xzlab.org/software.html.

Symposium on the Interface: Computing Science and Statistics (20th). Theme: Computationally Intensive Methods in Statistics Held in Reston, Virginia on April 20-23, 1988

DTIC Science & Technology

1988-08-20

34 William A. Link, Patuxent Wildlife Research Center "Increasing reliability of multiversion fault-tolerant software design by modulation," Junryo 3... Multiversion lault-Tolerant Software Design by Modularization Junryo Miyashita Department of Computer Science California state University at san Bernardino Fault...They shall beE refered to as " multiversion fault-tolerant software design". Onel problem of developing multi-versions of a program is the high cost

Twice random, once mixed: applying mixed models to simultaneously analyze random effects of language and participants.

PubMed

Janssen, Dirk P

2012-03-01

Psychologists, psycholinguists, and other researchers using language stimuli have been struggling for more than 30 years with the problem of how to analyze experimental data that contain two crossed random effects (items and participants). The classical analysis of variance does not apply; alternatives have been proposed but have failed to catch on, and a statistically unsatisfactory procedure of using two approximations (known as F(1) and F(2)) has become the standard. A simple and elegant solution using mixed model analysis has been available for 15 years, and recent improvements in statistical software have made mixed models analysis widely available. The aim of this article is to increase the use of mixed models by giving a concise practical introduction and by giving clear directions for undertaking the analysis in the most popular statistical packages. The article also introduces the DJMIXED: add-on package for SPSS, which makes entering the models and reporting their results as straightforward as possible.

Statistical Issues in Testing Conformance with the Quantitative Imaging Biomarker Alliance (QIBA) Profile Claims.

PubMed

Obuchowski, Nancy A; Buckler, Andrew; Kinahan, Paul; Chen-Mayer, Heather; Petrick, Nicholas; Barboriak, Daniel P; Bullen, Jennifer; Barnhart, Huiman; Sullivan, Daniel C

2016-04-01

A major initiative of the Quantitative Imaging Biomarker Alliance is to develop standards-based documents called "Profiles," which describe one or more technical performance claims for a given imaging modality. The term "actor" denotes any entity (device, software, or person) whose performance must meet certain specifications for the claim to be met. The objective of this paper is to present the statistical issues in testing actors' conformance with the specifications. In particular, we present the general rationale and interpretation of the claims, the minimum requirements for testing whether an actor achieves the performance requirements, the study designs used for testing conformity, and the statistical analysis plan. We use three examples to illustrate the process: apparent diffusion coefficient in solid tumors measured by MRI, change in Perc 15 as a biomarker for the progression of emphysema, and percent change in solid tumor volume by computed tomography as a biomarker for lung cancer progression. Copyright © 2016 The Association of University Radiologists. All rights reserved.

DECONV-TOOL: An IDL based deconvolution software package

NASA Technical Reports Server (NTRS)

Varosi, F.; Landsman, W. B.

1992-01-01

There are a variety of algorithms for deconvolution of blurred images, each having its own criteria or statistic to be optimized in order to estimate the original image data. Using the Interactive Data Language (IDL), we have implemented the Maximum Likelihood, Maximum Entropy, Maximum Residual Likelihood, and sigma-CLEAN algorithms in a unified environment called DeConv_Tool. Most of the algorithms have as their goal the optimization of statistics such as standard deviation and mean of residuals. Shannon entropy, log-likelihood, and chi-square of the residual auto-correlation are computed by DeConv_Tool for the purpose of determining the performance and convergence of any particular method and comparisons between methods. DeConv_Tool allows interactive monitoring of the statistics and the deconvolved image during computation. The final results, and optionally, the intermediate results, are stored in a structure convenient for comparison between methods and review of the deconvolution computation. The routines comprising DeConv_Tool are available via anonymous FTP through the IDL Astronomy User's Library.

Software database creature for investment property measurement according to international standards

NASA Astrophysics Data System (ADS)

Ponomareva, S. V.; Merzliakova, N. A.

2018-05-01

The article deals with investment property measurement and accounting problems at the international, national and enterprise levels. The need to create the software for investment property measurement according to International Accounting Standards was substantiated. The necessary software functions and the processes were described.

The Digital Shoreline Analysis System (DSAS) Version 4.0 - An ArcGIS extension for calculating shoreline change

USGS Publications Warehouse

Thieler, E. Robert; Himmelstoss, Emily A.; Zichichi, Jessica L.; Ergul, Ayhan

2009-01-01

The Digital Shoreline Analysis System (DSAS) version 4.0 is a software extension to ESRI ArcGIS v.9.2 and above that enables a user to calculate shoreline rate-of-change statistics from multiple historic shoreline positions. A user-friendly interface of simple buttons and menus guides the user through the major steps of shoreline change analysis. Components of the extension and user guide include (1) instruction on the proper way to define a reference baseline for measurements, (2) automated and manual generation of measurement transects and metadata based on user-specified parameters, and (3) output of calculated rates of shoreline change and other statistical information. DSAS computes shoreline rates of change using four different methods: (1) endpoint rate, (2) simple linear regression, (3) weighted linear regression, and (4) least median of squares. The standard error, correlation coefficient, and confidence interval are also computed for the simple and weighted linear-regression methods. The results of all rate calculations are output to a table that can be linked to the transect file by a common attribute field. DSAS is intended to facilitate the shoreline change-calculation process and to provide rate-of-change information and the statistical data necessary to establish the reliability of the calculated results. The software is also suitable for any generic application that calculates positional change over time, such as assessing rates of change of glacier limits in sequential aerial photos, river edge boundaries, land-cover changes, and so on.

Implementing informative priors for heterogeneity in meta-analysis using meta-regression and pseudo data.

PubMed

Rhodes, Kirsty M; Turner, Rebecca M; White, Ian R; Jackson, Dan; Spiegelhalter, David J; Higgins, Julian P T

2016-12-20

Many meta-analyses combine results from only a small number of studies, a situation in which the between-study variance is imprecisely estimated when standard methods are applied. Bayesian meta-analysis allows incorporation of external evidence on heterogeneity, providing the potential for more robust inference on the effect size of interest. We present a method for performing Bayesian meta-analysis using data augmentation, in which we represent an informative conjugate prior for between-study variance by pseudo data and use meta-regression for estimation. To assist in this, we derive predictive inverse-gamma distributions for the between-study variance expected in future meta-analyses. These may serve as priors for heterogeneity in new meta-analyses. In a simulation study, we compare approximate Bayesian methods using meta-regression and pseudo data against fully Bayesian approaches based on importance sampling techniques and Markov chain Monte Carlo (MCMC). We compare the frequentist properties of these Bayesian methods with those of the commonly used frequentist DerSimonian and Laird procedure. The method is implemented in standard statistical software and provides a less complex alternative to standard MCMC approaches. An importance sampling approach produces almost identical results to standard MCMC approaches, and results obtained through meta-regression and pseudo data are very similar. On average, data augmentation provides closer results to MCMC, if implemented using restricted maximum likelihood estimation rather than DerSimonian and Laird or maximum likelihood estimation. The methods are applied to real datasets, and an extension to network meta-analysis is described. The proposed method facilitates Bayesian meta-analysis in a way that is accessible to applied researchers. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

Tolerancing aspheres based on manufacturing knowledge

NASA Astrophysics Data System (ADS)

Wickenhagen, S.; Kokot, S.; Fuchs, U.

2017-10-01

A standard way of tolerancing optical elements or systems is to perform a Monte Carlo based analysis within a common optical design software package. Although, different weightings and distributions are assumed they are all counting on statistics, which usually means several hundreds or thousands of systems for reliable results. Thus, employing these methods for small batch sizes is unreliable, especially when aspheric surfaces are involved. The huge database of asphericon was used to investigate the correlation between the given tolerance values and measured data sets. The resulting probability distributions of these measured data were analyzed aiming for a robust optical tolerancing process.

Survey of Software Assurance Techniques for Highly Reliable Systems

NASA Technical Reports Server (NTRS)

Nelson, Stacy

2004-01-01

This document provides a survey of software assurance techniques for highly reliable systems including a discussion of relevant safety standards for various industries in the United States and Europe, as well as examples of methods used during software development projects. It contains one section for each industry surveyed: Aerospace, Defense, Nuclear Power, Medical Devices and Transportation. Each section provides an overview of applicable standards and examples of a mission or software development project, software assurance techniques used and reliability achieved.

Functional annotation of regulatory pathways.

PubMed

Pandey, Jayesh; Koyutürk, Mehmet; Kim, Yohan; Szpankowski, Wojciech; Subramaniam, Shankar; Grama, Ananth

2007-07-01

Standardized annotations of biomolecules in interaction networks (e.g. Gene Ontology) provide comprehensive understanding of the function of individual molecules. Extending such annotations to pathways is a critical component of functional characterization of cellular signaling at the systems level. We propose a framework for projecting gene regulatory networks onto the space of functional attributes using multigraph models, with the objective of deriving statistically significant pathway annotations. We first demonstrate that annotations of pairwise interactions do not generalize to indirect relationships between processes. Motivated by this result, we formalize the problem of identifying statistically overrepresented pathways of functional attributes. We establish the hardness of this problem by demonstrating the non-monotonicity of common statistical significance measures. We propose a statistical model that emphasizes the modularity of a pathway, evaluating its significance based on the coupling of its building blocks. We complement the statistical model by an efficient algorithm and software, Narada, for computing significant pathways in large regulatory networks. Comprehensive results from our methods applied to the Escherichia coli transcription network demonstrate that our approach is effective in identifying known, as well as novel biological pathway annotations. Narada is implemented in Java and is available at http://www.cs.purdue.edu/homes/jpandey/narada/.

Teaching Probability with the Support of the R Statistical Software

ERIC Educational Resources Information Center

dos Santos Ferreira, Robson; Kataoka, Verônica Yumi; Karrer, Monica

2014-01-01

The objective of this paper is to discuss aspects of high school students' learning of probability in a context where they are supported by the statistical software R. We report on the application of a teaching experiment, constructed using the perspective of Gal's probabilistic literacy and Papert's constructionism. The results show improvement…

Using Information Technology in Teaching of Business Statistics in Nigeria Business School

ERIC Educational Resources Information Center

Hamadu, Dallah; Adeleke, Ismaila; Ehie, Ike

2011-01-01

This paper discusses the use of Microsoft Excel software in the teaching of statistics in the Faculty of Business Administration at the University of Lagos, Nigeria. Problems associated with existing traditional methods are identified and a novel pedagogy using Excel is proposed. The advantages of using this software over other specialized…

25 CFR 543.7 - What are the minimum internal control standards for bingo?

Code of Federal Regulations, 2011 CFR

2011-04-01

... software upgrades, data storage media replacement, etc.). The information recorded must be used when...., draw objects and back-up draw objects); and (ii) Random number generator software. (Additional information technology security standards can be found in § 543.16 of this part.) (2) The game software...

25 CFR 543.7 - What are the minimum internal control standards for bingo?

Code of Federal Regulations, 2012 CFR

2012-04-01

... software upgrades, data storage media replacement, etc.). The information recorded must be used when...., draw objects and back-up draw objects); and (ii) Random number generator software. (Additional information technology security standards can be found in § 543.16 of this part.) (2) The game software...

Future of Software Engineering Standards

NASA Technical Reports Server (NTRS)

Poon, Peter T.

1997-01-01

In the new millennium, software engineering standards are expected to continue to influence the process of producing software-intensive systems which are cost-effetive and of high quality. These sytems may range from ground and flight systems used for planetary exploration to educational support systems used in schools as well as consumer-oriented systems.

Evolution of Secondary Software Businesses: Understanding Industry Dynamics

NASA Astrophysics Data System (ADS)

Tyrväinen, Pasi; Warsta, Juhani; Seppänen, Veikko

Primary software industry originates from IBM's decision to unbundle software-related computer system development activities to external partners. This kind of outsourcing from an enterprise internal software development activity is a common means to start a new software business serving a vertical software market. It combines knowledge of the vertical market process with competence in software development. In this research, we present and analyze the key figures of the Finnish secondary software industry, in order to quantify its interaction with the primary software industry during the period of 2000-2003. On the basis of the empirical data, we present a model for evolution of a secondary software business, which makes explicit the industry dynamics. It represents the shift from internal software developed for competitive advantage to development of products supporting standard business processes on top of standardized technologies. We also discuss the implications for software business strategies in each phase.

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.

Dynamic Weather Routes Architecture Overview

NASA Technical Reports Server (NTRS)

Eslami, Hassan; Eshow, Michelle

2014-01-01

Dynamic Weather Routes Architecture Overview, presents the high level software architecture of DWR, based on the CTAS software framework and the Direct-To automation tool. The document also covers external and internal data flows, required dataset, changes to the Direct-To software for DWR, collection of software statistics, and the code structure.

Safe Software for Space Applications: Building on the DO-178 Experience

NASA Astrophysics Data System (ADS)

Dorsey, Cheryl A.; Dorsey, Timothy A.

2013-09-01

DO-178, Software Considerations in Airborne Systems and Equipment Certification, is the well-known international standard dealing with the assurance of software used in airborne systems [1,2]. Insights into the DO-178 experiences, strengths and weaknesses can benefit the international space community. As DO-178 is an excellent standard for safe software development when used appropriately, this paper provides lessons learned and suggestions for using it effectively.

FAILSAFE Health Management for Embedded Systems

NASA Technical Reports Server (NTRS)

Horvath, Gregory A.; Wagner, David A.; Wen, Hui Ying; Barry, Matthew

2010-01-01

The FAILSAFE project is developing concepts and prototype implementations for software health management in mission- critical, real-time embedded systems. The project unites features of the industry-standard ARINC 653 Avionics Application Software Standard Interface and JPL s Mission Data System (MDS) technology (see figure). The ARINC 653 standard establishes requirements for the services provided by partitioned, real-time operating systems. The MDS technology provides a state analysis method, canonical architecture, and software framework that facilitates the design and implementation of software-intensive complex systems. The MDS technology has been used to provide the health management function for an ARINC 653 application implementation. In particular, the focus is on showing how this combination enables reasoning about, and recovering from, application software problems.

The Statistical Consulting Center for Astronomy (SCCA)

NASA Technical Reports Server (NTRS)

Akritas, Michael

2001-01-01

The process by which raw astronomical data acquisition is transformed into scientifically meaningful results and interpretation typically involves many statistical steps. Traditional astronomy limits itself to a narrow range of old and familiar statistical methods: means and standard deviations; least-squares methods like chi(sup 2) minimization; and simple nonparametric procedures such as the Kolmogorov-Smirnov tests. These tools are often inadequate for the complex problems and datasets under investigations, and recent years have witnessed an increased usage of maximum-likelihood, survival analysis, multivariate analysis, wavelet and advanced time-series methods. The Statistical Consulting Center for Astronomy (SCCA) assisted astronomers with the use of sophisticated tools, and to match these tools with specific problems. The SCCA operated with two professors of statistics and a professor of astronomy working together. Questions were received by e-mail, and were discussed in detail with the questioner. Summaries of those questions and answers leading to new approaches were posted on the Web (www.state.psu.edu/ mga/SCCA). In addition to serving individual astronomers, the SCCA established a Web site for general use that provides hypertext links to selected on-line public-domain statistical software and services. The StatCodes site (www.astro.psu.edu/statcodes) provides over 200 links in the areas of: Bayesian statistics; censored and truncated data; correlation and regression, density estimation and smoothing, general statistics packages and information; image analysis; interactive Web tools; multivariate analysis; multivariate clustering and classification; nonparametric analysis; software written by astronomers; spatial statistics; statistical distributions; time series analysis; and visualization tools. StatCodes has received a remarkable high and constant hit rate of 250 hits/week (over 10,000/year) since its inception in mid-1997. It is of interest to scientists both within and outside of astronomy. The most popular sections are multivariate techniques, image analysis, and time series analysis. Hundreds of copies of the ASURV, SLOPES and CENS-TAU codes developed by SCCA scientists were also downloaded from the StatCodes site. In addition to formal SCCA duties, SCCA scientists continued a variety of related activities in astrostatistics, including refereeing of statistically oriented papers submitted to the Astrophysical Journal, talks in meetings including Feigelson's talk to science journalists entitled "The reemergence of astrostatistics" at the American Association for the Advancement of Science meeting, and published papers of astrostatistical content.

Evaluation of computer-aided diagnosis (CAD) software for the detection of lung nodules on multidetector row computed tomography (MDCT): JAFROC study for the improvement in radiologists' diagnostic accuracy.

PubMed

Hirose, Tomohiro; Nitta, Norihisa; Shiraishi, Junji; Nagatani, Yukihiro; Takahashi, Masashi; Murata, Kiyoshi

2008-12-01

The aim of this study was to evaluate the usefulness of computer-aided diagnosis (CAD) software for the detection of lung nodules on multidetector-row computed tomography (MDCT) in terms of improvement in radiologists' diagnostic accuracy in detecting lung nodules, using jackknife free-response receiver-operating characteristic (JAFROC) analysis. Twenty-one patients (6 without and 15 with lung nodules) were selected randomly from 120 consecutive thoracic computed tomographic examinations. The gold standard for the presence or absence of nodules in the observer study was determined by consensus of two radiologists. Six expert radiologists participated in a free-response receiver operating characteristic study for the detection of lung nodules on MDCT, in which cases were interpreted first without and then with the output of CAD software. Radiologists were asked to indicate the locations of lung nodule candidates on the monitor with their confidence ratings for the presence of lung nodules. The performance of the CAD software indicated that the sensitivity in detecting lung nodules was 71.4%, with 0.95 false-positive results per case. When radiologists used the CAD software, the average sensitivity improved from 39.5% to 81.0%, with an increase in the average number of false-positive results from 0.14 to 0.89 per case. The average figure-of-merit values for the six radiologists were 0.390 without and 0.845 with the output of the CAD software, and there was a statistically significant difference (P < .0001) using the JAFROC analysis. The CAD software for the detection of lung nodules on MDCT has the potential to assist radiologists by increasing their accuracy.

Tool for Statistical Analysis and Display of Landing Sites

NASA Technical Reports Server (NTRS)

Wawrzyniak, Geoffrey; Kennedy, Brian; Knocke, Philip; Michel, John

2006-01-01

MarsLS is a software tool for analyzing statistical dispersion of spacecraft-landing sites and displaying the results of its analyses. Originally intended for the Mars Explorer Rover (MER) mission, MarsLS is also applicable to landing sites on Earth and non-MER sites on Mars. MarsLS is a collection of interdependent MATLAB scripts that utilize the MATLAB graphical-user-interface software environment to display landing-site data (see figure) on calibrated image-maps of the Martian or other terrain. The landing-site data comprise latitude/longitude pairs generated by Monte Carlo runs of other computer programs that simulate entry, descent, and landing. Using these data, MarsLS can compute a landing-site ellipse a standard means of depicting the area within which the spacecraft can be expected to land with a given probability. MarsLS incorporates several features for the user s convenience, including capabilities for drawing lines and ellipses, overlaying kilometer or latitude/longitude grids, drawing and/or specifying lines and/or points, entering notes, defining and/or displaying polygons to indicate hazards or areas of interest, and evaluating hazardous and/or scientifically interesting areas. As part of such an evaluation, MarsLS can compute the probability of landing in a specified polygonal area.

Effectiveness of a Computer-Based Training Program of Attention and Memory in Patients with Acquired Brain Damage

PubMed Central

Fernandez, Elizabeth; Bergado Rosado, Jorge A.; Rodriguez Perez, Daymi; Salazar Santana, Sonia; Torres Aguilar, Maydane; Bringas, Maria Luisa

2017-01-01

Many training programs have been designed using modern software to restore the impaired cognitive functions in patients with acquired brain damage (ABD). The objective of this study was to evaluate the effectiveness of a computer-based training program of attention and memory in patients with ABD, using a two-armed parallel group design, where the experimental group (n = 50) received cognitive stimulation using RehaCom software, and the control group (n = 30) received the standard cognitive stimulation (non-computerized) for eight weeks. In order to assess the possible cognitive changes after the treatment, a post-pre experimental design was employed using the following neuropsychological tests: Wechsler Memory Scale (WMS) and Trail Making test A and B. The effectiveness of the training procedure was statistically significant (p < 0.05) when it established the comparison between the performance in these scales, before and after the training period, in each patient and between the two groups. The training group had statistically significant (p < 0.001) changes in focused attention (Trail A), two subtests (digit span and logical memory), and the overall score of WMS. Finally, we discuss the advantages of computerized training rehabilitation and further directions of this line of work. PMID:29301194

SAO mission support software and data standards, version 1.0

NASA Technical Reports Server (NTRS)

Hsieh, P.

1993-01-01

This document defines the software developed by the SAO AXAF Mission Support (MS) Program and defines standards for the software development process and control of data products generated by the software. The SAO MS is tasked to develop and use software to perform a variety of functions in support of the AXAF mission. Software is developed by software engineers and scientists, and commercial off-the-shelf (COTS) software is used either directly or customized through the use of scripts to implement analysis procedures. Software controls real-time laboratory instruments, performs data archiving, displays data, and generates model predictions. Much software is used in the analysis of data to generate data products that are required by the AXAF project, for example, on-orbit mirror performance predictions or detailed characterization of the mirror reflection performance with energy.

Nasa-wide Standard Administrative Systems

NASA Technical Reports Server (NTRS)

Schneck, P.

1984-01-01

Factors to be considered in developing agency-wide standard administrative systems for NASA include uniformity of hardware and software; centralization vs. decentralization; risk exposure; and models for software development.

Guidance and Control Software Project Data - Volume 1: Planning Documents

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J. (Editor)

2008-01-01

The Guidance and Control Software (GCS) project was the last in a series of software reliability studies conducted at Langley Research Center between 1977 and 1994. The technical results of the GCS project were recorded after the experiment was completed. Some of the support documentation produced as part of the experiment, however, is serving an unexpected role far beyond its original project context. Some of the software used as part of the GCS project was developed to conform to the RTCA/DO-178B software standard, "Software Considerations in Airborne Systems and Equipment Certification," used in the civil aviation industry. That standard requires extensive documentation throughout the software development life cycle, including plans, software requirements, design and source code, verification cases and results, and configuration management and quality control data. The project documentation that includes this information is open for public scrutiny without the legal or safety implications associated with comparable data from an avionics manufacturer. This public availability has afforded an opportunity to use the GCS project documents for DO-178B training. This report provides a brief overview of the GCS project, describes the 4-volume set of documents and the role they are playing in training, and includes the planning documents from the GCS project. Volume 1 contains five appendices: A. Plan for Software Aspects of Certification for the Guidance and Control Software Project; B. Software Development Standards for the Guidance and Control Software Project; C. Software Verification Plan for the Guidance and Control Software Project; D. Software Configuration Management Plan for the Guidance and Control Software Project; and E. Software Quality Assurance Activities.

Data Analysis and Graphing in an Introductory Physics Laboratory: Spreadsheet versus Statistics Suite

ERIC Educational Resources Information Center

Peterlin, Primoz

2010-01-01

Two methods of data analysis are compared: spreadsheet software and a statistics software suite. Their use is compared analysing data collected in three selected experiments taken from an introductory physics laboratory, which include a linear dependence, a nonlinear dependence and a histogram. The merits of each method are compared. (Contains 7…

Descriptive and inferential statistical methods used in burns research.

PubMed

Al-Benna, Sammy; Al-Ajam, Yazan; Way, Benjamin; Steinstraesser, Lars

2010-05-01

Burns research articles utilise a variety of descriptive and inferential methods to present and analyse data. The aim of this study was to determine the descriptive methods (e.g. mean, median, SD, range, etc.) and survey the use of inferential methods (statistical tests) used in articles in the journal Burns. This study defined its population as all original articles published in the journal Burns in 2007. Letters to the editor, brief reports, reviews, and case reports were excluded. Study characteristics, use of descriptive statistics and the number and types of statistical methods employed were evaluated. Of the 51 articles analysed, 11(22%) were randomised controlled trials, 18(35%) were cohort studies, 11(22%) were case control studies and 11(22%) were case series. The study design and objectives were defined in all articles. All articles made use of continuous and descriptive data. Inferential statistics were used in 49(96%) articles. Data dispersion was calculated by standard deviation in 30(59%). Standard error of the mean was quoted in 19(37%). The statistical software product was named in 33(65%). Of the 49 articles that used inferential statistics, the tests were named in 47(96%). The 6 most common tests used (Student's t-test (53%), analysis of variance/co-variance (33%), chi(2) test (27%), Wilcoxon & Mann-Whitney tests (22%), Fisher's exact test (12%)) accounted for the majority (72%) of statistical methods employed. A specified significance level was named in 43(88%) and the exact significance levels were reported in 28(57%). Descriptive analysis and basic statistical techniques account for most of the statistical tests reported. This information should prove useful in deciding which tests should be emphasised in educating burn care professionals. These results highlight the need for burn care professionals to have a sound understanding of basic statistics, which is crucial in interpreting and reporting data. Advice should be sought from professionals in the fields of biostatistics and epidemiology when using more advanced statistical techniques. Copyright 2009 Elsevier Ltd and ISBI. All rights reserved.

Software architecture standard for simulation virtual machine, version 2.0

NASA Technical Reports Server (NTRS)

Sturtevant, Robert; Wessale, William

1994-01-01

The Simulation Virtual Machine (SBM) is an Ada architecture which eases the effort involved in the real-time software maintenance and sustaining engineering. The Software Architecture Standard defines the infrastructure which all the simulation models are built from. SVM was developed for and used in the Space Station Verification and Training Facility.

78 FR 22432 - Airworthiness Directives; Airbus Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-16

... electrical rudder], through Airbus Service Bulletin (SB) A330-27-3176, --software standard P12A/M21A on FCPC.... Since we issued that AD, we have determined that new software standards for the flight control primary.... This proposed AD would require that operators modify or replace all three FCPCs with new software...

Algorithms and software for U-Pb geochronology by LA-ICPMS

NASA Astrophysics Data System (ADS)

McLean, Noah M.; Bowring, James F.; Gehrels, George

2016-07-01

The past 15 years have produced numerous innovations in geochronology, including experimental methods, instrumentation, and software that are revolutionizing the acquisition and application of geochronological data. For example, exciting advances are being driven by Laser-Ablation ICP Mass Spectrometry (LA-ICPMS), which allows for rapid determination of U-Th-Pb ages with 10s of micrometer-scale spatial resolution. This method has become the most commonly applied tool for dating zircons, constraining a host of geological problems. The LA-ICPMS community is now faced with archiving these data with associated analytical results and, more importantly, ensuring that data meet the highest standards for precision and accuracy and that interlaboratory biases are minimized. However, there is little consensus with regard to analytical strategies and data reduction protocols for LA-ICPMS geochronology. The result is systematic interlaboratory bias and both underestimation and overestimation of uncertainties on calculated dates that, in turn, decrease the value of data in repositories such as EarthChem, which archives data and analytical results from participating laboratories. We present free open-source software that implements new algorithms for evaluating and resolving many of these discrepancies. This solution is the result of a collaborative effort to extend the U-Pb_Redux software for the ID-TIMS community to the LA-ICPMS community. Now named ET_Redux, our new software automates the analytical and scientific workflows of data acquisition, statistical filtering, data analysis and interpretation, publication, community-based archiving, and the compilation and comparison of data from different laboratories to support collaborative science.

ICESat (GLAS) Science Processing Software Document Series. Volume 2; Science Data Management Plan; 4.0

NASA Technical Reports Server (NTRS)

Jester, Peggy L.; Hancock, David W., III

1999-01-01

This document provides the Data Management Plan for the GLAS Standard Data Software (SDS) supporting the GLAS instrument of the EOS ICESat Spacecraft. The SDS encompasses the ICESat Science Investigator-led Processing System (I-SIPS) Software and the Instrument Support Facility (ISF) Software. This Plan addresses the identification, authority, and description of the interface nodes associated with the GLAS Standard Data Products and the GLAS Ancillary Data.

ICESat (GLAS) Science Processing Software Document Series. Volume 3; GLAS Science Software Requirements Document; Ver 2.1

NASA Technical Reports Server (NTRS)

Jester, Peggy L.; Lee, Jeffrey; Zukor, Dorothy J. (Technical Monitor)

2001-01-01

This document addresses the software requirements of the Geoscience Laser Altimeter System (GLAS) Standard Data Software (SDS) supporting the GLAS instrument on the EOS ICESat Spacecraft. This Software Requirements Document represents the initial collection of the technical engineering information for the GLAS SDS. This information is detailed within the second of four main volumes of the Standard documentation, the Product Specification volume. This document is a "roll-out" from the governing volume outline containing the Concept and Requirements sections.

Traceability of Software Safety Requirements in Legacy Safety Critical Systems

NASA Technical Reports Server (NTRS)

Hill, Janice L.

2007-01-01

How can traceability of software safety requirements be created for legacy safety critical systems? Requirements in safety standards are imposed most times during contract negotiations. On the other hand, there are instances where safety standards are levied on legacy safety critical systems, some of which may be considered for reuse for new applications. Safety standards often specify that software development documentation include process-oriented and technical safety requirements, and also require that system and software safety analyses are performed supporting technical safety requirements implementation. So what can be done if the requisite documents for establishing and maintaining safety requirements traceability are not available?

Validation of PC-based Sound Card with Biopac for Digitalization of ECG Recording in Short-term HRV Analysis.

PubMed

Maheshkumar, K; Dilara, K; Maruthy, K N; Sundareswaren, L

2016-07-01

Heart rate variability (HRV) analysis is a simple and noninvasive technique capable of assessing autonomic nervous system modulation on heart rate (HR) in healthy as well as disease conditions. The aim of the present study was to compare (validate) the HRV using a temporal series of electrocardiograms (ECG) obtained by simple analog amplifier with PC-based sound card (audacity) and Biopac MP36 module. Based on the inclusion criteria, 120 healthy participants, including 72 males and 48 females, participated in the present study. Following standard protocol, 5-min ECG was recorded after 10 min of supine rest by Portable simple analog amplifier PC-based sound card as well as by Biopac module with surface electrodes in Leads II position simultaneously. All the ECG data was visually screened and was found to be free of ectopic beats and noise. RR intervals from both ECG recordings were analyzed separately in Kubios software. Short-term HRV indexes in both time and frequency domain were used. The unpaired Student's t-test and Pearson correlation coefficient test were used for the analysis using the R statistical software. No statistically significant differences were observed when comparing the values analyzed by means of the two devices for HRV. Correlation analysis revealed perfect positive correlation (r = 0.99, P < 0.001) between the values in time and frequency domain obtained by the devices. On the basis of the results of the present study, we suggest that the calculation of HRV values in the time and frequency domains by RR series obtained from the PC-based sound card is probably as reliable as those obtained by the gold standard Biopac MP36.

Estimating a Service-Life Distribution Based on Production Counts and a Failure Database

DOE PAGES

Ryan, Kenneth J.; Hamada, Michael Scott; Vardeman, Stephen B.

2017-04-01

A manufacturer wanted to compare the service-life distributions of two similar products. These concern product lifetimes after installation (not manufacture). For each product, there were available production counts and an imperfect database providing information on failing units. In the real case, these units were expensive repairable units warrantied against repairs. Failure (of interest here) was relatively rare and driven by a different mode/mechanism than ordinary repair events (not of interest here). Approach: Data models for the service life based on a standard parametric lifetime distribution and a related limited failure population were developed. These models were used to develop expressionsmore » for the likelihood of the available data that properly accounts for information missing in the failure database. Results: A Bayesian approach was employed to obtain estimates of model parameters (with associated uncertainty) in order to investigate characteristics of the service-life distribution. Custom software was developed and is included as Supplemental Material to this case study. One part of a responsible approach to the original case was a simulation experiment used to validate the correctness of the software and the behavior of the statistical methodology before using its results in the application, and an example of such an experiment is included here. Because of confidentiality issues that prevent use of the original data, simulated data with characteristics like the manufacturer’s proprietary data are used to illustrate some aspects of our real analyses. Lastly, we also note that, although this case focuses on rare and complete product failure, the statistical methodology provided is directly applicable to more standard warranty data problems involving typically much larger warranty databases where entries are warranty claims (often for repairs) rather than reports of complete failures.« less

Exploiting Orbital Data and Observation Campaigns to Improve Space Debris Models

NASA Astrophysics Data System (ADS)

Braun, V.; Horstmann, A.; Reihs, B.; Lemmens, S.; Merz, K.; Krag, H.

The European Space Agency (ESA) has been developing the Meteoroid and Space Debris Terrestrial Environment Reference (MASTER) software as the European reference model for space debris for more than 25 years. It is an event-based simulation of all known individual debris-generating events since 1957, including breakups, solid rocket motor firings and nuclear reactor core ejections. In 2014, the upgraded Debris Risk Assessment and Mitigation Analysis (DRAMA) tool suite was released. In the same year an ESA instruction made the standard ISO 24113:2011 on space debris mitigation requirements, adopted via the European Cooperation for Space Standardization (ECSS), applicable to all ESA missions. In order to verify the compliance of a space mission with those requirements, the DRAMA software is used to assess collision avoidance statistics, estimate the remaining orbital lifetime and evaluate the on-ground risk for controlled and uncontrolled reentries. In this paper, the approach to validate the MASTER and DRAMA tools is outlined. For objects larger than 1 cm, thus potentially being observable from ground, the MASTER model has been validated through dedicated observation campaigns. Recent campaign results shall be discussed. Moreover, catalogue data from the Space Surveillance Network (SSN) has been used to correlate the larger objects. In DRAMA, the assessment of collision avoidance statistics is based on orbit uncertainty information derived from Conjunction Data Messages (CDM) provided by the Joint Space Operations Center (JSpOC). They were collected for more than 20 ESA spacecraft in the recent years. The way this information is going to be used in a future DRAMA version is outlined and the comparison of estimated manoeuvre rates with real manoeuvres from the operations of ESA spacecraft is shown.

Estimating a Service-Life Distribution Based on Production Counts and a Failure Database

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

Ryan, Kenneth J.; Hamada, Michael Scott; Vardeman, Stephen B.

A manufacturer wanted to compare the service-life distributions of two similar products. These concern product lifetimes after installation (not manufacture). For each product, there were available production counts and an imperfect database providing information on failing units. In the real case, these units were expensive repairable units warrantied against repairs. Failure (of interest here) was relatively rare and driven by a different mode/mechanism than ordinary repair events (not of interest here). Approach: Data models for the service life based on a standard parametric lifetime distribution and a related limited failure population were developed. These models were used to develop expressionsmore » for the likelihood of the available data that properly accounts for information missing in the failure database. Results: A Bayesian approach was employed to obtain estimates of model parameters (with associated uncertainty) in order to investigate characteristics of the service-life distribution. Custom software was developed and is included as Supplemental Material to this case study. One part of a responsible approach to the original case was a simulation experiment used to validate the correctness of the software and the behavior of the statistical methodology before using its results in the application, and an example of such an experiment is included here. Because of confidentiality issues that prevent use of the original data, simulated data with characteristics like the manufacturer’s proprietary data are used to illustrate some aspects of our real analyses. Lastly, we also note that, although this case focuses on rare and complete product failure, the statistical methodology provided is directly applicable to more standard warranty data problems involving typically much larger warranty databases where entries are warranty claims (often for repairs) rather than reports of complete failures.« less

The Role of Data Analysis Software in Graduate Programs in Education and Post-Graduate Research

ERIC Educational Resources Information Center

Harwell, Michael

2018-01-01

The importance of data analysis software in graduate programs in education and post-graduate educational research is self-evident. However the role of this software in facilitating supererogated statistical practice versus "cookbookery" is unclear. The need to rigorously document the role of data analysis software in students' graduate…

Information system life-cycle and documentation standards, volume 1

NASA Technical Reports Server (NTRS)

Callender, E. David; Steinbacher, Jody

1989-01-01

The Software Management and Assurance Program (SMAP) Information System Life-Cycle and Documentation Standards Document describes the Version 4 standard information system life-cycle in terms of processes, products, and reviews. The description of the products includes detailed documentation standards. The standards in this document set can be applied to the life-cycle, i.e., to each phase in the system's development, and to the documentation of all NASA information systems. This provides consistency across the agency as well as visibility into the completeness of the information recorded. An information system is software-intensive, but consists of any combination of software, hardware, and operational procedures required to process, store, or transmit data. This document defines a standard life-cycle model and content for associated documentation.

LEGOS: Object-based software components for mission-critical systems. Final report, June 1, 1995--December 31, 1997

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

NONE

1998-08-01

An estimated 85% of the installed base of software is a custom application with a production quantity of one. In practice, almost 100% of military software systems are custom software. Paradoxically, the marginal costs of producing additional units are near zero. So why hasn`t the software market, a market with high design costs and low productions costs evolved like other similar custom widget industries, such as automobiles and hardware chips? The military software industry seems immune to market pressures that have motivated a multilevel supply chain structure in other widget industries: design cost recovery, improve quality through specialization, and enablemore » rapid assembly from purchased components. The primary goal of the ComponentWare Consortium (CWC) technology plan was to overcome barriers to building and deploying mission-critical information systems by using verified, reusable software components (Component Ware). The adoption of the ComponentWare infrastructure is predicated upon a critical mass of the leading platform vendors` inevitable adoption of adopting emerging, object-based, distributed computing frameworks--initially CORBA and COM/OLE. The long-range goal of this work is to build and deploy military systems from verified reusable architectures. The promise of component-based applications is to enable developers to snap together new applications by mixing and matching prefabricated software components. A key result of this effort is the concept of reusable software architectures. A second important contribution is the notion that a software architecture is something that can be captured in a formal language and reused across multiple applications. The formalization and reuse of software architectures provide major cost and schedule improvements. The Unified Modeling Language (UML) is fast becoming the industry standard for object-oriented analysis and design notation for object-based systems. However, the lack of a standard real-time distributed object operating system, lack of a standard Computer-Aided Software Environment (CASE) tool notation and lack of a standard CASE tool repository has limited the realization of component software. The approach to fulfilling this need is the software component factory innovation. The factory approach takes advantage of emerging standards such as UML, CORBA, Java and the Internet. The key technical innovation of the software component factory is the ability to assemble and test new system configurations as well as assemble new tools on demand from existing tools and architecture design repositories.« less

Development and Evaluation of a Computer-Based Program for Assessing Quality of Family Medicine Teams Based on Accreditation Standards

PubMed Central

Valjevac, Salih; Ridjanovic, Zoran; Masic, Izet

2009-01-01

CONFLICT OF INTEREST: NONE DECLARED SUMMARY Introduction Agency for healthcare quality and accreditation in Federation of Bosnia and Herzegovina (AKAZ) is authorized body in the field of healthcare quality and safety improvement and accreditation of healthcare institutions. Beside accreditation standards for hospitals and primary health care centers, AKAZ has also developed accreditation standards for family medicine teams. Methods Software development was primarily based on Accreditation Standards for Family Medicine Teams. Seven chapters / topics: (1. Physical factors; 2. Equipment; 3. Organization and Management; 4. Health promotion and illness prevention; 5. Clinical services; 6. Patient survey; and 7. Patient’s rights and obligations) contain 35 standards describing expected level of family medicine team’s quality. Based on accreditation standards structure and needs of different potential users, it was concluded that software backbone should be a database containing all accreditation standards, self assessment and external assessment details. In this article we will present the development of standardized software for self and external evaluation of quality of service in family medicine, as well as plans for the future development of this software package. Conclusion Electronic data gathering and storing enhances the management, access and overall use of information. During this project we came to conclusion that software for self assessment and external assessment is ideal for accreditation standards distribution, their overview by the family medicine team members, their self assessment and external assessment. PMID:24109157

Mapping Norway - a Method to Register and Survey the Status of Accessibility

NASA Astrophysics Data System (ADS)

Michaelis, Sven; Bögelsack, Kathrin

2018-05-01

The Norwegian mapping authority has developed a standard method for mapping accessibility mostly for people with limited or no walking abilities in urban and recreational areas. We choose an object-orientated approach where points, lines and polygons represents objects in the environment. All data are stored in a geospatial database, so they can be presented as web map and analyzed using GIS software. By the end of 2016 more than 160 municipalities are mapped using that method. The aim of this project is to establish a national standard for mapping and to provide a geodatabase that shows the status of accessibility throughout Norway. The data provide a useful tool for national statistics, local planning authorities and private users. First results show that accessibility is low and Norway still faces many challenges to meet the government's goals for Universal Design.

Comparison of Scientific Calipers and Computer-Enabled CT Review for the Measurement of Skull Base and Craniomaxillofacial Dimensions

PubMed Central

Citardi, Martin J.; Herrmann, Brian; Hollenbeak, Chris S.; Stack, Brendan C.; Cooper, Margaret; Bucholz, Richard D.

2001-01-01

Traditionally, cadaveric studies and plain-film cephalometrics provided information about craniomaxillofacial proportions and measurements; however, advances in computer technology now permit software-based review of computed tomography (CT)-based models. Distances between standardized anatomic points were measured on five dried human skulls with standard scientific calipers (Geneva Gauge, Albany, NY) and through computer workstation (StealthStation 2.6.4, Medtronic Surgical Navigation Technology, Louisville, CO) review of corresponding CT scans. Differences in measurements between the caliper and CT model were not statistically significant for each parameter. Measurements obtained by computer workstation CT review of the cranial skull base are an accurate representation of actual bony anatomy. Such information has important implications for surgical planning and clinical research. ImagesFigure 1Figure 2Figure 3 PMID:17167599

Automatic thermographic image defect detection of composites

NASA Astrophysics Data System (ADS)

Luo, Bin; Liebenberg, Bjorn; Raymont, Jeff; Santospirito, SP

2011-05-01

Detecting defects, and especially reliably measuring defect sizes, are critical objectives in automatic NDT defect detection applications. In this work, the Sentence software is proposed for the analysis of pulsed thermography and near IR images of composite materials. Furthermore, the Sentence software delivers an end-to-end, user friendly platform for engineers to perform complete manual inspections, as well as tools that allow senior engineers to develop inspection templates and profiles, reducing the requisite thermographic skill level of the operating engineer. Finally, the Sentence software can also offer complete independence of operator decisions by the fully automated "Beep on Defect" detection functionality. The end-to-end automatic inspection system includes sub-systems for defining a panel profile, generating an inspection plan, controlling a robot-arm and capturing thermographic images to detect defects. A statistical model has been built to analyze the entire image, evaluate grey-scale ranges, import sentencing criteria and automatically detect impact damage defects. A full width half maximum algorithm has been used to quantify the flaw sizes. The identified defects are imported into the sentencing engine which then sentences (automatically compares analysis results against acceptance criteria) the inspection by comparing the most significant defect or group of defects against the inspection standards.

Simple solution to the medical instrumentation software problem

NASA Astrophysics Data System (ADS)

Leif, Robert C.; Leif, Suzanne B.; Leif, Stephanie H.; Bingue, E.

1995-04-01

Medical devices now include a substantial software component, which is both difficult and expensive to produce and maintain. Medical software must be developed according to `Good Manufacturing Practices', GMP. Good Manufacturing Practices as specified by the FDA and ISO requires the definition and compliance to a software processes which ensures quality products by specifying a detailed method of software construction. The software process should be based on accepted standards. US Department of Defense software standards and technology can both facilitate the development and improve the quality of medical systems. We describe the advantages of employing Mil-Std-498, Software Development and Documentation, and the Ada programming language. Ada provides the very broad range of functionalities, from embedded real-time to management information systems required by many medical devices. It also includes advanced facilities for object oriented programming and software engineering.

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PubMed Central

Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M.; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R.

2015-01-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/. PMID:26037908

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

PubMed

Qi, Da; Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R

2015-09-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation guide for class B software specification documents

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1979-01-01

General conceptual requirements and specific application rules and procedures are provided for the production of software specification documents in conformance with deep space network software standards and class B standards. Class B documentation is identified as the appropriate level applicable to implementation, sustaining engineering, and operational uses by qualified personnel. Special characteristics of class B documents are defined.

COGNATE: comparative gene annotation characterizer.

PubMed

Wilbrandt, Jeanne; Misof, Bernhard; Niehuis, Oliver

2017-07-17

The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https://github.com/ZFMK/COGNATE ). The tool COGNATE allows comparing genome assemblies and structural elements on multiples levels (e.g., scaffold or contig sequence, gene). It clearly enhances comparability between analyses. Thus, COGNATE can provide the important standardization of both genome and gene structure parameter disclosure as well as data acquisition for future comparative analyses. With the establishment of comprehensive descriptive standards and the extensive availability of genomes, an encompassing database will become possible.

Statistical Theory for the "RCT-YES" Software: Design-Based Causal Inference for RCTs. NCEE 2015-4011

ERIC Educational Resources Information Center

Schochet, Peter Z.

2015-01-01

This report presents the statistical theory underlying the "RCT-YES" software that estimates and reports impacts for RCTs for a wide range of designs used in social policy research. The report discusses a unified, non-parametric design-based approach for impact estimation using the building blocks of the Neyman-Rubin-Holland causal…

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

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

2017-11-01

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

The Software Maturity Matrix: A Software Performance Metric

DTIC Science & Technology

2003-01-28

are for Managing n Use Them! n Unused measurements have the same value as last night’s unused hotel room or an empty airline seat. n Be Prepared to...standard measurements are implicit n Organization standard verification is implicit n Organization standard SMM training can be the basis of an

Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie

2002-01-01

The Base Enivronmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists on an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign manditory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: It helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.

Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie

2003-01-01

The Base Environmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists of an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign mandatory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: it helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.

Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie; Selinsky, T.

2002-01-01

The Base Environmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists of an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign mandatory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: it helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.

Quantifying and reducing statistical uncertainty in sample-based health program costing studies in low- and middle-income countries.

PubMed

Rivera-Rodriguez, Claudia L; Resch, Stephen; Haneuse, Sebastien

2018-01-01

In many low- and middle-income countries, the costs of delivering public health programs such as for HIV/AIDS, nutrition, and immunization are not routinely tracked. A number of recent studies have sought to estimate program costs on the basis of detailed information collected on a subsample of facilities. While unbiased estimates can be obtained via accurate measurement and appropriate analyses, they are subject to statistical uncertainty. Quantification of this uncertainty, for example, via standard errors and/or 95% confidence intervals, provides important contextual information for decision-makers and for the design of future costing studies. While other forms of uncertainty, such as that due to model misspecification, are considered and can be investigated through sensitivity analyses, statistical uncertainty is often not reported in studies estimating the total program costs. This may be due to a lack of awareness/understanding of (1) the technical details regarding uncertainty estimation and (2) the availability of software with which to calculate uncertainty for estimators resulting from complex surveys. We provide an overview of statistical uncertainty in the context of complex costing surveys, emphasizing the various potential specific sources that contribute to overall uncertainty. We describe how analysts can compute measures of uncertainty, either via appropriately derived formulae or through resampling techniques such as the bootstrap. We also provide an overview of calibration as a means of using additional auxiliary information that is readily available for the entire program, such as the total number of doses administered, to decrease uncertainty and thereby improve decision-making and the planning of future studies. A recent study of the national program for routine immunization in Honduras shows that uncertainty can be reduced by using information available prior to the study. This method can not only be used when estimating the total cost of delivering established health programs but also to decrease uncertainty when the interest lies in assessing the incremental effect of an intervention. Measures of statistical uncertainty associated with survey-based estimates of program costs, such as standard errors and 95% confidence intervals, provide important contextual information for health policy decision-making and key inputs for the design of future costing studies. Such measures are often not reported, possibly because of technical challenges associated with their calculation and a lack of awareness of appropriate software. Modern statistical analysis methods for survey data, such as calibration, provide a means to exploit additional information that is readily available but was not used in the design of the study to significantly improve the estimation of total cost through the reduction of statistical uncertainty.

Quantifying and reducing statistical uncertainty in sample-based health program costing studies in low- and middle-income countries

PubMed Central

Resch, Stephen

2018-01-01

Objectives: In many low- and middle-income countries, the costs of delivering public health programs such as for HIV/AIDS, nutrition, and immunization are not routinely tracked. A number of recent studies have sought to estimate program costs on the basis of detailed information collected on a subsample of facilities. While unbiased estimates can be obtained via accurate measurement and appropriate analyses, they are subject to statistical uncertainty. Quantification of this uncertainty, for example, via standard errors and/or 95% confidence intervals, provides important contextual information for decision-makers and for the design of future costing studies. While other forms of uncertainty, such as that due to model misspecification, are considered and can be investigated through sensitivity analyses, statistical uncertainty is often not reported in studies estimating the total program costs. This may be due to a lack of awareness/understanding of (1) the technical details regarding uncertainty estimation and (2) the availability of software with which to calculate uncertainty for estimators resulting from complex surveys. We provide an overview of statistical uncertainty in the context of complex costing surveys, emphasizing the various potential specific sources that contribute to overall uncertainty. Methods: We describe how analysts can compute measures of uncertainty, either via appropriately derived formulae or through resampling techniques such as the bootstrap. We also provide an overview of calibration as a means of using additional auxiliary information that is readily available for the entire program, such as the total number of doses administered, to decrease uncertainty and thereby improve decision-making and the planning of future studies. Results: A recent study of the national program for routine immunization in Honduras shows that uncertainty can be reduced by using information available prior to the study. This method can not only be used when estimating the total cost of delivering established health programs but also to decrease uncertainty when the interest lies in assessing the incremental effect of an intervention. Conclusion: Measures of statistical uncertainty associated with survey-based estimates of program costs, such as standard errors and 95% confidence intervals, provide important contextual information for health policy decision-making and key inputs for the design of future costing studies. Such measures are often not reported, possibly because of technical challenges associated with their calculation and a lack of awareness of appropriate software. Modern statistical analysis methods for survey data, such as calibration, provide a means to exploit additional information that is readily available but was not used in the design of the study to significantly improve the estimation of total cost through the reduction of statistical uncertainty. PMID:29636964

SEDPAK—A comprehensive operational system and data-processing package in APPLESOFT BASIC for a settling tube, sediment analyzer

NASA Astrophysics Data System (ADS)

Goldbery, R.; Tehori, O.

SEDPAK provides a comprehensive software package for operation of a settling tube and sand analyzer (2-0.063 mm) and includes data-processing programs for statistical and graphic output of results. The programs are menu-driven and written in APPLESOFT BASIC, conforming with APPLE 3.3 DOS. Data storage and retrieval from disc is an important feature of SEDPAK. Additional features of SEDPAK include condensation of raw settling data via standard size-calibration curves to yield statistical grain-size parameters, plots of grain-size frequency distributions and cumulative log/probability curves. The program also has a module for processing of grain-size frequency data from sieved samples. An addition feature of SEDPAK is the option for automatic data processing and graphic output of a sequential or nonsequential array of samples on one side of a disc.

Imaging and quantification of endothelial cell loss in eye bank prepared DMEK grafts using trainable segmentation software.

PubMed

Jardine, Griffin J; Holiman, Jeffrey D; Stoeger, Christopher G; Chamberlain, Winston D

2014-09-01

To improve accuracy and efficiency in quantifying the endothelial cell loss (ECL) in eye bank preparation of corneal endothelial grafts. Eight cadaveric corneas were subjected to Descemet Membrane Endothelial Keratoplasty (DMEK) preparation. The endothelial surfaces were stained with a viability stain, calcein AM dye (CAM) and then captured by a digital camera. The ECL rates were quantified in these images by three separate readers using trainable segmentation, a plug-in feature from the imaging software, Fiji. Images were also analyzed by Adobe Photoshop for comparison. Mean times required to process the images were measured between the two modalities. The mean ECL (with standard deviation) as analyzed by Fiji was 22.5% (6.5%) and Adobe was 18.7% (7.0%; p = 0.04). The mean time required to process the images through the two different imaging methods was 19.9 min (7.5) for Fiji and 23.4 min (12.9) for Adobe (p = 0.17). Establishing an accurate, efficient and reproducible means of quantifying ECL in graft preparation and surgical techniques can provide insight to the safety, long-term potential of the graft tissues as well as provide a quality control measure for eye banks and surgeons. Trainable segmentation in Fiji software using CAM is a novel approach to measuring ECL that captured a statistically significantly higher percentage of ECL comparable to Adobe and was more accurate in standardized testing. Interestingly, ECL as determined using both methods in eye bank-prepared DMEK grafts exceeded 18% on average.

FlowCal: A user-friendly, open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units

PubMed Central

Castillo-Hair, Sebastian M.; Sexton, John T.; Landry, Brian P.; Olson, Evan J.; Igoshin, Oleg A.; Tabor, Jeffrey J.

2017-01-01

Flow cytometry is widely used to measure gene expression and other molecular biological processes with single cell resolution via fluorescent probes. Flow cytometers output data in arbitrary units (a.u.) that vary with the probe, instrument, and settings. Arbitrary units can be converted to the calibrated unit molecules of equivalent fluorophore (MEF) using commercially available calibration particles. However, there is no convenient, non-proprietary tool available to perform this calibration. Consequently, most researchers report data in a.u., limiting interpretation. Here, we report a software tool named FlowCal to overcome current limitations. FlowCal can be run using an intuitive Microsoft Excel interface, or customizable Python scripts. The software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Additionally, FlowCal automatically gates data, calculates common statistics, and produces publication quality plots. We validate FlowCal by calibrating a.u. measurements of E. coli expressing superfolder GFP (sfGFP) collected at 10 different detector sensitivity (gain) settings to a single MEF value. Additionally, we reduce day-to-day variability in replicate E. coli sfGFP expression measurements due to instrument drift by 33%, and calibrate S. cerevisiae mVenus expression data to MEF units. Finally, we demonstrate a simple method for using FlowCal to calibrate fluorescence units across different cytometers. FlowCal should ease the quantitative analysis of flow cytometry data within and across laboratories and facilitate the adoption of standard fluorescence units in synthetic biology and beyond. PMID:27110723

77 FR 50726 - Software Requirement Specifications for Digital Computer Software and Complex Electronics Used in...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... Computer Software and Complex Electronics Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear...-1209, ``Software Requirement Specifications for Digital Computer Software and Complex Electronics used... Electronics Engineers (ANSI/IEEE) Standard 830-1998, ``IEEE Recommended Practice for Software Requirements...

A new approach to aid the characterisation and identification of metabolites of a model drug; partial isotope enrichment combined with novel formula elucidation software.

PubMed

Hobby, Kirsten; Gallagher, Richard T; Caldwell, Patrick; Wilson, Ian D

2009-01-01

This work describes the identification of 'isotopically enriched' metabolites of 4-cyanoaniline using the unique features of the software package 'Spectral Simplicity'. The software is capable of creating the theoretical mass spectra for partially isotope-enriched compounds, and subsequently performing an elemental composition analysis to give the elemental formula for the 'isotopically enriched' metabolite. A novel mass spectral correlation method, called 'FuzzyFit', was employed. 'FuzzyFit' utilises the expected experimental distribution of errors in both mass accuracy and isotope pattern and enables discrimination between statistically probable and improbable candidate formulae. The software correctly determined the molecular formulae of ten previously described metabolites of 4-cyanoaniline confirming the technique of partial isotope enrichment can produce results analogous to standard methodologies. Six previously unknown species were also identified, based on the presence of the unique 'designer' isotope ratio. Three of the unknowns were tentatively identified as N-acetylglutamine, O-methyl-N acetylglucuronide and a putative fatty acid conjugate. The discovery of a significant number of unknown species of a model drug with a comprehensive history of investigation highlights the potential for enhancement to the analytical process by the use of 'designer' isotope ratio compounds. The 'FuzzyFit' methodology significantly aided the elucidation of candidate formulae, by provision of a vastly simplified candidate formula data set. Copyright (c) 2008 John Wiley & Sons, Ltd.

Development of quantitative screen for 1550 chemicals with GC-MS.

PubMed

Bergmann, Alan J; Points, Gary L; Scott, Richard P; Wilson, Glenn; Anderson, Kim A

2018-05-01

With hundreds of thousands of chemicals in the environment, effective monitoring requires high-throughput analytical techniques. This paper presents a quantitative screening method for 1550 chemicals based on statistical modeling of responses with identification and integration performed using deconvolution reporting software. The method was evaluated with representative environmental samples. We tested biological extracts, low-density polyethylene, and silicone passive sampling devices spiked with known concentrations of 196 representative chemicals. A multiple linear regression (R 2  = 0.80) was developed with molecular weight, logP, polar surface area, and fractional ion abundance to predict chemical responses within a factor of 2.5. Linearity beyond the calibration had R 2  > 0.97 for three orders of magnitude. Median limits of quantitation were estimated to be 201 pg/μL (1.9× standard deviation). The number of detected chemicals and the accuracy of quantitation were similar for environmental samples and standard solutions. To our knowledge, this is the most precise method for the largest number of semi-volatile organic chemicals lacking authentic standards. Accessible instrumentation and software make this method cost effective in quantifying a large, customizable list of chemicals. When paired with silicone wristband passive samplers, this quantitative screen will be very useful for epidemiology where binning of concentrations is common. Graphical abstract A multiple linear regression of chemical responses measured with GC-MS allowed quantitation of 1550 chemicals in samples such as silicone wristbands.

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.

Semiautomated Workflow for Clinically Streamlined Glioma Parametric Response Mapping

PubMed Central

Keith, Lauren; Ross, Brian D.; Galbán, Craig J.; Luker, Gary D.; Galbán, Stefanie; Zhao, Binsheng; Guo, Xiaotao; Chenevert, Thomas L.; Hoff, Benjamin A.

2017-01-01

Management of glioblastoma multiforme remains a challenging problem despite recent advances in targeted therapies. Timely assessment of therapeutic agents is hindered by the lack of standard quantitative imaging protocols for determining targeted response. Clinical response assessment for brain tumors is determined by volumetric changes assessed at 10 weeks post-treatment initiation. Further, current clinical criteria fail to use advanced quantitative imaging approaches, such as diffusion and perfusion magnetic resonance imaging. Development of the parametric response mapping (PRM) applied to diffusion-weighted magnetic resonance imaging has provided a sensitive and early biomarker of successful cytotoxic therapy in brain tumors while maintaining a spatial context within the tumor. Although PRM provides an earlier readout than volumetry and sometimes greater sensitivity compared with traditional whole-tumor diffusion statistics, it is not routinely used for patient management; an automated and standardized software for performing the analysis and for the generation of a clinical report document is required for this. We present a semiautomated and seamless workflow for image coregistration, segmentation, and PRM classification of glioblastoma multiforme diffusion-weighted magnetic resonance imaging scans. The software solution can be integrated using local hardware or performed remotely in the cloud while providing connectivity to existing picture archive and communication systems. This is an important step toward implementing PRM analysis of solid tumors in routine clinical practice. PMID:28286871

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

Head Circumference as a Useful Surrogate for Intracranial Volume in Older Adults

PubMed Central

Hshieh, Tammy T.; Fox, Meaghan L.; Kosar, Cyrus M.; Cavallari, Michele; Guttmann, Charles R.G.; Alsop, David; Marcantonio, Edward R.; Schmitt, Eva M.; Jones, Richard N.; Inouye, Sharon K.

2015-01-01

Background Intracranial volume (ICV) has been proposed as a measure of maximum lifetime brain size. Accurate ICV measures require neuroimaging which is not always feasible for epidemiologic investigations. We examined head circumference as a useful surrogate for intracranial volume in older adults. Methods 99 older adults underwent Magnetic Resonance Imaging (MRI). ICV was measured by Statistical Parametric Mapping 8 (SPM8) software or Functional MRI of the Brain Software Library (FSL) extraction with manual editing, typically considered the gold standard. Head circumferences were determined using standardized tape measurement. We examined estimated correlation coefficients between head circumference and the two MRI-based ICV measurements. Results Head circumference and ICV by SPM8 were moderately correlated (overall r=0.73, men r=0.67, women r=0.63). Head circumference and ICV by FSL were also moderately correlated (overall r=0.69, men r=0.63, women r=0.49). Conclusions Head circumference measurement was strongly correlated with MRI-derived ICV. Our study presents a simple method to approximate ICV among older patients, which may prove useful as a surrogate for cognitive reserve in large scale epidemiologic studies of cognitive outcomes. This study also suggests the stability of head circumference correlation with ICV throughout the lifespan. PMID:26631180

Intensity and duration of activity bouts decreases in healthy children between 7 and 13 years of age: a new, higher resolution method to analyze StepWatch Activity Monitor data.

PubMed

Tulchin-Francis, Kirsten; Stevens, Wilshaw; Jeans, Kelly A

2014-11-01

Assessment of physical, ambulatory, activity using accelerometer-based devices has been reported in healthy individuals across a wide range of ages, as well as in multiple patient populations. Many researchers who utilize the StepWatch Activity Monitor (SAM) rely on the default settings for data collection and analysis. A comparison was made between the standard output from the SAM software, and a novel method to evaluate all walking bouts using an Intensity-Duration-Volume (I-D-V) model in healthy children aged 7-13. 105 children without impairment wore the SAM for a total of 1691 d. Statistically significant differences were seen between 7-8-9 year olds and 10-11-12 year olds using the I-D-V model that were not seen using the standard SAM software default output. The increased sensitivity of this technique could be critical for observing the effect of various interventions on patients who experience physical limitations. This new analytical model also allows researchers to monitor activity and exercise-type behavior in a way which coincides with exercise prescription by assessing intensity, duration and volume of activity bouts.

Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra provides reduced effect of scanner for cortex volumetry with atlas-based method in healthy subjects.

PubMed

Goto, Masami; Abe, Osamu; Aoki, Shigeki; Hayashi, Naoto; Miyati, Tosiaki; Takao, Hidemasa; Iwatsubo, Takeshi; Yamashita, Fumio; Matsuda, Hiroshi; Mori, Harushi; Kunimatsu, Akira; Ino, Kenji; Yano, Keiichi; Ohtomo, Kuni

2013-07-01

This study aimed to investigate whether the effect of scanner for cortex volumetry with atlas-based method is reduced using Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) normalization compared with standard normalization. Three-dimensional T1-weighted magnetic resonance images (3D-T1WIs) of 21 healthy subjects were obtained and evaluated for effect of scanner in cortex volumetry. 3D-T1WIs of the 21 subjects were obtained with five MRI systems. Imaging of each subject was performed on each of five different MRI scanners. We used the Voxel-Based Morphometry 8 tool implemented in Statistical Parametric Mapping 8 and WFU PickAtlas software (Talairach brain atlas theory). The following software default settings were used as bilateral region-of-interest labels: "Frontal Lobe," "Hippocampus," "Occipital Lobe," "Orbital Gyrus," "Parietal Lobe," "Putamen," and "Temporal Lobe." Effect of scanner for cortex volumetry using the atlas-based method was reduced with DARTEL normalization compared with standard normalization in Frontal Lobe, Occipital Lobe, Orbital Gyrus, Putamen, and Temporal Lobe; was the same in Hippocampus and Parietal Lobe; and showed no increase with DARTEL normalization for any region of interest (ROI). DARTEL normalization reduces the effect of scanner, which is a major problem in multicenter studies.

Understanding the Perception of Very Small Software Companies towards the Adoption of Process Standards

NASA Astrophysics Data System (ADS)

Basri, Shuib; O'Connor, Rory V.

This paper is concerned with understanding the issues that affect the adoption of software process standards by Very Small Entities (VSEs), their needs from process standards and their willingness to engage with the new ISO/IEC 29110 standard in particular. In order to achieve this goal, a series of industry data collection studies were undertaken with a collection of VSEs. A twin track approach of a qualitative data collection (interviews and focus groups) and quantitative data collection (questionnaire) were undertaken. Data analysis was being completed separately and the final results were merged, using the coding mechanisms of grounded theory. This paper serves as a roadmap for both researchers wishing to understand the issues of process standards adoption by very small companies and also for the software process standards community.

Coordinate based random effect size meta-analysis of neuroimaging studies.

PubMed

Tench, C R; Tanasescu, Radu; Constantinescu, C S; Auer, D P; Cottam, W J

2017-06-01

Low power in neuroimaging studies can make them difficult to interpret, and Coordinate based meta-analysis (CBMA) may go some way to mitigating this issue. CBMA has been used in many analyses to detect where published functional MRI or voxel-based morphometry studies testing similar hypotheses report significant summary results (coordinates) consistently. Only the reported coordinates and possibly t statistics are analysed, and statistical significance of clusters is determined by coordinate density. Here a method of performing coordinate based random effect size meta-analysis and meta-regression is introduced. The algorithm (ClusterZ) analyses both coordinates and reported t statistic or Z score, standardised by the number of subjects. Statistical significance is determined not by coordinate density, but by a random effects meta-analyses of reported effects performed cluster-wise using standard statistical methods and taking account of censoring inherent in the published summary results. Type 1 error control is achieved using the false cluster discovery rate (FCDR), which is based on the false discovery rate. This controls both the family wise error rate under the null hypothesis that coordinates are randomly drawn from a standard stereotaxic space, and the proportion of significant clusters that are expected under the null. Such control is necessary to avoid propagating and even amplifying the very issues motivating the meta-analysis in the first place. ClusterZ is demonstrated on both numerically simulated data and on real data from reports of grey matter loss in multiple sclerosis (MS) and syndromes suggestive of MS, and of painful stimulus in healthy controls. The software implementation is available to download and use freely. Copyright © 2017 Elsevier Inc. All rights reserved.

Bladder cancer mapping in Libya based on standardized morbidity ratio and log-normal model

NASA Astrophysics Data System (ADS)

Alhdiri, Maryam Ahmed; Samat, Nor Azah; Mohamed, Zulkifley

2017-05-01

Disease mapping contains a set of statistical techniques that detail maps of rates based on estimated mortality, morbidity, and prevalence. A traditional approach to measure the relative risk of the disease is called Standardized Morbidity Ratio (SMR). It is the ratio of an observed and expected number of accounts in an area, which has the greatest uncertainty if the disease is rare or if geographical area is small. Therefore, Bayesian models or statistical smoothing based on Log-normal model are introduced which might solve SMR problem. This study estimates the relative risk for bladder cancer incidence in Libya from 2006 to 2007 based on the SMR and log-normal model, which were fitted to data using WinBUGS software. This study starts with a brief review of these models, starting with the SMR method and followed by the log-normal model, which is then applied to bladder cancer incidence in Libya. All results are compared using maps and tables. The study concludes that the log-normal model gives better relative risk estimates compared to the classical method. The log-normal model has can overcome the SMR problem when there is no observed bladder cancer in an area.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

First experiences with the implementation of the European standard EN 62304 on medical device software for the quality assurance of a radiotherapy unit

PubMed Central

2014-01-01

Background According to the latest amendment of the Medical Device Directive standalone software qualifies as a medical device when intended by the manufacturer to be used for medical purposes. In this context, the EN 62304 standard is applicable which defines the life-cycle requirements for the development and maintenance of medical device software. A pilot project was launched to acquire skills in implementing this standard in a hospital-based environment (in-house manufacture). Methods The EN 62304 standard outlines minimum requirements for each stage of the software life-cycle, defines the activities and tasks to be performed and scales documentation and testing according to its criticality. The required processes were established for the pre-existent decision-support software FlashDumpComparator (FDC) used during the quality assurance of treatment-relevant beam parameters. As the EN 62304 standard implicates compliance with the EN ISO 14971 standard on the application of risk management to medical devices, a risk analysis was carried out to identify potential hazards and reduce the associated risks to acceptable levels. Results The EN 62304 standard is difficult to implement without proper tools, thus open-source software was selected and integrated into a dedicated development platform. The control measures yielded by the risk analysis were independently implemented and verified, and a script-based test automation was retrofitted to reduce the associated test effort. After all documents facilitating the traceability of the specified requirements to the corresponding tests and of the control measures to the proof of execution were generated, the FDC was released as an accessory to the HIT facility. Conclusions The implementation of the EN 62304 standard was time-consuming, and a learning curve had to be overcome during the first iterations of the associated processes, but many process descriptions and all software tools can be re-utilized in follow-up projects. It has been demonstrated that a standards-compliant development of small and medium-sized medical software can be carried out by a small team with limited resources in a clinical setting. This is of particular relevance as the upcoming revision of the Medical Device Directive is expected to harmonize and tighten the current legal requirements for all European in-house manufacturers. PMID:24655818

First experiences with the implementation of the European standard EN 62304 on medical device software for the quality assurance of a radiotherapy unit.

PubMed

Höss, Angelika; Lampe, Christian; Panse, Ralf; Ackermann, Benjamin; Naumann, Jakob; Jäkel, Oliver

2014-03-21

According to the latest amendment of the Medical Device Directive standalone software qualifies as a medical device when intended by the manufacturer to be used for medical purposes. In this context, the EN 62304 standard is applicable which defines the life-cycle requirements for the development and maintenance of medical device software. A pilot project was launched to acquire skills in implementing this standard in a hospital-based environment (in-house manufacture). The EN 62304 standard outlines minimum requirements for each stage of the software life-cycle, defines the activities and tasks to be performed and scales documentation and testing according to its criticality. The required processes were established for the pre-existent decision-support software FlashDumpComparator (FDC) used during the quality assurance of treatment-relevant beam parameters. As the EN 62304 standard implicates compliance with the EN ISO 14971 standard on the application of risk management to medical devices, a risk analysis was carried out to identify potential hazards and reduce the associated risks to acceptable levels. The EN 62304 standard is difficult to implement without proper tools, thus open-source software was selected and integrated into a dedicated development platform. The control measures yielded by the risk analysis were independently implemented and verified, and a script-based test automation was retrofitted to reduce the associated test effort. After all documents facilitating the traceability of the specified requirements to the corresponding tests and of the control measures to the proof of execution were generated, the FDC was released as an accessory to the HIT facility. The implementation of the EN 62304 standard was time-consuming, and a learning curve had to be overcome during the first iterations of the associated processes, but many process descriptions and all software tools can be re-utilized in follow-up projects. It has been demonstrated that a standards-compliant development of small and medium-sized medical software can be carried out by a small team with limited resources in a clinical setting. This is of particular relevance as the upcoming revision of the Medical Device Directive is expected to harmonize and tighten the current legal requirements for all European in-house manufacturers.

A Strategy for Improved System Assurance

DTIC Science & Technology

2007-06-20

Quality (Measurements Life Cycle Safety, Security & Others) ISO /IEC 12207 * Software Life Cycle Processes ISO 9001 Quality Management System...14598 Software Product Evaluation Related ISO /IEC 90003 Guidelines for the Application of ISO 9001:2000 to Computer Software IEEE 12207 Industry...Implementation of International Standard ISO /IEC 12207 IEEE 1220 Standard for Application and Management of the System Engineering Process Use in

BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters.

PubMed

Huang, Hailiang; Tata, Sandeep; Prill, Robert J

2013-01-01

Computational workloads for genome-wide association studies (GWAS) are growing in scale and complexity outpacing the capabilities of single-threaded software designed for personal computers. The BlueSNP R package implements GWAS statistical tests in the R programming language and executes the calculations across computer clusters configured with Apache Hadoop, a de facto standard framework for distributed data processing using the MapReduce formalism. BlueSNP makes computationally intensive analyses, such as estimating empirical p-values via data permutation, and searching for expression quantitative trait loci over thousands of genes, feasible for large genotype-phenotype datasets. http://github.com/ibm-bioinformatics/bluesnp

Adaptive statistical iterative reconstruction use for radiation dose reduction in pediatric lower-extremity CT: impact on diagnostic image quality.

PubMed

Shah, Amisha; Rees, Mitchell; Kar, Erica; Bolton, Kimberly; Lee, Vincent; Panigrahy, Ashok

2018-06-01

For the past several years, increased levels of imaging radiation and cumulative radiation to children has been a significant concern. Although several measures have been taken to reduce radiation dose during computed tomography (CT) scan, the newer dose reduction software adaptive statistical iterative reconstruction (ASIR) has been an effective technique in reducing radiation dose. To our knowledge, no studies are published that assess the effect of ASIR on extremity CT scans in children. To compare radiation dose, image noise, and subjective image quality in pediatric lower extremity CT scans acquired with and without ASIR. The study group consisted of 53 patients imaged on a CT scanner equipped with ASIR software. The control group consisted of 37 patients whose CT images were acquired without ASIR. Image noise, Computed Tomography Dose Index (CTDI) and dose length product (DLP) were measured. Two pediatric radiologists rated the studies in subjective categories: image sharpness, noise, diagnostic acceptability, and artifacts. The CTDI (p value = 0.0184) and DLP (p value <0.0002) were significantly decreased with the use of ASIR compared with non-ASIR studies. However, the subjective ratings for sharpness (p < 0.0001) and diagnostic acceptability of the ASIR images (p < 0.0128) were decreased compared with standard, non-ASIR CT studies. Adaptive statistical iterative reconstruction reduces radiation dose for lower extremity CTs in children, but at the expense of diagnostic imaging quality. Further studies are warranted to determine the specific utility of ASIR for pediatric musculoskeletal CT imaging.

The Cardiac Atlas Project--an imaging database for computational modeling and statistical atlases of the heart.

PubMed

Fonseca, Carissa G; Backhaus, Michael; Bluemke, David A; Britten, Randall D; Chung, Jae Do; Cowan, Brett R; Dinov, Ivo D; Finn, J Paul; Hunter, Peter J; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Medrano-Gracia, Pau; Shivkumar, Kalyanam; Suinesiaputra, Avan; Tao, Wenchao; Young, Alistair A

2011-08-15

Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups. Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt). http://www.cardiacatlas.org a.young@auckland.ac.nz Supplementary data are available at Bioinformatics online.

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.

PubMed

Pasaniuc, Bogdan; Zaitlen, Noah; Shi, Huwenbo; Bhatia, Gaurav; Gusev, Alexander; Pickrell, Joseph; Hirschhorn, Joel; Strachan, David P; Patterson, Nick; Price, Alkes L

2014-10-15

Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1-5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case-control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of [Formula: see text] association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses. Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/. bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu Supplementary materials are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Flow Chamber System for the Statistical Evaluation of Bacterial Colonization on Materials

PubMed Central

Menzel, Friederike; Conradi, Bianca; Rodenacker, Karsten; Gorbushina, Anna A.; Schwibbert, Karin

2016-01-01

Biofilm formation on materials leads to high costs in industrial processes, as well as in medical applications. This fact has stimulated interest in the development of new materials with improved surfaces to reduce bacterial colonization. Standardized tests relying on statistical evidence are indispensable to evaluate the quality and safety of these new materials. We describe here a flow chamber system for biofilm cultivation under controlled conditions with a total capacity for testing up to 32 samples in parallel. In order to quantify the surface colonization, bacterial cells were DAPI (4`,6-diamidino-2-phenylindole)-stained and examined with epifluorescence microscopy. More than 100 images of each sample were automatically taken and the surface coverage was estimated using the free open source software g’mic, followed by a precise statistical evaluation. Overview images of all gathered pictures were generated to dissect the colonization characteristics of the selected model organism Escherichia coli W3310 on different materials (glass and implant steel). With our approach, differences in bacterial colonization on different materials can be quantified in a statistically validated manner. This reliable test procedure will support the design of improved materials for medical, industrial, and environmental (subaquatic or subaerial) applications. PMID:28773891

How to Deal with Interval-Censored Data Practically while Assessing the Progression-Free Survival: A Step-by-Step Guide Using SAS and R Software.

PubMed

Dugué, Audrey Emmanuelle; Pulido, Marina; Chabaud, Sylvie; Belin, Lisa; Gal, Jocelyn

2016-12-01

We describe how to estimate progression-free survival while dealing with interval-censored data in the setting of clinical trials in oncology. Three procedures with SAS and R statistical software are described: one allowing for a nonparametric maximum likelihood estimation of the survival curve using the EM-ICM (Expectation and Maximization-Iterative Convex Minorant) algorithm as described by Wellner and Zhan in 1997; a sensitivity analysis procedure in which the progression time is assigned (i) at the midpoint, (ii) at the upper limit (reflecting the standard analysis when the progression time is assigned at the first radiologic exam showing progressive disease), or (iii) at the lower limit of the censoring interval; and finally, two multiple imputations are described considering a uniform or the nonparametric maximum likelihood estimation (NPMLE) distribution. Clin Cancer Res; 22(23); 5629-35. ©2016 AACR. ©2016 American Association for Cancer Research.

Dynamic Hurricane Data Analysis Tool

NASA Technical Reports Server (NTRS)

Knosp, Brian W.; Li, Peggy; Vu, Quoc A.

2009-01-01

A dynamic hurricane data analysis tool allows users of the JPL Tropical Cyclone Information System (TCIS) to analyze data over a Web medium. The TCIS software is described in the previous article, Tropical Cyclone Information System (TCIS) (NPO-45748). This tool interfaces with the TCIS database to pull in data from several different atmospheric and oceanic data sets, both observed by instruments. Users can use this information to generate histograms, maps, and profile plots for specific storms. The tool also displays statistical values for the user-selected parameter for the mean, standard deviation, median, minimum, and maximum values. There is little wait time, allowing for fast data plots over date and spatial ranges. Users may also zoom-in for a closer look at a particular spatial range. This is version 1 of the software. Researchers will use the data and tools on the TCIS to understand hurricane processes, improve hurricane forecast models and identify what types of measurements the next generation of instruments will need to collect.

Progress on automated data analysis algorithms for ultrasonic inspection of composites

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Forsyth, David S.; Welter, John T.

2015-03-01

Progress is presented on the development and demonstration of automated data analysis (ADA) software to address the burden in interpreting ultrasonic inspection data for large composite structures. The automated data analysis algorithm is presented in detail, which follows standard procedures for analyzing signals for time-of-flight indications and backwall amplitude dropout. New algorithms have been implemented to reliably identify indications in time-of-flight images near the front and back walls of composite panels. Adaptive call criteria have also been applied to address sensitivity to variation in backwall signal level, panel thickness variation, and internal signal noise. ADA processing results are presented for a variety of test specimens that include inserted materials and discontinuities produced under poor manufacturing conditions. Software tools have been developed to support both ADA algorithm design and certification, producing a statistical evaluation of indication results and false calls using a matching process with predefined truth tables. Parametric studies were performed to evaluate detection and false call results with respect to varying algorithm settings.

LH750 hematology analyzers to identify malaria and dengue and distinguish them from other febrile illnesses.

PubMed

Sharma, P; Bhargava, M; Sukhachev, D; Datta, S; Wattal, C

2014-02-01

Tropical febrile illnesses such as malaria and dengue are challenging to differentiate clinically. Automated cellular indices from hematology analyzers may afford a preliminary rapid distinction. Blood count and VCS parameters from 114 malaria patients, 105 dengue patients, and 105 febrile controls without dengue or malaria were analyzed. Statistical discriminant functions were generated, and their diagnostic performances were assessed by ROC curve analysis. Three statistical functions were generated: (i) malaria-vs.-controls factor incorporating platelet count and standard deviations of lymphocyte volume and conductivity that identified malaria with 90.4% sensitivity, 88.6% specificity; (ii) dengue-vs.-controls factor incorporating platelet count, lymphocyte percentage and standard deviation of lymphocyte conductivity that identified dengue with 81.0% sensitivity and 77.1% specificity; and (iii) febrile-controls-vs.-malaria/dengue factor incorporating mean corpuscular hemoglobin concentration, neutrophil percentage, mean lymphocyte and monocyte volumes, and standard deviation of monocyte volume that distinguished malaria and dengue from other febrile illnesses with 85.1% sensitivity and 91.4% specificity. Leukocyte abnormalities quantitated by automated analyzers successfully identified malaria and dengue and distinguished them from other fevers. These economic discriminant functions can be rapidly calculated by analyzer software programs to generate electronic flags to trigger-specific testing. They could potentially transform diagnostic approaches to tropical febrile illnesses in cost-constrained settings. © 2013 John Wiley & Sons Ltd.

RAD-ADAPT: Software for modelling clonogenic assay data in radiation biology.

PubMed

Zhang, Yaping; Hu, Kaiqiang; Beumer, Jan H; Bakkenist, Christopher J; D'Argenio, David Z

2017-04-01

We present a comprehensive software program, RAD-ADAPT, for the quantitative analysis of clonogenic assays in radiation biology. Two commonly used models for clonogenic assay analysis, the linear-quadratic model and single-hit multi-target model, are included in the software. RAD-ADAPT uses maximum likelihood estimation method to obtain parameter estimates with the assumption that cell colony count data follow a Poisson distribution. The program has an intuitive interface, generates model prediction plots, tabulates model parameter estimates, and allows automatic statistical comparison of parameters between different groups. The RAD-ADAPT interface is written using the statistical software R and the underlying computations are accomplished by the ADAPT software system for pharmacokinetic/pharmacodynamic systems analysis. The use of RAD-ADAPT is demonstrated using an example that examines the impact of pharmacologic ATM and ATR kinase inhibition on human lung cancer cell line A549 after ionizing radiation. Copyright © 2017 Elsevier B.V. All rights reserved.

Systematic on-site monitoring of compliance dust samples

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

Grayson, R.L.; Gandy, J.R.

1996-12-31

Maintaining compliance with U.S. respirable coal mine dust standards can be difficult on high-productivity longwall panels. Comprehensive and systematic analysis of compliance dust sample data, coupled with access to the U.S. Bureau of Mines (USBM) DUSTPRO, can yield important information for use in maintaining compliance. The objective of this study was to develop and apply a customized software for the collection, storage, modification, and analysis of respirable dust data while providing for flexible export of data and linking with the USBM`s expert advisory system on dust control. An executable, IBM-compatible software was created and customized for use by the personmore » in charge of collecting, submitting, analyzing, and monitoring respirable dust compliance samples. Both descriptive statistics and multiple regression analysis were incorporated. The software allows ASCH files to be exported and directly links with DUSTPRO. After development and validation of the software, longwall compliance data from two different mines was analyzed to evaluate the value of the software. Data included variables on respirable dust concentration, tons produced, the existence of roof/floor rock (dummy variable), and the sampling cycle (dummy variables). Because of confidentiality, specific data will not be presented, only the equations and ANOVA tables. The final regression models explained 83.8% and 61.1% of the variation in the data for the two panels. Important correlations among variables within sampling cycles showed the value of using dummy variables for sampling cycles. The software proved flexible and fast for its intended use. The insights obtained from use improved the systematic monitoring of respirable dust compliance data, especially for pinpointing the most effective dust control methods during specific sampling cycles.« less

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

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

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternativelymore » available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).« less

Determining the status quo of infection prevention and control standards in the hospitals of iran: a case study in 23 hospitals.

PubMed

Shojaee, Jalil; Moosazadeh, Mahmood

2014-02-01

Applying Prevention and Control of Infection (PCI) standards in hospitals reduces probable risks to patients, staff and visitors; it also increases efficiency, and ultimately improves productivity of hospitals. The current study aimed to determine the status quo of international standards of PCI in hospitals located in the north of Iran. This cross-sectional study was conducted in 23 hospitals. Data collection tool was a questionnaire with confirmed validity and reliability. . In this regard, 260 managers, section supervisors and infection control nurses participated in the study according to census basis. SPSS software version 16 was employed to analyze the data through descriptive and analytical statistics. Among the studied hospitals, 18 hospitals were public. Hospitals enjoyed 77.2% of leadership and programming, 80.8% of focus of programs, 67.4% of isolating methods, 88.2% of hand health and protection techniques, 78.8% of improving patient's safety and quality, 90.3% of training personnel, and 78.7% of the average status quo of PCI standards. This study revealed that PCI standards were significantly observed in the studied hospitals and that there were necessary conditions for full deployment of nosocomial infection surveillance.

Comparison of measurement methods with a mixed effects procedure accounting for replicated evaluations (COM3PARE): method comparison algorithm implementation for head and neck IGRT positional verification.

PubMed

Roy, Anuradha; Fuller, Clifton D; Rosenthal, David I; Thomas, Charles R

2015-08-28

Comparison of imaging measurement devices in the absence of a gold-standard comparator remains a vexing problem; especially in scenarios where multiple, non-paired, replicated measurements occur, as in image-guided radiotherapy (IGRT). As the number of commercially available IGRT presents a challenge to determine whether different IGRT methods may be used interchangeably, an unmet need conceptually parsimonious and statistically robust method to evaluate the agreement between two methods with replicated observations. Consequently, we sought to determine, using an previously reported head and neck positional verification dataset, the feasibility and utility of a Comparison of Measurement Methods with the Mixed Effects Procedure Accounting for Replicated Evaluations (COM3PARE), a unified conceptual schema and analytic algorithm based upon Roy's linear mixed effects (LME) model with Kronecker product covariance structure in a doubly multivariate set-up, for IGRT method comparison. An anonymized dataset consisting of 100 paired coordinate (X/ measurements from a sequential series of head and neck cancer patients imaged near-simultaneously with cone beam CT (CBCT) and kilovoltage X-ray (KVX) imaging was used for model implementation. Software-suggested CBCT and KVX shifts for the lateral (X), vertical (Y) and longitudinal (Z) dimensions were evaluated for bias, inter-method (between-subject variation), intra-method (within-subject variation), and overall agreement using with a script implementing COM3PARE with the MIXED procedure of the statistical software package SAS (SAS Institute, Cary, NC, USA). COM3PARE showed statistically significant bias agreement and difference in inter-method between CBCT and KVX was observed in the Z-axis (both p - value<0.01). Intra-method and overall agreement differences were noted as statistically significant for both the X- and Z-axes (all p - value<0.01). Using pre-specified criteria, based on intra-method agreement, CBCT was deemed preferable for X-axis positional verification, with KVX preferred for superoinferior alignment. The COM3PARE methodology was validated as feasible and useful in this pilot head and neck cancer positional verification dataset. COM3PARE represents a flexible and robust standardized analytic methodology for IGRT comparison. The implemented SAS script is included to encourage other groups to implement COM3PARE in other anatomic sites or IGRT platforms.

A study of software standards used in the avionics industry

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.

1994-01-01

Within the past decade, software has become an increasingly common element in computing systems. In particular, the role of software used in the aerospace industry, especially in life- or safety-critical applications, is rapidly expanding. This intensifies the need to use effective techniques for achieving and verifying the reliability of avionics software. Although certain software development processes and techniques are mandated by government regulating agencies, no one methodology has been shown to consistently produce reliable software. The knowledge base for designing reliable software simply has not reached the maturity of its hardware counterpart. In an effort to increase our understanding of software, the Langley Research Center conducted a series of experiments over 15 years with the goal of understanding why and how software fails. As part of this program, the effectiveness of current industry standards for the development of avionics is being investigated. This study involves the generation of a controlled environment to conduct scientific experiments on software processes.

Announcing a Community Effort to Create an Information Model for Research Software Archives

NASA Astrophysics Data System (ADS)

Million, C.; Brazier, A.; King, T.; Hayes, A.

2018-04-01

An effort has started to create recommendations and standards for the archiving of planetary science research software. The primary goal is to define an information model that is consistent with OAIS standards.

A Statistical Testing Approach for Quantifying Software Reliability; Application to an Example System

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

Chu, Tsong-Lun; Varuttamaseni, Athi; Baek, Joo-Seok

The U.S. Nuclear Regulatory Commission (NRC) encourages the use of probabilistic risk assessment (PRA) technology in all regulatory matters, to the extent supported by the state-of-the-art in PRA methods and data. Although much has been accomplished in the area of risk-informed regulation, risk assessment for digital systems has not been fully developed. The NRC established a plan for research on digital systems to identify and develop methods, analytical tools, and regulatory guidance for (1) including models of digital systems in the PRAs of nuclear power plants (NPPs), and (2) incorporating digital systems in the NRC's risk-informed licensing and oversight activities.more » Under NRC's sponsorship, Brookhaven National Laboratory (BNL) explored approaches for addressing the failures of digital instrumentation and control (I and C) systems in the current NPP PRA framework. Specific areas investigated included PRA modeling digital hardware, development of a philosophical basis for defining software failure, and identification of desirable attributes of quantitative software reliability methods. Based on the earlier research, statistical testing is considered a promising method for quantifying software reliability. This paper describes a statistical software testing approach for quantifying software reliability and applies it to the loop-operating control system (LOCS) of an experimental loop of the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL).« less

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

PubMed Central

Höhna, Sebastian; Landis, Michael J.

2016-01-01

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

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

PubMed

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

2016-07-01

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

78 FR 47011 - Software Unit Testing for Digital Computer Software Used in Safety Systems of Nuclear Power Plants

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0195] Software Unit Testing for Digital Computer Software... revised regulatory guide (RG), revision 1 of RG 1.171, ``Software Unit Testing for Digital Computer Software Used in Safety Systems of Nuclear Power Plants.'' This RG endorses American National Standards...

Health Disparities Calculator (HD*Calc) - SEER Software

Cancer.gov

Statistical software that generates summary measures to evaluate and monitor health disparities. Users can import SEER data or other population-based health data to calculate 11 disparity measurements.

Voice Response System Statistics Program : Operational Handbook.

DOT National Transportation Integrated Search

1980-06-01

This report documents the Voice Response System (VRS) Statistics Program developed for the preflight weather briefing VRS. It describes the VRS statistical report format and contents, the software program structure, and the program operation.

Methods to ensure the standardization of FORTRAN software. [PFORT, DAVE, POLISH, and BRNANL, for analysis and editing of codes, in FORTRAN for PDP-10 and IBM 360 and 370

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

Gaffney, P.W.; Wooten, J.W.

1980-05-01

Four software tools PFORT, DAVE, POLISH, and BRNANL, which may be used to ensure the standardization of FORTRAN software are introduced. First, FORTRAN computer programs are loosely classified into three groups. Then reasons are given why the program in two of these groups should adhere to a portable subset of the American National Standard (ANS) First FORTRAN 1966. Next, the software tools PFORT, DAVE, POLISH, and BRNANL, are briefly described, and an example of the output from PFORT, DAVE, and POLISH are given. Finally, the dissemination of information pertaining to the tools together with their availability is outlined. 11 figures.

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.

Software for improving the quality of project management, a case study: international manufacture of electrical equipment

NASA Astrophysics Data System (ADS)

Preradović, D. M.; Mićić, Lj S.; Barz, C.

2017-05-01

Production conditions in today’s world require software support at every stage of production and development of new products, for quality assurance and compliance with ISO standards. In addition to ISO standards such as usual metrics of quality, companies today are focused on other optional standards, such as CMMI (Capability Maturity Model Integrated) or prescribing they own standards. However, while there is intensive progress being made in the PM (project management), there is still a significant number of projects, at the global level, that are failures. These have failed to achieve their goals, within budget or timeframe. This paper focuses on checking the role of software tools through the rate of success in projects implemented in the case of internationally manufactured electrical equipment. The results of this research show the level of contribution of the project management software used to manage and develop new products to improve PM processes and PM functions, and how selection of the software tools affects the quality of PM processes and successfully completed projects.

Evaluation of bond strength of resin cements using different general-purpose statistical software packages for two-parameter Weibull statistics.

PubMed

Roos, Malgorzata; Stawarczyk, Bogna

2012-07-01

This study evaluated and compared Weibull parameters of resin bond strength values using six different general-purpose statistical software packages for two-parameter Weibull distribution. Two-hundred human teeth were randomly divided into 4 groups (n=50), prepared and bonded on dentin according to the manufacturers' instructions using the following resin cements: (i) Variolink (VAN, conventional resin cement), (ii) Panavia21 (PAN, conventional resin cement), (iii) RelyX Unicem (RXU, self-adhesive resin cement) and (iv) G-Cem (GCM, self-adhesive resin cement). Subsequently, all specimens were stored in water for 24h at 37°C. Shear bond strength was measured and the data were analyzed using Anderson-Darling goodness-of-fit (MINITAB 16) and two-parameter Weibull statistics with the following statistical software packages: Excel 2011, SPSS 19, MINITAB 16, R 2.12.1, SAS 9.1.3. and STATA 11.2 (p≤0.05). Additionally, the three-parameter Weibull was fitted using MNITAB 16. Two-parameter Weibull calculated with MINITAB and STATA can be compared using an omnibus test and using 95% CI. In SAS only 95% CI were directly obtained from the output. R provided no estimates of 95% CI. In both SAS and R the global comparison of the characteristic bond strength among groups is provided by means of the Weibull regression. EXCEL and SPSS provided no default information about 95% CI and no significance test for the comparison of Weibull parameters among the groups. In summary, conventional resin cement VAN showed the highest Weibull modulus and characteristic bond strength. There are discrepancies in the Weibull statistics depending on the software package and the estimation method. The information content in the default output provided by the software packages differs to very high extent. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Joint models for longitudinal and time-to-event data: a review of reporting quality with a view to meta-analysis.

PubMed

Sudell, Maria; Kolamunnage-Dona, Ruwanthi; Tudur-Smith, Catrin

2016-12-05

Joint models for longitudinal and time-to-event data are commonly used to simultaneously analyse correlated data in single study cases. Synthesis of evidence from multiple studies using meta-analysis is a natural next step but its feasibility depends heavily on the standard of reporting of joint models in the medical literature. During this review we aim to assess the current standard of reporting of joint models applied in the literature, and to determine whether current reporting standards would allow or hinder future aggregate data meta-analyses of model results. We undertook a literature review of non-methodological studies that involved joint modelling of longitudinal and time-to-event medical data. Study characteristics were extracted and an assessment of whether separate meta-analyses for longitudinal, time-to-event and association parameters were possible was made. The 65 studies identified used a wide range of joint modelling methods in a selection of software. Identified studies concerned a variety of disease areas. The majority of studies reported adequate information to conduct a meta-analysis (67.7% for longitudinal parameter aggregate data meta-analysis, 69.2% for time-to-event parameter aggregate data meta-analysis, 76.9% for association parameter aggregate data meta-analysis). In some cases model structure was difficult to ascertain from the published reports. Whilst extraction of sufficient information to permit meta-analyses was possible in a majority of cases, the standard of reporting of joint models should be maintained and improved. Recommendations for future practice include clear statement of model structure, of values of estimated parameters, of software used and of statistical methods applied.

GRO/EGRET data analysis software: An integrated system of custom and commercial software using standard interfaces

NASA Technical Reports Server (NTRS)

Laubenthal, N. A.; Bertsch, D.; Lal, N.; Etienne, A.; Mcdonald, L.; Mattox, J.; Sreekumar, P.; Nolan, P.; Fierro, J.

1992-01-01

The Energetic Gamma Ray Telescope Experiment (EGRET) on the Compton Gamma Ray Observatory has been in orbit for more than a year and is being used to map the full sky for gamma rays in a wide energy range from 30 to 20,000 MeV. Already these measurements have resulted in a wide range of exciting new information on quasars, pulsars, galactic sources, and diffuse gamma ray emission. The central part of the analysis is done with sky maps that typically cover an 80 x 80 degree section of the sky for an exposure time of several days. Specific software developed for this program generates the counts, exposure, and intensity maps. The analysis is done on a network of UNIX based workstations and takes full advantage of a custom-built user interface called X-dialog. The maps that are generated are stored in the FITS format for a collection of energies. These, along with similar diffuse emission background maps generated from a model calculation, serve as input to a maximum likelihood program that produces maps of likelihood with optional contours that are used to evaluate regions for sources. Likelihood also evaluates the background corrected intensity at each location for each energy interval from which spectra can be generated. Being in a standard FITS format permits all of the maps to be easily accessed by the full complement of tools available in several commercial astronomical analysis systems. In the EGRET case, IDL is used to produce graphics plots in two and three dimensions and to quickly implement any special evaluation that might be desired. Other custom-built software, such as the spectral and pulsar analyses, take advantage of the XView toolkit for display and Postscript output for the color hard copy. This poster paper outlines the data flow and provides examples of the user interfaces and output products. It stresses the advantages that are derived from the integration of the specific instrument-unique software and powerful commercial tools for graphics and statistical evaluation. This approach has several proven advantages including flexibility, a minimum of development effort, ease of use, and portability.

The best motivator priorities parents choose via analytical hierarchy process

NASA Astrophysics Data System (ADS)

Farah, R. N.; Latha, P.

2015-05-01

Motivation is probably the most important factor that educators can target in order to improve learning. Numerous cross-disciplinary theories have been postulated to explain motivation. While each of these theories has some truth, no single theory seems to adequately explain all human motivation. The fact is that human beings in general and pupils in particular are complex creatures with complex needs and desires. In this paper, Analytic Hierarchy Process (AHP) has been proposed as an emerging solution to move towards too large, dynamic and complex real world multi-criteria decision making problems in selecting the most suitable motivator when choosing school for their children. Data were analyzed using SPSS 17.0 ("Statistical Package for Social Science") software. Statistic testing used are descriptive and inferential statistic. Descriptive statistic used to identify respondent pupils and parents demographic factors. The statistical testing used to determine the pupils and parents highest motivator priorities and parents' best priorities using AHP to determine the criteria chosen by parents such as school principals, teachers, pupils and parents. The moderating factors are selected schools based on "Standard Kualiti Pendidikan Malaysia" (SKPM) in Ampang. Inferential statistics such as One-way ANOVA used to get the significant and data used to calculate the weightage of AHP. School principals is found to be the best motivator for parents in choosing school for their pupils followed by teachers, parents and pupils.

Concentration of Donepezil in the Cerebrospinal Fluid of AD Patients: Evaluation of Dosage Sufficiency in Standard Treatment Strategy.

PubMed

Valis, Martin; Masopust, Jiri; Vysata, Oldrich; Hort, Jakub; Dolezal, Rafael; Tomek, Jiri; Misik, Jan; Kuca, Kamil; Karasova, Jana Zdarova

2017-01-01

Although some studies have described the pharmacokinetics and pharmacodynamics of donepezil in the peripheral compartment, studies focused on drug transport across the blood-brain barrier are still very rare. To our knowledge, the fluctuation in the cerebrospinal fluid concentration of donepezil after administration of the drug has not been described in the literature so far. We recruited 16 patients regularly taking a standard therapeutic dose of donepezil (10 mg per day). All patients (Caucasian race) were treated for at least three months with a stable dose of 10 mg per day prior to sample collection. Patients were divided into two groups depending on the time of plasma and cerebrospinal fluid sampling: 12 h (n = 9; 4 M/5F aged 78.68 ± 7.35 years) and 24 h (n = 7; 3 M/4F aged 77.14 ± 5.87 years) after donepezil administration. The cerebrospinal fluid sample was collected by standard lumbar puncture technique using a single-use traumatic needle. The samples were analysed on an Agilent 1260 Series liquid chromatograph comprising a degasser, a quaternary pump, a light-tight autosampler unit set, a thermostated column compartment, and a UV/VIS detector. Agilent ChemStation software, the statistical software Prism4, version 5.0 (GraphPad Software, USA), and IBM ® SPSS ® Statistics were used for the analysis of the results. The difference in plasma concentration of donepezil after 12 h (mean ± SEM; 39.99 ± 5.90 ng/ml) and after 24 h (29.38 ± 1.71 ng/ml) was nonsignificant. In contrast, the donepezil concentration in the cerebrospinal fluid was significantly higher in the 24-h interval (7.54 ± 0.55 ng/ml) compared with the 12-h interval (5.19 ± 0.83 ng/ml, which is ~70 % based on mean cerebrospinal fluid values). Based on these data, it is plausible to predict that donepezil might produce a stronger AChE inhibition in the brain at 24 h compared with 12 h following the administration. This information may help physicians individually adjust the time of drug administration in the patients according to time course of the disease symptoms.

EEG and MEG data analysis in SPM8.

PubMed

Litvak, Vladimir; Mattout, Jérémie; Kiebel, Stefan; Phillips, Christophe; Henson, Richard; Kilner, James; Barnes, Gareth; Oostenveld, Robert; Daunizeau, Jean; Flandin, Guillaume; Penny, Will; Friston, Karl

2011-01-01

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools.

Lamprey: tracking users on the World Wide Web.

PubMed

Felciano, R M; Altman, R B

1996-01-01

Tracking individual web sessions provides valuable information about user behavior. This information can be used for general purpose evaluation of web-based user interfaces to biomedical information systems. To this end, we have developed Lamprey, a tool for doing quantitative and qualitative analysis of Web-based user interfaces. Lamprey can be used from any conforming browser, and does not require modification of server or client software. By rerouting WWW navigation through a centralized filter, Lamprey collects the sequence and timing of hyperlinks used by individual users to move through the web. Instead of providing marginal statistics, it retains the full information required to recreate a user session. We have built Lamprey as a standard Common Gateway Interface (CGI) that works with all standard WWW browsers and servers. In this paper, we describe Lamprey and provide a short demonstration of this approach for evaluating web usage patterns.

EEG and MEG Data Analysis in SPM8

PubMed Central

Litvak, Vladimir; Mattout, Jérémie; Kiebel, Stefan; Phillips, Christophe; Henson, Richard; Kilner, James; Barnes, Gareth; Oostenveld, Robert; Daunizeau, Jean; Flandin, Guillaume; Penny, Will; Friston, Karl

2011-01-01

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools. PMID:21437221

Identifying fMRI Model Violations with Lagrange Multiplier Tests

PubMed Central

Cassidy, Ben; Long, Christopher J; Rae, Caroline; Solo, Victor

2013-01-01

The standard modeling framework in Functional Magnetic Resonance Imaging (fMRI) is predicated on assumptions of linearity, time invariance and stationarity. These assumptions are rarely checked because doing so requires specialised software, although failure to do so can lead to bias and mistaken inference. Identifying model violations is an essential but largely neglected step in standard fMRI data analysis. Using Lagrange Multiplier testing methods we have developed simple and efficient procedures for detecting model violations such as non-linearity, non-stationarity and validity of the common Double Gamma specification for hemodynamic response. These procedures are computationally cheap and can easily be added to a conventional analysis. The test statistic is calculated at each voxel and displayed as a spatial anomaly map which shows regions where a model is violated. The methodology is illustrated with a large number of real data examples. PMID:22542665

Software Reviews.

ERIC Educational Resources Information Center

Mathematics and Computer Education, 1988

1988-01-01

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

CIDR

Science.gov Websites

Targeted Informatics General Information Software Posters NIH Program Projects and Statistics QC Statistics Completed Projects Publications Contact Information NIH Contacts CIDR Contacts ___________________ -Contact

Company's Unusual Plan to Package Commercial Software with Business Textbooks Produces a Measure of Success.

ERIC Educational Resources Information Center

Watkins, Beverly T.

1992-01-01

Course Technology Inc. has developed 10 products combining textbooks with commercial software for college accounting, business, computer science, and statistics courses. Five of the products use Lotus 1-2-3 spreadsheet software. The products have been positively received by teachers and students. (DB)

Leveraging Code Comments to Improve Software Reliability

ERIC Educational Resources Information Center

Tan, Lin

2009-01-01

Commenting source code has long been a common practice in software development. This thesis, consisting of three pieces of work, made novel use of the code comments written in natural language to improve software reliability. Our solution combines Natural Language Processing (NLP), Machine Learning, Statistics, and Program Analysis techniques to…

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…

Starworld: Preparing Accountants for the Future: A Case-Based Approach to Teach International Financial Reporting Standards Using ERP Software

ERIC Educational Resources Information Center

Ragan, Joseph M.; Savino, Christopher J.; Parashac, Paul; Hosler, Jonathan C.

2010-01-01

International Financial Reporting Standards now constitute an important part of educating young professional accountants. This paper looks at a case based process to teach International Financial Reporting Standards using integrated Enterprise Resource Planning software. The case contained within the paper can be used within a variety of courses…

Software handlers for process interfaces

NASA Technical Reports Server (NTRS)

Bercaw, R. W.

1976-01-01

The principles involved in the development of software handlers for custom interfacing problems are discussed. Handlers for the CAMAC standard are examined in detail. The types of transactions that must be supported have been established by standards groups, eliminating conflicting requirements arising out of different design philosophies and applications. Implementation of the standard handlers has been facilititated by standardization of hardware. The necessary local processors can be placed in the handler when it is written or at run time by means of input/output directives, or they can be built into a high-performance input/output processor. The full benefits of these process interfaces will only be realized when software requirements are incorporated uniformly into the hardware.

Demonstration of a software design and statistical analysis methodology with application to patient outcomes data sets

PubMed Central

Mayo, Charles; Conners, Steve; Warren, Christopher; Miller, Robert; Court, Laurence; Popple, Richard

2013-01-01

Purpose: With emergence of clinical outcomes databases as tools utilized routinely within institutions, comes need for software tools to support automated statistical analysis of these large data sets and intrainstitutional exchange from independent federated databases to support data pooling. In this paper, the authors present a design approach and analysis methodology that addresses both issues. Methods: A software application was constructed to automate analysis of patient outcomes data using a wide range of statistical metrics, by combining use of C#.Net and R code. The accuracy and speed of the code was evaluated using benchmark data sets. Results: The approach provides data needed to evaluate combinations of statistical measurements for ability to identify patterns of interest in the data. Through application of the tools to a benchmark data set for dose-response threshold and to SBRT lung data sets, an algorithm was developed that uses receiver operator characteristic curves to identify a threshold value and combines use of contingency tables, Fisher exact tests, Welch t-tests, and Kolmogorov-Smirnov tests to filter the large data set to identify values demonstrating dose-response. Kullback-Leibler divergences were used to provide additional confirmation. Conclusions: The work demonstrates the viability of the design approach and the software tool for analysis of large data sets. PMID:24320426

Demonstration of a software design and statistical analysis methodology with application to patient outcomes data sets.

PubMed

Mayo, Charles; Conners, Steve; Warren, Christopher; Miller, Robert; Court, Laurence; Popple, Richard

2013-11-01

With emergence of clinical outcomes databases as tools utilized routinely within institutions, comes need for software tools to support automated statistical analysis of these large data sets and intrainstitutional exchange from independent federated databases to support data pooling. In this paper, the authors present a design approach and analysis methodology that addresses both issues. A software application was constructed to automate analysis of patient outcomes data using a wide range of statistical metrics, by combining use of C#.Net and R code. The accuracy and speed of the code was evaluated using benchmark data sets. The approach provides data needed to evaluate combinations of statistical measurements for ability to identify patterns of interest in the data. Through application of the tools to a benchmark data set for dose-response threshold and to SBRT lung data sets, an algorithm was developed that uses receiver operator characteristic curves to identify a threshold value and combines use of contingency tables, Fisher exact tests, Welch t-tests, and Kolmogorov-Smirnov tests to filter the large data set to identify values demonstrating dose-response. Kullback-Leibler divergences were used to provide additional confirmation. The work demonstrates the viability of the design approach and the software tool for analysis of large data sets.

LFSTAT - Low-Flow Analysis in R

NASA Astrophysics Data System (ADS)

Koffler, Daniel; Laaha, Gregor

2013-04-01

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

NASA/NBS (National Aeronautics and Space Administration/National Bureau of Standards) standard reference model for telerobot control system architecture (NASREM)

NASA Technical Reports Server (NTRS)

Albus, James S.; Mccain, Harry G.; Lumia, Ronald

1989-01-01

The document describes the NASA Standard Reference Model (NASREM) Architecture for the Space Station Telerobot Control System. It defines the functional requirements and high level specifications of the control system for the NASA space Station document for the functional specification, and a guideline for the development of the control system architecture, of the 10C Flight Telerobot Servicer. The NASREM telerobot control system architecture defines a set of standard modules and interfaces which facilitates software design, development, validation, and test, and make possible the integration of telerobotics software from a wide variety of sources. Standard interfaces also provide the software hooks necessary to incrementally upgrade future Flight Telerobot Systems as new capabilities develop in computer science, robotics, and autonomous system control.

Selected Streamflow Statistics for Streamgaging Stationsin Northeastern Maryland, 2006

USGS Publications Warehouse

Ries, Kernell G.

2006-01-01

Streamflow statistics were calculated for 47 U.S. Geological Survey (USGS) streamgaging stations in northeastern Maryland, in cooperation with (1) the University of Maryland, Baltimore County, Center for Urban Environmental Research and Education; (2) the Baltimore City Department of Public Works; and (3) the Baltimore County Department of Environmental Protection and Resource Management. The statistics include the mean, minimum, maximum, and standard deviation of the daily mean discharges for the periods of record at the stations, as well as flow-duration and low-flow frequency statistics. The flow-duration statistics include the 1-, 2-, 5-, 10-, 15-, 20-, 25-, 30-, 40-, 50-, 60-, 70-, 75-, 80-, 85-, 90-, 95-, 98-, and 99-percent duration discharges. The low-flow frequency statistics include the average discharges for 1, 7, 14, and 30 days that recur, on average, once in 1.01, 2, 5, 10, 20, 50, and 100 years. The statistics were computed only for the 25 stations with periods of record of 10 years or more. The statistics were computed from records available through September 30, 2004 using standard methods and computer software developed by the USGS. A comparison between low-flow frequency statistics computed for this study and for a previous study that used data available through September 30, 1989 was done for seven stations. The comparison indicated that, for the 7-day mean low flow, the newer values were 19.8 and 15.3 percent lower for the 20- and 10-year recurrence intervals, respectively, and 2.1 percent higher for the 2-year recurrence interval, than the older values. For the 14-day mean low flow, the newer 20- and 10-year values were 25.2 and 15.5 percent lower, respectively, and the 2-year value was 2.9 percent higher than the older values. For the 30-day mean low flow, the newer 20-, 10-, and 2-year values were 10.8, 7.9, and 0.8 percent lower, respectively, than the older values. The newer values are generally lower than the older ones most likely because two major droughts have occurred since the older study was completed.

Statistical Validation for Clinical Measures: Repeatability and Agreement of Kinect™-Based Software.

PubMed

Lopez, Natalia; Perez, Elisa; Tello, Emanuel; Rodrigo, Alejandro; Valentinuzzi, Max E

2018-01-01

The rehabilitation process is a fundamental stage for recovery of people's capabilities. However, the evaluation of the process is performed by physiatrists and medical doctors, mostly based on their observations, that is, a subjective appreciation of the patient's evolution. This paper proposes a tracking platform of the movement made by an individual's upper limb using Kinect sensor(s) to be applied for the patient during the rehabilitation process. The main contribution is the development of quantifying software and the statistical validation of its performance, repeatability, and clinical use in the rehabilitation process. The software determines joint angles and upper limb trajectories for the construction of a specific rehabilitation protocol and quantifies the treatment evolution. In turn, the information is presented via a graphical interface that allows the recording, storage, and report of the patient's data. For clinical purposes, the software information is statistically validated with three different methodologies, comparing the measures with a goniometer in terms of agreement and repeatability. The agreement of joint angles measured with the proposed software and goniometer is evaluated with Bland-Altman plots; all measurements fell well within the limits of agreement, meaning interchangeability of both techniques. Additionally, the results of Bland-Altman analysis of repeatability show 95% confidence. Finally, the physiotherapists' qualitative assessment shows encouraging results for the clinical use. The main conclusion is that the software is capable of offering a clinical history of the patient and is useful for quantification of the rehabilitation success. The simplicity, low cost, and visualization possibilities enhance the use of the software Kinect for rehabilitation and other applications, and the expert's opinion endorses the choice of our approach for clinical practice. Comparison of the new measurement technique with established goniometric methods determines that the proposed software agrees sufficiently to be used interchangeably.

Developing Confidence Limits For Reliability Of Software

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.

1991-01-01

Technique developed for estimating reliability of software by use of Moranda geometric de-eutrophication model. Pivotal method enables straightforward construction of exact bounds with associated degree of statistical confidence about reliability of software. Confidence limits thus derived provide precise means of assessing quality of software. Limits take into account number of bugs found while testing and effects of sampling variation associated with random order of discovering bugs.

ProUCL version 4.1.00 Documentation Downloads

EPA Pesticide Factsheets

ProUCL version 4.1.00 represents a comprehensive statistical software package equipped with statistical methods and graphical tools needed to address many environmental sampling and statistical issues as described in various these guidance documents.

RipleyGUI: software for analyzing spatial patterns in 3D cell distributions

PubMed Central

Hansson, Kristin; Jafari-Mamaghani, Mehrdad; Krieger, Patrik

2013-01-01

The true revolution in the age of digital neuroanatomy is the ability to extensively quantify anatomical structures and thus investigate structure-function relationships in great detail. To facilitate the quantification of neuronal cell patterns we have developed RipleyGUI, a MATLAB-based software that can be used to detect patterns in the 3D distribution of cells. RipleyGUI uses Ripley's K-function to analyze spatial distributions. In addition the software contains statistical tools to determine quantitative statistical differences, and tools for spatial transformations that are useful for analyzing non-stationary point patterns. The software has a graphical user interface making it easy to use without programming experience, and an extensive user manual explaining the basic concepts underlying the different statistical tools used to analyze spatial point patterns. The described analysis tool can be used for determining the spatial organization of neurons that is important for a detailed study of structure-function relationships. For example, neocortex that can be subdivided into six layers based on cell density and cell types can also be analyzed in terms of organizational principles distinguishing the layers. PMID:23658544

The Effective Use of System and Software Architecture Standards for Software Technology Readiness Assessments

DTIC Science & Technology

2011-05-01

IEC 42010 Technology Viewpoint • Case Study – Multimedia Conferencing System – Technology Specification • Risks of Software TRL Determination...fully support the required threshold functionality . • Relevant Environment for Space* – A satellite from launch to standard operation in space is...Analytical and experimental critical function and/or characteristic f f t TRL 4 TRL 3 proo o concep Technology concept and/or application

The role of open-source software in innovation and standardization in radiology.

PubMed

Erickson, Bradley J; Langer, Steve; Nagy, Paul

2005-11-01

The use of open-source software (OSS), in which developers release the source code to applications they have developed, is popular in the software industry. This is done to allow others to modify and improve software (which may or may not be shared back to the community) and to allow others to learn from the software. Radiology was an early participant in this model, supporting OSS that implemented the ACR-National Electrical Manufacturers Association (now Digital Imaging and Communications in Medicine) standard for medical image communications. In radiology and in other fields, OSS has promoted innovation and the adoption of standards. Popular OSS is of high quality because access to source code allows many people to identify and resolve errors. Open-source software is analogous to the peer-review scientific process: one must be able to see and reproduce results to understand and promote what is shared. The authors emphasize that support for OSS need not threaten vendors; most vendors embrace and benefit from standards. Open-source development does not replace vendors but more clearly defines their roles, typically focusing on areas in which proprietary differentiators benefit customers and on professional services such as implementation planning and service. Continued support for OSS is essential for the success of our field.

Analysis of High-Throughput ELISA Microarray Data

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

White, Amanda M.; Daly, Don S.; Zangar, Richard C.

Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

The effect on prospective teachers of the learning environment supported by dynamic statistics software

NASA Astrophysics Data System (ADS)

Koparan, Timur

2016-02-01

In this study, the effect on the achievement and attitudes of prospective teachers is examined. With this aim ahead, achievement test, attitude scale for statistics and interviews were used as data collection tools. The achievement test comprises 8 problems based on statistical data, and the attitude scale comprises 13 Likert-type items. The study was carried out in 2014-2015 academic year fall semester at a university in Turkey. The study, which employed the pre-test-post-test control group design of quasi-experimental research method, was carried out on a group of 80 prospective teachers, 40 in the control group and 40 in the experimental group. Both groups had four-hour classes about descriptive statistics. The classes with the control group were carried out through traditional methods while dynamic statistics software was used in the experimental group. Five prospective teachers from the experimental group were interviewed clinically after the application for a deeper examination of their views about application. Qualitative data gained are presented under various themes. At the end of the study, it was found that there is a significant difference in favour of the experimental group in terms of achievement and attitudes, the prospective teachers have affirmative approach to the use of dynamic software and see it as an effective tool to enrich maths classes. In accordance with the findings of the study, it is suggested that dynamic software, which offers unique opportunities, be used in classes by teachers and students.

Statistical Energy Analysis (SEA) and Energy Finite Element Analysis (EFEA) Predictions for a Floor-Equipped Composite Cylinder

NASA Technical Reports Server (NTRS)

Grosveld, Ferdinand W.; Schiller, Noah H.; Cabell, Randolph H.

2011-01-01

Comet Enflow is a commercially available, high frequency vibroacoustic analysis software founded on Energy Finite Element Analysis (EFEA) and Energy Boundary Element Analysis (EBEA). Energy Finite Element Analysis (EFEA) was validated on a floor-equipped composite cylinder by comparing EFEA vibroacoustic response predictions with Statistical Energy Analysis (SEA) and experimental results. Statistical Energy Analysis (SEA) predictions were made using the commercial software program VA One 2009 from ESI Group. The frequency region of interest for this study covers the one-third octave bands with center frequencies from 100 Hz to 4000 Hz.

CALIPSO Data Read Software

Atmospheric Science Data Center

2018-06-14

  CALIPSO Data Read Software Callable routines in Interactive Data Language (IDL) provide basic read access to CALIPSO science data files. ... Release 4.30  (PDF) Standard Data Sets: LIDAR L1:  CAL_LID_L1-Standard-V4-10 LIDAR L2: ...

The Minnesota Grading System Using Fundus Autofluorescence of Eye Bank Eyes: A Correlation To Age-Related Macular Degeneration (An AOS Thesis)

PubMed Central

Olsen, Timothy W.

2008-01-01

Purpose To establish a grading system of eye bank eyes using fundus autofluorescence (FAF) and identify a methodology that correlates FAF to age-related macular degeneration (AMD) with clinical correlation to the Age-Related Eye Disease Study (AREDS). Methods Two hundred sixty-two eye bank eyes were evaluated using a standardized analysis of FAF. Measurements were taken with the confocal scanning laser ophthalmoscope (cSLO). First, high-resolution, digital, stereoscopic, color images were obtained and graded according to AREDS criteria. With the neurosensory retina removed, mean FAF values were obtained from cSLO images using software analysis that excludes areas of atrophy and other artifact, generating an FAF value from a grading template. Age and AMD grade were compared to FAF values. An internal fluorescence reference standard was tested. Results Standardization of the cSLO machine demonstrated that reliable data could be acquired after a 1-hour warm-up. Images obtained prior to 1 hour had falsely elevated levels of FAF. In this initial analysis, there was no statistical correlation of age to mean FAF. There was a statistically significant decrease in FAF from AREDS grade 1, 2 to 3, 4 (P < .0001). An internal fluorescent standard may serve as a quantitative reference. Conclusions The Minnesota Grading System (MGS) of FAF (MGS-FAF) establishes a standardized methodology for grading eye bank tissue to quantify FAF compounds in the retinal pigment epithelium and correlate these findings to the AREDS. Future studies could then correlate specific FAF to the aging process, histopathology AMD phenotypes, and other maculopathies, as well as to analyze the biochemistry of autofluorescent fluorophores. PMID:19277247

The Minnesota Grading System using fundus autofluorescence of eye bank eyes: a correlation to age-related macular degeneration (an AOS thesis).

PubMed

Olsen, Timothy W

2008-01-01

To establish a grading system of eye bank eyes using fundus autofluorescence (FAF) and identify a methodology that correlates FAF to age-related macular degeneration (AMD) with clinical correlation to the Age-Related Eye Disease Study (AREDS). Two hundred sixty-two eye bank eyes were evaluated using a standardized analysis of FAF. Measurements were taken with the confocal scanning laser ophthalmoscope (cSLO). First, high-resolution, digital, stereoscopic, color images were obtained and graded according to AREDS criteria. With the neurosensory retina removed, mean FAF values were obtained from cSLO images using software analysis that excludes areas of atrophy and other artifact, generating an FAF value from a grading template. Age and AMD grade were compared to FAF values. An internal fluorescence reference standard was tested. Standardization of the cSLO machine demonstrated that reliable data could be acquired after a 1-hour warm-up. Images obtained prior to 1 hour had falsely elevated levels of FAF. In this initial analysis, there was no statistical correlation of age to mean FAF. There was a statistically significant decrease in FAF from AREDS grade 1, 2 to 3, 4 (P < .0001). An internal fluorescent standard may serve as a quantitative reference. The Minnesota Grading System (MGS) of FAF (MGS-FAF) establishes a standardized methodology for grading eye bank tissue to quantify FAF compounds in the retinal pigment epithelium and correlate these findings to the AREDS. Future studies could then correlate specific FAF to the aging process, histopathology AMD phenotypes, and other maculopathies, as well as to analyze the biochemistry of autofluorescent fluorophores.

A Study on the Development of Service Quality Index for Incheon International Airport

NASA Technical Reports Server (NTRS)

Lee, Kang Seok; Lee, Seung Chang; Hong, Soon Kil

2003-01-01

The main purpose of this study is located at developing Ominibus Monitors System(OMS) for internal management, which will enable to establish standards, finding out matters to be improved, and appreciation for its treatment in a systematic way. It is through developing subjective or objective estimation tool with use importance, perceived level, and complex index at international airport by each principal service items. The direction of this study came towards for the purpose of developing a metric analysis tool, utilizing the Quantitative Second Data, Analysing Perceived Data through airport user surveys, systemizing the data collection-input-analysis process, making data image according to graph of results, planning Service Encounter and endowing control attribution, and ensuring competitiveness at the minimal international standards. It is much important to set up a pre-investigation plan on the base of existent foreign literature and actual inspection to international airport. Two tasks have been executed together on the base of this pre-investigation; one is developing subjective estimation standards for departing party, entering party, and airport residence and the other is developing objective standards as complementary methods. The study has processed for the purpose of monitoring services at airports regularly and irregularly through developing software system for operating standards after ensuring credibility and feasibility of estimation standards with substantial and statistical way.

A Simple Graphical Method for Quantification of Disaster Management Surge Capacity Using Computer Simulation and Process-control Tools.

PubMed

Franc, Jeffrey Michael; Ingrassia, Pier Luigi; Verde, Manuela; Colombo, Davide; Della Corte, Francesco

2015-02-01

Surge capacity, or the ability to manage an extraordinary volume of patients, is fundamental for hospital management of mass-casualty incidents. However, quantification of surge capacity is difficult and no universal standard for its measurement has emerged, nor has a standardized statistical method been advocated. As mass-casualty incidents are rare, simulation may represent a viable alternative to measure surge capacity. Hypothesis/Problem The objective of the current study was to develop a statistical method for the quantification of surge capacity using a combination of computer simulation and simple process-control statistical tools. Length-of-stay (LOS) and patient volume (PV) were used as metrics. The use of this method was then demonstrated on a subsequent computer simulation of an emergency department (ED) response to a mass-casualty incident. In the derivation phase, 357 participants in five countries performed 62 computer simulations of an ED response to a mass-casualty incident. Benchmarks for ED response were derived from these simulations, including LOS and PV metrics for triage, bed assignment, physician assessment, and disposition. In the application phase, 13 students of the European Master in Disaster Medicine (EMDM) program completed the same simulation scenario, and the results were compared to the standards obtained in the derivation phase. Patient-volume metrics included number of patients to be triaged, assigned to rooms, assessed by a physician, and disposed. Length-of-stay metrics included median time to triage, room assignment, physician assessment, and disposition. Simple graphical methods were used to compare the application phase group to the derived benchmarks using process-control statistical tools. The group in the application phase failed to meet the indicated standard for LOS from admission to disposition decision. This study demonstrates how simulation software can be used to derive values for objective benchmarks of ED surge capacity using PV and LOS metrics. These objective metrics can then be applied to other simulation groups using simple graphical process-control tools to provide a numeric measure of surge capacity. Repeated use in simulations of actual EDs may represent a potential means of objectively quantifying disaster management surge capacity. It is hoped that the described statistical method, which is simple and reusable, will be useful for investigators in this field to apply to their own research.

[Statistical analysis using freely-available "EZR (Easy R)" software].

PubMed

Kanda, Yoshinobu

2015-10-01

Clinicians must often perform statistical analyses for purposes such evaluating preexisting evidence and designing or executing clinical studies. R is a free software environment for statistical computing. R supports many statistical analysis functions, but does not incorporate a statistical graphical user interface (GUI). The R commander provides an easy-to-use basic-statistics GUI for R. However, the statistical function of the R commander is limited, especially in the field of biostatistics. Therefore, the author added several important statistical functions to the R commander and named it "EZR (Easy R)", which is now being distributed on the following website: http://www.jichi.ac.jp/saitama-sct/. EZR allows the application of statistical functions that are frequently used in clinical studies, such as survival analyses, including competing risk analyses and the use of time-dependent covariates and so on, by point-and-click access. In addition, by saving the script automatically created by EZR, users can learn R script writing, maintain the traceability of the analysis, and assure that the statistical process is overseen by a supervisor.

ESML for Earth Science Data Sets and Analysis

NASA Technical Reports Server (NTRS)

Graves, Sara; Ramachandran, Rahul

2003-01-01

The primary objective of this research project was to transition ESML from design to application. The resulting schema and prototype software will foster community acceptance for the Define once, use anywhere concept central to ESML. Supporting goals include: 1) Refinement of the ESML schema and software libraries in cooperation with the user community; 2) Application of the ESML schema and software to a variety of Earth science data sets and analysis tools; 3) Development of supporting prototype software for enhanced ease of use; 4) Cooperation with standards bodies in order to assure ESML is aligned with related metadata standards as appropriate; and 5) Widespread publication of the ESML approach, schema, and software.

Earth Science Markup Language: Transitioning From Design to Application

NASA Technical Reports Server (NTRS)

Moe, Karen; Graves, Sara; Ramachandran, Rahul

2002-01-01

The primary objective of the proposed Earth Science Markup Language (ESML) research is to transition from design to application. The resulting schema and prototype software will foster community acceptance for the "define once, use anywhere" concept central to ESML. Supporting goals include: 1. Refinement of the ESML schema and software libraries in cooperation with the user community. 2. Application of the ESML schema and software libraries to a variety of Earth science data sets and analysis tools. 3. Development of supporting prototype software for enhanced ease of use. 4. Cooperation with standards bodies in order to assure ESML is aligned with related metadata standards as appropriate. 5. Widespread publication of the ESML approach, schema, and software.

Process air quality data

NASA Technical Reports Server (NTRS)

Butler, C. M.; Hogge, J. E.

1978-01-01

Air quality sampling was conducted. Data for air quality parameters, recorded on written forms, punched cards or magnetic tape, are available for 1972 through 1975. Computer software was developed to (1) calculate several daily statistical measures of location, (2) plot time histories of data or the calculated daily statistics, (3) calculate simple correlation coefficients, and (4) plot scatter diagrams. Computer software was developed for processing air quality data to include time series analysis and goodness of fit tests. Computer software was developed to (1) calculate a larger number of daily statistical measures of location, and a number of daily monthly and yearly measures of location, dispersion, skewness and kurtosis, (2) decompose the extended time series model and (3) perform some goodness of fit tests. The computer program is described, documented and illustrated by examples. Recommendations are made for continuation of the development of research on processing air quality data.

Standards guide for space and earth sciences computer software

NASA Technical Reports Server (NTRS)

Mason, G.; Chapman, R.; Klinglesmith, D.; Linnekin, J.; Putney, W.; Shaffer, F.; Dapice, R.

1972-01-01

Guidelines for the preparation of systems analysis and programming work statements are presented. The data is geared toward the efficient administration of available monetary and equipment resources. Language standards and the application of good management techniques to software development are emphasized.

ASAP (Automatic Software for ASL Processing): A toolbox for processing Arterial Spin Labeling images.

PubMed

Mato Abad, Virginia; García-Polo, Pablo; O'Daly, Owen; Hernández-Tamames, Juan Antonio; Zelaya, Fernando

2016-04-01

The method of Arterial Spin Labeling (ASL) has experienced a significant rise in its application to functional imaging, since it is the only technique capable of measuring blood perfusion in a truly non-invasive manner. Currently, there are no commercial packages for processing ASL data and there is no recognized standard for normalizing ASL data to a common frame of reference. This work describes a new Automated Software for ASL Processing (ASAP) that can automatically process several ASL datasets. ASAP includes functions for all stages of image pre-processing: quantification, skull-stripping, co-registration, partial volume correction and normalization. To assess the applicability and validity of the toolbox, this work shows its application in the study of hypoperfusion in a sample of healthy subjects at risk of progressing to Alzheimer's disease. ASAP requires limited user intervention, minimizing the possibility of random and systematic errors, and produces cerebral blood flow maps that are ready for statistical group analysis. The software is easy to operate and results in excellent quality of spatial normalization. The results found in this evaluation study are consistent with previous studies that find decreased perfusion in Alzheimer's patients in similar regions and demonstrate the applicability of ASAP. Copyright © 2015 Elsevier Inc. All rights reserved.

Chapter 16: text mining for translational bioinformatics.

PubMed

Cohen, K Bretonnel; Hunter, Lawrence E

2013-04-01

Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

A benchmarking tool to evaluate computer tomography perfusion infarct core predictions against a DWI standard.

PubMed

Cereda, Carlo W; Christensen, Søren; Campbell, Bruce Cv; Mishra, Nishant K; Mlynash, Michael; Levi, Christopher; Straka, Matus; Wintermark, Max; Bammer, Roland; Albers, Gregory W; Parsons, Mark W; Lansberg, Maarten G

2016-10-01

Differences in research methodology have hampered the optimization of Computer Tomography Perfusion (CTP) for identification of the ischemic core. We aim to optimize CTP core identification using a novel benchmarking tool. The benchmarking tool consists of an imaging library and a statistical analysis algorithm to evaluate the performance of CTP. The tool was used to optimize and evaluate an in-house developed CTP-software algorithm. Imaging data of 103 acute stroke patients were included in the benchmarking tool. Median time from stroke onset to CT was 185 min (IQR 180-238), and the median time between completion of CT and start of MRI was 36 min (IQR 25-79). Volumetric accuracy of the CTP-ROIs was optimal at an rCBF threshold of <38%; at this threshold, the mean difference was 0.3 ml (SD 19.8 ml), the mean absolute difference was 14.3 (SD 13.7) ml, and CTP was 67% sensitive and 87% specific for identification of DWI positive tissue voxels. The benchmarking tool can play an important role in optimizing CTP software as it provides investigators with a novel method to directly compare the performance of alternative CTP software packages. © The Author(s) 2015.

Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1981-01-01

A parametric software cost estimation model prepared for Jet PRopulsion Laboratory (JPL) Deep Space Network (DSN) Data System implementation tasks is described. The resource estimation mdel modifies and combines a number of existing models. The model calibrates the task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit JPL software life-cycle statistics.

TMS communications software. Volume 1: Computer interfaces

NASA Technical Reports Server (NTRS)

Brown, J. S.; Lenker, M. D.

1979-01-01

A prototype bus communications system, which is being used to support the Trend Monitoring System (TMS) as well as for evaluation of the bus concept is considered. Hardware and software interfaces to the MODCOMP and NOVA minicomputers are included. The system software required to drive the interfaces in each TMS computer is described. Documentation of other software for bus statistics monitoring and for transferring files across the bus is also included.

Making the Business Case for Software Assurance

DTIC Science & Technology

2009-04-01

and Capability dEtermination-SPICE, ISO /IEC 15504, 1998. [ ISO 2007] International Organization for Standardization. " ISO /IEC 27001 & 27002 ...Implementing the Process Areas 6.2.7 Differences Between the CMMI and Software CMM Process Areas 6.3 The CMMI Appraisal Process 6.4 Adapting ISO 15504 to...Secure Software Assurance 6.4.1 Assessment and the Secure Life Cycle 6.4.2 ISO 15504 Capability Levels 6.5 Adapting the ISOIIEC 21287 Standard Approach to

A compliance assessment of midpoint formative assessments completed by APPE preceptors.

PubMed

Lea Bonner, C; Staton, April G; Naro, Patricia B; McCullough, Elizabeth; Lynn Stevenson, T; Williamson, Margaret; Sheffield, Melody C; Miller, Mindi; Fetterman, James W; Fan, Shirley; Momary, Kathryn M

Experiential pharmacy preceptors should provide formative and summative feedback during a learning experience. Preceptors are required to provide colleges and schools of pharmacy with assessments or evaluations of students' performance. Students and experiential programs value on-time completion of midpoint evaluations by preceptors. The objective of this study was to determine the number of on-time electronically documented formative midpoint evaluations completed by preceptors during advanced pharmacy practice experiences (APPEs). Compliance rates of on-time electronically documented formative midpoint evaluations were reviewed by the Office of Experiential Education of a five-member consortium during the two-year study period prior to the adoption of Standards 2016. Pearson chi-square test and generalized linear models were used to determine if statistically significant differences were present. Average midpoint compliance rates for the two-year research period were 40.7% and 41% respectively. No statistical significance was noted comparing compliance rates for year one versus year two. However, statistical significance was present when comparing compliance rates between schools during year two. Feedback from students and preceptors pointed to the need for brief formal midpoint evaluations that require minimal time to complete, user friendly experiential management software, and methods for documenting verbal feedback through student self-reflection. Additional education and training to both affiliate and faculty preceptors on the importance of written formative feedback at midpoint is critical to remaining in compliance with Standards 2016. Copyright © 2017 Elsevier Inc. All rights reserved.

Final Report of the NASA Office of Safety and Mission Assurance Agile Benchmarking Team

NASA Technical Reports Server (NTRS)

Wetherholt, Martha

2016-01-01

To ensure that the NASA Safety and Mission Assurance (SMA) community remains in a position to perform reliable Software Assurance (SA) on NASAs critical software (SW) systems with the software industry rapidly transitioning from waterfall to Agile processes, Terry Wilcutt, Chief, Safety and Mission Assurance, Office of Safety and Mission Assurance (OSMA) established the Agile Benchmarking Team (ABT). The Team's tasks were: 1. Research background literature on current Agile processes, 2. Perform benchmark activities with other organizations that are involved in software Agile processes to determine best practices, 3. Collect information on Agile-developed systems to enable improvements to the current NASA standards and processes to enhance their ability to perform reliable software assurance on NASA Agile-developed systems, 4. Suggest additional guidance and recommendations for updates to those standards and processes, as needed. The ABT's findings and recommendations for software management, engineering and software assurance are addressed herein.

Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.

PubMed

Zakrzewski, Martha; Proietti, Carla; Ellis, Jonathan J; Hasan, Shihab; Brion, Marie-Jo; Berger, Bernard; Krause, Lutz

2017-03-01

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo ( https://zenodo.org/record/50931 ). The software is freely available for non-commercial users. l.krause@uq.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

CRAX. Cassandra Exoskeleton

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

Robinson, D.G.; Eubanks, L.

1998-03-01

This software assists the engineering designer in characterizing the statistical uncertainty in the performance of complex systems as a result of variations in manufacturing processes, material properties, system geometry or operating environment. The software is composed of a graphical user interface that provides the user with easy access to Cassandra uncertainty analysis routines. Together this interface and the Cassandra routines are referred to as CRAX (CassandRA eXoskeleton). The software is flexible enough, that with minor modification, it is able to interface with large modeling and analysis codes such as heat transfer or finite element analysis software. The current version permitsmore » the user to manually input a performance function, the number of random variables and their associated statistical characteristics: density function, mean, coefficients of variation. Additional uncertainity analysis modules are continuously being added to the Cassandra core.« less

Cassandra Exoskeleton

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

Robiinson, David G.

1999-02-20

This software assists the engineering designer in characterizing the statistical uncertainty in the performance of complex systems as a result of variations in manufacturing processes, material properties, system geometry or operating environment. The software is composed of a graphical user interface that provides the user with easy access to Cassandra uncertainty analysis routines. Together this interface and the Cassandra routines are referred to as CRAX (CassandRA eXoskeleton). The software is flexible enough, that with minor modification, it is able to interface with large modeling and analysis codes such as heat transfer or finite element analysis software. The current version permitsmore » the user to manually input a performance function, the number of random variables and their associated statistical characteristics: density function, mean, coefficients of variation. Additional uncertainity analysis modules are continuously being added to the Cassandra core.« less

Database Performance Monitoring for the Photovoltaic Systems

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

Klise, Katherine A.

The Database Performance Monitoring (DPM) software (copyright in processes) is being developed at Sandia National Laboratories to perform quality control analysis on time series data. The software loads time indexed databases (currently csv format), performs a series of quality control tests defined by the user, and creates reports which include summary statistics, tables, and graphics. DPM can be setup to run on an automated schedule defined by the user. For example, the software can be run once per day to analyze data collected on the previous day. HTML formatted reports can be sent via email or hosted on a website.more » To compare performance of several databases, summary statistics and graphics can be gathered in a dashboard view which links to detailed reporting information for each database. The software can be customized for specific applications.« less

Compression Algorithm Analysis of In-Situ (S)TEM Video: Towards Automatic Event Detection and Characterization

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

Teuton, Jeremy R.; Griswold, Richard L.; Mehdi, Beata L.

Precise analysis of both (S)TEM images and video are time and labor intensive processes. As an example, determining when crystal growth and shrinkage occurs during the dynamic process of Li dendrite deposition and stripping involves manually scanning through each frame in the video to extract a specific set of frames/images. For large numbers of images, this process can be very time consuming, so a fast and accurate automated method is desirable. Given this need, we developed software that uses analysis of video compression statistics for detecting and characterizing events in large data sets. This software works by converting the datamore » into a series of images which it compresses into an MPEG-2 video using the open source “avconv” utility [1]. The software does not use the video itself, but rather analyzes the video statistics from the first pass of the video encoding that avconv records in the log file. This file contains statistics for each frame of the video including the frame quality, intra-texture and predicted texture bits, forward and backward motion vector resolution, among others. In all, avconv records 15 statistics for each frame. By combining different statistics, we have been able to detect events in various types of data. We have developed an interactive tool for exploring the data and the statistics that aids the analyst in selecting useful statistics for each analysis. Going forward, an algorithm for detecting and possibly describing events automatically can be written based on statistic(s) for each data type.« less

Navigating freely-available software tools for metabolomics analysis.

PubMed

Spicer, Rachel; Salek, Reza M; Moreno, Pablo; Cañueto, Daniel; Steinbeck, Christoph

2017-01-01

The field of metabolomics has expanded greatly over the past two decades, both as an experimental science with applications in many areas, as well as in regards to data standards and bioinformatics software tools. The diversity of experimental designs and instrumental technologies used for metabolomics has led to the need for distinct data analysis methods and the development of many software tools. To compile a comprehensive list of the most widely used freely available software and tools that are used primarily in metabolomics. The most widely used tools were selected for inclusion in the review by either ≥ 50 citations on Web of Science (as of 08/09/16) or the use of the tool being reported in the recent Metabolomics Society survey. Tools were then categorised by the type of instrumental data (i.e. LC-MS, GC-MS or NMR) and the functionality (i.e. pre- and post-processing, statistical analysis, workflow and other functions) they are designed for. A comprehensive list of the most used tools was compiled. Each tool is discussed within the context of its application domain and in relation to comparable tools of the same domain. An extended list including additional tools is available at https://github.com/RASpicer/MetabolomicsTools which is classified and searchable via a simple controlled vocabulary. This review presents the most widely used tools for metabolomics analysis, categorised based on their main functionality. As future work, we suggest a direct comparison of tools' abilities to perform specific data analysis tasks e.g. peak picking.

Data storage technology: Hardware and software, Appendix B

NASA Technical Reports Server (NTRS)

Sable, J. D.

1972-01-01

This project involves the development of more economical ways of integrating and interfacing new storage devices and data processing programs into a computer system. It involves developing interface standards and a software/hardware architecture which will make it possible to develop machine independent devices and programs. These will interface with the machine dependent operating systems of particular computers. The development project will not be to develop the software which would ordinarily be the responsibility of the manufacturer to supply, but to develop the standards with which that software is expected to confirm in providing an interface with the user or storage system.

How to choose the right statistical software?-a method increasing the post-purchase satisfaction.

PubMed

Cavaliere, Roberto

2015-12-01

Nowadays, we live in the "data era" where the use of statistical or data analysis software is inevitable, in any research field. This means that the choice of the right software tool or platform is a strategic issue for a research department. Nevertheless, in many cases decision makers do not pay the right attention to a comprehensive and appropriate evaluation of what the market offers. Indeed, the choice still depends on few factors like, for instance, researcher's personal inclination, e.g., which software have been used at the university or is already known. This is not wrong in principle, but in some cases it's not enough at all and might lead to a "dead end" situation, typically after months or years of investments already done on the wrong software. This article, far from being a full and complete guide to statistical software evaluation, aims to illustrate some key points of the decision process and introduce an extended range of factors which can help to undertake the right choice, at least in potential. There is not enough literature about that topic, most of the time underestimated, both in the traditional literature and even in the so called "gray literature", even if some documents or short pages can be found online. Anyhow, it seems there is not a common and known standpoint about the process of software evaluation from the final user perspective. We suggests a multi-factor analysis leading to an evaluation matrix tool, to be intended as a flexible and customizable tool, aimed to provide a clearer picture of the software alternatives available, not in abstract but related to the researcher's own context and needs. This method is a result of about twenty years of experience of the author in the field of evaluating and using technical-computing software and partially arises from a research made about such topics as part of a project funded by European Commission under the Lifelong Learning Programme 2011.

Comparison of Segmental Versus Longitudinal Intravascular Ultrasound Analysis for Pediatric Cardiac Allograft Vasculopathy.

PubMed

Kuhn, M A; Burch, M; Chinnock, R E; Fenton, M J

2017-10-01

Intravascular ultrasound (IVUS) has been routinely used in some centers to investigate cardiac allograft vasculopathy in pediatric heart transplant recipients. We present an alternative method using more sophisticated imaging software. This study presents a comparison of this method with an established standard method. All patients who had IVUS performed in 2014 were retrospectively evaluated. The standard technique consisted of analysis of 10 operator-selected segments along the vessel. Each study was re-evaluated using a longitudinal technique, taken at every third cardiac cycle, along the entire vessel. Semiautomatic edge detection software was used to detect vessel imaging planes. Measurements included outer and inner diameter, total and luminal area, maximal intimal thickness (MIT), and intimal index. Each IVUS was graded for severity using the Stanford classification. All results were given as mean ± standard deviation (SD). Groups were compared using Student t test. A P value <.05 was considered significant. There were 59 IVUS studies performed on 58 patients. There was no statistically significant difference between outer diameter, inner diameter, or total area. In the longitudinal group, there was a significantly smaller luminal area, higher MIT, and higher intimal index. Using the longitudinal technique, there was an increase in Stanford classification in 20 patients. The longitudinal technique appeared more sensitive in assessing the degree of cardiac allograft vasculopathy and may play a role in the increase in the degree of thickening seen. It may offer an alternative way of grading severity of cardiac allograft vasculopathy in pediatric heart transplant recipients. Copyright © 2017 Elsevier Inc. All rights reserved.

The integration of the risk management process with the lifecycle of medical device software.

PubMed

Pecoraro, F; Luzi, D

2014-01-01

The application of software in the Medical Device (MD) domain has become central to the improvement of diagnoses and treatments. The new European regulations that specifically address software as an important component of MD, require complex procedures to make software compliant with safety requirements, introducing thereby new challenges in the qualification and classification of MD software as well as in the performance of risk management activities. Under this perspective, the aim of this paper is to propose an integrated framework that combines the activities to be carried out by the manufacturer to develop safe software within the development lifecycle based on the regulatory requirements reported in US and European regulations as well as in the relevant standards and guidelines. A comparative analysis was carried out to identify the main issues related to the application of the current new regulations. In addition, standards and guidelines recently released to harmonise procedures for the validation of MD software have been used to define the risk management activities to be carried out by the manufacturer during the software development process. This paper highlights the main issues related to the qualification and classification of MD software, providing an analysis of the different regulations applied in Europe and the US. A model that integrates the risk management process within the software development lifecycle has been proposed too. It is based on regulatory requirements and considers software risk analysis as a central input to be managed by the manufacturer already at the initial stages of the software design, in order to prevent MD failures. Relevant changes in the process of MD development have been introduced with the recognition of software being an important component of MDs as stated in regulations and standards. This implies the performance of highly iterative processes that have to integrate the risk management in the framework of software development. It also makes it necessary to involve both medical and software engineering competences to safeguard patient and user safety.

Toward Software Both Seen and Heard.

ERIC Educational Resources Information Center

Lazzaro, Joseph J.

1996-01-01

Visually impaired users are hampered by current PC software written for graphical user interfaces. Screen readers that vocalize displayed text require standardization that remains missing in the programming industry; the readers cannot interpret many cues in the Windows environment. More programming standards and adaptive technology for computers…

TOAD Editor

NASA Technical Reports Server (NTRS)

Bingle, Bradford D.; Shea, Anne L.; Hofler, Alicia S.

1993-01-01

Transferable Output ASCII Data (TOAD) computer program (LAR-13755), implements format designed to facilitate transfer of data across communication networks and dissimilar host computer systems. Any data file conforming to TOAD format standard called TOAD file. TOAD Editor is interactive software tool for manipulating contents of TOAD files. Commonly used to extract filtered subsets of data for visualization of results of computation. Also offers such user-oriented features as on-line help, clear English error messages, startup file, macroinstructions defined by user, command history, user variables, UNDO features, and full complement of mathematical statistical, and conversion functions. Companion program, TOAD Gateway (LAR-14484), converts data files from variety of other file formats to that of TOAD. TOAD Editor written in FORTRAN 77.

Play It Again: Teaching Statistics with Monte Carlo Simulation

ERIC Educational Resources Information Center

Sigal, Matthew J.; Chalmers, R. Philip

2016-01-01

Monte Carlo simulations (MCSs) provide important information about statistical phenomena that would be impossible to assess otherwise. This article introduces MCS methods and their applications to research and statistical pedagogy using a novel software package for the R Project for Statistical Computing constructed to lessen the often steep…

A Statistics Curriculum for the Undergraduate Chemistry Major

ERIC Educational Resources Information Center

Schlotter, Nicholas E.

2013-01-01

Our ability to statistically analyze data has grown significantly with the maturing of computer hardware and software. However, the evolution of our statistics capabilities has taken place without a corresponding evolution in the curriculum for the undergraduate chemistry major. Most faculty understands the need for a statistical educational…

USL/DBMS NASA/PC R and D project system testing standards

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Kavi, Srinu; Moreau, Dennis R.; Yan, Lin

1984-01-01

A set of system testing standards to be used in the development of all C software within the NASA/PC Research and Development Project is established. Testing will be considered in two phases: the program testing phase and the system testing phase. The objective of these standards is to provide guidelines for the planning and conduct of program and software system testing.

20 CFR 634.4 - Statistical standards.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 20 Employees' Benefits 3 2011-04-01 2011-04-01 false Statistical standards. 634.4 Section 634.4... System § 634.4 Statistical standards. Recipients shall agree to provide required data following the statistical standards prescribed by the Bureau of Labor Statistics for cooperative statistical programs. ...

20 CFR 634.4 - Statistical standards.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Statistical standards. 634.4 Section 634.4... System § 634.4 Statistical standards. Recipients shall agree to provide required data following the statistical standards prescribed by the Bureau of Labor Statistics for cooperative statistical programs. ...

Product specification documentation standard and Data Item Descriptions (DID). Volume of the information system life-cycle and documentation standards, volume 3

NASA Technical Reports Server (NTRS)

Callender, E. David; Steinbacher, Jody

1989-01-01

This is the third of five volumes on Information System Life-Cycle and Documentation Standards which present a well organized, easily used standard for providing technical information needed for developing information systems, components, and related processes. This volume states the Software Management and Assurance Program documentation standard for a product specification document and for data item descriptions. The framework can be applied to any NASA information system, software, hardware, operational procedures components, and related processes.

Application of industry-standard guidelines for the validation of avionics software

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.; Shagnea, Anita M.

1990-01-01

The application of industry standards to the development of avionics software is discussed, focusing on verification and validation activities. It is pointed out that the procedures that guide the avionics software development and testing process are under increased scrutiny. The DO-178A guidelines, Software Considerations in Airborne Systems and Equipment Certification, are used by the FAA for certifying avionics software. To investigate the effectiveness of the DO-178A guidelines for improving the quality of avionics software, guidance and control software (GCS) is being developed according to the DO-178A development method. It is noted that, due to the extent of the data collection and configuration management procedures, any phase in the life cycle of a GCS implementation can be reconstructed. Hence, a fundamental development and testing platform has been established that is suitable for investigating the adequacy of various software development processes. In particular, the overall effectiveness and efficiency of the development method recommended by the DO-178A guidelines are being closely examined.

Engineering Documentation and Data Control

NASA Technical Reports Server (NTRS)

Matteson, Michael J.; Bramley, Craig; Ciaruffoli, Veronica

2001-01-01

Mississippi Space Services (MSS) the facility services contractor for NASA's John C. Stennis Space Center (SSC), is utilizing technology to improve engineering documentation and data control. Two identified improvement areas, labor intensive documentation research and outdated drafting standards, were targeted as top priority. MSS selected AutoManager(R) WorkFlow from Cyco software to manage engineering documentation. The software is currently installed on over 150 desctops. The outdated SSC drafting standard was written for pre-CADD drafting methods, in other words, board drafting. Implementation of COTS software solutions to manage engineering documentation and update the drafting standard resulted in significant increases in productivity by reducing the time spent searching for documents.

Software Reviews.

ERIC Educational Resources Information Center

Science Software Quarterly, 1984

1984-01-01

Provides extensive reviews of computer software, examining documentation, ease of use, performance, error handling, special features, and system requirements. Includes statistics, problem-solving (TK Solver), label printing, database management, experimental psychology, Encyclopedia Britannica biology, and DNA-sequencing programs. A program for…

A Data-Driven Solution for Performance Improvement

NASA Technical Reports Server (NTRS)

2002-01-01

Marketed as the "Software of the Future," Optimal Engineering Systems P.I. EXPERT(TM) technology offers statistical process control and optimization techniques that are critical to businesses looking to restructure or accelerate operations in order to gain a competitive edge. Kennedy Space Center granted Optimal Engineering Systems the funding and aid necessary to develop a prototype of the process monitoring and improvement software. Completion of this prototype demonstrated that it was possible to integrate traditional statistical quality assurance tools with robust optimization techniques in a user- friendly format that is visually compelling. Using an expert system knowledge base, the software allows the user to determine objectives, capture constraints and out-of-control processes, predict results, and compute optimal process settings.

ASSIP Study of Real-Time Safety-Critical Embedded Software-Intensive System Engineering Practices

DTIC Science & Technology

2008-02-01

and assessment 2. product engineering processes 3. tooling processes 6 | CMU/SEI-2008-SR-001 Slide 1 Process Standards IEC/ ISO 12207 Software...and technical effort to align with 12207 IEC/ ISO 15026 System & Software Integrity Levels Generic Safety SAE ARP 4754 Certification Considerations...Process Frameworks in revision – ISO 9001, ISO 9004 – ISO 15288/ ISO 12207 harmonization – RTCA DO-178B, MOD Standard UK 00-56/3, … • Methods & Tools

ResidPlots-2: Computer Software for IRT Graphical Residual Analyses

ERIC Educational Resources Information Center

Liang, Tie; Han, Kyung T.; Hambleton, Ronald K.

2009-01-01

This article discusses the ResidPlots-2, a computer software that provides a powerful tool for IRT graphical residual analyses. ResidPlots-2 consists of two components: a component for computing residual statistics and another component for communicating with users and for plotting the residual graphs. The features of the ResidPlots-2 software are…

Expert system verification and validation guidelines/workshop task. Deliverable no. 1: ES V/V guidelines

NASA Technical Reports Server (NTRS)

French, Scott W.

1991-01-01

The goals are to show that verifying and validating a software system is a required part of software development and has a direct impact on the software's design and structure. Workshop tasks are given in the areas of statistics, integration/system test, unit and architectural testing, and a traffic controller problem.

Improving the Effectiveness of Program Managers

DTIC Science & Technology

2006-05-03

Improving the Effectiveness of Program Managers Systems and Software Technology Conference Salt Lake City, Utah May 3, 2006 Presented by GAO’s...Companies’ best practices Motorola Caterpillar Toyota FedEx NCR Teradata Boeing Hughes Space and Communications Disciplined software and management...and total ownership costs Collection of metrics data to improve software reliability Technology readiness levels and design maturity Statistical

Real time computer data system for the 40 x 80 ft wind tunnel facility at Ames Research Center

NASA Technical Reports Server (NTRS)

Cambra, J. M.; Tolari, G. P.

1974-01-01

The wind tunnel realtime computer system is a distributed data gathering system that features a master computer subsystem, a high speed data gathering subsystem, a quick look dynamic analysis and vibration control subsystem, an analog recording back-up subsystem, a pulse code modulation (PCM) on-board subsystem, a communications subsystem, and a transducer excitation and calibration subsystem. The subsystems are married to the master computer through an executive software system and standard hardware and FORTRAN software interfaces. The executive software system has four basic software routines. These are the playback, setup, record, and monitor routines. The standard hardware interfaces along with the software interfaces provide the system with the capability of adapting to new environments.

Software For Computing Reliability Of Other Software

NASA Technical Reports Server (NTRS)

Nikora, Allen; Antczak, Thomas M.; Lyu, Michael

1995-01-01

Computer Aided Software Reliability Estimation (CASRE) computer program developed for use in measuring reliability of other software. Easier for non-specialists in reliability to use than many other currently available programs developed for same purpose. CASRE incorporates mathematical modeling capabilities of public-domain Statistical Modeling and Estimation of Reliability Functions for Software (SMERFS) computer program and runs in Windows software environment. Provides menu-driven command interface; enabling and disabling of menu options guides user through (1) selection of set of failure data, (2) execution of mathematical model, and (3) analysis of results from model. Written in C language.

Study Frequency of Hypertension and Obesity and their Relationship with Lifestyle Factors (Nutritional Habits, Physical Activity, Cigarette Consumption) in Ardabil City Physicians, 2012-13.

PubMed

Fathi, Afshin; Ahari, Saeid Sadeghieh; Amani, Firouz; Nikneghad, Mohammad Reza

2016-01-01

Few studies have been done on lifestyle of Iranian physicians. As physicians have important role in health promotion, the main goal of the study was to assess the lifestyle of this influential group. A cross-sectional descriptive study was conducted on lifestyle of all registered physicians of Ardabil hospitals, Iran, 2012-13. In this research, 225 physicians were selected, by using simple random sampling. Demographic and lifestyle data were obtained by self-report using standard questionnaires, physical activity by official Iranian short-version of the international physical activity questionnaire, and dietary intake by food frequency questionnaire. Weight and height was performed according to standard protocols by using standardized and zero calibrated instruments. Data were analyzed by inferential statistics using Statistical Package for the Social Sciences. 16 software. Findings showed that 8% of participants were hypertensive, 21.3% smoker, 40%-47% inactive, 51.1% overweight, and 18.2% obese. There was a significant relationship between blood pressure and self-reported lifestyle habits ( P < 0.05). And 70.7% of males and 74.1% of females had regular 10-min walking each day and moderate activity of males was significantly higher than females ( P < 0.05). Food frequency weekly consumption of overweight and obese physicians were significantly higher than normal weight physicians ( P < 0.05). Few doctors follow a healthy lifestyle; this may have a negative effect on society attitude about health.

Virtual file system for PSDS

NASA Technical Reports Server (NTRS)

Runnels, Tyson D.

1993-01-01

This is a case study. It deals with the use of a 'virtual file system' (VFS) for Boeing's UNIX-based Product Standards Data System (PSDS). One of the objectives of PSDS is to store digital standards documents. The file-storage requirements are that the files must be rapidly accessible, stored for long periods of time - as though they were paper, protected from disaster, and accumulative to about 80 billion characters (80 gigabytes). This volume of data will be approached in the first two years of the project's operation. The approach chosen is to install a hierarchical file migration system using optical disk cartridges. Files are migrated from high-performance media to lower performance optical media based on a least-frequency-used algorithm. The optical media are less expensive per character stored and are removable. Vital statistics about the removable optical disk cartridges are maintained in a database. The assembly of hardware and software acts as a single virtual file system transparent to the PSDS user. The files are copied to 'backup-and-recover' media whose vital statistics are also stored in the database. Seventeen months into operation, PSDS is storing 49 gigabytes. A number of operational and performance problems were overcome. Costs are under control. New and/or alternative uses for the VFS are being considered.

Identifying the impact of social determinants of health on disease rates using correlation analysis of area-based summary information.

PubMed

Song, Ruiguang; Hall, H Irene; Harrison, Kathleen McDavid; Sharpe, Tanya Telfair; Lin, Lillian S; Dean, Hazel D

2011-01-01

We developed a statistical tool that brings together standard, accessible, and well-understood analytic approaches and uses area-based information and other publicly available data to identify social determinants of health (SDH) that significantly affect the morbidity of a specific disease. We specified AIDS as the disease of interest and used data from the American Community Survey and the National HIV Surveillance System. Morbidity and socioeconomic variables in the two data systems were linked through geographic areas that can be identified in both systems. Correlation and partial correlation coefficients were used to measure the impact of socioeconomic factors on AIDS diagnosis rates in certain geographic areas. We developed an easily explained approach that can be used by a data analyst with access to publicly available datasets and standard statistical software to identify the impact of SDH. We found that the AIDS diagnosis rate was highly correlated with the distribution of race/ethnicity, population density, and marital status in an area. The impact of poverty, education level, and unemployment depended on other SDH variables. Area-based measures of socioeconomic variables can be used to identify risk factors associated with a disease of interest. When correlation analysis is used to identify risk factors, potential confounding from other variables must be taken into account.

School furniture and work surface lighting impacts on the body posture of Paraíba's public school students.

PubMed

da Silva, Luiz Bueno; Coutinho, Antonio Souto; da Costa Eulálio, Eliza Juliana; Soares, Elaine Victor Gonçalves

2012-01-01

The main objective of this study is to evaluate the impact of school furniture and work surface lighting on the body posture of public Middle School students from Paraíba (Brazil). The survey was carried out in two public schools and the target population for the study included 8th grade groups involving a total of 31 students. Brazilian standards for lighting levels, the CEBRACE standards for furniture measurements and the Postural Assessment Software (SAPO) for the postural misalignment assay were adopted for the measurements comparison. The statistic analysis includes analyses of parametric and non-parametric correlations. The results show that the students' most affected parts of the body were the spine, the regions of the knees and head and neck, with 90% of the total number of students presenting postural misalignment. The lighting levels were usually found below 300 lux, below recommended levels. The statistic analysis show that the more adequate the furniture seems to be to the user, the less the user will complain of pain. Such results indicate the need of investments in more suitable school furniture and structural reforms aimed at improving the lighting in the classrooms, which could fulfill the students' profile and reduce their complaints.

Bootstrap-based methods for estimating standard errors in Cox's regression analyses of clustered event times.

PubMed

Xiao, Yongling; Abrahamowicz, Michal

2010-03-30

We propose two bootstrap-based methods to correct the standard errors (SEs) from Cox's model for within-cluster correlation of right-censored event times. The cluster-bootstrap method resamples, with replacement, only the clusters, whereas the two-step bootstrap method resamples (i) the clusters, and (ii) individuals within each selected cluster, with replacement. In simulations, we evaluate both methods and compare them with the existing robust variance estimator and the shared gamma frailty model, which are available in statistical software packages. We simulate clustered event time data, with latent cluster-level random effects, which are ignored in the conventional Cox's model. For cluster-level covariates, both proposed bootstrap methods yield accurate SEs, and type I error rates, and acceptable coverage rates, regardless of the true random effects distribution, and avoid serious variance under-estimation by conventional Cox-based standard errors. However, the two-step bootstrap method over-estimates the variance for individual-level covariates. We also apply the proposed bootstrap methods to obtain confidence bands around flexible estimates of time-dependent effects in a real-life analysis of cluster event times.

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses

PubMed Central

Park, Danny S.; Brown, Brielin; Eng, Celeste; Huntsman, Scott; Hu, Donglei; Torgerson, Dara G.; Burchard, Esteban G.; Zaitlen, Noah

2015-01-01

Motivation: Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global ‘best guess’ reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Results: We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of ‘best guess’ reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing. Availability and implementation: Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix. Contact: noah.zaitlen@ucsf.edu PMID:26072481

Implementation of statistical process control for proteomic experiments via LC MS/MS.

PubMed

Bereman, Michael S; Johnson, Richard; Bollinger, James; Boss, Yuval; Shulman, Nick; MacLean, Brendan; Hoofnagle, Andrew N; MacCoss, Michael J

2014-04-01

Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. The source code, written in the R statistical language, runs directly from the Skyline interface, which supports the use of raw data files from several of the mass spectrometry vendors. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution), and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts. Thresholds are experiment- and instrument-specific and are determined empirically from user-defined quality control standards that enable the separation of random noise and systematic error. Finally, Pareto analysis provides a summary of performance metrics and guides the user to metrics with high variance. The utility of these charts to evaluate proteomic experiments is illustrated in two case studies.

User systems guidelines for software projects

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

Abrahamson, L.

1986-04-01

This manual presents guidelines for software standards which were developed so that software project-development teams and management involved in approving the software could have a generalized view of all phases in the software production procedure and the steps involved in completing each phase. Guidelines are presented for six phases of software development: project definition, building a user interface, designing software, writing code, testing code, and preparing software documentation. The discussions for each phase include examples illustrating the recommended guidelines. 45 refs. (DWL)

HRVanalysis: A Free Software for Analyzing Cardiac Autonomic Activity

PubMed Central

Pichot, Vincent; Roche, Frédéric; Celle, Sébastien; Barthélémy, Jean-Claude; Chouchou, Florian

2016-01-01

Since the pioneering studies of the 1960s, heart rate variability (HRV) has become an increasingly used non-invasive tool for examining cardiac autonomic functions and dysfunctions in various populations and conditions. Many calculation methods have been developed to address these issues, each with their strengths and weaknesses. Although, its interpretation may remain difficult, this technique provides, from a non-invasive approach, reliable physiological information that was previously inaccessible, in many fields including death and health prediction, training and overtraining, cardiac and respiratory rehabilitation, sleep-disordered breathing, large cohort follow-ups, children's autonomic status, anesthesia, or neurophysiological studies. In this context, we developed HRVanalysis, a software to analyse HRV, used and improved for over 20 years and, thus, designed to meet laboratory requirements. The main strength of HRVanalysis is its wide application scope. In addition to standard analysis over short and long periods of RR intervals, the software allows time-frequency analysis using wavelet transform as well as analysis of autonomic nervous system status on surrounding scored events and on preselected labeled areas. Moreover, the interface is designed for easy study of large cohorts, including batch mode signal processing to avoid running repetitive operations. Results are displayed as figures or saved in TXT files directly employable in statistical softwares. Recordings can arise from RR or EKG files of different types such as cardiofrequencemeters, holters EKG, polygraphs, and data acquisition systems. HRVanalysis can be downloaded freely from the Web page at: https://anslabtools.univ-st-etienne.fr HRVanalysis is meticulously maintained and developed for in-house laboratory use. In this article, after a brief description of the context, we present an overall view of HRV analysis and we describe the methodological approach of the different techniques provided by the software. PMID:27920726

One Burn, One Standard

DTIC Science & Technology

2014-09-01

Johannes Kepler University Linz Software GmbH Research Department Medical Informatics Hagenberg, Austria Herbert L. Haller, MD Trauma Hospital Linz of...0000000000000004 Address correspondence to M. Giretzlehner, PhD, Johannes Kepler University Linz, RISC Software GmbH, Research Department Medical Informatics, Softwarepark 35, 4232 Hagenberg, Austria. One Burn, One Standard LETTER TO THE EDITOR

Home noninvasive positive pressure ventilation with built-in software in stable hypercapnic COPD: a short-term prospective, multicenter, randomized, controlled trial.

PubMed

Zhou, Luqian; Li, Xiaoying; Guan, Lili; Chen, Jianhua; Guo, Bingpeng; Wu, Weiliang; Huo, Yating; Zhou, Ziqing; Liang, Zhenyu; Zhou, Yuqi; Tan, Jie; Chen, Xin; Song, Yuanlin; Chen, Rongchang

2017-01-01

The benefits of noninvasive positive pressure ventilation (NPPV) in patients with hypercapnic COPD are controversial. It is presumed that methodology and appropriate use of NIV ventilator might be crucial for the outcomes. With the new built-in software, the performance of NIV can be monitored at home, which can guarantee the compliance and appropriate use. This study investigated effects of home use of NIV in hypercapnia in COPD patients using the NIV ventilator with built-in software for monitoring. The current multicenter prospective, randomized, controlled trial enrolled patients with stable GOLD stages III and IV hypercapnic COPD. Patients were randomly assigned via a computer-generated randomization sequence, with a block size of four patients, to continue optimized treatment (control group) or to receive additional NPPV (intervention group) for 3 months. The primary outcome was arterial carbon dioxide pressure (PaCO 2 ). Data were derived from built-in software and analyzed every 4 weeks. Analysis was carried out with the intention to treat. This study is registered with ClinicalTrials.gov, number NCT02499718. Patients were recruited from 20 respiratory units in China from October 1, 2015, and recruitment was terminated with a record of the vital statistics on May 31, 2016. A total of 115 patients were randomly assigned to the NPPV group (n=57) or the control group (n=58). Patients complied well with NPPV therapy (mean [± standard deviation] day use 5.6±1.4 h). The mean estimation of leaks was 37.99±13.71 L/min. The changes in PaCO 2 (-10.41±0.97 vs -4.32±0.68 mmHg, P =0.03) and 6-min walk distance (6MWD) (38.2% vs 18.2%, P =0.02) were statistically significant in the NPPV group versus the control group. COPD assessment test (CAT) showed a positive trend ( P =0.06) in favor of the NPPV group. Pulmonary function and dyspnea were not different between groups. Ventilators equipped with built-in software provided methodology for monitoring NIV use at home, which could facilitate the improvement of compliance and quality control of NIV use. It was shown that three months use of NIV at home could reduce the PaCO 2 and improve exercise tolerance (6MWD) in chronic hypercapnic COPD patients.

SEER*Stat Software

Cancer.gov

If you have access to SEER Research Data, use SEER*Stat to analyze SEER and other cancer-related databases. View individual records and produce statistics including incidence, mortality, survival, prevalence, and multiple primary. Tutorials and related analytic software tools are available.

CADDIS Volume 4. Data Analysis: Download Software

EPA Pesticide Factsheets

Overview of the data analysis tools available for download on CADDIS. Provides instructions for downloading and installing CADStat, access to Microsoft Excel macro for computing SSDs, a brief overview of command line use of R, a statistical software.

Genetic Programming as Alternative for Predicting Development Effort of Individual Software Projects

PubMed Central

Chavoya, Arturo; Lopez-Martin, Cuauhtemoc; Andalon-Garcia, Irma R.; Meda-Campaña, M. E.

2012-01-01

Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, whereas another sample of 130 projects developed by 38 practitioners was used for validating them. The models used two kinds of lines of code as well as programming language experience as independent variables. Accuracy results from the model obtained with genetic programming suggest that it could be used to predict the software development effort of individual projects when these projects have been developed in a disciplined manner within a development-controlled environment. PMID:23226305

Coupling Sensing Hardware with Data Interrogation Software for Structural Health Monitoring

DOE PAGES

Farrar, Charles R.; Allen, David W.; Park, Gyuhae; ...

2006-01-01

The process of implementing a damage detection strategy for aerospace, civil and mechanical engineering infrastructure is referred to as structural health monitoring (SHM). The authors' approach is to address the SHM problem in the context of a statistical pattern recognition paradigm. In this paradigm, the process can be broken down into four parts: (1) Operational Evaluation, (2) Data Acquisition and Cleansing, (3) Feature Extraction and Data Compression, and (4) Statistical Model Development for Feature Discrimination. These processes must be implemented through hardware or software and, in general, some combination of these two approaches will be used. This paper will discussmore » each portion of the SHM process with particular emphasis on the coupling of a general purpose data interrogation software package for structural health monitoring with a modular wireless sensing and processing platform. More specifically, this paper will address the need to take an integrated hardware/software approach to developing SHM solutions.« less

Proceedings, Conference on the Computing Environment for Mathematical Software

NASA Technical Reports Server (NTRS)

1981-01-01

Recent advances in software and hardware technology which make it economical to create computing environments appropriate for specialized applications are addressed. Topics included software tools, FORTRAN standards activity, and features of languages, operating systems, and hardware that are important for the development, testing, and maintenance of mathematical software.

SU-E-CAMPUS-J-05: Quantitative Investigation of Random and Systematic Uncertainties From Hardware and Software Components in the Frameless 6DBrainLAB ExacTrac System

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

Keeling, V; Jin, H; Hossain, S

2014-06-15

Purpose: To evaluate setup accuracy and quantify individual systematic and random errors for the various hardware and software components of the frameless 6D-BrainLAB ExacTrac system. Methods: 35 patients with cranial lesions, some with multiple isocenters (50 total lesions treated in 1, 3, 5 fractions), were investigated. All patients were simulated with a rigid head-and-neck mask and the BrainLAB localizer. CT images were transferred to the IPLAN treatment planning system where optimized plans were generated using stereotactic reference frame based on the localizer. The patients were setup initially with infrared (IR) positioning ExacTrac system. Stereoscopic X-ray images (XC: X-ray Correction) weremore » registered to their corresponding digitally-reconstructed-radiographs, based on bony anatomy matching, to calculate 6D-translational and rotational (Lateral, Longitudinal, Vertical, Pitch, Roll, Yaw) shifts. XC combines systematic errors of the mask, localizer, image registration, frame, and IR. If shifts were below tolerance (0.7 mm translational and 1 degree rotational), treatment was initiated; otherwise corrections were applied and additional X-rays were acquired to verify patient position (XV: X-ray Verification). Statistical analysis was used to extract systematic and random errors of the different components of the 6D-ExacTrac system and evaluate the cumulative setup accuracy. Results: Mask systematic errors (translational; rotational) were the largest and varied from one patient to another in the range (−15 to 4mm; −2.5 to 2.5degree) obtained from mean of XC for each patient. Setup uncertainty in IR positioning (0.97,2.47,1.62mm;0.65,0.84,0.96degree) was extracted from standard-deviation of XC. Combined systematic errors of the frame and localizer (0.32,−0.42,−1.21mm; −0.27,0.34,0.26degree) was extracted from mean of means of XC distributions. Final patient setup uncertainty was obtained from the standard deviations of XV (0.57,0.77,0.67mm,0.39,0.35,0.30degree). Conclusion: Statistical analysis was used to calculate cumulative and individual systematic errors from the different hardware and software components of the 6D-ExacTrac-system. Patients were treated with cumulative errors (<1mm,<1degree) with XV image guidance.« less

Classification software technique assessment

NASA Technical Reports Server (NTRS)

Jayroe, R. R., Jr.; Atkinson, R.; Dasarathy, B. V.; Lybanon, M.; Ramapryian, H. K.

1976-01-01

A catalog of software options is presented for the use of local user communities to obtain software for analyzing remotely sensed multispectral imagery. The resources required to utilize a particular software program are described. Descriptions of how a particular program analyzes data and the performance of that program for an application and data set provided by the user are shown. An effort is made to establish a statistical performance base for various software programs with regard to different data sets and analysis applications, to determine the status of the state-of-the-art.

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

ERIC Educational Resources Information Center

Meletiou-Mavrotheris, Maria

2004-01-01

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

Sulfur in Cometary Dust

NASA Technical Reports Server (NTRS)

Fomenkova, M. N.

1997-01-01

The computer-intensive project consisted of the analysis and synthesis of existing data on composition of comet Halley dust particles. The main objective was to obtain a complete inventory of sulfur containing compounds in the comet Halley dust by building upon the existing classification of organic and inorganic compounds and applying a variety of statistical techniques for cluster and cross-correlational analyses. A student hired for this project wrote and tested the software to perform cluster analysis. The following tasks were carried out: (1) selecting the data from existing database for the proposed project; (2) finding access to a standard library of statistical routines for cluster analysis; (3) reformatting the data as necessary for input into the library routines; (4) performing cluster analysis and constructing hierarchical cluster trees using three methods to define the proximity of clusters; (5) presenting the output results in different formats to facilitate the interpretation of the obtained cluster trees; (6) selecting groups of data points common for all three trees as stable clusters. We have also considered the chemistry of sulfur in inorganic compounds.

Quantitative Analysis of Venus Radar Backscatter Data in ArcGIS

NASA Technical Reports Server (NTRS)

Long, S. M.; Grosfils, E. B.

2005-01-01

Ongoing mapping of the Ganiki Planitia (V14) quadrangle of Venus and definition of material units has involved an integrated but qualitative analysis of Magellan radar backscatter images and topography using standard geomorphological mapping techniques. However, such analyses do not take full advantage of the quantitative information contained within the images. Analysis of the backscatter coefficient allows a much more rigorous statistical comparison between mapped units, permitting first order selfsimilarity tests of geographically separated materials assigned identical geomorphological labels. Such analyses cannot be performed directly on pixel (DN) values from Magellan backscatter images, because the pixels are scaled to the Muhleman law for radar echoes on Venus and are not corrected for latitudinal variations in incidence angle. Therefore, DN values must be converted based on pixel latitude back to their backscatter coefficient values before accurate statistical analysis can occur. Here we present a method for performing the conversions and analysis of Magellan backscatter data using commonly available ArcGIS software and illustrate the advantages of the process for geological mapping.

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

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

Jin, Ye; Ma, Xiaosong; Liu, Qing Gary

2015-01-01

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters tomore » create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.« less

Novel application of windowed beamforming function imaging for FLGPR

NASA Astrophysics Data System (ADS)

Xique, Ismael J.; Burns, Joseph W.; Thelen, Brian J.; LaRose, Ryan M.

2018-04-01

Backprojection of cross-correlated array data, using algorithms such as coherent interferometric imaging (Borcea, et al., 2006), has been advanced as a method to improve the statistical stability of images of targets in an inhomogeneous medium. Recently, the Windowed Beamforming Energy (WBE) function algorithm has been introduced as a functionally equivalent approach, which is significantly less computationally burdensome (Borcea, et al., 2011). WBE produces similar results through the use of a quadratic function summing signals after beamforming in transmission and reception, and windowing in the time domain. We investigate the application of WBE to improve the detection of buried targets with forward looking ground penetrating MIMO radar (FLGPR) data. The formulation of WBE as well the software implementation of WBE for the FLGPR data collection will be discussed. WBE imaging results are compared to standard backprojection and Coherence Factor imaging. Additionally, the effectiveness of WBE on field-collected data is demonstrated qualitatively through images and quantitatively through the use of a CFAR statistic on buried targets of a variety of contrast levels.

Software Quality Assurance and Controls Standard

DTIC Science & Technology

2010-04-27

Software Quality Assurance d C t l St d dan on ro s an ar Sue Carroll Principal Software Quality Analyst, SAS John Wal z VP Technology and...for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that...Cycle (SLC) process? • What is in a SQA Process? • Where are SQA Controls? • What is the SQA standards history? Wh t i h i i SQA?• a s c ang ng n

Software And Systems Engineering Risk Management

DTIC Science & Technology

2010-04-01

RSKM 2004 COSO Enterprise RSKM Framework 2006 ISO/IEC 16085 Risk Management Process 2008 ISO/IEC 12207 Software Lifecycle Processes 2009 ISO/IEC...1 Software And Systems Engineering Risk Management John Walz VP Technical and Conferences Activities, IEEE Computer Society Vice-Chair Planning...Software & Systems Engineering Standards Committee, IEEE Computer Society US TAG to ISO TMB Risk Management Working Group Systems and Software

Evaluating Software Assurance Knowledge and Competency of Acquisition Professionals

DTIC Science & Technology

2014-10-01

of ISO 12207 -2008, both internationally and in the United States [7]. That standard documents a comprehensive set of activities and supporting...grows, organizations must ensure that their procurement agents acquire high quality, secure software. ISO 12207 and the Software Assurance Competency...cyberattacks grows, organizations must ensure that their procurement agents acquire high quality, secure software. ISO 12207 and the Software Assurance

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

Acoustic Emission Analysis Applet (AEAA) Software

NASA Technical Reports Server (NTRS)

Nichols, Charles T.; Roth, Don J.

2013-01-01

NASA Glenn Research and NASA White Sands Test Facility have developed software supporting an automated pressure vessel structural health monitoring (SHM) system based on acoustic emissions (AE). The software, referred to as the Acoustic Emission Analysis Applet (AEAA), provides analysts with a tool that can interrogate data collected on Digital Wave Corp. and Physical Acoustics Corp. software using a wide spectrum of powerful filters and charts. This software can be made to work with any data once the data format is known. The applet will compute basic AE statistics, and statistics as a function of time and pressure (see figure). AEAA provides value added beyond the analysis provided by the respective vendors' analysis software. The software can handle data sets of unlimited size. A wide variety of government and commercial applications could benefit from this technology, notably requalification and usage tests for compressed gas and hydrogen-fueled vehicles. Future enhancements will add features similar to a "check engine" light on a vehicle. Once installed, the system will ultimately be used to alert International Space Station crewmembers to critical structural instabilities, but will have little impact to missions otherwise. Diagnostic information could then be transmitted to experienced technicians on the ground in a timely manner to determine whether pressure vessels have been impacted, are structurally unsound, or can be safely used to complete the mission.

The discounting model selector: Statistical software for delay discounting applications.

PubMed

Gilroy, Shawn P; Franck, Christopher T; Hantula, Donald A

2017-05-01

Original, open-source computer software was developed and validated against established delay discounting methods in the literature. The software executed approximate Bayesian model selection methods from user-supplied temporal discounting data and computed the effective delay 50 (ED50) from the best performing model. Software was custom-designed to enable behavior analysts to conveniently apply recent statistical methods to temporal discounting data with the aid of a graphical user interface (GUI). The results of independent validation of the approximate Bayesian model selection methods indicated that the program provided results identical to that of the original source paper and its methods. Monte Carlo simulation (n = 50,000) confirmed that true model was selected most often in each setting. Simulation code and data for this study were posted to an online repository for use by other researchers. The model selection approach was applied to three existing delay discounting data sets from the literature in addition to the data from the source paper. Comparisons of model selected ED50 were consistent with traditional indices of discounting. Conceptual issues related to the development and use of computer software by behavior analysts and the opportunities afforded by free and open-sourced software are discussed and a review of possible expansions of this software are provided. © 2017 Society for the Experimental Analysis of Behavior.

Software Reliability, Measurement, and Testing. Volume 2. Guidebook for Software Reliability Measurement and Testing

DTIC Science & Technology

1992-04-01

contractor’s existing data collection, analysis and corrective action system shall be utilized, with modification only as necessary to meet the...either from test or from analysis of field data . The procedures of MIL-STD-756B assume that the reliability of a 18 DEFINE IDENTIFY SOFTWARE LIFE CYCLE...to generate sufficient data to report a statistically valid reliability figure for a class of software. Casual data gathering accumulates data more

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction

PubMed Central

Gallistel, C. R.; Balci, Fuat; Freestone, David; Kheifets, Aaron; King, Adam

2014-01-01

We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be controlled by one computer. PMID:24637442

Automated, quantitative cognitive/behavioral screening of mice: for genetics, pharmacology, animal cognition and undergraduate instruction.

PubMed

Gallistel, C R; Balci, Fuat; Freestone, David; Kheifets, Aaron; King, Adam

2014-02-26

We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be controlled by one computer.

Autonomous Real Time Requirements Tracing

NASA Technical Reports Server (NTRS)

Plattsmier, George I.; Stetson, Howard K.

2014-01-01

One of the more challenging aspects of software development is the ability to verify and validate the functional software requirements dictated by the Software Requirements Specification (SRS) and the Software Detail Design (SDD). Insuring the software has achieved the intended requirements is the responsibility of the Software Quality team and the Software Test team. The utilization of Timeliner-TLX(sup TM) Auto-Procedures for relocating ground operations positions to ISS automated on-board operations has begun the transition that would be required for manned deep space missions with minimal crew requirements. This transition also moves the auto-procedures from the procedure realm into the flight software arena and as such the operational requirements and testing will be more structured and rigorous. The autoprocedures would be required to meet NASA software standards as specified in the Software Safety Standard (NASASTD- 8719), the Software Engineering Requirements (NPR 7150), the Software Assurance Standard (NASA-STD-8739) and also the Human Rating Requirements (NPR-8705). The Autonomous Fluid Transfer System (AFTS) test-bed utilizes the Timeliner-TLX(sup TM) Language for development of autonomous command and control software. The Timeliner- TLX(sup TM) system has the unique feature of providing the current line of the statement in execution during real-time execution of the software. The feature of execution line number internal reporting unlocks the capability of monitoring the execution autonomously by use of a companion Timeliner-TLX(sup TM) sequence as the line number reporting is embedded inside the Timeliner-TLX(sup TM) execution engine. This negates I/O processing of this type data as the line number status of executing sequences is built-in as a function reference. This paper will outline the design and capabilities of the AFTS Autonomous Requirements Tracker, which traces and logs SRS requirements as they are being met during real-time execution of the targeted system. It is envisioned that real time requirements tracing will greatly assist the movement of autoprocedures to flight software enhancing the software assurance of auto-procedures and also their acceptance as reliable commanders

Autonomous Real Time Requirements Tracing

NASA Technical Reports Server (NTRS)

Plattsmier, George; Stetson, Howard

2014-01-01

One of the more challenging aspects of software development is the ability to verify and validate the functional software requirements dictated by the Software Requirements Specification (SRS) and the Software Detail Design (SDD). Insuring the software has achieved the intended requirements is the responsibility of the Software Quality team and the Software Test team. The utilization of Timeliner-TLX(sup TM) Auto- Procedures for relocating ground operations positions to ISS automated on-board operations has begun the transition that would be required for manned deep space missions with minimal crew requirements. This transition also moves the auto-procedures from the procedure realm into the flight software arena and as such the operational requirements and testing will be more structured and rigorous. The autoprocedures would be required to meet NASA software standards as specified in the Software Safety Standard (NASASTD- 8719), the Software Engineering Requirements (NPR 7150), the Software Assurance Standard (NASA-STD-8739) and also the Human Rating Requirements (NPR-8705). The Autonomous Fluid Transfer System (AFTS) test-bed utilizes the Timeliner-TLX(sup TM) Language for development of autonomous command and control software. The Timeliner-TLX(sup TM) system has the unique feature of providing the current line of the statement in execution during real-time execution of the software. The feature of execution line number internal reporting unlocks the capability of monitoring the execution autonomously by use of a companion Timeliner-TLX(sup TM) sequence as the line number reporting is embedded inside the Timeliner-TLX(sup TM) execution engine. This negates I/O processing of this type data as the line number status of executing sequences is built-in as a function reference. This paper will outline the design and capabilities of the AFTS Autonomous Requirements Tracker, which traces and logs SRS requirements as they are being met during real-time execution of the targeted system. It is envisioned that real time requirements tracing will greatly assist the movement of autoprocedures to flight software enhancing the software assurance of auto-procedures and also their acceptance as reliable commanders.

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

PubMed

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

2015-03-01

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

ExAtlas: An interactive online tool for meta-analysis of gene expression data.

PubMed

Sharov, Alexei A; Schlessinger, David; Ko, Minoru S H

2015-12-01

We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users' own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher's methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data sets (e.g. GNF/BioGPS, Gene Ontology, KEGG, GAD phenotypes, BrainScan, ENCODE ChIP-seq, and protein-protein interaction) are pre-loaded and can be used for functional annotations.

A probabilistic sizing tool and Monte Carlo analysis for entry vehicle ablative thermal protection systems

NASA Astrophysics Data System (ADS)

Mazzaracchio, Antonio; Marchetti, Mario

2010-03-01

Implicit ablation and thermal response software was developed to analyse and size charring ablative thermal protection systems for entry vehicles. A statistical monitor integrated into the tool, which uses the Monte Carlo technique, allows a simulation to run over stochastic series. This performs an uncertainty and sensitivity analysis, which estimates the probability of maintaining the temperature of the underlying material within specified requirements. This approach and the associated software are primarily helpful during the preliminary design phases of spacecraft thermal protection systems. They are proposed as an alternative to traditional approaches, such as the Root-Sum-Square method. The developed tool was verified by comparing the results with those from previous work on thermal protection system probabilistic sizing methodologies, which are based on an industry standard high-fidelity ablation and thermal response program. New case studies were analysed to establish thickness margins on sizing heat shields that are currently proposed for vehicles using rigid aeroshells for future aerocapture missions at Neptune, and identifying the major sources of uncertainty in the material response.

Astroinformatics as a New Research Field. UkrVO Astroinformation Resources: Tasks and Prospective

NASA Astrophysics Data System (ADS)

Vavilova, I. B.

The data-oriented astronomy has allowed classifying the Astroinformatics as a new academic research field, which covers various multi-disciplinary applications of the e-Astronomy. Among them are the data modeling, data mining, metadata standards development, data access, digital astronomical databases, image archives and visualization, machine learning, statistics and other computational methods and software for work with astronomical survey and catalogues with their teta- topeta-scale astroinformation resource. In this review we describe briefly the astroinformatics applications and software/services performed for different astronomical tasks in frame of the VIrtual Roentgen and Gamma Observatory (VIRGO) and Ukrainian VirtualObservatory (UkrVO). Among them there are projects based on the archival space-born data of X-ray and gamma space observatories and on the Joint Digitized Archive (JDA) database of astroplate network collections. The UkrVO JDA DR1 deals with the star catalogues (FON, Polar zone, open clusters, GRB star fields) as well as the UkrVO JDA DR2 deals with the Solar System bodies (giant and small planets, satellites, astronomical heritage images).

Expert system verification and validation study. Delivery 3A and 3B: Trip summaries

NASA Technical Reports Server (NTRS)

French, Scott

1991-01-01

Key results are documented from attending the 4th workshop on verification, validation, and testing. The most interesting part of the workshop was when representatives from the U.S., Japan, and Europe presented surveys of VV&T within their respective regions. Another interesting part focused on current efforts to define industry standards for artificial intelligence and how that might affect approaches to VV&T of expert systems. The next part of the workshop focused on VV&T methods of applying mathematical techniques to verification of rule bases and techniques for capturing information relating to the process of developing software. The final part focused on software tools. A summary is also presented of the EPRI conference on 'Methodologies, Tools, and Standards for Cost Effective Reliable Software Verification and Validation. The conference was divided into discussion sessions on the following issues: development process, automated tools, software reliability, methods, standards, and cost/benefit considerations.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

PubMed

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

Non-standard analysis and embedded software

NASA Technical Reports Server (NTRS)

Platek, Richard

1995-01-01

One model for computing in the future is ubiquitous, embedded computational devices analogous to embedded electrical motors. Many of these computers will control physical objects and processes. Such hidden computerized environments introduce new safety and correctness concerns whose treatment go beyond present Formal Methods. In particular, one has to begin to speak about Real Space software in analogy with Real Time software. By this we mean, computerized systems which have to meet requirements expressed in the real geometry of space. How to translate such requirements into ordinary software specifications and how to carry out proofs is a major challenge. In this talk we propose a research program based on the use of no-standard analysis. Much detail remains to be carried out. The purpose of the talk is to inform the Formal Methods community that Non-Standard Analysis provides a possible avenue to attack which we believe will be fruitful.

Patient Safety—Incorporating Drawing Software into Root Cause Analysis Software

PubMed Central

Williams, Linda; Grayson, Diana; Gosbee, John

2001-01-01

Drawing software from Lassalle Technologies1 (France) designed for Visual Basic is the tool we used to standardize the creation, storage, and retrieval of flow diagrams containing information about adverse events and close calls.

Patient Safety—Incorporating Drawing Software into Root Cause Analysis Software

PubMed Central

Williams, Linda; Grayson, Diana; Gosbee, John

2002-01-01

Drawing software from Lassalle Technologies1 (France) designed for Visual Basic is the tool we used to standardize the creation, storage, and retrieval of flow diagrams containing information about adverse events and close calls.

The Missing Link: The Use of Link Words and Phrases as a Link to Manuscript Quality

ERIC Educational Resources Information Center

Onwuegbuzie, Anthony J.

2016-01-01

In this article, I provide a typology of transition words/phrases. This typology comprises 12 dimensions of link words/phrases that capture 277 link words/phrases. Using QDA Miner, WordStat, and SPSS--a computer-assisted mixed methods data analysis software, content analysis software, and statistical software, respectively--I analyzed 74…

Standardized development of computer software. Part 1: Methods

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1976-01-01

This work is a two-volume set on standards for modern software engineering methodology. This volume presents a tutorial and practical guide to the efficient development of reliable computer software, a unified and coordinated discipline for design, coding, testing, documentation, and project organization and management. The aim of the monograph is to provide formal disciplines for increasing the probability of securing software that is characterized by high degrees of initial correctness, readability, and maintainability, and to promote practices which aid in the consistent and orderly development of a total software system within schedule and budgetary constraints. These disciplines are set forth as a set of rules to be applied during software development to drastically reduce the time traditionally spent in debugging, to increase documentation quality, to foster understandability among those who must come in contact with it, and to facilitate operations and alterations of the program as requirements on the program environment change.

Health software: a new CEI Guide for software management in medical environment.

PubMed

Giacomozzi, Claudia; Martelli, Francesco

2016-01-01

The increasing spread of software components in the healthcare context renders explanatory guides relevant and mandatory to interpret laws and standards, and to support safe management of software products in healthcare. In 2012 a working group has been settled for the above purposes at Italian Electrotechnical Committee (CEI), made of experts from Italian National Institute of Health (ISS), representatives of industry, and representatives of the healthcare organizations. As a first outcome of the group activity, Guide CEI 62-237 was published in February 2015. The Guide incorporates an innovative approach based on the proper contextualization of software products, either medical devices or not, to the specific healthcare scenario, and addresses the risk management of IT systems. The Guide provides operators and manufacturers with an interpretative support with many detailed examples to facilitate the proper contextualization and management of health software, in compliance with related European and international regulations and standards.

Implementation of AAPG exchange format

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

Keiser, K.; Guerrero, I.

1989-03-01

The American Association of Petroleum Geologists (AAPG) has proposed a format for exchanging geologic and other petroleum data. The AAPG Computer Applications Committee approved the proposal at the March 1988 AAPG annual meeting in Houston, Texas. By adopting this format, data input into application software and data exchange between software packages are greatly simplified. Benefits to both users and suppliers of software are substantial. The AAPG exchange format supports a flexible, generic data structure. This flexibility allows application software to use the standard format for storing internal control data. In some cases, extensions to the standard format, such as separationmore » of header and data files and use of data delimiters, permits the use of AAPG format translator programs on data that were defined and generated before the emergence of the exchange format. Translation software, programmed in C, has been written and contributes to successful implementation of the AAPG exchange format in application software.« less

Technical Support Document for Version 3.6.1 of the COMcheck Software

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

Bartlett, Rosemarie; Connell, Linda M.; Gowri, Krishnan

2009-09-29

This technical support document (TSD) is designed to explain the technical basis for the COMcheck software as originally developed based on the ANSI/ASHRAE/IES Standard 90.1-1989 (Standard 90.1-1989). Documentation for other national model codes and standards and specific state energy codes supported in COMcheck has been added to this report as appendices. These appendices are intended to provide technical documentation for features specific to the supported codes and for any changes made for state-specific codes that differ from the standard features that support compliance with the national model codes and standards.

Statistical Validation for Clinical Measures: Repeatability and Agreement of Kinect™-Based Software

PubMed Central

Tello, Emanuel; Rodrigo, Alejandro; Valentinuzzi, Max E.

2018-01-01

Background The rehabilitation process is a fundamental stage for recovery of people's capabilities. However, the evaluation of the process is performed by physiatrists and medical doctors, mostly based on their observations, that is, a subjective appreciation of the patient's evolution. This paper proposes a tracking platform of the movement made by an individual's upper limb using Kinect sensor(s) to be applied for the patient during the rehabilitation process. The main contribution is the development of quantifying software and the statistical validation of its performance, repeatability, and clinical use in the rehabilitation process. Methods The software determines joint angles and upper limb trajectories for the construction of a specific rehabilitation protocol and quantifies the treatment evolution. In turn, the information is presented via a graphical interface that allows the recording, storage, and report of the patient's data. For clinical purposes, the software information is statistically validated with three different methodologies, comparing the measures with a goniometer in terms of agreement and repeatability. Results The agreement of joint angles measured with the proposed software and goniometer is evaluated with Bland-Altman plots; all measurements fell well within the limits of agreement, meaning interchangeability of both techniques. Additionally, the results of Bland-Altman analysis of repeatability show 95% confidence. Finally, the physiotherapists' qualitative assessment shows encouraging results for the clinical use. Conclusion The main conclusion is that the software is capable of offering a clinical history of the patient and is useful for quantification of the rehabilitation success. The simplicity, low cost, and visualization possibilities enhance the use of the software Kinect for rehabilitation and other applications, and the expert's opinion endorses the choice of our approach for clinical practice. Comparison of the new measurement technique with established goniometric methods determines that the proposed software agrees sufficiently to be used interchangeably. PMID:29750166

AN INITIAL EVALUATION OF THE BTRACKS BALANCE PLATE AND SPORTS BALANCE SOFTWARE FOR CONCUSSION DIAGNOSIS

PubMed Central

Manyak, Kristin A.; Abdenour, Thomas E.; Rauh, Mitchell J.; Baweja, Harsimran S.

2016-01-01

Background As recently dictated by the American Medical Society, balance testing is an important component in the clinical evaluation of concussion. Despite this, previous research on the efficacy of balance testing for concussion diagnosis suggests low sensitivity (∼30%), based primarily on the popular Balance Error Scoring System (BESS). The Balance Tracking System (BTrackS, Balance Tracking Systems Inc., San Diego, CA, USA) consists of a force plate (BTrackS Balance Plate) and software (BTrackS Sport Balance) which can quickly (<2 min) perform concussion balance testing with gold standard accuracy. Purpose The present study aimed to determine the sensitivity of the BTrackS Balance Plate and Sports Balance Software for concussion diagnosis. Study Design Cross-Sectional Study Methods Preseason baseline balance testing of 519 healthy Division I college athletes playing sports with a relatively high risk for concussions was performed with the BTrackS Balance Test. Testing was administered by certified athletic training staff using the BTrackS Balance Plate and Sport Balance software. Of the baselined athletes, 25 later experienced a concussion during the ensuing sport season. Post-injury balance testing was performed on these concussed athletes within 48 of injury and the sensitivity of the BTrackS Balance Plate and Sport Balance software was estimated based on the number of athletes showing a balance decline according to the criteria specified in the Sport Balance software. This criteria is based on the minimal detectable change statistic with a 90% confidence level (i.e. 90% specificity). Results Of 25 athletes who experienced concussions, 16 had balance declines relative to baseline testing results according to the BTrackS Sport Balance software criteria. This corresponds to an estimated concussion sensitivity of 64%, which is twice as great as that reported previously for the BESS. Conclusions The BTrackS Balance Plate and Sport Balance software has the greatest concussion sensitivity of any balance testing instrument reported to date. Level of Evidence Level 2 (Individual cross sectional diagnostic study) PMID:27104048

A Mathematics Software Database Update.

ERIC Educational Resources Information Center

Cunningham, R. S.; Smith, David A.

1987-01-01

Contains an update of an earlier listing of software for mathematics instruction at the college level. Topics are: advanced mathematics, algebra, calculus, differential equations, discrete mathematics, equation solving, general mathematics, geometry, linear and matrix algebra, logic, statistics and probability, and trigonometry. (PK)

[The planning of resource support of secondary medical care in hospital].

PubMed

Kungurov, N V; Zil'berberg, N V

2010-01-01

The Ural Institute of dermatovenerology and immunopathology developed and implemented the software concerning the personalized total recording of medical services and pharmaceuticals. The Institute also presents such software as listing of medical services, software module of calculation of financial costs of implementing full standards of secondary medical care in case of chronic dermatopathy, reference book of standards of direct specific costs on laboratory and physiotherapy services, reference book of pharmaceuticals, testing systems and consumables. The unified information system of management recording is a good technique to substantiate the costs of the implementation of standards of medical care, including high-tech care with taking into account the results of total calculation of provided medical services.

Revealing the ISO/IEC 9126-1 Clique Tree for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2007-01-01

Previous research has shown that acyclic dependency models, if they exist, can be extracted from software quality standards and that these models can be used to assess software safety and product quality. In the case of commercial off-the-shelf (COTS) software, the extracted dependency model can be used in a probabilistic Bayesian network context for COTS software evaluation. Furthermore, while experts typically employ Bayesian networks to encode domain knowledge, secondary structures (clique trees) from Bayesian network graphs can be used to determine the probabilistic distribution of any software variable (attribute) using any clique that contains that variable. Secondary structures, therefore, provide insight into the fundamental nature of graphical networks. This paper will apply secondary structure calculations to reveal the clique tree of the acyclic dependency model extracted from the ISO/IEC 9126-1 software quality standard. Suggestions will be provided to describe how the clique tree may be exploited to aid efficient transformation of an evaluation model.

Effects of Medical Device Regulations on the Development of Stand-Alone Medical Software: A Pilot Study.

PubMed

Blagec, Kathrin; Jungwirth, David; Haluza, Daniela; Samwald, Matthias

2018-01-01

Medical device regulations which aim to ensure safety standards do not only apply to hardware devices but also to standalone medical software, e.g. mobile apps. To explore the effects of these regulations on the development and distribution of medical standalone software. We invited a convenience sample of 130 domain experts to participate in an online survey about the impact of current regulations on the development and distribution of medical standalone software. 21 respondents completed the questionnaire. Participants reported slight positive effects on usability, reliability, and data security of their products, whereas the ability to modify already deployed software and customization by end users were negatively impacted. The additional time and costs needed to go through the regulatory process were perceived as the greatest obstacles in developing and distributing medical software. Further research is needed to compare positive effects on software quality with negative impacts on market access and innovation. Strategies for avoiding over-regulation while still ensuring safety standards need to be devised.

Secure software practices among Malaysian software practitioners: An exploratory study

NASA Astrophysics Data System (ADS)

Mohamed, Shafinah Farvin Packeer; Baharom, Fauziah; Deraman, Aziz; Yahya, Jamaiah; Mohd, Haslina

2016-08-01

Secure software practices is increasingly gaining much importance among software practitioners and researchers due to the rise of computer crimes in the software industry. It has become as one of the determinant factors for producing high quality software. Even though its importance has been revealed, its current practice in the software industry is still scarce, particularly in Malaysia. Thus, an exploratory study is conducted among software practitioners in Malaysia to study their experiences and practices in the real-world projects. This paper discusses the findings from the study, which involved 93 software practitioners. Structured questionnaire is utilized for data collection purpose whilst statistical methods such as frequency, mean, and cross tabulation are used for data analysis. Outcomes from this study reveal that software practitioners are becoming increasingly aware on the importance of secure software practices, however, they lack of appropriate implementation, which could affect the quality of produced software.

Information Interface Related Standards, Guidelines, and Recommended Practices.

DTIC Science & Technology

1985-07-01

Application Workshop, IEEE, October 1984 (11) Software Portability and Standards, by Ingemar Dahlstrand, Ellis Horwood Ltd., 1984 (12) World of EDP...March 29, 1985, p. 42-48 * 9. "IBM’s Topview Plays to Poor Reviews of Early Users," Computer World , March 4, 1985, p. 5 10. "Lack of Software Standards...Information Symbols ISOiTR 7239-1984 - Development and Principles for Application of Public Information Symbols ISO/TR 8545 -1984 - Technical Drawings

Software component quality evaluation

NASA Technical Reports Server (NTRS)

Clough, A. J.

1991-01-01

The paper describes a software inspection process that can be used to evaluate the quality of software components. Quality criteria, process application, independent testing of the process and proposed associated tool support are covered. Early results indicate that this technique is well suited for assessing software component quality in a standardized fashion. With automated machine assistance to facilitate both the evaluation and selection of software components, such a technique should promote effective reuse of software components.

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

PubMed Central

Fischer, Sandra; Kumar, Neeraj

2017-01-01

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea. PMID:28097056

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons.

PubMed

Lagkouvardos, Ilias; Fischer, Sandra; Kumar, Neeraj; Clavel, Thomas

2017-01-01

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha - and beta -diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

Index of mechanical work in gait of children with cerebral palsy.

PubMed

Dziuba, Alicja Katarzyna; Tylkowska, Małgorzata; Jaroszczuk, Sebastian

2014-01-01

The pathological gait of children with cerebral palsy involves higher mechanical work, which limits their ability to function properly in society. Mechanical work is directly related to walking speed and, although a number of studies have been carried out in this field, few of them analysed the effect of the speed. The study aimed to develop standards for mechanical work during gait of children with cerebral palsy depending on the walking speed. The study covered 18 children with cerebral palsy and 14 healthy children. The BTS Smart software and the author's software were used to evaluate mechanical work, kinetic, potential and rotational energy connected with motion of the children body during walk. Compared to healthy subjects, mechanical work in children with cerebral palsy increases with the degree of disability. It can be expressed as a linear function of walking speed and shows strong and statistically significant correlations with walking gait. A negative statistically significant correlation between the degree of disability and walking speed can be observed. The highest contribution to the total mechanical energy during gait is from mechanical energy of the feet. Instantaneous value of rotational energy is 700 times lower than the instantaneous mechanical energy. An increase in walking speed causes the increase in the effect of the index of kinetic energy on total mechanical work. The method described can provide an objective supplementation for doctors and physical therapists to perform a simple and immediate diagnosis without much technical knowledge.

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

75 FR 25165 - Defense Federal Acquisition Regulation Supplement; Cost and Software Data Reporting System

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... 215, 234, 242, and 252 Defense Federal Acquisition Regulation Supplement; Cost and Software Data... Regulation Supplement (DFARS) to set forth DoD Cost and Software Data Reporting system requirements for major... set forth the DoD requirement for offerors to: Describe the standard Cost and Software Data Reporting...

Tips on Creating Complex Geometry Using Solid Modeling Software

ERIC Educational Resources Information Center

Gow, George

2008-01-01

Three-dimensional computer-aided drafting (CAD) software, sometimes referred to as "solid modeling" software, is easy to learn, fun to use, and becoming the standard in industry. However, many users have difficulty creating complex geometry with the solid modeling software. And the problem is not entirely a student problem. Even some teachers and…

Analysis of Software Development Methodologies to Build Safety Software Applications for the SATEX-II: A Mexican Experimental Satellite

NASA Astrophysics Data System (ADS)

Aguilar Cisneros, Jorge; Vargas Martinez, Hector; Pedroza Melendez, Alejandro; Alonso Arevalo, Miguel

2013-09-01

Mexico is a country where the experience to build software for satellite applications is beginning. This is a delicate situation because in the near future we will need to develop software for the SATEX-II (Mexican Experimental Satellite). SATEX- II is a SOMECyTA's project (the Mexican Society of Aerospace Science and Technology). We have experienced applying software development methodologies, like TSP (Team Software Process) and SCRUM in other areas. Then, we analyzed these methodologies and we concluded: these can be applied to develop software for the SATEX-II, also, we supported these methodologies with SSP-05-0 Standard in particular with ESA PSS-05-11. Our analysis was focusing on main characteristics of each methodology and how these methodologies could be used with the ESA PSS 05-0 Standards. Our outcomes, in general, may be used by teams who need to build small satellites, but, in particular, these are going to be used when we will build the on board software applications for the SATEX-II.

OHD/HL - Staff

Science.gov Websites

Laboratory Branches Hydrologic Software Engineering Branch (HSEB) Hydrologic Science and Modeling Branch (HSMB) General Info Publications Documentation Software Standard and Guidelines Contact Us HL Staff resources and services. Staff Directory Chief, Hydrology Laboratory; Chief, Hydrologic Software Engineering

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

Evidential evaluation of DNA profiles using a discrete statistical model implemented in the DNA LiRa software.

PubMed

Puch-Solis, Roberto; Clayton, Tim

2014-07-01

The high sensitivity of the technology for producing profiles means that it has become routine to produce profiles from relatively small quantities of DNA. The profiles obtained from low template DNA (LTDNA) are affected by several phenomena which must be taken into consideration when interpreting and evaluating this evidence. Furthermore, many of the same phenomena affect profiles from higher amounts of DNA (e.g. where complex mixtures has been revealed). In this article we present a statistical model, which forms the basis of software DNA LiRa, and that is able to calculate likelihood ratios where one to four donors are postulated and for any number of replicates. The model can take into account dropin and allelic dropout for different contributors, template degradation and uncertain allele designations. In this statistical model unknown parameters are treated following the Empirical Bayesian paradigm. The performance of LiRa is tested using examples and the outputs are compared with those generated using two other statistical software packages likeLTD and LRmix. The concept of ban efficiency is introduced as a measure for assessing model sensitivity. Copyright © 2014. Published by Elsevier Ireland Ltd.

Software Suite to Support In-Flight Characterization of Remote Sensing Systems

NASA Technical Reports Server (NTRS)

Stanley, Thomas; Holekamp, Kara; Gasser, Gerald; Tabor, Wes; Vaughan, Ronald; Ryan, Robert; Pagnutti, Mary; Blonski, Slawomir; Kenton, Ross

2014-01-01

A characterization software suite was developed to facilitate NASA's in-flight characterization of commercial remote sensing systems. Characterization of aerial and satellite systems requires knowledge of ground characteristics, or ground truth. This information is typically obtained with instruments taking measurements prior to or during a remote sensing system overpass. Acquired ground-truth data, which can consist of hundreds of measurements with different data formats, must be processed before it can be used in the characterization. Accurate in-flight characterization of remote sensing systems relies on multiple field data acquisitions that are efficiently processed, with minimal error. To address the need for timely, reproducible ground-truth data, a characterization software suite was developed to automate the data processing methods. The characterization software suite is engineering code, requiring some prior knowledge and expertise to run. The suite consists of component scripts for each of the three main in-flight characterization types: radiometric, geometric, and spatial. The component scripts for the radiometric characterization operate primarily by reading the raw data acquired by the field instruments, combining it with other applicable information, and then reducing it to a format that is appropriate for input into MODTRAN (MODerate resolution atmospheric TRANsmission), an Air Force Research Laboratory-developed radiative transport code used to predict at-sensor measurements. The geometric scripts operate by comparing identified target locations from the remote sensing image to known target locations, producing circular error statistics defined by the Federal Geographic Data Committee Standards. The spatial scripts analyze a target edge within the image, and produce estimates of Relative Edge Response and the value of the Modulation Transfer Function at the Nyquist frequency. The software suite enables rapid, efficient, automated processing of ground truth data, which has been used to provide reproducible characterizations on a number of commercial remote sensing systems. Overall, this characterization software suite improves the reliability of ground-truth data processing techniques that are required for remote sensing system in-flight characterizations.

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.; Dateo, C.; Pires, A.

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

Not so Fast My Friend: The Rush to R and the Need for Rigorous Evaluation of Data Analysis and Software in Education

ERIC Educational Resources Information Center

Harwell, Michael

2014-01-01

Commercial data analysis software has been a fixture of quantitative analyses in education for more than three decades. Despite its apparent widespread use there is no formal evidence cataloging what software is used in educational research and educational statistics classes, by whom and for what purpose, and whether some programs should be…

The Application of Software Safety to the Constellation Program Launch Control System

NASA Technical Reports Server (NTRS)

Kania, James; Hill, Janice

2011-01-01

The application of software safety practices on the LCS project resulted in the successful implementation of the NASA Software Safety Standard NASA-STD-8719.138 and CxP software safety requirements. The GOP-GEN-GSW-011 Hazard Report was the first report developed at KSC to identify software hazard causes and their controls. This approach can be applied to similar large software - intensive systems where loss of control can lead to a hazard.

How to choose the right statistical software?—a method increasing the post-purchase satisfaction

PubMed Central

2015-01-01

Nowadays, we live in the “data era” where the use of statistical or data analysis software is inevitable, in any research field. This means that the choice of the right software tool or platform is a strategic issue for a research department. Nevertheless, in many cases decision makers do not pay the right attention to a comprehensive and appropriate evaluation of what the market offers. Indeed, the choice still depends on few factors like, for instance, researcher’s personal inclination, e.g., which software have been used at the university or is already known. This is not wrong in principle, but in some cases it’s not enough at all and might lead to a “dead end” situation, typically after months or years of investments already done on the wrong software. This article, far from being a full and complete guide to statistical software evaluation, aims to illustrate some key points of the decision process and introduce an extended range of factors which can help to undertake the right choice, at least in potential. There is not enough literature about that topic, most of the time underestimated, both in the traditional literature and even in the so called “gray literature”, even if some documents or short pages can be found online. Anyhow, it seems there is not a common and known standpoint about the process of software evaluation from the final user perspective. We suggests a multi-factor analysis leading to an evaluation matrix tool, to be intended as a flexible and customizable tool, aimed to provide a clearer picture of the software alternatives available, not in abstract but related to the researcher’s own context and needs. This method is a result of about twenty years of experience of the author in the field of evaluating and using technical-computing software and partially arises from a research made about such topics as part of a project funded by European Commission under the Lifelong Learning Programme 2011. PMID:26793368

Software production methodology tested project

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1976-01-01

The history and results of a 3 1/2-year study in software development methodology are reported. The findings of this study have become the basis for DSN software development guidelines and standard practices. The article discusses accomplishments, discoveries, problems, recommendations and future directions.

Accuracy of a remote quantitative image analysis in the whole slide images.

PubMed

Słodkowska, Janina; Markiewicz, Tomasz; Grala, Bartłomiej; Kozłowski, Wojciech; Papierz, Wielisław; Pleskacz, Katarzyna; Murawski, Piotr

2011-03-30

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and oligodendrogliomas could be successfully used as an alternative method to the manual reading as well as to the digital images quantitation with CAMI software. According to our observation a need of a remote supervision/consultation and training for the effective use of remote quantitative analysis of WSI is necessary.

How Statistics "Excel" Online.

ERIC Educational Resources Information Center

Chao, Faith; Davis, James

2000-01-01

Discusses the use of Microsoft Excel software and provides examples of its use in an online statistics course at Golden Gate University in the areas of randomness and probability, sampling distributions, confidence intervals, and regression analysis. (LRW)

Establishment of a new relationship between posed smile width and lower facial height: A cross-sectional study

PubMed Central

Abraham, Aby; George, Jinu; Peter, Elbe; Philip, Koshi; Chankramath, Rajesh; Johns, Dexton Antony; Bhaskar, Anitha

2015-01-01

Objective: The present study is intended to add a new parameter that would be useful in orthodontic clinical evaluation, treatment planning, and determination of vertical dimension (at occlusion). Materials and Methods: Standardized videographic recording of 79 subjects during posed smile was captured. Each video was then cut into 30 photos using the free studio software. The widest commissure-to-commissure posed smile frame (posed smile width [SW]) was selected as one of 10 or more frames showing an identical smile. Lower third of the face is measured from subnasale to soft tissue menton using a digital vernier caliper. Two values were then compared. Ratio between lower facial height and posed SW was calculated. Results: The co-relation between smiling width and lower facial height was found to be statistically significant (P < 0.01). The ratio of lower facial height and smiling width was calculated as 1.0016 with a standard deviation (SD) = 0.04 in males and 1.0301 with an SD = 0.07 in females. The difference between the mean lower facial height in males and females was statistically significant with a t = 10.231 and P = 0.000. The difference between the mean smiling width in males and females was also statistically significant with a t = 5.653 and P = 0.000. Conclusion: In class I subjects with pleasing appearance, normal facial proportions, normal overjet and overbite, and average Frankfort mandibular angle, the lower facial height (subnasale to soft tissue menton) is equal to posed SW. PMID:26430369

Logic integer programming models for signaling networks.

PubMed

Haus, Utz-Uwe; Niermann, Kathrin; Truemper, Klaus; Weismantel, Robert

2009-05-01

We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this, we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in molecular biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included.