Automatic Rock Detection and Mapping from HiRISE Imagery

NASA Technical Reports Server (NTRS)

Huertas, Andres; Adams, Douglas S.; Cheng, Yang

2008-01-01

This system includes a C-code software program and a set of MATLAB software tools for statistical analysis and rock distribution mapping. The major functions include rock detection and rock detection validation. The rock detection code has been evolved into a production tool that can be used by engineers and geologists with minor training.

Testing expert systems

NASA Technical Reports Server (NTRS)

Chang, C. L.; Stachowitz, R. A.

1988-01-01

Software quality is of primary concern in all large-scale expert system development efforts. Building appropriate validation and test tools for ensuring software reliability of expert systems is therefore required. The Expert Systems Validation Associate (EVA) is a validation system under development at the Lockheed Artificial Intelligence Center. EVA provides a wide range of validation and test tools to check correctness, consistency, and completeness of an expert system. Testing a major function of EVA. It means executing an expert system with test cases with the intent of finding errors. In this paper, we describe many different types of testing such as function-based testing, structure-based testing, and data-based testing. We describe how appropriate test cases may be selected in order to perform good and thorough testing of an expert system.

A software tool to analyze clinical workflows from direct observations.

PubMed

Schweitzer, Marco; Lasierra, Nelia; Hoerbst, Alexander

2015-01-01

Observational data of clinical processes need to be managed in a convenient way, so that process information is reliable, valid and viable for further analysis. However, existing tools for allocating observations fail in systematic data collection of specific workflow recordings. We present a software tool which was developed to facilitate the analysis of clinical process observations. The tool was successfully used in the project OntoHealth, to build, store and analyze observations of diabetes routine consultations.

Independent Verification and Validation of Complex User Interfaces: A Human Factors Approach

NASA Technical Reports Server (NTRS)

Whitmore, Mihriban; Berman, Andrea; Chmielewski, Cynthia

1996-01-01

The Usability Testing and Analysis Facility (UTAF) at the NASA Johnson Space Center has identified and evaluated a potential automated software interface inspection tool capable of assessing the degree to which space-related critical and high-risk software system user interfaces meet objective human factors standards across each NASA program and project. Testing consisted of two distinct phases. Phase 1 compared analysis times and similarity of results for the automated tool and for human-computer interface (HCI) experts. In Phase 2, HCI experts critiqued the prototype tool's user interface. Based on this evaluation, it appears that a more fully developed version of the tool will be a promising complement to a human factors-oriented independent verification and validation (IV&V) process.

A digital flight control system verification laboratory

NASA Technical Reports Server (NTRS)

De Feo, P.; Saib, S.

1982-01-01

A NASA/FAA program has been established for the verification and validation of digital flight control systems (DFCS), with the primary objective being the development and analysis of automated verification tools. In order to enhance the capabilities, effectiveness, and ease of using the test environment, software verification tools can be applied. Tool design includes a static analyzer, an assertion generator, a symbolic executor, a dynamic analysis instrument, and an automated documentation generator. Static and dynamic tools are integrated with error detection capabilities, resulting in a facility which analyzes a representative testbed of DFCS software. Future investigations will ensue particularly in the areas of increase in the number of software test tools, and a cost effectiveness assessment.

Design, Development and Delivery of Active Learning Tools in Software Verification & Validation Education

ERIC Educational Resources Information Center

Acharya, Sushil; Manohar, Priyadarshan Anant; Wu, Peter; Maxim, Bruce; Hansen, Mary

2018-01-01

Active learning tools are critical in imparting real world experiences to the students within a classroom environment. This is important because graduates are expected to develop software that meets rigorous quality standards in functional and application domains with little to no training. However, there is a well-recognized need for the…

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

The Design and Evaluation of Class Exercises as Active Learning Tools in Software Verification and Validation

ERIC Educational Resources Information Center

Wu, Peter Y.; Manohar, Priyadarshan A.; Acharya, Sushil

2016-01-01

It is well known that interesting questions can stimulate thinking and invite participation. Class exercises are designed to make use of questions to engage students in active learning. In a project toward building a community skilled in software verification and validation (SV&V), we critically review and further develop course materials in…

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Records Inventory Data Collection Software

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

Cole, Brian A.

1995-03-01

DATALINK was created to provide an easy to use data collection program for records management software products. It provides several useful tools for capturing and validating record index data in the field. It also allows users to easily create a comma delimited, ASCII text file for data export into most records management software products.

A cross-validation package driving Netica with python

USGS Publications Warehouse

Fienen, Michael N.; Plant, Nathaniel G.

2014-01-01

Bayesian networks (BNs) are powerful tools for probabilistically simulating natural systems and emulating process models. Cross validation is a technique to avoid overfitting resulting from overly complex BNs. Overfitting reduces predictive skill. Cross-validation for BNs is known but rarely implemented due partly to a lack of software tools designed to work with available BN packages. CVNetica is open-source, written in Python, and extends the Netica software package to perform cross-validation and read, rebuild, and learn BNs from data. Insights gained from cross-validation and implications on prediction versus description are illustrated with: a data-driven oceanographic application; and a model-emulation application. These examples show that overfitting occurs when BNs become more complex than allowed by supporting data and overfitting incurs computational costs as well as causing a reduction in prediction skill. CVNetica evaluates overfitting using several complexity metrics (we used level of discretization) and its impact on performance metrics (we used skill).

Data-driven traffic impact assessment tool for work zones.

DOT National Transportation Integrated Search

2017-03-01

Traditionally, traffic impacts of work zones have been assessed using planning software such as Quick Zone, custom spreadsheets, and others. These software programs generate delay, queuing, and other mobility measures but are difficult to validate du...

Web-based Quality Control Tool used to validate CERES products on a cluster of Linux servers

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Mlynczak, P.; Mitrescu, C.; Doelling, D.

2014-12-01

There have been a few popular desktop tools used in the Earth Science community to validate science data. Because of the limitation on the capacity of desktop hardware such as disk space and CPUs, those softwares are not able to display large amount of data from files.This poster will talk about an in-house developed web-based software built on a cluster of Linux servers. That allows users to take advantage of a few Linux servers working in parallel to generate hundreds images in a short period of time. The poster will demonstrate:(1) The hardware and software architecture is used to provide high throughput of images. (2) The software structure that can incorporate new products and new requirement quickly. (3) The user interface about how users can manipulate the data and users can control how the images are displayed.

Development and assessment of a digital X-ray software tool to determine vertebral rotation in adolescent idiopathic scoliosis.

PubMed

Eijgenraam, Susanne M; Boselie, Toon F M; Sieben, Judith M; Bastiaenen, Caroline H G; Willems, Paul C; Arts, Jacobus J; Lataster, Arno

2017-02-01

The amount of vertebral rotation in the axial plane is of key importance in the prognosis and treatment of adolescent idiopathic scoliosis (AIS). Current methods to determine vertebral rotation are either designed for use in analogue plain radiographs and not useful in digital images, or lack measurement precision and are therefore less suitable for the follow-up of rotation in AIS patients. This study aimed to develop a digital X-ray software tool with high measurement precision to determine vertebral rotation in AIS, and to assess its (concurrent) validity and reliability. In this study a combination of basic science and reliability methodology applied in both laboratory and clinical settings was used. Software was developed using the algorithm of the Perdriolle torsion meter for analogue AP plain radiographs of the spine. Software was then assessed for (1) concurrent validity and (2) intra- and interobserver reliability. Plain radiographs of both human cadaver vertebrae and outpatient AIS patients were used. Concurrent validity was measured by two independent observers, both experienced in the assessment of plain radiographs. Reliability-measurements were performed by three independent spine surgeons. Pearson correlation of the software compared with the analogue Perdriolle torsion meter for mid-thoracic vertebrae was 0.98, for low-thoracic vertebrae 0.97 and for lumbar vertebrae 0.97. Measurement exactness of the software was within 5° in 62% of cases and within 10° in 97% of cases. Intraclass correlation coefficient (ICC) for inter-observer reliability was 0.92 (0.91-0.95), ICC for intra-observer reliability was 0.96 (0.94-0.97). We developed a digital X-ray software tool to determine vertebral rotation in AIS with a substantial concurrent validity and reliability, which may be useful for the follow-up of vertebral rotation in AIS patients. Copyright © 2015 Elsevier Inc. All rights reserved.

Fast scattering simulation tool for multi-energy x-ray imaging

NASA Astrophysics Data System (ADS)

Sossin, A.; Tabary, J.; Rebuffel, V.; Létang, J. M.; Freud, N.; Verger, L.

2015-12-01

A combination of Monte Carlo (MC) and deterministic approaches was employed as a means of creating a simulation tool capable of providing energy resolved x-ray primary and scatter images within a reasonable time interval. Libraries of Sindbad, a previously developed x-ray simulation software, were used in the development. The scatter simulation capabilities of the tool were validated through simulation with the aid of GATE and through experimentation by using a spectrometric CdTe detector. A simple cylindrical phantom with cavities and an aluminum insert was used. Cross-validation with GATE showed good agreement with a global spatial error of 1.5% and a maximum scatter spectrum error of around 6%. Experimental validation also supported the accuracy of the simulations obtained from the developed software with a global spatial error of 1.8% and a maximum error of around 8.5% in the scatter spectra.

Cross-platform validation and analysis environment for particle physics

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

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

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

Formal verification and testing: An integrated approach to validating Ada programs

NASA Technical Reports Server (NTRS)

Cohen, Norman H.

1986-01-01

An integrated set of tools called a validation environment is proposed to support the validation of Ada programs by a combination of methods. A Modular Ada Validation Environment (MAVEN) is described which proposes a context in which formal verification can fit into the industrial development of Ada software.

Design and validation of an improved graphical user interface with the 'Tool ball'.

PubMed

Lee, Kuo-Wei; Lee, Ying-Chu

2012-01-01

The purpose of this research is introduce the design of an improved graphical user interface (GUI) and verifies the operational efficiency of the proposed interface. Until now, clicking the toolbar with the mouse is the usual way to operate software functions. In our research, we designed an improved graphical user interface - a tool ball that is operated by a mouse wheel to perform software functions. Several experiments are conducted to measure the time needed to operate certain software functions with the traditional combination of "mouse click + tool button" and the proposed integration of "mouse wheel + tool ball". The results indicate that the tool ball design can accelerate the speed of operating software functions, decrease the number of icons on the screen, and enlarge the applications of the mouse wheel. Copyright © 2011 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Software tool for portal dosimetry research.

PubMed

Vial, P; Hunt, P; Greer, P B; Oliver, L; Baldock, C

2008-09-01

This paper describes a software tool developed for research into the use of an electronic portal imaging device (EPID) to verify dose for intensity modulated radiation therapy (IMRT) beams. A portal dose image prediction (PDIP) model that predicts the EPID response to IMRT beams has been implemented into a commercially available treatment planning system (TPS). The software tool described in this work was developed to modify the TPS PDIP model by incorporating correction factors into the predicted EPID image to account for the difference in EPID response to open beam radiation and multileaf collimator (MLC) transmitted radiation. The processes performed by the software tool include; i) read the MLC file and the PDIP from the TPS, ii) calculate the fraction of beam-on time that each point in the IMRT beam is shielded by MLC leaves, iii) interpolate correction factors from look-up tables, iv) create a corrected PDIP image from the product of the original PDIP and the correction factors and write the corrected image to file, v) display, analyse, and export various image datasets. The software tool was developed using the Microsoft Visual Studio.NET framework with the C# compiler. The operation of the software tool was validated. This software provided useful tools for EPID dosimetry research, and it is being utilised and further developed in ongoing EPID dosimetry and IMRT dosimetry projects.

OPTHYLIC: An Optimised Tool for Hybrid Limits Computation

NASA Astrophysics Data System (ADS)

Busato, Emmanuel; Calvet, David; Theveneaux-Pelzer, Timothée

2018-05-01

A software tool, computing observed and expected upper limits on Poissonian process rates using a hybrid frequentist-Bayesian CLs method, is presented. This tool can be used for simple counting experiments where only signal, background and observed yields are provided or for multi-bin experiments where binned distributions of discriminating variables are provided. It allows the combination of several channels and takes into account statistical and systematic uncertainties, as well as correlations of systematic uncertainties between channels. It has been validated against other software tools and analytical calculations, for several realistic cases.

DATALINK. Records Inventory Data Collection Software

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

Cole, B.

1995-03-01

DATALINK was created to provide an easy to use data collection program for records management software products. It provides several useful tools for capturing and validating record index data in the field. It also allows users to easily create a comma delimited, ASCII text file for data export into most records management software products.

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

PubMed

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

2014-03-01

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

Identification of peptide features in precursor spectra using Hardklör and Krönik

PubMed Central

Hoopmann, Michael R.; MacCoss, Michael J.; Moritz, Robert L.

2013-01-01

Hardklör and Krönik are software tools for feature detection and data reduction of high resolution mass spectra. Hardklör is used to reduce peptide isotope distributions to a single monoisotopic mass and charge state, and can deconvolve overlapping peptide isotope distributions. Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). Both software tools contain a simple user interface and can be run from nearly any desktop computer. These tools are freely available from http://proteome.gs.washington.edu/software/hardklor. PMID:22389013

Developing sustainable software solutions for bioinformatics by the “ Butterfly” paradigm

PubMed Central

Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas

2014-01-01

Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (“ Butterfly” paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions. PMID:25383181

A Validation Metrics Framework for Safety-Critical Software-Intensive Systems

DTIC Science & Technology

2009-03-01

so does its definition, tools, and techniques, including means for measuring the validation activity, its outputs, and impact on development...independent of the SDLP. When considering the above SDLPs from the safety engineering team’s perspective, there are also large impacts on the way... impact . Interpretation of any actionable metric data will need to be undertaken in the context of the SDLP. 2. Safety Input The software safety

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.

Development of Advanced Verification and Validation Procedures and Tools for the Certification of Learning Systems in Aerospace Applications

NASA Technical Reports Server (NTRS)

Jacklin, Stephen; Schumann, Johann; Gupta, Pramod; Richard, Michael; Guenther, Kurt; Soares, Fola

2005-01-01

Adaptive control technologies that incorporate learning algorithms have been proposed to enable automatic flight control and vehicle recovery, autonomous flight, and to maintain vehicle performance in the face of unknown, changing, or poorly defined operating environments. In order for adaptive control systems to be used in safety-critical aerospace applications, they must be proven to be highly safe and reliable. Rigorous methods for adaptive software verification and validation must be developed to ensure that control system software failures will not occur. Of central importance in this regard is the need to establish reliable methods that guarantee convergent learning, rapid convergence (learning) rate, and algorithm stability. This paper presents the major problems of adaptive control systems that use learning to improve performance. The paper then presents the major procedures and tools presently developed or currently being developed to enable the verification, validation, and ultimate certification of these adaptive control systems. These technologies include the application of automated program analysis methods, techniques to improve the learning process, analytical methods to verify stability, methods to automatically synthesize code, simulation and test methods, and tools to provide on-line software assurance.

An overview of 3D software visualization.

PubMed

Teyseyre, Alfredo R; Campo, Marcelo R

2009-01-01

Software visualization studies techniques and methods for graphically representing different aspects of software. Its main goal is to enhance, simplify and clarify the mental representation a software engineer has of a computer system. During many years, visualization in 2D space has been actively studied, but in the last decade, researchers have begun to explore new 3D representations for visualizing software. In this article, we present an overview of current research in the area, describing several major aspects like: visual representations, interaction issues, evaluation methods and development tools. We also perform a survey of some representative tools to support different tasks, i.e., software maintenance and comprehension, requirements validation and algorithm animation for educational purposes, among others. Finally, we conclude identifying future research directions.

Global Precipitation Mission Visualization Tool

NASA Technical Reports Server (NTRS)

Schwaller, Mathew

2011-01-01

The Global Precipitation Mission (GPM) software provides graphic visualization tools that enable easy comparison of ground- and space-based radar observations. It was initially designed to compare ground radar reflectivity from operational, ground-based, S- and C-band meteorological radars with comparable measurements from the Tropical Rainfall Measuring Mission (TRMM) satellite's precipitation radar instrument. This design is also applicable to other groundbased and space-based radars, and allows both ground- and space-based radar data to be compared for validation purposes. The tool creates an operational system that routinely performs several steps. It ingests satellite radar data (precipitation radar data from TRMM) and groundbased meteorological radar data from a number of sources. Principally, the ground radar data comes from national networks of weather radars (see figure). The data ingested by the visualization tool must conform to the data formats used in GPM Validation Network Geometry-matched data product generation. The software also performs match-ups of the radar volume data for the ground- and space-based data, as well as statistical and graphical analysis (including two-dimensional graphical displays) on the match-up data. The visualization tool software is written in IDL, and can be operated either in the IDL development environment or as a stand-alone executable function.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

PubMed Central

Cai, Wenxuan; Guner, Huseyin; Gregorich, Zachery R.; Chen, Albert J.; Ayaz-Guner, Serife; Peng, Ying; Valeja, Santosh G.; Liu, Xiaowen; Ge, Ying

2016-01-01

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics. PMID:26598644

Campus Energy Model for Control and Performance Validation

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

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

Software risk management through independent verification and validation

NASA Technical Reports Server (NTRS)

Callahan, John R.; Zhou, Tong C.; Wood, Ralph

1995-01-01

Software project managers need tools to estimate and track project goals in a continuous fashion before, during, and after development of a system. In addition, they need an ability to compare the current project status with past project profiles to validate management intuition, identify problems, and then direct appropriate resources to the sources of problems. This paper describes a measurement-based approach to calculating the risk inherent in meeting project goals that leverages past project metrics and existing estimation and tracking models. We introduce the IV&V Goal/Questions/Metrics model, explain its use in the software development life cycle, and describe our attempts to validate the model through the reverse engineering of existing projects.

MVP-CA Methodology for the Expert System Advocate's Advisor (ESAA)

DOT National Transportation Integrated Search

1997-11-01

The Multi-Viewpoint Clustering Analysis (MVP-CA) tool is a semi-automated tool to provide a valuable aid for comprehension, verification, validation, maintenance, integration, and evolution of complex knowledge-based software systems. In this report,...

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Software Maintenance Exercises for a Software Engineering Project Course

DTIC Science & Technology

1989-02-01

what is program style and how can it be measured? Program style has been defined as a "followed convention with respect to punctuation, capitalization ...convention with respect to punctuation, capitalization , and typographic arrangement and display." *DASC is a software tool that takes a syntactically...Specilleauons: A Frarnewo* * CM-12 Software Metrws CM- 13 Introduction to Softwarell Verification and Validation CM-14 Intelectual Property Protection for

Stability analysis using SDSA tool

NASA Astrophysics Data System (ADS)

Goetzendorf-Grabowski, Tomasz; Mieszalski, Dawid; Marcinkiewicz, Ewa

2011-11-01

The SDSA (Simulation and Dynamic Stability Analysis) application is presented as a tool for analysing the dynamic characteristics of the aircraft just in the conceptual design stage. SDSA is part of the CEASIOM (Computerized Environment for Aircraft Synthesis and Integrated Optimization Methods) software environment which was developed within the SimSAC (Simulating Aircraft Stability And Control Characteristics for Use in Conceptual Design) project, funded by the European Commission 6th Framework Program. SDSA can also be used as stand alone software, and integrated with other design and optimisation systems using software wrappers. This paper focuses on the main functionalities of SDSA and presents both computational and free flight experimental results to compare and validate the presented software. Two aircraft are considered, the EADS Ranger 2000 and the Warsaw University designed PW-6 glider. For the two cases considered here the SDSA software is shown to be an excellent tool for predicting dynamic characteristics of an aircraft.

Verification and Validation in a Rapid Software Development Process

NASA Technical Reports Server (NTRS)

Callahan, John R.; Easterbrook, Steve M.

1997-01-01

The high cost of software production is driving development organizations to adopt more automated design and analysis methods such as rapid prototyping, computer-aided software engineering (CASE) tools, and high-level code generators. Even developers of safety-critical software system have adopted many of these new methods while striving to achieve high levels Of quality and reliability. While these new methods may enhance productivity and quality in many cases, we examine some of the risks involved in the use of new methods in safety-critical contexts. We examine a case study involving the use of a CASE tool that automatically generates code from high-level system designs. We show that while high-level testing on the system structure is highly desirable, significant risks exist in the automatically generated code and in re-validating releases of the generated code after subsequent design changes. We identify these risks and suggest process improvements that retain the advantages of rapid, automated development methods within the quality and reliability contexts of safety-critical projects.

Validation of the Mobile Information Software Evaluation Tool (MISET) With Nursing Students.

PubMed

Secco, M Loretta; Furlong, Karen E; Doyle, Glynda; Bailey, Judy

2016-07-01

This study evaluated the Mobile Information Software Evaluation Tool (MISET) with a sample of Canadian undergraduate nursing students (N = 240). Psychometric analyses determined how well the MISET assessed the extent that nursing students find mobile device-based information resources useful and supportive of learning in the clinical and classroom settings. The MISET has a valid three-factor structure with high explained variance (74.7%). Internal consistency reliabilities were high for the MISET total (.90) and three subscales: Usefulness/Helpfulness, Information Literacy Support, and Use of Evidence-Based Sources (.87 to .94). Construct validity evidence included significantly higher mean total MISET, Helpfulness/Usefulness, and Information Literacy Support scores for senior students and those with higher computer competence. The MISET is a promising tool to evaluate mobile information technologies and information literacy support; however, longitudinal assessment of changes in scores over time would determine scale sensitivity and responsiveness. [J Nurs Educ. 2016;55(7):385-390.]. Copyright 2016, SLACK Incorporated.

Open source cardiology electronic health record development for DIGICARDIAC implementation

NASA Astrophysics Data System (ADS)

Dugarte, Nelson; Medina, Rubén.; Huiracocha, Lourdes; Rojas, Rubén.

2015-12-01

This article presents the development of a Cardiology Electronic Health Record (CEHR) system. Software consists of a structured algorithm designed under Health Level-7 (HL7) international standards. Novelty of the system is the integration of high resolution ECG (HRECG) signal acquisition and processing tools, patient information management tools and telecardiology tools. Acquisition tools are for management and control of the DIGICARDIAC electrocardiograph functions. Processing tools allow management of HRECG signal analysis searching for indicative patterns of cardiovascular pathologies. Telecardiology tools incorporation allows system communication with other health care centers decreasing access time to the patient information. CEHR system was completely developed using open source software. Preliminary results of process validation showed the system efficiency.

Computer applications making rapid advances in high throughput microbial proteomics (HTMP).

PubMed

Anandkumar, Balakrishna; Haga, Steve W; Wu, Hui-Fen

2014-02-01

The last few decades have seen the rise of widely-available proteomics tools. From new data acquisition devices, such as MALDI-MS and 2DE to new database searching softwares, these new products have paved the way for high throughput microbial proteomics (HTMP). These tools are enabling researchers to gain new insights into microbial metabolism, and are opening up new areas of study, such as protein-protein interactions (interactomics) discovery. Computer software is a key part of these emerging fields. This current review considers: 1) software tools for identifying the proteome, such as MASCOT or PDQuest, 2) online databases of proteomes, such as SWISS-PROT, Proteome Web, or the Proteomics Facility of the Pathogen Functional Genomics Resource Center, and 3) software tools for applying proteomic data, such as PSI-BLAST or VESPA. These tools allow for research in network biology, protein identification, functional annotation, target identification/validation, protein expression, protein structural analysis, metabolic pathway engineering and drug discovery.

Verification and Validation of the Malicious Activity Simulation Tool (MAST) for Network Administrator Training and Evaluation

DTIC Science & Technology

2012-03-01

to sell fake antivirus software ; Gammima, which was used to steal gaming login information; and Zeus, which was used to steal banking information...13 3. Viruses ......................................14 C. PROOF OF CONCEPT OF SOFTWARE TRAINING USING MALWARE MIMICS...33 2. Software .....................................34 3. COMPOSE CG-71 Virtual Machines ...............37 a. Integrated Shipboard Network System

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Design of a Syntax Validation Tool for Requirements Analysis Using Structured Analysis and Design Technique (SADT)

DTIC Science & Technology

1988-09-01

analysis phase of the software life cycle (16:1-1). While editing a SADT diagram, the tool should be able to check whether or not structured analysis...diag-ams are valid for the SADT’s syntax, produce error messages, do error recovery, and perform editing suggestions. Thus, this tool must have the...directed editors are editors which use the syn- tax of the programming language while editing a program. While text editors treat programs as text, syntax

Static and Dynamic Verification of Critical Software for Space Applications

NASA Astrophysics Data System (ADS)

Moreira, F.; Maia, R.; Costa, D.; Duro, N.; Rodríguez-Dapena, P.; Hjortnaes, K.

Space technology is no longer used only for much specialised research activities or for sophisticated manned space missions. Modern society relies more and more on space technology and applications for every day activities. Worldwide telecommunications, Earth observation, navigation and remote sensing are only a few examples of space applications on which we rely daily. The European driven global navigation system Galileo and its associated applications, e.g. air traffic management, vessel and car navigation, will significantly expand the already stringent safety requirements for space based applications Apart from their usefulness and practical applications, every single piece of onboard software deployed into the space represents an enormous investment. With a long lifetime operation and being extremely difficult to maintain and upgrade, at least when comparing with "mainstream" software development, the importance of ensuring their correctness before deployment is immense. Verification &Validation techniques and technologies have a key role in ensuring that the onboard software is correct and error free, or at least free from errors that can potentially lead to catastrophic failures. Many RAMS techniques including both static criticality analysis and dynamic verification techniques have been used as a means to verify and validate critical software and to ensure its correctness. But, traditionally, these have been isolated applied. One of the main reasons is the immaturity of this field in what concerns to its application to the increasing software product(s) within space systems. This paper presents an innovative way of combining both static and dynamic techniques exploiting their synergy and complementarity for software fault removal. The methodology proposed is based on the combination of Software FMEA and FTA with Fault-injection techniques. The case study herein described is implemented with support from two tools: The SoftCare tool for the SFMEA and SFTA, and the Xception tool for fault-injection. Keywords: Verification &Validation, RAMS, Onboard software, SFMEA, STA, Fault-injection 1 This work is being performed under the project STADY Applied Static And Dynamic Verification Of Critical Software, ESA/ESTEC Contract Nr. 15751/02/NL/LvH.

Simulation validation and management

NASA Astrophysics Data System (ADS)

Illgen, John D.

1995-06-01

Illgen Simulation Technologies, Inc., has been working interactive verification and validation programs for the past six years. As a result, they have evolved a methodology that has been adopted and successfully implemented by a number of different verification and validation programs. This methodology employs a unique case of computer-assisted software engineering (CASE) tools to reverse engineer source code and produce analytical outputs (flow charts and tables) that aid the engineer/analyst in the verification and validation process. We have found that the use of CASE tools saves time,which equate to improvements in both schedule and cost. This paper will describe the ISTI-developed methodology and how CASe tools are used in its support. Case studies will be discussed.

Adaptation and development of software simulation methodologies for cardiovascular engineering: present and future challenges from an end-user perspective

PubMed Central

Díaz-Zuccarini, V.; Narracott, A.J.; Burriesci, G.; Zervides, C.; Rafiroiu, D.; Jones, D.; Hose, D.R.; Lawford, P.V.

2009-01-01

This paper describes the use of diverse software tools in cardiovascular applications. These tools were primarily developed in the field of engineering and the applications presented push the boundaries of the software to address events related to venous and arterial valve closure, exploration of dynamic boundary conditions or the inclusion of multi-scale boundary conditions from protein to organ levels. The future of cardiovascular research and the challenges that modellers and clinicians face from validation to clinical uptake are discussed from an end-user perspective. PMID:19487202

Adaptation and development of software simulation methodologies for cardiovascular engineering: present and future challenges from an end-user perspective.

PubMed

Díaz-Zuccarini, V; Narracott, A J; Burriesci, G; Zervides, C; Rafiroiu, D; Jones, D; Hose, D R; Lawford, P V

2009-07-13

This paper describes the use of diverse software tools in cardiovascular applications. These tools were primarily developed in the field of engineering and the applications presented push the boundaries of the software to address events related to venous and arterial valve closure, exploration of dynamic boundary conditions or the inclusion of multi-scale boundary conditions from protein to organ levels. The future of cardiovascular research and the challenges that modellers and clinicians face from validation to clinical uptake are discussed from an end-user perspective.

Improvement of Simulation Method in Validation of Software of the Coordinate Measuring Systems

NASA Astrophysics Data System (ADS)

Nieciąg, Halina

2015-10-01

Software is used in order to accomplish various tasks at each stage of the functioning of modern measuring systems. Before metrological confirmation of measuring equipment, the system has to be validated. This paper discusses the method for conducting validation studies of a fragment of software to calculate the values of measurands. Due to the number and nature of the variables affecting the coordinate measurement results and the complex character and multi-dimensionality of measurands, the study used the Monte Carlo method of numerical simulation. The article presents an attempt of possible improvement of results obtained by classic Monte Carlo tools. The algorithm LHS (Latin Hypercube Sampling) was implemented as alternative to the simple sampling schema of classic algorithm.

Quantitative fluorescence angiography for neurosurgical interventions.

PubMed

Weichelt, Claudia; Duscha, Philipp; Steinmeier, Ralf; Meyer, Tobias; Kuß, Julia; Cimalla, Peter; Kirsch, Matthias; Sobottka, Stephan B; Koch, Edmund; Schackert, Gabriele; Morgenstern, Ute

2013-06-01

Present methods for quantitative measurement of cerebral perfusion during neurosurgical operations require additional technology for measurement, data acquisition, and processing. This study used conventional fluorescence video angiography--as an established method to visualize blood flow in brain vessels--enhanced by a quantifying perfusion software tool. For these purposes, the fluorescence dye indocyanine green is given intravenously, and after activation by a near-infrared light source the fluorescence signal is recorded. Video data are analyzed by software algorithms to allow quantification of the blood flow. Additionally, perfusion is measured intraoperatively by a reference system. Furthermore, comparing reference measurements using a flow phantom were performed to verify the quantitative blood flow results of the software and to validate the software algorithm. Analysis of intraoperative video data provides characteristic biological parameters. These parameters were implemented in the special flow phantom for experimental validation of the developed software algorithms. Furthermore, various factors that influence the determination of perfusion parameters were analyzed by means of mathematical simulation. Comparing patient measurement, phantom experiment, and computer simulation under certain conditions (variable frame rate, vessel diameter, etc.), the results of the software algorithms are within the range of parameter accuracy of the reference methods. Therefore, the software algorithm for calculating cortical perfusion parameters from video data presents a helpful intraoperative tool without complex additional measurement technology.

Production of Reliable Flight Crucial Software: Validation Methods Research for Fault Tolerant Avionics and Control Systems Sub-Working Group Meeting

NASA Technical Reports Server (NTRS)

Dunham, J. R. (Editor); Knight, J. C. (Editor)

1982-01-01

The state of the art in the production of crucial software for flight control applications was addressed. The association between reliability metrics and software is considered. Thirteen software development projects are discussed. A short term need for research in the areas of tool development and software fault tolerance was indicated. For the long term, research in format verification or proof methods was recommended. Formal specification and software reliability modeling, were recommended as topics for both short and long term research.

A survey of ground operations tools developed to simulate the pointing of space telescopes and the design for WISE

NASA Technical Reports Server (NTRS)

Fabinsky, Beth

2006-01-01

WISE, the Wide Field Infrared Survey Explorer, is scheduled for launch in June 2010. The mission operations system for WISE requires a software modeling tool to help plan, integrate and simulate all spacecraft pointing and verify that no attitude constraints are violated. In the course of developing the requirements for this tool, an investigation was conducted into the design of similar tools for other space-based telescopes. This paper summarizes the ground software and processes used to plan and validate pointing for a selection of space telescopes; with this information as background, the design for WISE is presented.

DATALINK: Records inventory data collection software. User`s guide

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

Cole, B.A.

1995-03-01

DATALINK was created to provide an easy to use data collection program for records management software products. It provides several useful tools for capturing and validating record index data in the field. It also allows users to easily create a comma delimited, ASCII text file for data export into most records management software products. It runs on virtually any computer us MS-DOS.

TEAMS Model Analyzer

NASA Technical Reports Server (NTRS)

Tijidjian, Raffi P.

2010-01-01

The TEAMS model analyzer is a supporting tool developed to work with models created with TEAMS (Testability, Engineering, and Maintenance System), which was developed by QSI. In an effort to reduce the time spent in the manual process that each TEAMS modeler must perform in the preparation of reporting for model reviews, a new tool has been developed as an aid to models developed in TEAMS. The software allows for the viewing, reporting, and checking of TEAMS models that are checked into the TEAMS model database. The software allows the user to selectively model in a hierarchical tree outline view that displays the components, failure modes, and ports. The reporting features allow the user to quickly gather statistics about the model, and generate an input/output report pertaining to all of the components. Rules can be automatically validated against the model, with a report generated containing resulting inconsistencies. In addition to reducing manual effort, this software also provides an automated process framework for the Verification and Validation (V&V) effort that will follow development of these models. The aid of such an automated tool would have a significant impact on the V&V process.

MS Data Miner: a web-based software tool to analyze, compare, and share mass spectrometry protein identifications.

PubMed

Dyrlund, Thomas F; Poulsen, Ebbe T; Scavenius, Carsten; Sanggaard, Kristian W; Enghild, Jan J

2012-09-01

Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science), and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a Gene Ontology term analysis function and a tool for generating comparative Excel data reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Software reliability through fault-avoidance and fault-tolerance

NASA Technical Reports Server (NTRS)

Vouk, Mladen A.; Mcallister, David F.

1993-01-01

Strategies and tools for the testing, risk assessment and risk control of dependable software-based systems were developed. Part of this project consists of studies to enable the transfer of technology to industry, for example the risk management techniques for safety-concious systems. Theoretical investigations of Boolean and Relational Operator (BRO) testing strategy were conducted for condition-based testing. The Basic Graph Generation and Analysis tool (BGG) was extended to fully incorporate several variants of the BRO metric. Single- and multi-phase risk, coverage and time-based models are being developed to provide additional theoretical and empirical basis for estimation of the reliability and availability of large, highly dependable software. A model for software process and risk management was developed. The use of cause-effect graphing for software specification and validation was investigated. Lastly, advanced software fault-tolerance models were studied to provide alternatives and improvements in situations where simple software fault-tolerance strategies break down.

Digital-flight-control-system software written in automated-engineering-design language: A user's guide of verification and validation tools

NASA Technical Reports Server (NTRS)

Saito, Jim

1987-01-01

The user guide of verification and validation (V&V) tools for the Automated Engineering Design (AED) language is specifically written to update the information found in several documents pertaining to the automated verification of flight software tools. The intent is to provide, in one document, all the information necessary to adequately prepare a run to use the AED V&V tools. No attempt is made to discuss the FORTRAN V&V tools since they were not updated and are not currently active. Additionally, the current descriptions of the AED V&V tools are contained and provides information to augment the NASA TM 84276. The AED V&V tools are accessed from the digital flight control systems verification laboratory (DFCSVL) via a PDP-11/60 digital computer. The AED V&V tool interface handlers on the PDP-11/60 generate a Univac run stream which is transmitted to the Univac via a Remote Job Entry (RJE) link. Job execution takes place on the Univac 1100 and the job output is transmitted back to the DFCSVL and stored as a PDP-11/60 printfile.

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

NASA Astrophysics Data System (ADS)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical models.

Validation of a Magnetic Resonance Imaging-based Auto-contouring Software Tool for Gross Tumour Delineation in Head and Neck Cancer Radiotherapy Planning.

PubMed

Doshi, T; Wilson, C; Paterson, C; Lamb, C; James, A; MacKenzie, K; Soraghan, J; Petropoulakis, L; Di Caterina, G; Grose, D

2017-01-01

To carry out statistical validation of a newly developed magnetic resonance imaging (MRI) auto-contouring software tool for gross tumour volume (GTV) delineation in head and neck tumours to assist in radiotherapy planning. Axial MRI baseline scans were obtained for 10 oropharyngeal and laryngeal cancer patients. GTV was present on 102 axial slices and auto-contoured using the modified fuzzy c-means clustering integrated with the level set method (FCLSM). Peer-reviewed (C-gold) manual contours were used as the reference standard to validate auto-contoured GTVs (C-auto) and mean manual contours (C-manual) from two expert clinicians (C1 and C2). Multiple geometric metrics, including the Dice similarity coefficient (DSC), were used for quantitative validation. A DSC≥0.7 was deemed acceptable. Inter- and intra-variabilities among the manual contours were also validated. The two-dimensional contours were then reconstructed in three dimensions for GTV volume calculation, comparison and three-dimensional visualisation. The mean DSC between C-gold and C-auto was 0.79. The mean DSC between C-gold and C-manual was 0.79 and that between C1 and C2 was 0.80. The average time for GTV auto-contouring per patient was 8 min (range 6-13 min; mean 45 s per axial slice) compared with 15 min (range 6-23 min; mean 88 s per axial slice) for C1. The average volume concordance between C-gold and C-auto volumes was 86.51% compared with 74.16% between C-gold and C-manual. The average volume concordance between C1 and C2 volumes was 86.82%. This newly designed MRI-based auto-contouring software tool shows initial acceptable results in GTV delineation of oropharyngeal and laryngeal tumours using FCLSM. This auto-contouring software tool may help reduce inter- and intra-variability and can assist clinical oncologists with time-consuming, complex radiotherapy planning. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Review of Software Tools for Design and Analysis of Large scale MRM Proteomic Datasets

PubMed Central

Colangelo, Christopher M.; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

2013-01-01

Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. PMID:23702368

Reliability and validity assessment of gastrointestinal dystemperaments questionnaire: a novel scale in Persian traditional medicine

PubMed Central

Hoseinzadeh, Hamidreza; Taghipour, Ali; Yousefi, Mahdi

2018-01-01

Background Development of a questionnaire based on the resources of Persian traditional medicine seems necessary. One of the problems faced by practitioners of traditional medicine is the different opinions regarding the diagnosis of general temperament or temperament of member. One of the reasons is the lack of validity tools, and it has led to difficulties in training the student of traditional medicine and the treatment of patients. The differences in the detection methods, have given rise to several treatment methods. Objective The present study aimed to develop a questionnaire and standard software for diagnosis of gastrointestinal dystemperaments. Methods The present research is a tool developing study which included 8 stages of developing the items, determining the statements based on items, assessing the face validity, assessing the content validity, assessing the reliability, rating the items, developing a software for calculation of the total score of the questionnaire named GDS v.1.1, and evaluating the concurrent validity using statistical tests including Cronbach’s alpha coefficient, Cohen’s kappa coefficient. Results Based on the results, 112 notes including 62 symptoms were extracted from resources, and 58 items were obtained from in-person interview sessions with a panel of experts. A statement was selected for each item and, after merging a number of statements, a total of 49 statements were finally obtained. By calculating the score of statement impact and determining the content validity, respectively, 6 and 10 other items were removed from the list of statements. Standardized Cronbach’s alpha for this questionnaire was obtained 0.795 and its concurrent validity was equal to 0.8. Conclusion A quantitative tool was developed for diagnosis and examination of gastrointestinal dystemperaments. The developed questionnaire is adequately reliable and valid for this purpose. In addition, the software can be used for clinical diagnosis. PMID:29629060

PT-SAFE: a software tool for development and annunciation of medical audible alarms.

PubMed

Bennett, Christopher L; McNeer, Richard R

2012-03-01

Recent reports by The Joint Commission as well as the Anesthesia Patient Safety Foundation have indicated that medical audible alarm effectiveness needs to be improved. Several recent studies have explored various approaches to improving the audible alarms, motivating the authors to develop real-time software capable of comparing such alarms. We sought to devise software that would allow for the development of a variety of audible alarm designs that could also integrate into existing operating room equipment configurations. The software is meant to be used as a tool for alarm researchers to quickly evaluate novel alarm designs. A software tool was developed for the purpose of creating and annunciating audible alarms. The alarms consisted of annunciators that were mapped to vital sign data received from a patient monitor. An object-oriented approach to software design was used to create a tool that is flexible and modular at run-time, can annunciate wave-files from disk, and can be programmed with MATLAB by the user to create custom alarm algorithms. The software was tested in a simulated operating room to measure technical performance and to validate the time-to-annunciation against existing equipment alarms. The software tool showed efficacy in a simulated operating room environment by providing alarm annunciation in response to physiologic and ventilator signals generated by a human patient simulator, on average 6.2 seconds faster than existing equipment alarms. Performance analysis showed that the software was capable of supporting up to 15 audible alarms on a mid-grade laptop computer before audio dropouts occurred. These results suggest that this software tool provides a foundation for rapidly staging multiple audible alarm sets from the laboratory to a simulation environment for the purpose of evaluating novel alarm designs, thus producing valuable findings for medical audible alarm standardization.

Knowledge-based assistance in costing the space station DMS

NASA Technical Reports Server (NTRS)

Henson, Troy; Rone, Kyle

1988-01-01

The Software Cost Engineering (SCE) methodology developed over the last two decades at IBM Systems Integration Division (SID) in Houston is utilized to cost the NASA Space Station Data Management System (DMS). An ongoing project to capture this methodology, which is built on a foundation of experiences and lessons learned, has resulted in the development of an internal-use-only, PC-based prototype that integrates algorithmic tools with knowledge-based decision support assistants. This prototype Software Cost Engineering Automation Tool (SCEAT) is being employed to assist in the DMS costing exercises. At the same time, DMS costing serves as a forcing function and provides a platform for the continuing, iterative development, calibration, and validation and verification of SCEAT. The data that forms the cost engineering database is derived from more than 15 years of development of NASA Space Shuttle software, ranging from low criticality, low complexity support tools to highly complex and highly critical onboard software.

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

PubMed

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

2015-03-01

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

Software for Automated Testing of Mission-Control Displays

NASA Technical Reports Server (NTRS)

OHagan, Brian

2004-01-01

MCC Display Cert Tool is a set of software tools for automated testing of computerterminal displays in spacecraft mission-control centers, including those of the space shuttle and the International Space Station. This software makes it possible to perform tests that are more thorough, take less time, and are less likely to lead to erroneous results, relative to tests performed manually. This software enables comparison of two sets of displays to report command and telemetry differences, generates test scripts for verifying telemetry and commands, and generates a documentary record containing display information, including version and corrective-maintenance data. At the time of reporting the information for this article, work was continuing to add a capability for validation of display parameters against a reconfiguration file.

Simulator validation results and proposed reporting format from flight testing a software model of a complex, high-performance airplane.

DOT National Transportation Integrated Search

2008-01-01

Computer simulations are often used in aviation studies. These simulation tools may require complex, high-fidelity aircraft models. Since many of the flight models used are third-party developed products, independent validation is desired prior to im...

LATUX: An Iterative Workflow for Designing, Validating, and Deploying Learning Analytics Visualizations

ERIC Educational Resources Information Center

Martinez-Maldonado, Roberto; Pardo, Abelardo; Mirriahi, Negin; Yacef, Kalina; Kay, Judy; Clayphan, Andrew

2015-01-01

Designing, validating, and deploying learning analytics tools for instructors or students is a challenge that requires techniques and methods from different disciplines, such as software engineering, human-computer interaction, computer graphics, educational design, and psychology. Whilst each has established its own design methodologies, we now…

Validation of the PCN Concept: Mobility, Traffic Flow Confidentiality and Protection Against Directed Attacks

DTIC Science & Technology

2010-11-01

peer, racoon (IKE-daemon) will start authenticating using certificates. After a successful authentication, IPSec security associations will be set up...colour had credentials from one CA. Racoon and ipsec-tools are open-source software, implementing IKE and IPSec. Validation of the PCN Concept; Mobility

A Software Tool for Integrated Optical Design Analysis

NASA Technical Reports Server (NTRS)

Moore, Jim; Troy, Ed; DePlachett, Charles; Montgomery, Edward (Technical Monitor)

2001-01-01

Design of large precision optical systems requires multi-disciplinary analysis, modeling, and design. Thermal, structural and optical characteristics of the hardware must be accurately understood in order to design a system capable of accomplishing the performance requirements. The interactions between each of the disciplines become stronger as systems are designed lighter weight for space applications. This coupling dictates a concurrent engineering design approach. In the past, integrated modeling tools have been developed that attempt to integrate all of the complex analysis within the framework of a single model. This often results in modeling simplifications and it requires engineering specialist to learn new applications. The software described in this presentation addresses the concurrent engineering task using a different approach. The software tool, Integrated Optical Design Analysis (IODA), uses data fusion technology to enable a cross discipline team of engineering experts to concurrently design an optical system using their standard validated engineering design tools.

LACO-Wiki: A land cover validation tool and a new, innovative teaching resource for remote sensing and the geosciences

NASA Astrophysics Data System (ADS)

See, Linda; Perger, Christoph; Dresel, Christopher; Hofer, Martin; Weichselbaum, Juergen; Mondel, Thomas; Steffen, Fritz

2016-04-01

The validation of land cover products is an important step in the workflow of generating a land cover map from remotely-sensed imagery. Many students of remote sensing will be given exercises on classifying a land cover map followed by the validation process. Many algorithms exist for classification, embedded within proprietary image processing software or increasingly as open source tools. However, there is little standardization for land cover validation, nor a set of open tools available for implementing this process. The LACO-Wiki tool was developed as a way of filling this gap, bringing together standardized land cover validation methods and workflows into a single portal. This includes the storage and management of land cover maps and validation data; step-by-step instructions to guide users through the validation process; sound sampling designs; an easy-to-use environment for validation sample interpretation; and the generation of accuracy reports based on the validation process. The tool was developed for a range of users including producers of land cover maps, researchers, teachers and students. The use of such a tool could be embedded within the curriculum of remote sensing courses at a university level but is simple enough for use by students aged 13-18. A beta version of the tool is available for testing at: http://www.laco-wiki.net.

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

The prediction of the number of clusters in a dataset, in particular microarrays, is a fundamental task in biological data analysis, usually performed via validation measures. Unfortunately, it has received very little attention and in fact there is a growing need for software tools/libraries dedicated to it. Here we present ValWorkBench, a software library consisting of eleven well known validation measures, together with novel heuristic approximations for some of them. The main objective of this paper is to provide the interested researcher with the full software documentation of an open source cluster validation platform having the main features of being easily extendible in a homogeneous way and of offering software components that can be readily re-used. Consequently, the focus of the presentation is on the architecture of the library, since it provides an essential map that can be used to access the full software documentation, which is available at the supplementary material website [1]. The mentioned main features of ValWorkBench are also discussed and exemplified, with emphasis on software abstraction design and re-usability. A comparison with existing cluster validation software libraries, mainly in terms of the mentioned features, is also offered. It suggests that ValWorkBench is a much needed contribution to the microarray software development/algorithm engineering community. For completeness, it is important to mention that previous accurate algorithmic experimental analysis of the relative merits of each of the implemented measures [19,23,25], carried out specifically on microarray data, gives useful insights on the effectiveness of ValWorkBench for cluster validation to researchers in the microarray community interested in its use for the mentioned task. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Experimental Evaluation of Verification and Validation Tools on Martian Rover Software

NASA Technical Reports Server (NTRS)

Brat, Guillaume; Giannakopoulou, Dimitra; Goldberg, Allen; Havelund, Klaus; Lowry, Mike; Pasareanu, Corina; Venet, Arnaud; Visser, Willem

2003-01-01

To achieve its science objectives in deep space exploration, NASA has a need for science platform vehicles to autonomously make control decisions in a time frame that excludes intervention from Earth-based controllers. Round-trip light-time is one significant factor motivating autonomy capability, another factor is the need to reduce ground support operations cost. An unsolved problem potentially impeding the adoption of autonomy capability is the verification and validation of such software systems, which exhibit far more behaviors (and hence distinct execution paths in the software) than is typical in current deepspace platforms. Hence the need for a study to benchmark advanced Verification and Validation (V&V) tools on representative autonomy software. The objective of the study was to access the maturity of different technologies, to provide data indicative of potential synergies between them, and to identify gaps in the technologies with respect to the challenge of autonomy V&V. The study consisted of two parts: first, a set of relatively independent case studies of different tools on the same autonomy code, second a carefully controlled experiment with human participants on a subset of these technologies. This paper describes the second part of the study. Overall, nearly four hundred hours of data on human use of three different advanced V&V tools were accumulated, with a control group that used conventional testing methods. The experiment simulated four independent V&V teams debugging three successive versions of an executive controller for a Martian Rover. Defects were carefully seeded into the three versions based on a profile of defects from CVS logs that occurred in the actual development of the executive controller. The rest of the document is structured a s follows. In section 2 and 3, we respectively describe the tools used in the study and the rover software that was analyzed. In section 4 the methodology for the experiment is described; this includes the code preparation, seeding of defects, participant training and experimental setup. Next we give a qualitative overview of how the experiment went from the point of view of each technology; model checking (section 5), static analysis (section 6), runtime analysis (section 7) and testing (section 8). The find section gives some preliminary quantitative results on how the tools compared.

Applicability of SREM to the Verification of Management Information System Software Requirements. Volume I.

DTIC Science & Technology

1981-04-30

However, SREM was not designed to harmonize these kinds of problems. Rather, it is a tool to investigate the logic of the processing specified in the... design . Supoorting programs were also conducted to perform basic research into such areas as software reliability, static and dynamic validation techniques...development. 0 Maintain requirements development independent of the target machine and the eventual software design . 0. Allow for easy response to

Structure and software tools of AIDA.

PubMed

Duisterhout, J S; Franken, B; Witte, F

1987-01-01

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write implementation-specific code which can be selected and loaded by a special source loader, being part of the AIDA software. This feature is also accessible for maintaining software on different sites and on different installations.

Translating expert system rules into Ada code with validation and verification

NASA Technical Reports Server (NTRS)

Becker, Lee; Duckworth, R. James; Green, Peter; Michalson, Bill; Gosselin, Dave; Nainani, Krishan; Pease, Adam

1991-01-01

The purpose of this ongoing research and development program is to develop software tools which enable the rapid development, upgrading, and maintenance of embedded real-time artificial intelligence systems. The goals of this phase of the research were to investigate the feasibility of developing software tools which automatically translate expert system rules into Ada code and develop methods for performing validation and verification testing of the resultant expert system. A prototype system was demonstrated which automatically translated rules from an Air Force expert system was demonstrated which detected errors in the execution of the resultant system. The method and prototype tools for converting AI representations into Ada code by converting the rules into Ada code modules and then linking them with an Activation Framework based run-time environment to form an executable load module are discussed. This method is based upon the use of Evidence Flow Graphs which are a data flow representation for intelligent systems. The development of prototype test generation and evaluation software which was used to test the resultant code is discussed. This testing was performed automatically using Monte-Carlo techniques based upon a constraint based description of the required performance for the system.

Review of software tools for design and analysis of large scale MRM proteomic datasets.

PubMed

Colangelo, Christopher M; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

2013-06-15

Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Quantifying Uncertainties in Navigation and Orbit Propagation Analyses

NASA Technical Reports Server (NTRS)

Krieger, Andrew W.; Welch, Bryan W.

2017-01-01

A tool used to calculate dilution of precision (DOP) was created in order to assist the Space Communications and Navigation (SCaN) program to analyze current and future user missions. The SCaN Center for Engineering, Networks, Integration, and Communication (SCENIC) is developing a new user interface (UI) to augment and replace the capabilities of currently used commercial software, such as Systems Tool Kit (STK). The DOP tool will be integrated in the SCENIC UI and will be used to analyze the accuracy of navigation solutions. This tool was developed using MATLAB and free and open-source tools to save cost and to use already existing orbital software libraries. GPS DOP data was collected and used for validation purposes. The similarities between the DOP tool results and GPS data show that the DOP tool is performing correctly. Additional improvements can be made in the DOP tool to improve its accuracy and performance in analyzing navigation solutions.

Building Diagnostic Market Deployment - Final Report

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

Katipamula, S.; Gayeski, N.

2012-04-30

Operational faults are pervasive across the commercial buildings sector, wasting energy and increasing energy costs by up to about 30% (Mills 2009, Liu et al. 2003, Claridge et al. 2000, Katipamula and Brambley 2008, and Brambley and Katipamula 2009). Automated fault detection and diagnostic (AFDD) tools provide capabilities essential for detecting and correcting these problems and eliminating the associated energy waste and costs. The U.S. Department of Energy's (DOE) Building Technology Program (BTP) has previously invested in developing and testing of such diagnostic tools for whole-building (and major system) energy use, air handlers, chillers, cooling towers, chilled-water distribution systems, andmore » boilers. These diagnostic processes can be used to make the commercial buildings more energy efficient. The work described in this report was done as part of a Cooperative Research and Development Agreement (CRADA) between the U.S. Department of Energy's Pacific Northwest National Laboratory (PNNL) and KGS Building LLC (KGS). PNNL and KGS both believe that the widespread adoption of AFDD tools will result in significant reduction to energy and peak energy consumption. The report provides an introduction and summary of the various tasks performed under the CRADA. The CRADA project had three major focus areas: (1) Technical Assistance for Whole Building Energy Diagnostician (WBE) Commercialization, (2) Market Transfer of the Outdoor Air/Economizer Diagnostician (OAE), and (3) Development and Deployment of Automated Diagnostics to Improve Large Commercial Building Operations. PNNL has previously developed two diagnostic tools: (1) whole building energy (WBE) diagnostician and (2) outdoor air/economizer (OAE) diagnostician. WBE diagnostician is currently licensed non-exclusively to one company. As part of this CRADA, PNNL developed implementation documentation and provided technical support to KGS to implement the tool into their software suite, Clockworks. PNNL also provided validation data sets and the WBE software tool to validate the KGS implementation. OAE diagnostician automatically detects and diagnoses problems with outdoor air ventilation and economizer operation for air handling units (AHUs) in commercial buildings using data available from building automation systems (BASs). As part of this CRADA, PNNL developed implementation documentation and provided technical support to KGS to implement the tool into their software suite. PNNL also provided validation data sets and the OAE software tool to validate the KGS implementation. Finally, as part of this CRADA project, PNNL developed new processes to automate parts of the re-tuning process and transfer those process to KGS for integration into their software product. The transfer of DOE-funded technologies will transform the commercial buildings sector by making buildings more energy efficient and also reducing the carbon footprint from the buildings. As part of the CRADA with PNNL, KGS implemented the whole building energy diagnostician, a portion of outdoor air economizer diagnostician and a number of measures that automate the identification of re-tuning measures.« less

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.

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

Carr, Francis; Evans, Antony; Feron, Eric; Clarke, John-Paul

2003-01-01

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

Proceedings of the Workshop on software tools for distributed intelligent control systems

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

Herget, C.J.

1990-09-01

The Workshop on Software Tools for Distributed Intelligent Control Systems was organized by Lawrence Livermore National Laboratory for the United States Army Headquarters Training and Doctrine Command and the Defense Advanced Research Projects Agency. The goals of the workshop were to the identify the current state of the art in tools which support control systems engineering design and implementation, identify research issues associated with writing software tools which would provide a design environment to assist engineers in multidisciplinary control design and implementation, formulate a potential investment strategy to resolve the research issues and develop public domain code which can formmore » the core of more powerful engineering design tools, and recommend test cases to focus the software development process and test associated performance metrics. Recognizing that the development of software tools for distributed intelligent control systems will require a multidisciplinary effort, experts in systems engineering, control systems engineering, and compute science were invited to participate in the workshop. In particular, experts who could address the following topics were selected: operating systems, engineering data representation and manipulation, emerging standards for manufacturing data, mathematical foundations, coupling of symbolic and numerical computation, user interface, system identification, system representation at different levels of abstraction, system specification, system design, verification and validation, automatic code generation, and integration of modular, reusable code.« less

A Tool for Verification and Validation of Neural Network Based Adaptive Controllers for High Assurance Systems

NASA Technical Reports Server (NTRS)

Gupta, Pramod; Schumann, Johann

2004-01-01

High reliability of mission- and safety-critical software systems has been identified by NASA as a high-priority technology challenge. We present an approach for the performance analysis of a neural network (NN) in an advanced adaptive control system. This problem is important in the context of safety-critical applications that require certification, such as flight software in aircraft. We have developed a tool to measure the performance of the NN during operation by calculating a confidence interval (error bar) around the NN's output. Our tool can be used during pre-deployment verification as well as monitoring the network performance during operation. The tool has been implemented in Simulink and simulation results on a F-15 aircraft are presented.

Software testing

NASA Astrophysics Data System (ADS)

Price-Whelan, Adrian M.

2016-01-01

Now more than ever, scientific results are dependent on sophisticated software and analysis. Why should we trust code written by others? How do you ensure your own code produces sensible results? How do you make sure it continues to do so as you update, modify, and add functionality? Software testing is an integral part of code validation and writing tests should be a requirement for any software project. I will talk about Python-based tools that make managing and running tests much easier and explore some statistics for projects hosted on GitHub that contain tests.

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

PubMed

Mariano, Diego C B; Pereira, Felipe L; Aguiar, Edgar L; Oliveira, Letícia C; Benevides, Leandro; Guimarães, Luís C; Folador, Edson L; Sousa, Thiago J; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique C P; Silva, Artur; Ramos, Rommel T J; Azevedo, Vasco A C

2016-12-15

The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

PubMed Central

2011-01-01

Background The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. Results A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. Conclusions The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim. PMID:21586134

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

PubMed

Luna, Augustin; Karac, Evrim I; Sunshine, Margot; Chang, Lucas; Nussinov, Ruth; Aladjem, Mirit I; Kohn, Kurt W

2011-05-17

The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.

Development and validation of a novel large field of view phantom and a software module for the quality assurance of geometric distortion in magnetic resonance imaging.

PubMed

Torfeh, Tarraf; Hammoud, Rabih; McGarry, Maeve; Al-Hammadi, Noora; Perkins, Gregory

2015-09-01

To develop and validate a large field of view phantom and quality assurance software tool for the assessment and characterization of geometric distortion in MRI scanners commissioned for radiation therapy planning. A purpose built phantom was developed consisting of 357 rods (6mm in diameter) of polymethyl-methacrylat separated by 20mm intervals, providing a three dimensional array of control points at known spatial locations covering a large field of view up to a diameter of 420mm. An in-house software module was developed to allow automatic geometric distortion assessment. This software module was validated against a virtual dataset of the phantom that reproduced the exact geometry of the physical phantom, but with known translational and rotational displacements and warping. For validation experiments, clinical MRI sequences were acquired with and without the application of a commercial 3D distortion correction algorithm (Gradwarp™). The software module was used to characterize and assess system-related geometric distortion in the sequences relative to a benchmark CT dataset, and the efficacy of the vendor geometric distortion correction algorithms (GDC) was also assessed. Results issued from the validation of the software against virtual images demonstrate the algorithm's ability to accurately calculate geometric distortion with sub-pixel precision by the extraction of rods and quantization of displacements. Geometric distortion was assessed for the typical sequences used in radiotherapy applications and over a clinically relevant 420mm field of view (FOV). As expected and towards the edges of the field of view (FOV), distortion increased with increasing FOV. For all assessed sequences, the vendor GDC was able to reduce the mean distortion to below 1mm over a field of view of 5, 10, 15 and 20cm radius respectively. Results issued from the application of the developed phantoms and algorithms demonstrate a high level of precision. The results indicate that this platform represents an important, robust and objective tool to perform routine quality assurance of MR-guided therapeutic applications, where spatial accuracy is paramount. Copyright © 2015 Elsevier Inc. All rights reserved.

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

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

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

Excavator Design Validation

NASA Technical Reports Server (NTRS)

Pholsiri, Chalongrath; English, James; Seberino, Charles; Lim, Yi-Je

2010-01-01

The Excavator Design Validation tool verifies excavator designs by automatically generating control systems and modeling their performance in an accurate simulation of their expected environment. Part of this software design includes interfacing with human operations that can be included in simulation-based studies and validation. This is essential for assessing productivity, versatility, and reliability. This software combines automatic control system generation from CAD (computer-aided design) models, rapid validation of complex mechanism designs, and detailed models of the environment including soil, dust, temperature, remote supervision, and communication latency to create a system of high value. Unique algorithms have been created for controlling and simulating complex robotic mechanisms automatically from just a CAD description. These algorithms are implemented as a commercial cross-platform C++ software toolkit that is configurable using the Extensible Markup Language (XML). The algorithms work with virtually any mobile robotic mechanisms using module descriptions that adhere to the XML standard. In addition, high-fidelity, real-time physics-based simulation algorithms have also been developed that include models of internal forces and the forces produced when a mechanism interacts with the outside world. This capability is combined with an innovative organization for simulation algorithms, new regolith simulation methods, and a unique control and study architecture to make powerful tools with the potential to transform the way NASA verifies and compares excavator designs. Energid's Actin software has been leveraged for this design validation. The architecture includes parametric and Monte Carlo studies tailored for validation of excavator designs and their control by remote human operators. It also includes the ability to interface with third-party software and human-input devices. Two types of simulation models have been adapted: high-fidelity discrete element models and fast analytical models. By using the first to establish parameters for the second, a system has been created that can be executed in real time, or faster than real time, on a desktop PC. This allows Monte Carlo simulations to be performed on a computer platform available to all researchers, and it allows human interaction to be included in a real-time simulation process. Metrics on excavator performance are established that work with the simulation architecture. Both static and dynamic metrics are included.

XMI2USE: A Tool for Transforming XMI to USE Specifications

NASA Astrophysics Data System (ADS)

Sun, Wuliang; Song, Eunjee; Grabow, Paul C.; Simmonds, Devon M.

The UML-based Specification Environment (USE) tool supports syntactic analysis, type checking, consistency checking, and dynamic validation of invariants and pre-/post conditions specified in the Object Constraint Language (OCL). Due to its animation and analysis power, it is useful when checking critical non-functional properties such as security policies. However, the USE tool requires one to specify (i.e., "write") a model using its own textual language and does not allow one to import any model specification files created by other UML modeling tools. Hence, to make the best use of existing UML tools, we often create a model with OCL constraints using a modeling tool such as the IBM Rational Software Architect (RSA) and then use the USE tool for model validation. This approach, however, requires a manual transformation between the specifications of two different tool formats, which is error-prone and diminishes the benefit of automated model-level validations. In this paper, we describe our own implementation of a specification transformation engine that is based on the Model Driven Architecture (MDA) framework and currently supports automatic tool-level transformations from RSA to USE.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.

PubMed

Prior, Fred W; Erickson, Bradley J; Tarbox, Lawrence

2007-11-01

The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.

A tool to include gamma analysis software into a quality assurance program.

PubMed

Agnew, Christina E; McGarry, Conor K

2016-03-01

To provide a tool to enable gamma analysis software algorithms to be included in a quality assurance (QA) program. Four image sets were created comprising two geometric images to independently test the distance to agreement (DTA) and dose difference (DD) elements of the gamma algorithm, a clinical step and shoot IMRT field and a clinical VMAT arc. The images were analysed using global and local gamma analysis with 2 in-house and 8 commercially available software encompassing 15 software versions. The effect of image resolution on gamma pass rates was also investigated. All but one software accurately calculated the gamma passing rate for the geometric images. Variation in global gamma passing rates of 1% at 3%/3mm and over 2% at 1%/1mm was measured between software and software versions with analysis of appropriately sampled images. This study provides a suite of test images and the gamma pass rates achieved for a selection of commercially available software. This image suite will enable validation of gamma analysis software within a QA program and provide a frame of reference by which to compare results reported in the literature from various manufacturers and software versions. Copyright © 2015. Published by Elsevier Ireland Ltd.

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

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

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

Advanced Structural Optimization Under Consideration of Cost Tracking

NASA Astrophysics Data System (ADS)

Zell, D.; Link, T.; Bickelmaier, S.; Albinger, J.; Weikert, S.; Cremaschi, F.; Wiegand, A.

2014-06-01

In order to improve the design process of launcher configurations in the early development phase, the software Multidisciplinary Optimization (MDO) was developed. The tool combines different efficient software tools such as Optimal Design Investigations (ODIN) for structural optimizations, Aerospace Trajectory Optimization Software (ASTOS) for trajectory and vehicle design optimization for a defined payload and mission.The present paper focuses to the integration and validation of ODIN. ODIN enables the user to optimize typical axis-symmetric structures by means of sizing the stiffening designs concerning strength and stability while minimizing the structural mass. In addition a fully automatic finite element model (FEM) generator module creates ready-to-run FEM models of a complete stage or launcher assembly.Cost tracking respectively future improvements concerning cost optimization are indicated.

Adaption of G-TAG Software for Validating Touch and Go Asteroid Sample Return Design Methodology

NASA Technical Reports Server (NTRS)

Blackmore, Lars James C.; Acikmese, Behcet; Mandic, Milan

2012-01-01

A software tool is used to demonstrate the feasibility of Touch and Go (TAG) sampling for Asteroid Sample Return missions. TAG is a concept whereby a spacecraft is in contact with the surface of a small body, such as a comet or asteroid, for a few seconds or less before ascending to a safe location away from the small body. Previous work at JPL developed the G-TAG simulation tool, which provides a software environment for fast, multi-body simulations of the TAG event. G-TAG is described in Multibody Simulation Software Testbed for Small-Body Exploration and Sampling, (NPO-47196) NASA Tech Briefs, Vol. 35, No. 11 (November 2011), p.54. This current innovation adapts this tool to a mission that intends to return a sample from the surface of an asteroid. In order to demonstrate the feasibility of the TAG concept, the new software tool was used to generate extensive simulations that demonstrate the designed spacecraft meets key requirements. These requirements state that contact force and duration must be sufficient to ensure that enough material from the surface is collected in the brushwheel sampler (BWS), and that the spacecraft must survive the contact and must be able to recover and ascend to a safe position, and maintain velocity and orientation after the contact.

Application of Architectural Patterns and Lightweight Formal Method for the Validation and Verification of Safety Critical Systems

DTIC Science & Technology

2013-09-01

to a XML file, a code that Bonine in [21] developed for a similar purpose. Using the StateRover XML log file import tool, we are able to generate a...C. Bonine , M. Shing, T.W. Otani, “Computer-aided process and tools for mobile software acquisition,” NPS, Monterey, CA, Tech. Rep. NPS-SE-13...C10P07R05– 075, 2013. [21] C. Bonine , “Specification, validation and verification of mobile application behavior,” M.S. thesis, Dept. Comp. Science, NPS

Microstructure Modeling of 3rd Generation Disk Alloys

NASA Technical Reports Server (NTRS)

Jou, Herng-Jeng

2010-01-01

The objective of this program is to model, validate, and predict the precipitation microstructure evolution, using PrecipiCalc (QuesTek Innovations LLC) software, for 3rd generation Ni-based gas turbine disc superalloys during processing and service, with a set of logical and consistent experiments and characterizations. Furthermore, within this program, the originally research-oriented microstructure simulation tool will be further improved and implemented to be a useful and user-friendly engineering tool. In this report, the key accomplishment achieved during the second year (2008) of the program is summarized. The activities of this year include final selection of multicomponent thermodynamics and mobility databases, precipitate surface energy determination from nucleation experiment, multiscale comparison of predicted versus measured intragrain precipitation microstructure in quench samples showing good agreement, isothermal coarsening experiment and interaction of grain boundary and intergrain precipitates, primary microstructure of subsolvus treatment, and finally the software implementation plan for the third year of the project. In the following year, the calibrated models and simulation tools will be validated against an independently developed experimental data set, with actual disc heat treatment process conditions. Furthermore, software integration and implementation will be developed to provide material engineers valuable information in order to optimize the processing of the 3rd generation gas turbine disc alloys.

Analysis of key technologies for virtual instruments metrology

NASA Astrophysics Data System (ADS)

Liu, Guixiong; Xu, Qingui; Gao, Furong; Guan, Qiuju; Fang, Qiang

2008-12-01

Virtual instruments (VIs) require metrological verification when applied as measuring instruments. Owing to the software-centered architecture, metrological evaluation of VIs includes two aspects: measurement functions and software characteristics. Complexity of software imposes difficulties on metrological testing of VIs. Key approaches and technologies for metrology evaluation of virtual instruments are investigated and analyzed in this paper. The principal issue is evaluation of measurement uncertainty. The nature and regularity of measurement uncertainty caused by software and algorithms can be evaluated by modeling, simulation, analysis, testing and statistics with support of powerful computing capability of PC. Another concern is evaluation of software features like correctness, reliability, stability, security and real-time of VIs. Technologies from software engineering, software testing and computer security domain can be used for these purposes. For example, a variety of black-box testing, white-box testing and modeling approaches can be used to evaluate the reliability of modules, components, applications and the whole VI software. The security of a VI can be assessed by methods like vulnerability scanning and penetration analysis. In order to facilitate metrology institutions to perform metrological verification of VIs efficiently, an automatic metrological tool for the above validation is essential. Based on technologies of numerical simulation, software testing and system benchmarking, a framework for the automatic tool is proposed in this paper. Investigation on implementation of existing automatic tools that perform calculation of measurement uncertainty, software testing and security assessment demonstrates the feasibility of the automatic framework advanced.

A new dataset validation system for the Planetary Science Archive

NASA Astrophysics Data System (ADS)

Manaud, N.; Zender, J.; Heather, D.; Martinez, S.

2007-08-01

The Planetary Science Archive is the official archive for the Mars Express mission. It has received its first data by the end of 2004. These data are delivered by the PI teams to the PSA team as datasets, which are formatted conform to the Planetary Data System (PDS). The PI teams are responsible for analyzing and calibrating the instrument data as well as the production of reduced and calibrated data. They are also responsible of the scientific validation of these data. ESA is responsible of the long-term data archiving and distribution to the scientific community and must ensure, in this regard, that all archived products meet quality. To do so, an archive peer-review is used to control the quality of the Mars Express science data archiving process. However a full validation of its content is missing. An independent review board recently recommended that the completeness of the archive as well as the consistency of the delivered data should be validated following well-defined procedures. A new validation software tool is being developed to complete the overall data quality control system functionality. This new tool aims to improve the quality of data and services provided to the scientific community through the PSA, and shall allow to track anomalies in and to control the completeness of datasets. It shall ensure that the PSA end-users: (1) can rely on the result of their queries, (2) will get data products that are suitable for scientific analysis, (3) can find all science data acquired during a mission. We defined dataset validation as the verification and assessment process to check the dataset content against pre-defined top-level criteria, which represent the general characteristics of good quality datasets. The dataset content that is checked includes the data and all types of information that are essential in the process of deriving scientific results and those interfacing with the PSA database. The validation software tool is a multi-mission tool that has been designed to provide the user with the flexibility of defining and implementing various types of validation criteria, to iteratively and incrementally validate datasets, and to generate validation reports.

Federal Emergency Management Information System (FEMIS) system administration guide. Version 1.3

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

Burford, M.J.; Burnett, R.A.; Downing, T.R.

The Federal Emergency Management Information System (FEMIS) is an emergency management planning and analysis tool that was developed by the (Pacific Northwest National Laboratory) (PNNL) under the direction of the U.S. Army Chemical Biological Defense Command. The FEMIS System Administration Guide defines FEMIS hardware and software requirements and gives instructions for installing the FEMIS software package. 91 This document also contains information on the following: software installation for the FEMIS data servers, communication server, mail server, and the emergency management workstations; distribution media loading and FEMIS installation validation and troubleshooting; and system management of FEMIS users, login, privileges, and usage.more » The system administration utilities (tools), available in the FEMIS client software, are described for user accounts and site profile. This document also describes the installation and use of system and database administration utilities that will assist in keeping the FEMIS system running in an operational environment.« less

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.

Case Study: Test Results of a Tool and Method for In-Flight, Adaptive Control System Verification on a NASA F-15 Flight Research Aircraft

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.; Schumann, Johann; Guenther, Kurt; Bosworth, John

2006-01-01

Adaptive control technologies that incorporate learning algorithms have been proposed to enable autonomous flight control and to maintain vehicle performance in the face of unknown, changing, or poorly defined operating environments [1-2]. At the present time, however, it is unknown how adaptive algorithms can be routinely verified, validated, and certified for use in safety-critical applications. Rigorous methods for adaptive software verification end validation must be developed to ensure that. the control software functions as required and is highly safe and reliable. A large gap appears to exist between the point at which control system designers feel the verification process is complete, and when FAA certification officials agree it is complete. Certification of adaptive flight control software verification is complicated by the use of learning algorithms (e.g., neural networks) and degrees of system non-determinism. Of course, analytical efforts must be made in the verification process to place guarantees on learning algorithm stability, rate of convergence, and convergence accuracy. However, to satisfy FAA certification requirements, it must be demonstrated that the adaptive flight control system is also able to fail and still allow the aircraft to be flown safely or to land, while at the same time providing a means of crew notification of the (impending) failure. It was for this purpose that the NASA Ames Confidence Tool was developed [3]. This paper presents the Confidence Tool as a means of providing in-flight software assurance monitoring of an adaptive flight control system. The paper will present the data obtained from flight testing the tool on a specially modified F-15 aircraft designed to simulate loss of flight control faces.

Projecting manpower to attain quality

NASA Technical Reports Server (NTRS)

Rone, K. Y.

1983-01-01

The resulting model is useful as a projection tool but must be validated in order to be used as an on-going software cost engineering tool. A procedure is developed to facilitate the tracking of model projections and actual data to allow the model to be tuned. Finally, since the model must be used in an environment of overlapping development activities on a progression of software elements in development and maintenance, a manpower allocation model is developed for use in a steady state development/maintenance environment. In these days of soaring software costs it becomes increasingly important to properly manage a software development project. One element of the management task is the projection and tracking of manpower required to perform the task. In addition, since the total cost of the task is directly related to the initial quality built into the software, it becomes a necessity to project the development manpower in a way to attain that quality. An approach to projecting and tracking manpower with quality in mind is described.

An Update on Design Tools for Optimization of CMC 3D Fiber Architectures

NASA Technical Reports Server (NTRS)

Lang, J.; DiCarlo, J.

2012-01-01

Objective: Describe and up-date progress for NASA's efforts to develop 3D architectural design tools for CMC in general and for SIC/SiC composites in particular. Describe past and current sequential work efforts aimed at: Understanding key fiber and tow physical characteristics in conventional 2D and 3D woven architectures as revealed by microstructures in the literature. Developing an Excel program for down-selecting and predicting key geometric properties and resulting key fiber-controlled properties for various conventional 3D architectures. Developing a software tool for accurately visualizing all the key geometric details of conventional 3D architectures. Validating tools by visualizing and predicting the Internal geometry and key mechanical properties of a NASA SIC/SIC panel with a 3D orthogonal architecture. Applying the predictive and visualization tools toward advanced 3D orthogonal SiC/SIC composites, and combining them into a user-friendly software program.

Calibration of a COTS Integration Cost Model Using Local Project Data

NASA Technical Reports Server (NTRS)

Boland, Dillard; Coon, Richard; Byers, Kathryn; Levitt, David

1997-01-01

The software measures and estimation techniques appropriate to a Commercial Off the Shelf (COTS) integration project differ from those commonly used for custom software development. Labor and schedule estimation tools that model COTS integration are available. Like all estimation tools, they must be calibrated with the organization's local project data. This paper describes the calibration of a commercial model using data collected by the Flight Dynamics Division (FDD) of the NASA Goddard Spaceflight Center (GSFC). The model calibrated is SLIM Release 4.0 from Quantitative Software Management (QSM). By adopting the SLIM reuse model and by treating configuration parameters as lines of code, we were able to establish a consistent calibration for COTS integration projects. The paper summarizes the metrics, the calibration process and results, and the validation of the calibration.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

2016-09-01

Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools.

Experimental Evaluation of Verification and Validation Tools on Martian Rover Software

NASA Technical Reports Server (NTRS)

Brat, Guillaume; Giannakopoulou, Dimitra; Goldberg, Allen; Havelund, Klaus; Lowry, Mike; Pasareani, Corina; Venet, Arnaud; Visser, Willem; Washington, Rich

2003-01-01

We report on a study to determine the maturity of different verification and validation technologies (V&V) on a representative example of NASA flight software. The study consisted of a controlled experiment where three technologies (static analysis, runtime analysis and model checking) were compared to traditional testing with respect to their ability to find seeded errors in a prototype Mars Rover. What makes this study unique is that it is the first (to the best of our knowledge) to do a controlled experiment to compare formal methods based tools to testing on a realistic industrial-size example where the emphasis was on collecting as much data on the performance of the tools and the participants as possible. The paper includes a description of the Rover code that was analyzed, the tools used as well as a detailed description of the experimental setup and the results. Due to the complexity of setting up the experiment, our results can not be generalized, but we believe it can still serve as a valuable point of reference for future studies of this kind. It did confirm the belief we had that advanced tools can outperform testing when trying to locate concurrency errors. Furthermore the results of the experiment inspired a novel framework for testing the next generation of the Rover.

Knickpoint finder: A software tool that improves neotectonic analysis

NASA Astrophysics Data System (ADS)

Queiroz, G. L.; Salamuni, E.; Nascimento, E. R.

2015-03-01

This work presents a new software tool for morphometric analysis of drainage networks based on the methods of Hack (1973) and Etchebehere et al. (2004). This tool is applicable to studies of morphotectonics and neotectonics. The software used a digital elevation model (DEM) to identify the relief breakpoints along drainage profiles (knickpoints). The program was coded in Python for use on the ArcGIS platform and is called Knickpoint Finder. A study area was selected to test and evaluate the software's ability to analyze and identify neotectonic morphostructures based on the morphology of the terrain. For an assessment of its validity, we chose an area of the James River basin, which covers most of the Piedmont area of Virginia (USA), which is an area of constant intraplate seismicity and non-orogenic active tectonics and exhibits a relatively homogeneous geodesic surface currently being altered by the seismogenic features of the region. After using the tool in the chosen area, we found that the knickpoint locations are associated with the geologic structures, epicenters of recent earthquakes, and drainages with rectilinear anomalies. The regional analysis demanded the use of a spatial representation of the data after processing using Knickpoint Finder. The results were satisfactory in terms of the correlation of dense areas of knickpoints with active lineaments and the rapidity of the identification of deformed areas. Therefore, this software tool may be considered useful in neotectonic analyses of large areas and may be applied to any area where there is DEM coverage.

CEMENTITIOUS BARRIERS PARTNERSHIP FY13 MID-YEAR REPORT

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

Burns, H.; Flach, G.; Langton, C.

2013-05-01

In FY2013, the Cementitious Barriers Partnership (CBP) is continuing in its effort to develop and enhance software tools demonstrating tangible progress toward fulfilling the objective of developing a set of tools to improve understanding and prediction of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. In FY2012, the CBP released the initial inhouse “Beta-version” of the CBP Software Toolbox, a suite of software for simulating reactive transport in cementitious materials and important degradation phenomena. The current primary software components are LeachXS/ORCHESTRA, STADIUM, and a GoldSim interface for probabilistic analysis of selected degradation scenarios. THAMESmore » is a planned future CBP Toolbox component (FY13/14) focused on simulation of the microstructure of cementitious materials and calculation of resultant hydraulic and constituent mass transfer parameters needed in modeling. This past November, the CBP Software Toolbox Version 1.0 was released that supports analysis of external sulfate attack (including damage mechanics), carbonation, and primary constituent leaching. The LeachXS component embodies an extensive material property measurements database along with chemical speciation and reactive mass transport simulation cases with emphasis on leaching of major, trace and radionuclide constituents from cementitious materials used in DOE facilities, such as Saltstone (Savannah River) and Cast Stone (Hanford), tank closure grouts, and barrier concretes. STADIUM focuses on the physical and structural service life of materials and components based on chemical speciation and reactive mass transport of major cement constituents and aggressive species (e.g., chloride, sulfate, etc.). The CBP issued numerous reports and other documentation that accompanied the “Version 1.0” release including a CBP Software Toolbox User Guide and Installation Guide. These documents, as well as, the presentations from the CBP Software Toolbox Demonstration and User Workshop, which are briefly described below, can be accessed from the CBP webpage at http://cementbarriers.org/. The website was recently modified to describe the CBP Software Toolbox and includes an interest form for application to use the software. The CBP FY13 program is continuing research to improve and enhance the simulation tools as well as develop new tools that model other key degradation phenomena not addressed in Version 1.0. Also efforts to continue to verify the various simulation tools thru laboratory experiments and analysis of field specimens are ongoing to quantify and reduce the uncertainty associated with performance assessments are ongoing. This mid-year report also includes both a summary on the FY13 software accomplishments in addition to the release of Version 1.0 of the CBP Software Toolbox and the various experimental programs that are providing data for calibration and validation of the CBP developed software. The focus this year for experimental studies was to measure transport in cementitious material by utilization of a leaching method and reduction capacity of saltstone field samples. Results are being used to calibrate and validate the updated carbonation model.« less

Improving Flight Software Module Validation Efforts : a Modular, Extendable Testbed Software Framework

NASA Technical Reports Server (NTRS)

Lange, R. Connor

2012-01-01

Ever since Explorer-1, the United States' first Earth satellite, was developed and launched in 1958, JPL has developed many more spacecraft, including landers and orbiters. While these spacecraft vary greatly in their missions, capabilities,and destination, they all have something in common. All of the components of these spacecraft had to be comprehensively tested. While thorough testing is important to mitigate risk, it is also a very expensive and time consuming process. Thankfully,since virtually all of the software testing procedures for SMAP are computer controlled, these procedures can be automated. Most people testing SMAP flight software (FSW) would only need to write tests that exercise specific requirements and then check the filtered results to verify everything occurred as planned. This gives developers the ability to automatically launch tests on the testbed, distill the resulting logs into only the important information, generate validation documentation, and then deliver the documentation to management. With many of the steps in FSW testing automated, developers can use their limited time more effectively and can validate SMAP FSW modules quicker and test them more rigorously. As a result of the various benefits of automating much of the testing process, management is considering this automated tools use in future FSW validation efforts.

XTCE GOVSAT Tool Suite 1.0

NASA Technical Reports Server (NTRS)

Rice, J. Kevin

2013-01-01

The XTCE GOVSAT software suite contains three tools: validation, search, and reporting. The Extensible Markup Language (XML) Telemetric and Command Exchange (XTCE) GOVSAT Tool Suite is written in Java for manipulating XTCE XML files. XTCE is a Consultative Committee for Space Data Systems (CCSDS) and Object Management Group (OMG) specification for describing the format and information in telemetry and command packet streams. These descriptions are files that are used to configure real-time telemetry and command systems for mission operations. XTCE s purpose is to exchange database information between different systems. XTCE GOVSAT consists of rules for narrowing the use of XTCE for missions. The Validation Tool is used to syntax check GOVSAT XML files. The Search Tool is used to search (i.e. command and telemetry mnemonics) the GOVSAT XML files and view the results. Finally, the Reporting Tool is used to create command and telemetry reports. These reports can be displayed or printed for use by the operations team.

Software tool for mining liquid chromatography/multi-stage mass spectrometry data for comprehensive glycerophospholipid profiling.

PubMed

Hein, Eva-Maria; Bödeker, Bertram; Nolte, Jürgen; Hayen, Heiko

2010-07-30

Electrospray ionization mass spectrometry (ESI-MS) has emerged as an indispensable tool in the field of lipidomics. Despite the growing interest in lipid analysis, there are only a few software tools available for data evaluation, as compared for example to proteomics applications. This makes comprehensive lipid analysis a complex challenge. Thus, a computational tool for harnessing the raw data from liquid chromatography/mass spectrometry (LC/MS) experiments was developed in this study and is available from the authors on request. The Profiler-Merger-Viewer tool is a software package for automatic processing of raw-data from data-dependent experiments, measured by high-performance liquid chromatography hyphenated to electrospray ionization hybrid linear ion trap Fourier transform mass spectrometry (FTICR-MS and Orbitrap) in single and multi-stage mode. The software contains three parts: processing of the raw data by Profiler for lipid identification, summarizing of replicate measurements by Merger and visualization of all relevant data (chromatograms as well as mass spectra) for validation of the results by Viewer. The tool is easily accessible, since it is implemented in Java and uses Microsoft Excel (XLS) as output format. The motivation was to develop a tool which supports and accelerates the manual data evaluation (identification and relative quantification) significantly but does not make a complete data analysis within a black-box system. The software's mode of operation, usage and options will be demonstrated on the basis of a lipid extract of baker's yeast (S. cerevisiae). In this study, we focused on three important representatives of lipids: glycerophospholipids, lyso-glycerophospholipids and free fatty acids. Copyright 2010 John Wiley & Sons, Ltd.

Validation of measures from the smartphone sway balance application: a pilot study.

PubMed

Patterson, Jeremy A; Amick, Ryan Z; Thummar, Tarunkumar; Rogers, Michael E

2014-04-01

A number of different balance assessment techniques are currently available and widely used. These include both subjective and objective assessments. The ability to provide quantitative measures of balance and posture is the benefit of objective tools, however these instruments are not generally utilized outside of research laboratory settings due to cost, complexity of operation, size, duration of assessment, and general practicality. The purpose of this pilot study was to assess the value and validity of using software developed to access the iPod and iPhone accelerometers output and translate that to the measurement of human balance. Thirty healthy college-aged individuals (13 male, 17 female; age = 26.1 ± 8.5 years) volunteered. Participants performed a static Athlete's Single Leg Test protocol for 10 sec, on a Biodex Balance System SD while concurrently utilizing a mobile device with balance software. Anterior/posterior stability was recorded using both devices, described as the displacement in degrees from level, and was termed the "balance score." There were no significant differences between the two reported balance scores (p = 0.818. Mean balance score on the balance platform was 1.41 ± 0.90, as compared to 1.38 ± 0.72 using the mobile device. There is a need for a valid, convenient, and cost-effective tool to objectively measure balance. Results of this study are promising, as balance score derived from the Smartphone accelerometers were consistent with balance scores obtained from a previously validated balance system. However, further investigation is necessary as this version of the mobile software only assessed balance in the anterior/posterior direction. Additionally, further testing is necessary on a healthy populations and as well as those with impairment of the motor control system. Level 2b (Observational study of validity)(1.)

OTEC Cold Water Pipe-Platform Subsystem Dynamic Interaction Validation

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

Varley, Robert; Halkyard, John; Johnson, Peter

A commercial floating 100-megawatt (MW) ocean thermal energy conversion (OTEC) power plant will require a cold water pipe (CWP) with a diameter of 10-meter (m) and length of up to 1,000 m. The mass of the cold water pipe, including entrained water, can exceed the mass of the platform supporting it. The offshore industry uses software-modeling tools to develop platform and riser (pipe) designs to survive the offshore environment. These tools are typically validated by scale model tests in facilities able to replicate real at-sea meteorological and ocean (metocean) conditions to provide the understanding and confidence to proceed to finalmore » design and full-scale fabrication. However, today’s offshore platforms (similar to and usually larger than those needed for OTEC applications) incorporate risers (or pipes) with diameters well under one meter. Secondly, the preferred construction method for large diameter OTEC CWPs is the use of composite materials, primarily a form of fiber-reinforced plastic (FRP). The use of these material results in relatively low pipe stiffness and large strains compared to steel construction. These factors suggest the need for further validation of offshore industry software tools. The purpose of this project was to validate the ability to model numerically the dynamic interaction between a large cold water-filled fiberglass pipe and a floating OTEC platform excited by metocean weather conditions using measurements from a scale model tested in an ocean basin test facility.« less

Landsat-7 Simulation and Testing Environments

NASA Technical Reports Server (NTRS)

Holmes, E.; Ha, K.; Hawkins, K.; Lombardo, J.; Ram, M.; Sabelhaus, P.; Scott, S.; Phillips, R.

1999-01-01

A spacecraft Attitude Control and Determination Subsystem (ACDS) is heavily dependent upon simulation throughout its entire development, implementation and ground test cycle. Engineering simulation tools are typically developed to design and analyze control systems to validate the design and software simulation tools are required to qualify the flight software. However, the need for simulation does not end here. Operating the ACDS of a spacecraft on the ground requires the simulation of spacecraft dynamics, disturbance modeling and celestial body motion. Sensor data must also be simulated and substituted for actual sensor data on the ground so that the spacecraft will respond by sending commands to the actuators as they will on orbit. And finally, the simulators is the primary training tool and test-bed for the Flight Operations Team. In this paper various ACDS simulation, developed for or used by the Landsat 7 project will be described. The paper will include a description of each tool, its unique attributes, and its role in the overall development and testing of the ACDS. Finally, a section is included which discusses how the coordinated use of these simulation tools can maximize the probability of uncovering software, hardware and operations errors during the ground test process.

Telemetry-Enhancing Scripts

NASA Technical Reports Server (NTRS)

Maimone, Mark W.

2009-01-01

Scripts Providing a Cool Kit of Telemetry Enhancing Tools (SPACKLE) is a set of software tools that fill gaps in capabilities of other software used in processing downlinked data in the Mars Exploration Rovers (MER) flight and test-bed operations. SPACKLE tools have helped to accelerate the automatic processing and interpretation of MER mission data, enabling non-experts to understand and/or use MER query and data product command simulation software tools more effectively. SPACKLE has greatly accelerated some operations and provides new capabilities. The tools of SPACKLE are written, variously, in Perl or the C or C++ language. They perform a variety of search and shortcut functions that include the following: Generating text-only, Event Report-annotated, and Web-enhanced views of command sequences; Labeling integer enumerations with their symbolic meanings in text messages and engineering channels; Systematic detecting of corruption within data products; Generating text-only displays of data-product catalogs including downlink status; Validating and labeling of commands related to data products; Performing of convenient searches of detailed engineering data spanning multiple Martian solar days; Generating tables of initial conditions pertaining to engineering, health, and accountability data; Simplified construction and simulation of command sequences; and Fast time format conversions and sorting.

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator: Preprint

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Agreement between clinical estimation and a new quantitative analysis by Photoshop software in fundus and angiographic image variables.

PubMed

Ramezani, Alireza; Ahmadieh, Hamid; Azarmina, Mohsen; Soheilian, Masoud; Dehghan, Mohammad H; Mohebbi, Mohammad R

2009-12-01

To evaluate the validity of a new method for the quantitative analysis of fundus or angiographic images using Photoshop 7.0 (Adobe, USA) software by comparing with clinical evaluation. Four hundred and eighteen fundus and angiographic images of diabetic patients were evaluated by three retina specialists and then by computing using Photoshop 7.0 software. Four variables were selected for comparison: amount of hard exudates (HE) on color pictures, amount of HE on red-free pictures, severity of leakage, and the size of the foveal avascular zone (FAZ). The coefficient of agreement (Kappa) between the two methods in the amount of HE on color and red-free photographs were 85% (0.69) and 79% (0.59), respectively. The agreement for severity of leakage was 72% (0.46). In the two methods for the evaluation of the FAZ size using the magic and lasso software tools, the agreement was 54% (0.09) and 89% (0.77), respectively. Agreement in the estimation of the FAZ size by the lasso magnetic tool was excellent and was almost as good in the quantification of HE on color and on red-free images. Considering the agreement of this new technique for the measurement of variables in fundus images using Photoshop software with the clinical evaluation, this method seems to have sufficient validity to be used for the quantitative analysis of HE, leakage, and FAZ size on the angiograms of diabetic patients.

Developing Teaching Material Software Assisted for Numerical Methods

NASA Astrophysics Data System (ADS)

Handayani, A. D.; Herman, T.; Fatimah, S.

2017-09-01

The NCTM vision shows the importance of two things in school mathematics, which is knowing the mathematics of the 21st century and the need to continue to improve mathematics education to answer the challenges of a changing world. One of the competencies associated with the great challenges of the 21st century is the use of help and tools (including IT), such as: knowing the existence of various tools for mathematical activity. One of the significant challenges in mathematical learning is how to teach students about abstract concepts. In this case, technology in the form of mathematics learning software can be used more widely to embed the abstract concept in mathematics. In mathematics learning, the use of mathematical software can make high level math activity become easier accepted by student. Technology can strengthen student learning by delivering numerical, graphic, and symbolic content without spending the time to calculate complex computing problems manually. The purpose of this research is to design and develop teaching materials software assisted for numerical method. The process of developing the teaching material starts from the defining step, the process of designing the learning material developed based on information obtained from the step of early analysis, learners, materials, tasks that support then done the design step or design, then the last step is the development step. The development of teaching materials software assisted for numerical methods is valid in content. While validator assessment for teaching material in numerical methods is good and can be used with little revision.

Development and validation of a nursing professionalism evaluation model in a career ladder system.

PubMed

Kim, Yeon Hee; Jung, Young Sun; Min, Ja; Song, Eun Young; Ok, Jung Hui; Lim, Changwon; Kim, Kyunghee; Kim, Ji-Su

2017-01-01

The clinical ladder system categorizes the degree of nursing professionalism and rewards and is an important human resource tool for managing nursing. We developed a model to evaluate nursing professionalism, which determines the clinical ladder system levels, and verified its validity. Data were collected using a clinical competence tool developed in this study, and existing methods such as the nursing professionalism evaluation tool, peer reviews, and face-to-face interviews to evaluate promotions and verify the presented content in a medical institution. Reliability and convergent and discriminant validity of the clinical competence evaluation tool were verified using SmartPLS software. The validity of the model for evaluating overall nursing professionalism was also analyzed. Clinical competence was determined by five dimensions of nursing practice: scientific, technical, ethical, aesthetic, and existential. The structural model explained 66% of the variance. Clinical competence scales, peer reviews, and face-to-face interviews directly determined nursing professionalism levels. The evaluation system can be used for evaluating nurses' professionalism in actual medical institutions from a nursing practice perspective. A conceptual framework for establishing a human resources management system for nurses and a tool for evaluating nursing professionalism at medical institutions is provided.

System diagnostic builder

NASA Technical Reports Server (NTRS)

Nieten, Joseph L.; Burke, Roger

1992-01-01

The System Diagnostic Builder (SDB) is an automated software verification and validation tool using state-of-the-art Artificial Intelligence (AI) technologies. The SDB is used extensively by project BURKE at NASA-JSC as one component of a software re-engineering toolkit. The SDB is applicable to any government or commercial organization which performs verification and validation tasks. The SDB has an X-window interface, which allows the user to 'train' a set of rules for use in a rule-based evaluator. The interface has a window that allows the user to plot up to five data parameters (attributes) at a time. Using these plots and a mouse, the user can identify and classify a particular behavior of the subject software. Once the user has identified the general behavior patterns of the software, he can train a set of rules to represent his knowledge of that behavior. The training process builds rules and fuzzy sets to use in the evaluator. The fuzzy sets classify those data points not clearly identified as a particular classification. Once an initial set of rules is trained, each additional data set given to the SDB will be used by a machine learning mechanism to refine the rules and fuzzy sets. This is a passive process and, therefore, it does not require any additional operator time. The evaluation component of the SDB can be used to validate a single software system using some number of different data sets, such as a simulator. Moreover, it can be used to validate software systems which have been re-engineered from one language and design methodology to a totally new implementation.

New Automotive Air Conditioning System Simulation Tool Developed in MATLAB/Simulink

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

Kiss, T.; Chaney, L.; Meyer, J.

Further improvements in vehicle fuel efficiency require accurate evaluation of the vehicle's transient total power requirement. When operated, the air conditioning (A/C) system is the largest auxiliary load on a vehicle; therefore, accurate evaluation of the load it places on the vehicle's engine and/or energy storage system is especially important. Vehicle simulation software, such as 'Autonomie,' has been used by OEMs to evaluate vehicles' energy performance. A transient A/C simulation tool incorporated into vehicle simulation models would also provide a tool for developing more efficient A/C systems through a thorough consideration of the transient A/C system performance. The dynamic systemmore » simulation software Matlab/Simulink was used to develop new and more efficient vehicle energy system controls. The various modeling methods used for the new simulation tool are described in detail. Comparison with measured data is provided to demonstrate the validity of the model.« less

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

PubMed

Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

2005-04-01

We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

Software Validation via Model Animation

NASA Technical Reports Server (NTRS)

Dutle, Aaron M.; Munoz, Cesar A.; Narkawicz, Anthony J.; Butler, Ricky W.

2015-01-01

This paper explores a new approach to validating software implementations that have been produced from formally-verified algorithms. Although visual inspection gives some confidence that the implementations faithfully reflect the formal models, it does not provide complete assurance that the software is correct. The proposed approach, which is based on animation of formal specifications, compares the outputs computed by the software implementations on a given suite of input values to the outputs computed by the formal models on the same inputs, and determines if they are equal up to a given tolerance. The approach is illustrated on a prototype air traffic management system that computes simple kinematic trajectories for aircraft. Proofs for the mathematical models of the system's algorithms are carried out in the Prototype Verification System (PVS). The animation tool PVSio is used to evaluate the formal models on a set of randomly generated test cases. Output values computed by PVSio are compared against output values computed by the actual software. This comparison improves the assurance that the translation from formal models to code is faithful and that, for example, floating point errors do not greatly affect correctness and safety properties.

Tools for open geospatial science

NASA Astrophysics Data System (ADS)

Petras, V.; Petrasova, A.; Mitasova, H.

2017-12-01

Open science uses open source to deal with reproducibility challenges in data and computational sciences. However, just using open source software or making the code public does not make the research reproducible. Moreover, the scientists face the challenge of learning new unfamiliar tools and workflows. In this contribution, we will look at a graduate-level course syllabus covering several software tools which make validation and reuse by a wider professional community possible. For the novices in the open science arena, we will look at how scripting languages such as Python and Bash help us reproduce research (starting with our own work). Jupyter Notebook will be introduced as a code editor, data exploration tool, and a lab notebook. We will see how Git helps us not to get lost in revisions and how Docker is used to wrap all the parts together using a single text file so that figures for a scientific paper or a technical report can be generated with a single command. We will look at examples of software and publications in the geospatial domain which use these tools and principles. Scientific contributions to GRASS GIS, a powerful open source desktop GIS and geoprocessing backend, will serve as an example of why and how to publish new algorithms and tools as part of a bigger open source project.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

The ATLAS Simulation Infrastructure

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2010-09-25

The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, andmore » the validation of the simulated output against known physics processes.« less

Autonomy Software: V&V Challenges and Characteristics

NASA Technical Reports Server (NTRS)

Schumann, Johann; Visser, Willem

2006-01-01

The successful operation of unmanned air vehicles requires software with a high degree of autonomy. Only if high level functions can be carried out without human control and intervention, complex missions in a changing and potentially unknown environment can be carried out successfully. Autonomy software is highly mission and safety critical: failures, caused by flaws in the software cannot only jeopardize the mission, but could also endanger human life (e.g., a crash of an UAV in a densely populated area). Due to its large size, high complexity, and use of specialized algorithms (planner, constraint-solver, etc.), autonomy software poses specific challenges for its verification, validation, and certification. -- - we have carried out a survey among researchers aid scientists at NASA to study these issues. In this paper, we will present major results of this study, discussing the broad spectrum. of notions and characteristics of autonomy software and its challenges for design and development. A main focus of this survey was to evaluate verification and validation (V&V) issues and challenges, compared to the development of "traditional" safety-critical software. We will discuss important issues in V&V of autonomous software and advanced V&V tools which can help to mitigate software risks. Results of this survey will help to identify and understand safety concerns in autonomy software and will lead to improved strategies for mitigation of these risks.

AdViSHE: A Validation-Assessment Tool of Health-Economic Models for Decision Makers and Model Users.

PubMed

Vemer, P; Corro Ramos, I; van Voorn, G A K; Al, M J; Feenstra, T L

2016-04-01

A trade-off exists between building confidence in health-economic (HE) decision models and the use of scarce resources. We aimed to create a practical tool providing model users with a structured view into the validation status of HE decision models, to address this trade-off. A Delphi panel was organized, and was completed by a workshop during an international conference. The proposed tool was constructed iteratively based on comments from, and the discussion amongst, panellists. During the Delphi process, comments were solicited on the importance and feasibility of possible validation techniques for modellers, their relevance for decision makers, and the overall structure and formulation in the tool. The panel consisted of 47 experts in HE modelling and HE decision making from various professional and international backgrounds. In addition, 50 discussants actively engaged in the discussion at the conference workshop and returned 19 questionnaires with additional comments. The final version consists of 13 items covering all relevant aspects of HE decision models: the conceptual model, the input data, the implemented software program, and the model outcomes. Assessment of the Validation Status of Health-Economic decision models (AdViSHE) is a validation-assessment tool in which model developers report in a systematic way both on validation efforts performed and on their outcomes. Subsequently, model users can establish whether confidence in the model is justified or whether additional validation efforts should be undertaken. In this way, AdViSHE enhances transparency of the validation status of HE models and supports efficient model validation.

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

PubMed

Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

2016-09-02

Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNP(xl) for UV-induced peptide-RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark ( Ramus, C.; J. Proteomics 2016 , 132 , 51 - 62 ). The second workflow, RNP(xl), represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

Software Quality Control at Belle II

NASA Astrophysics Data System (ADS)

Ritter, M.; Kuhr, T.; Hauth, T.; Gebard, T.; Kristof, M.; Pulvermacher, C.; Belle Software Group, II

2017-10-01

Over the last seven years the software stack of the next generation B factory experiment Belle II has grown to over one million lines of C++ and Python code, counting only the part included in offline software releases. There are several thousand commits to the central repository by about 100 individual developers per year. To keep a coherent software stack of high quality that it can be sustained and used efficiently for data acquisition, simulation, reconstruction, and analysis over the lifetime of the Belle II experiment is a challenge. A set of tools is employed to monitor the quality of the software and provide fast feedback to the developers. They are integrated in a machinery that is controlled by a buildbot master and automates the quality checks. The tools include different compilers, cppcheck, the clang static analyzer, valgrind memcheck, doxygen, a geometry overlap checker, a check for missing or extra library links, unit tests, steering file level tests, a sophisticated high-level validation suite, and an issue tracker. The technological development infrastructure is complemented by organizational means to coordinate the development.

Desiderata for a Computer-Assisted Audit Tool for Clinical Data Source Verification Audits

PubMed Central

Duda, Stephany N.; Wehbe, Firas H.; Gadd, Cynthia S.

2013-01-01

Clinical data auditing often requires validating the contents of clinical research databases against source documents available in health care settings. Currently available data audit software, however, does not provide features necessary to compare the contents of such databases to source data in paper medical records. This work enumerates the primary weaknesses of using paper forms for clinical data audits and identifies the shortcomings of existing data audit software, as informed by the experiences of an audit team evaluating data quality for an international research consortium. The authors propose a set of attributes to guide the development of a computer-assisted clinical data audit tool to simplify and standardize the audit process. PMID:20841814

Software Development Technologies for Reactive, Real-Time, and Hybrid Systems

NASA Technical Reports Server (NTRS)

Manna, Zohar

1996-01-01

The research is directed towards the design and implementation of a comprehensive deductive environment for the development of high-assurance systems, especially reactive (concurrent, real-time, and hybrid) systems. Reactive systems maintain an ongoing interaction with their environment, and are among the most difficult to design and verify. The project aims to provide engineers with a wide variety of tools within a single, general, formal framework in which the tools will be most effective. The entire development process is considered, including the construction, transformation, validation, verification, debugging, and maintenance of computer systems. The goal is to automate the process as much as possible and reduce the errors that pervade hardware and software development.

CFD Fuel Slosh Modeling of Fluid-Structure Interaction in Spacecraft Propellant Tanks with Diaphragms

NASA Technical Reports Server (NTRS)

Sances, Dillon J.; Gangadharan, Sathya N.; Sudermann, James E.; Marsell, Brandon

2010-01-01

Liquid sloshing within spacecraft propellant tanks causes rapid energy dissipation at resonant modes, which can result in attitude destabilization of the vehicle. Identifying resonant slosh modes currently requires experimental testing and mechanical pendulum analogs to characterize the slosh dynamics. Computational Fluid Dynamics (CFD) techniques have recently been validated as an effective tool for simulating fuel slosh within free-surface propellant tanks. Propellant tanks often incorporate an internal flexible diaphragm to separate ullage and propellant which increases modeling complexity. A coupled fluid-structure CFD model is required to capture the damping effects of a flexible diaphragm on the propellant. ANSYS multidisciplinary engineering software employs a coupled solver for analyzing two-way Fluid Structure Interaction (FSI) cases such as the diaphragm propellant tank system. Slosh models generated by ANSYS software are validated by experimental lateral slosh test results. Accurate data correlation would produce an innovative technique for modeling fuel slosh within diaphragm tanks and provide an accurate and efficient tool for identifying resonant modes and the slosh dynamic response.

Implementing Lumberjacks and Black Swans Into Model-Based Tools to Support Human-Automation Interaction.

PubMed

Sebok, Angelia; Wickens, Christopher D

2017-03-01

The objectives were to (a) implement theoretical perspectives regarding human-automation interaction (HAI) into model-based tools to assist designers in developing systems that support effective performance and (b) conduct validations to assess the ability of the models to predict operator performance. Two key concepts in HAI, the lumberjack analogy and black swan events, have been studied extensively. The lumberjack analogy describes the effects of imperfect automation on operator performance. In routine operations, an increased degree of automation supports performance, but in failure conditions, increased automation results in more significantly impaired performance. Black swans are the rare and unexpected failures of imperfect automation. The lumberjack analogy and black swan concepts have been implemented into three model-based tools that predict operator performance in different systems. These tools include a flight management system, a remotely controlled robotic arm, and an environmental process control system. Each modeling effort included a corresponding validation. In one validation, the software tool was used to compare three flight management system designs, which were ranked in the same order as predicted by subject matter experts. The second validation compared model-predicted operator complacency with empirical performance in the same conditions. The third validation compared model-predicted and empirically determined time to detect and repair faults in four automation conditions. The three model-based tools offer useful ways to predict operator performance in complex systems. The three tools offer ways to predict the effects of different automation designs on operator performance.

Reliability and Validity of the Footprint Assessment Method Using Photoshop CS5 Software.

PubMed

Gutiérrez-Vilahú, Lourdes; Massó-Ortigosa, Núria; Costa-Tutusaus, Lluís; Guerra-Balic, Myriam

2015-05-01

Several sophisticated methods of footprint analysis currently exist. However, it is sometimes useful to apply standard measurement methods of recognized evidence with an easy and quick application. We sought to assess the reliability and validity of a new method of footprint assessment in a healthy population using Photoshop CS5 software (Adobe Systems Inc, San Jose, California). Forty-two footprints, corresponding to 21 healthy individuals (11 men with a mean ± SD age of 20.45 ± 2.16 years and 10 women with a mean ± SD age of 20.00 ± 1.70 years) were analyzed. Footprints were recorded in static bipedal standing position using optical podography and digital photography. Three trials for each participant were performed. The Hernández-Corvo, Chippaux-Smirak, and Staheli indices and the Clarke angle were calculated by manual method and by computerized method using Photoshop CS5 software. Test-retest was used to determine reliability. Validity was obtained by intraclass correlation coefficient (ICC). The reliability test for all of the indices showed high values (ICC, 0.98-0.99). Moreover, the validity test clearly showed no difference between techniques (ICC, 0.99-1). The reliability and validity of a method to measure, assess, and record the podometric indices using Photoshop CS5 software has been demonstrated. This provides a quick and accurate tool useful for the digital recording of morphostatic foot study parameters and their control.

Integrated software for the detection of epileptogenic zones in refractory epilepsy.

PubMed

Mottini, Alejandro; Miceli, Franco; Albin, Germán; Nuñez, Margarita; Ferrándo, Rodolfo; Aguerrebere, Cecilia; Fernandez, Alicia

2010-01-01

In this paper we present an integrated software designed to help nuclear medicine physicians in the detection of epileptogenic zones (EZ) by means of ictal-interictal SPECT and MR images. This tool was designed to be flexible, friendly and efficient. A novel detection method was included (A-contrario) along with the classical detection method (Subtraction analysis). The software's performance was evaluated with two separate sets of validation studies: visual interpretation of 12 patient images by an experimented observer and objective analysis of virtual brain phantom experiments by proposed numerical observers. Our results support the potential use of the proposed software to help nuclear medicine physicians in the detection of EZ in clinical practice.

Validation of a Custom-made Software for DQE Assessment in Mammography Digital Detectors

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

Ayala-Dominguez, L.; Perez-Ponce, H.; Brandan, M. E.

2010-12-07

This works presents the validation of a custom-made software, designed and developed in Matlab, intended for routine evaluation of detective quantum efficiency DQE, according to algorithms described in the IEC 62220-1-2 standard. DQE, normalized noise power spectrum NNPS and pre-sampling modulation transfer function MTF were calculated from RAW images from a GE Senographe DS (FineView disabled) and a Siemens Novation system. Calculated MTF is in close agreement with results obtained with alternative codes: MTF lowbar tool (Maidment), ImageJ plug-in (Perez-Ponce) and MIQuaELa (Ayala). Overall agreement better than {approx_equal}90% was found in MTF; the largest differences were observed at frequencies closemore » to the Nyquist limit. For the measurement of NNPS and DQE, agreement is similar to that obtained in the MTF. These results suggest that the developed software can be used with confidence for image quality assessment.« less

Kedalion: NASA's Adaptable and Agile Hardware/Software Integration and Test Lab

NASA Technical Reports Server (NTRS)

Mangieri, Mark L.; Vice, Jason

2011-01-01

NASA fs Kedalion engineering analysis lab at Johnson Space Center is on the forefront of validating and using many contemporary avionics hardware/software development and integration techniques, which represent new paradigms to heritage NASA culture. Kedalion has validated many of the Orion hardware/software engineering techniques borrowed from the adjacent commercial aircraft avionics solution space, with the intention to build upon such techniques to better align with today fs aerospace market. Using agile techniques, commercial products, early rapid prototyping, in-house expertise and tools, and customer collaboration, Kedalion has demonstrated that cost effective contemporary paradigms hold the promise to serve future NASA endeavors within a diverse range of system domains. Kedalion provides a readily adaptable solution for medium/large scale integration projects. The Kedalion lab is currently serving as an in-line resource for the project and the Multipurpose Crew Vehicle (MPCV) program.

GLUE 2 deployment: Ensuring quality in the EGI/WLCG information system

NASA Astrophysics Data System (ADS)

Burke, Stephen; Alandes Pradillo, Maria; Field, Laurence; Keeble, Oliver

2014-06-01

The GLUE 2 information model is now fully supported in the production EGI/WLCG information system. However, to make it usable and allow clients to rely on the published information it is important that the meaning is clearly defined, and that information providers and site configurations are validated to ensure as far as possible that what they publish is correct. In this paper we describe the definition of a detailed schema usage profile, the implementation of a software tool to validate published information according to the profile and the use of the tool in the production Grid, and also summarise the overall state of GLUE 2 deployment.

Revisiting Information Technology tools serving authorship and editorship: a case-guided tutorial to statistical analysis and plagiarism detection

PubMed Central

Bamidis, P D; Lithari, C; Konstantinidis, S T

2010-01-01

With the number of scientific papers published in journals, conference proceedings, and international literature ever increasing, authors and reviewers are not only facilitated with an abundance of information, but unfortunately continuously confronted with risks associated with the erroneous copy of another's material. In parallel, Information Communication Technology (ICT) tools provide to researchers novel and continuously more effective ways to analyze and present their work. Software tools regarding statistical analysis offer scientists the chance to validate their work and enhance the quality of published papers. Moreover, from the reviewers and the editor's perspective, it is now possible to ensure the (text-content) originality of a scientific article with automated software tools for plagiarism detection. In this paper, we provide a step-bystep demonstration of two categories of tools, namely, statistical analysis and plagiarism detection. The aim is not to come up with a specific tool recommendation, but rather to provide useful guidelines on the proper use and efficiency of either category of tools. In the context of this special issue, this paper offers a useful tutorial to specific problems concerned with scientific writing and review discourse. A specific neuroscience experimental case example is utilized to illustrate the young researcher's statistical analysis burden, while a test scenario is purpose-built using open access journal articles to exemplify the use and comparative outputs of seven plagiarism detection software pieces. PMID:21487489

Revisiting Information Technology tools serving authorship and editorship: a case-guided tutorial to statistical analysis and plagiarism detection.

PubMed

Bamidis, P D; Lithari, C; Konstantinidis, S T

2010-12-01

With the number of scientific papers published in journals, conference proceedings, and international literature ever increasing, authors and reviewers are not only facilitated with an abundance of information, but unfortunately continuously confronted with risks associated with the erroneous copy of another's material. In parallel, Information Communication Technology (ICT) tools provide to researchers novel and continuously more effective ways to analyze and present their work. Software tools regarding statistical analysis offer scientists the chance to validate their work and enhance the quality of published papers. Moreover, from the reviewers and the editor's perspective, it is now possible to ensure the (text-content) originality of a scientific article with automated software tools for plagiarism detection. In this paper, we provide a step-bystep demonstration of two categories of tools, namely, statistical analysis and plagiarism detection. The aim is not to come up with a specific tool recommendation, but rather to provide useful guidelines on the proper use and efficiency of either category of tools. In the context of this special issue, this paper offers a useful tutorial to specific problems concerned with scientific writing and review discourse. A specific neuroscience experimental case example is utilized to illustrate the young researcher's statistical analysis burden, while a test scenario is purpose-built using open access journal articles to exemplify the use and comparative outputs of seven plagiarism detection software pieces.

Validity and reliability of balance assessment software using the Nintendo Wii balance board: usability and validation

PubMed Central

2014-01-01

Background A balance test provides important information such as the standard to judge an individual’s functional recovery or make the prediction of falls. The development of a tool for a balance test that is inexpensive and widely available is needed, especially in clinical settings. The Wii Balance Board (WBB) is designed to test balance, but there is little software used in balance tests, and there are few studies on reliability and validity. Thus, we developed a balance assessment software using the Nintendo Wii Balance Board, investigated its reliability and validity, and compared it with a laboratory-grade force platform. Methods Twenty healthy adults participated in our study. The participants participated in the test for inter-rater reliability, intra-rater reliability, and concurrent validity. The tests were performed with balance assessment software using the Nintendo Wii balance board and a laboratory-grade force platform. Data such as Center of Pressure (COP) path length and COP velocity were acquired from the assessment systems. The inter-rater reliability, the intra-rater reliability, and concurrent validity were analyzed by an intraclass correlation coefficient (ICC) value and a standard error of measurement (SEM). Results The inter-rater reliability (ICC: 0.89-0.79, SEM in path length: 7.14-1.90, SEM in velocity: 0.74-0.07), intra-rater reliability (ICC: 0.92-0.70, SEM in path length: 7.59-2.04, SEM in velocity: 0.80-0.07), and concurrent validity (ICC: 0.87-0.73, SEM in path length: 5.94-0.32, SEM in velocity: 0.62-0.08) were high in terms of COP path length and COP velocity. Conclusion The balance assessment software incorporating the Nintendo Wii balance board was used in our study and was found to be a reliable assessment device. In clinical settings, the device can be remarkably inexpensive, portable, and convenient for the balance assessment. PMID:24912769

Validity and reliability of balance assessment software using the Nintendo Wii balance board: usability and validation.

PubMed

Park, Dae-Sung; Lee, GyuChang

2014-06-10

A balance test provides important information such as the standard to judge an individual's functional recovery or make the prediction of falls. The development of a tool for a balance test that is inexpensive and widely available is needed, especially in clinical settings. The Wii Balance Board (WBB) is designed to test balance, but there is little software used in balance tests, and there are few studies on reliability and validity. Thus, we developed a balance assessment software using the Nintendo Wii Balance Board, investigated its reliability and validity, and compared it with a laboratory-grade force platform. Twenty healthy adults participated in our study. The participants participated in the test for inter-rater reliability, intra-rater reliability, and concurrent validity. The tests were performed with balance assessment software using the Nintendo Wii balance board and a laboratory-grade force platform. Data such as Center of Pressure (COP) path length and COP velocity were acquired from the assessment systems. The inter-rater reliability, the intra-rater reliability, and concurrent validity were analyzed by an intraclass correlation coefficient (ICC) value and a standard error of measurement (SEM). The inter-rater reliability (ICC: 0.89-0.79, SEM in path length: 7.14-1.90, SEM in velocity: 0.74-0.07), intra-rater reliability (ICC: 0.92-0.70, SEM in path length: 7.59-2.04, SEM in velocity: 0.80-0.07), and concurrent validity (ICC: 0.87-0.73, SEM in path length: 5.94-0.32, SEM in velocity: 0.62-0.08) were high in terms of COP path length and COP velocity. The balance assessment software incorporating the Nintendo Wii balance board was used in our study and was found to be a reliable assessment device. In clinical settings, the device can be remarkably inexpensive, portable, and convenient for the balance assessment.

Applications of the pipeline environment for visual informatics and genomics computations

PubMed Central

2011-01-01

Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community. PMID:21791102

Expert system verification and validation study. Phase 2: Requirements Identification. Delivery 2: Current requirements applicability

NASA Technical Reports Server (NTRS)

1991-01-01

The second phase of a task is described which has the ultimate purpose of ensuring that adequate Expert Systems (ESs) Verification and Validation (V and V) tools and techniques are available for Space Station Freedom Program Knowledge Based Systems development. The purpose of this phase is to recommend modifications to current software V and V requirements which will extend the applicability of the requirements to NASA ESs.

Reviews of Selected System and Software Tools for Strategic Defense Applications

DTIC Science & Technology

1990-02-01

Interleaf and FrameMaker . IStatic Diagnostics Basic testing includes validating flows, detecting orphan activity, and checking completeness of activities...Publisher, Aldus PageMaker, Unix pic, Apple .pict metafile, Interleaf, Framemaker , or Postscript format. There are no forms for standard documents such as 3

SLDAssay: A software package and web tool for analyzing limiting dilution assays.

PubMed

Trumble, Ilana M; Allmon, Andrew G; Archin, Nancie M; Rigdon, Joseph; Francis, Owen; Baldoni, Pedro L; Hudgens, Michael G

2017-11-01

Serial limiting dilution (SLD) assays are used in many areas of infectious disease related research. This paper presents SLDAssay, a free and publicly available R software package and web tool for analyzing data from SLD assays. SLDAssay computes the maximum likelihood estimate (MLE) for the concentration of target cells, with corresponding exact and asymptotic confidence intervals. Exact and asymptotic goodness of fit p-values, and a bias-corrected (BC) MLE are also provided. No other publicly available software currently implements the BC MLE or the exact methods. For validation of SLDAssay, results from Myers et al. (1994) are replicated. Simulations demonstrate the BC MLE is less biased than the MLE. Additionally, simulations demonstrate that exact methods tend to give better confidence interval coverage and goodness-of-fit tests with lower type I error than the asymptotic methods. Additional advantages of using exact methods are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Software support for SBGN maps: SBGN-ML and LibSBGN.

PubMed

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

The AAO fiber instrument data simulator

NASA Astrophysics Data System (ADS)

Goodwin, Michael; Farrell, Tony; Smedley, Scott; Heald, Ron; Heijmans, Jeroen; De Silva, Gayandhi; Carollo, Daniela

2012-09-01

The fiber instrument data simulator is an in-house software tool that simulates detector images of fiber-fed spectrographs developed by the Australian Astronomical Observatory (AAO). In addition to helping validate the instrument designs, the resulting simulated images are used to develop the required data reduction software. Example applications that have benefited from the tool usage are the HERMES and SAMI instrumental projects for the Anglo-Australian Telescope (AAT). Given the sophistication of these projects an end-to-end data simulator that accurately models the predicted detector images is required. The data simulator encompasses all aspects of the transmission and optical aberrations of the light path: from the science object, through the atmosphere, telescope, fibers, spectrograph and finally the camera detectors. The simulator runs under a Linux environment that uses pre-calculated information derived from ZEMAX models and processed data from MATLAB. In this paper, we discuss the aspects of the model, software, example simulations and verification.

Current Practice in Software Development for Computational Neuroscience and How to Improve It

PubMed Central

Gewaltig, Marc-Oliver; Cannon, Robert

2014-01-01

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness. We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research. PMID:24465191

Current practice in software development for computational neuroscience and how to improve it.

PubMed

Gewaltig, Marc-Oliver; Cannon, Robert

2014-01-01

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness. We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research.

MASH Suite: a user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization.

PubMed

Guner, Huseyin; Close, Patrick L; Cai, Wenxuan; Zhang, Han; Peng, Ying; Gregorich, Zachery R; Ge, Ying

2014-03-01

The rapid advancements in mass spectrometry (MS) instrumentation, particularly in Fourier transform (FT) MS, have made the acquisition of high-resolution and high-accuracy mass measurements routine. However, the software tools for the interpretation of high-resolution MS data are underdeveloped. Although several algorithms for the automatic processing of high-resolution MS data are available, there is still an urgent need for a user-friendly interface with functions that allow users to visualize and validate the computational output. Therefore, we have developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution MS data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution MS data, and manually validate automatically processed results. Furthermore, it provides easy, fast, and reliable interpretation of top-down, middle-down, and bottom-up MS data. MASH Suite is convenient, easily operated, and freely available. It can greatly facilitate the comprehensive interpretation and validation of high-resolution MS data with high accuracy and reliability.

A method for the complete analysis of NORM building materials by γ-ray spectrometry using HPGe detectors.

PubMed

Quintana, B; Pedrosa, M C; Vázquez-Canelas, L; Santamaría, R; Sanjuán, M A; Puertas, F

2018-04-01

A methodology including software tools for analysing NORM building materials and residues by low-level gamma-ray spectrometry has been developed. It comprises deconvolution of gamma-ray spectra using the software GALEA with focus on the natural radionuclides and Monte Carlo simulations for efficiency and true coincidence summing corrections. The methodology has been tested on a range of building materials and validated against reference materials. Copyright © 2017 Elsevier Ltd. All rights reserved.

Software Development Cost Estimation Executive Summary

NASA Technical Reports Server (NTRS)

Hihn, Jairus M.; Menzies, Tim

2006-01-01

Identify simple fully validated cost models that provide estimation uncertainty with cost estimate. Based on COCOMO variable set. Use machine learning techniques to determine: a) Minimum number of cost drivers required for NASA domain based cost models; b) Minimum number of data records required and c) Estimation Uncertainty. Build a repository of software cost estimation information. Coordinating tool development and data collection with: a) Tasks funded by PA&E Cost Analysis; b) IV&V Effort Estimation Task and c) NASA SEPG activities.

Automatic control system generation for robot design validation

NASA Technical Reports Server (NTRS)

Bacon, James A. (Inventor); English, James D. (Inventor)

2012-01-01

The specification and drawings present a new method, system and software product for and apparatus for generating a robotic validation system for a robot design. The robotic validation system for the robot design of a robotic system is automatically generated by converting a robot design into a generic robotic description using a predetermined format, then generating a control system from the generic robotic description and finally updating robot design parameters of the robotic system with an analysis tool using both the generic robot description and the control system.

Validation of a Video Analysis Software Package for Quantifying Movement Velocity in Resistance Exercises.

PubMed

Sañudo, Borja; Rueda, David; Pozo-Cruz, Borja Del; de Hoyo, Moisés; Carrasco, Luis

2016-10-01

Sañudo, B, Rueda, D, del Pozo-Cruz, B, de Hoyo, M, and Carrasco, L. Validation of a video analysis software package for quantifying movement velocity in resistance exercises. J Strength Cond Res 30(10): 2934-2941, 2016-The aim of this study was to establish the validity of a video analysis software package in measuring mean propulsive velocity (MPV) and the maximal velocity during bench press. Twenty-one healthy males (21 ± 1 year) with weight training experience were recruited, and the MPV and the maximal velocity of the concentric phase (Vmax) were compared with a linear position transducer system during a standard bench press exercise. Participants performed a 1 repetition maximum test using the supine bench press exercise. The testing procedures involved the simultaneous assessment of bench press propulsive velocity using 2 kinematic (linear position transducer and semi-automated tracking software) systems. High Pearson's correlation coefficients for MPV and Vmax between both devices (r = 0.473 to 0.993) were observed. The intraclass correlation coefficients for barbell velocity data and the kinematic data obtained from video analysis were high (>0.79). In addition, the low coefficients of variation indicate that measurements had low variability. Finally, Bland-Altman plots with the limits of agreement of the MPV and Vmax with different loads showed a negative trend, which indicated that the video analysis had higher values than the linear transducer. In conclusion, this study has demonstrated that the software used for the video analysis was an easy to use and cost-effective tool with a very high degree of concurrent validity. This software can be used to evaluate changes in velocity of training load in resistance training, which may be important for the prescription and monitoring of training programmes.

SimDoseCT: dose reporting software based on Monte Carlo simulation for a 320 detector-row cone-beam CT scanner and ICRP computational adult phantoms

NASA Astrophysics Data System (ADS)

Cros, Maria; Joemai, Raoul M. S.; Geleijns, Jacob; Molina, Diego; Salvadó, Marçal

2017-08-01

This study aims to develop and test software for assessing and reporting doses for standard patients undergoing computed tomography (CT) examinations in a 320 detector-row cone-beam scanner. The software, called SimDoseCT, is based on the Monte Carlo (MC) simulation code, which was developed to calculate organ doses and effective doses in ICRP anthropomorphic adult reference computational phantoms for acquisitions with the Aquilion ONE CT scanner (Toshiba). MC simulation was validated by comparing CTDI measurements within standard CT dose phantoms with results from simulation under the same conditions. SimDoseCT consists of a graphical user interface connected to a MySQL database, which contains the look-up-tables that were generated with MC simulations for volumetric acquisitions at different scan positions along the phantom using any tube voltage, bow tie filter, focal spot and nine different beam widths. Two different methods were developed to estimate organ doses and effective doses from acquisitions using other available beam widths in the scanner. A correction factor was used to estimate doses in helical acquisitions. Hence, the user can select any available protocol in the Aquilion ONE scanner for a standard adult male or female and obtain the dose results through the software interface. Agreement within 9% between CTDI measurements and simulations allowed the validation of the MC program. Additionally, the algorithm for dose reporting in SimDoseCT was validated by comparing dose results from this tool with those obtained from MC simulations for three volumetric acquisitions (head, thorax and abdomen). The comparison was repeated using eight different collimations and also for another collimation in a helical abdomen examination. The results showed differences of 0.1 mSv or less for absolute dose in most organs and also in the effective dose calculation. The software provides a suitable tool for dose assessment in standard adult patients undergoing CT examinations in a 320 detector-row cone-beam scanner.

SimDoseCT: dose reporting software based on Monte Carlo simulation for a 320 detector-row cone-beam CT scanner and ICRP computational adult phantoms.

PubMed

Cros, Maria; Joemai, Raoul M S; Geleijns, Jacob; Molina, Diego; Salvadó, Marçal

2017-07-17

This study aims to develop and test software for assessing and reporting doses for standard patients undergoing computed tomography (CT) examinations in a 320 detector-row cone-beam scanner. The software, called SimDoseCT, is based on the Monte Carlo (MC) simulation code, which was developed to calculate organ doses and effective doses in ICRP anthropomorphic adult reference computational phantoms for acquisitions with the Aquilion ONE CT scanner (Toshiba). MC simulation was validated by comparing CTDI measurements within standard CT dose phantoms with results from simulation under the same conditions. SimDoseCT consists of a graphical user interface connected to a MySQL database, which contains the look-up-tables that were generated with MC simulations for volumetric acquisitions at different scan positions along the phantom using any tube voltage, bow tie filter, focal spot and nine different beam widths. Two different methods were developed to estimate organ doses and effective doses from acquisitions using other available beam widths in the scanner. A correction factor was used to estimate doses in helical acquisitions. Hence, the user can select any available protocol in the Aquilion ONE scanner for a standard adult male or female and obtain the dose results through the software interface. Agreement within 9% between CTDI measurements and simulations allowed the validation of the MC program. Additionally, the algorithm for dose reporting in SimDoseCT was validated by comparing dose results from this tool with those obtained from MC simulations for three volumetric acquisitions (head, thorax and abdomen). The comparison was repeated using eight different collimations and also for another collimation in a helical abdomen examination. The results showed differences of 0.1 mSv or less for absolute dose in most organs and also in the effective dose calculation. The software provides a suitable tool for dose assessment in standard adult patients undergoing CT examinations in a 320 detector-row cone-beam scanner.

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

Fault Injection Validation of a Safety-Critical TMR Sysem

NASA Astrophysics Data System (ADS)

Irrera, Ivano; Madeira, Henrique; Zentai, Andras; Hergovics, Beata

2016-08-01

Digital systems and their software are the core technology for controlling and monitoring industrial systems in practically all activity domains. Functional safety standards such as the European standard EN 50128 for railway applications define the procedures and technical requirements for the development of software for railway control and protection systems. The validation of such systems is a highly demanding task. In this paper we discuss the use of fault injection techniques, which have been used extensively in several domains, particularly in the space domain, to complement the traditional procedures to validate a SIL (Safety Integrity Level) 4 system for railway signalling, implementing a TMR (Triple Modular Redundancy) architecture. The fault injection tool is based on JTAG technology. The results of our injection campaign showed a high degree of tolerance to most of the injected faults, but several cases of unexpected behaviour have also been observed, helping understanding worst-case scenarios.

Electric Vehicle Battery Development Gains Momentum - Continuum Magazine

Science.gov Websites

to improve and accelerate battery design and boost EDV performance and consumer appeal - and chemistry, cell design, and battery pack options for particular vehicle platforms Factor in electrochemical separate, competitive, validated, and easy-to-use CAEBAT software tools for battery pack design. The three

extrap: Software to assist the selection of extrapolation methods for moving-boat ADCP streamflow measurements

NASA Astrophysics Data System (ADS)

Mueller, David S.

2013-04-01

Selection of the appropriate extrapolation methods for computing the discharge in the unmeasured top and bottom parts of a moving-boat acoustic Doppler current profiler (ADCP) streamflow measurement is critical to the total discharge computation. The software tool, extrap, combines normalized velocity profiles from the entire cross section and multiple transects to determine a mean profile for the measurement. The use of an exponent derived from normalized data from the entire cross section is shown to be valid for application of the power velocity distribution law in the computation of the unmeasured discharge in a cross section. Selected statistics are combined with empirically derived criteria to automatically select the appropriate extrapolation methods. A graphical user interface (GUI) provides the user tools to visually evaluate the automatically selected extrapolation methods and manually change them, as necessary. The sensitivity of the total discharge to available extrapolation methods is presented in the GUI. Use of extrap by field hydrographers has demonstrated that extrap is a more accurate and efficient method of determining the appropriate extrapolation methods compared with tools currently (2012) provided in the ADCP manufacturers' software.

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

2018-03-27

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

Hekate: Software Suite for the Mass Spectrometric Analysis and Three-Dimensional Visualization of Cross-Linked Protein Samples

PubMed Central

2013-01-01

Chemical cross-linking of proteins combined with mass spectrometry provides an attractive and novel method for the analysis of native protein structures and protein complexes. Analysis of the data however is complex. Only a small number of cross-linked peptides are produced during sample preparation and must be identified against a background of more abundant native peptides. To facilitate the search and identification of cross-linked peptides, we have developed a novel software suite, named Hekate. Hekate is a suite of tools that address the challenges involved in analyzing protein cross-linking experiments when combined with mass spectrometry. The software is an integrated pipeline for the automation of the data analysis workflow and provides a novel scoring system based on principles of linear peptide analysis. In addition, it provides a tool for the visualization of identified cross-links using three-dimensional models, which is particularly useful when combining chemical cross-linking with other structural techniques. Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight into the previously uncharacterized C-terminal domain of the protein. PMID:24010795

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

Chandra X-ray Center Science Data Systems Regression Testing of CIAO

NASA Astrophysics Data System (ADS)

Lee, N. P.; Karovska, M.; Galle, E. C.; Bonaventura, N. R.

2011-07-01

The Chandra Interactive Analysis of Observations (CIAO) is a software system developed for the analysis of Chandra X-ray Observatory observations. An important component of a successful CIAO release is the repeated testing of the tools across various platforms to ensure consistent and scientifically valid results. We describe the procedures of the scientific regression testing of CIAO and the enhancements made to the testing system to increase the efficiency of run time and result validation.

Nurturing reliable and robust open-source scientific software

NASA Astrophysics Data System (ADS)

Uieda, L.; Wessel, P.

2017-12-01

Scientific results are increasingly the product of software. The reproducibility and validity of published results cannot be ensured without access to the source code of the software used to produce them. Therefore, the code itself is a fundamental part of the methodology and must be published along with the results. With such a reliance on software, it is troubling that most scientists do not receive formal training in software development. Tools such as version control, continuous integration, and automated testing are routinely used in industry to ensure the correctness and robustness of software. However, many scientist do not even know of their existence (although efforts like Software Carpentry are having an impact on this issue; software-carpentry.org). Publishing the source code is only the first step in creating an open-source project. For a project to grow it must provide documentation, participation guidelines, and a welcoming environment for new contributors. Expanding the project community is often more challenging than the technical aspects of software development. Maintainers must invest time to enforce the rules of the project and to onboard new members, which can be difficult to justify in the context of the "publish or perish" mentality. This problem will continue as long as software contributions are not recognized as valid scholarship by hiring and tenure committees. Furthermore, there are still unsolved problems in providing attribution for software contributions. Many journals and metrics of academic productivity do not recognize citations to sources other than traditional publications. Thus, some authors choose to publish an article about the software and use it as a citation marker. One issue with this approach is that updating the reference to include new contributors involves writing and publishing a new article. A better approach would be to cite a permanent archive of individual versions of the source code in services such as Zenodo (zenodo.org). However, citations to these sources are not always recognized when computing citation metrics. In summary, the widespread development of reliable and robust open-source software relies on the creation of formal training programs in software development best practices and the recognition of software as a valid form of scholarship.

Next Generation Nuclear Plant Methods Research and Development Technical Program Plan -- PLN-2498

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

Richard R. Schultz; Abderrafi M. Ougouag; David W. Nigg

2008-09-01

One of the great challenges of designing and licensing the Very High Temperature Reactor (VHTR) is to confirm that the intended VHTR analysis tools can be used confidently to make decisions and to assure all that the reactor systems are safe and meet the performance objectives of the Generation IV Program. The research and development (R&D) projects defined in the Next Generation Nuclear Plant (NGNP) Design Methods Development and Validation Program will ensure that the tools used to perform the required calculations and analyses can be trusted. The Methods R&D tasks are designed to ensure that the calculational envelope ofmore » the tools used to analyze the VHTR reactor systems encompasses, or is larger than, the operational and transient envelope of the VHTR itself. The Methods R&D focuses on the development of tools to assess the neutronic and thermal fluid behavior of the plant. The fuel behavior and fission product transport models are discussed in the Advanced Gas Reactor (AGR) program plan. Various stress analysis and mechanical design tools will also need to be developed and validated and will ultimately also be included in the Methods R&D Program Plan. The calculational envelope of the neutronics and thermal-fluids software tools intended to be used on the NGNP is defined by the scenarios and phenomena that these tools can calculate with confidence. The software tools can only be used confidently when the results they produce have been shown to be in reasonable agreement with first-principle results, thought-problems, and data that describe the “highly ranked” phenomena inherent in all operational conditions and important accident scenarios for the VHTR.« less

Next Generation Nuclear Plant Methods Technical Program Plan

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

Richard R. Schultz; Abderrafi M. Ougouag; David W. Nigg

2010-12-01

One of the great challenges of designing and licensing the Very High Temperature Reactor (VHTR) is to confirm that the intended VHTR analysis tools can be used confidently to make decisions and to assure all that the reactor systems are safe and meet the performance objectives of the Generation IV Program. The research and development (R&D) projects defined in the Next Generation Nuclear Plant (NGNP) Design Methods Development and Validation Program will ensure that the tools used to perform the required calculations and analyses can be trusted. The Methods R&D tasks are designed to ensure that the calculational envelope ofmore » the tools used to analyze the VHTR reactor systems encompasses, or is larger than, the operational and transient envelope of the VHTR itself. The Methods R&D focuses on the development of tools to assess the neutronic and thermal fluid behavior of the plant. The fuel behavior and fission product transport models are discussed in the Advanced Gas Reactor (AGR) program plan. Various stress analysis and mechanical design tools will also need to be developed and validated and will ultimately also be included in the Methods R&D Program Plan. The calculational envelope of the neutronics and thermal-fluids software tools intended to be used on the NGNP is defined by the scenarios and phenomena that these tools can calculate with confidence. The software tools can only be used confidently when the results they produce have been shown to be in reasonable agreement with first-principle results, thought-problems, and data that describe the “highly ranked” phenomena inherent in all operational conditions and important accident scenarios for the VHTR.« less

Next Generation Nuclear Plant Methods Technical Program Plan -- PLN-2498

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

Richard R. Schultz; Abderrafi M. Ougouag; David W. Nigg

2010-09-01

One of the great challenges of designing and licensing the Very High Temperature Reactor (VHTR) is to confirm that the intended VHTR analysis tools can be used confidently to make decisions and to assure all that the reactor systems are safe and meet the performance objectives of the Generation IV Program. The research and development (R&D) projects defined in the Next Generation Nuclear Plant (NGNP) Design Methods Development and Validation Program will ensure that the tools used to perform the required calculations and analyses can be trusted. The Methods R&D tasks are designed to ensure that the calculational envelope ofmore » the tools used to analyze the VHTR reactor systems encompasses, or is larger than, the operational and transient envelope of the VHTR itself. The Methods R&D focuses on the development of tools to assess the neutronic and thermal fluid behavior of the plant. The fuel behavior and fission product transport models are discussed in the Advanced Gas Reactor (AGR) program plan. Various stress analysis and mechanical design tools will also need to be developed and validated and will ultimately also be included in the Methods R&D Program Plan. The calculational envelope of the neutronics and thermal-fluids software tools intended to be used on the NGNP is defined by the scenarios and phenomena that these tools can calculate with confidence. The software tools can only be used confidently when the results they produce have been shown to be in reasonable agreement with first-principle results, thought-problems, and data that describe the “highly ranked” phenomena inherent in all operational conditions and important accident scenarios for the VHTR.« less

CaveMan Enterprise version 1.0 Software Validation and Verification.

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

Hart, David

The U.S. Department of Energy Strategic Petroleum Reserve stores crude oil in caverns solution-mined in salt domes along the Gulf Coast of Louisiana and Texas. The CaveMan software program has been used since the late 1990s as one tool to analyze pressure mea- surements monitored at each cavern. The purpose of this monitoring is to catch potential cavern integrity issues as soon as possible. The CaveMan software was written in Microsoft Visual Basic, and embedded in a Microsoft Excel workbook; this method of running the CaveMan software is no longer sustainable. As such, a new version called CaveMan Enter- prisemore » has been developed. CaveMan Enterprise version 1.0 does not have any changes to the CaveMan numerical models. CaveMan Enterprise represents, instead, a change from desktop-managed work- books to an enterprise framework, moving data management into coordinated databases and porting the numerical modeling codes into the Python programming language. This document provides a report of the code validation and verification testing.« less

Advances in the production of freeform optical surfaces

NASA Astrophysics Data System (ADS)

Tohme, Yazid E.; Luniya, Suneet S.

2007-05-01

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

NASA Operational Simulator for Small Satellites: Tools for Software Based Validation and Verification of Small Satellites

NASA Technical Reports Server (NTRS)

Grubb, Matt

2016-01-01

The NASA Operational Simulator for Small Satellites (NOS3) is a suite of tools to aid in areas such as software development, integration test (IT), mission operations training, verification and validation (VV), and software systems check-out. NOS3 provides a software development environment, a multi-target build system, an operator interface-ground station, dynamics and environment simulations, and software-based hardware models. NOS3 enables the development of flight software (FSW) early in the project life cycle, when access to hardware is typically not available. For small satellites there are extensive lead times on many of the commercial-off-the-shelf (COTS) components as well as limited funding for engineering test units (ETU). Considering the difficulty of providing a hardware test-bed to each developer tester, hardware models are modeled based upon characteristic data or manufacturers data sheets for each individual component. The fidelity of each hardware models is such that FSW executes unaware that physical hardware is not present. This allows binaries to be compiled for both the simulation environment, and the flight computer, without changing the FSW source code. For hardware models that provide data dependent on the environment, such as a GPS receiver or magnetometer, an open-source tool from NASA GSFC (42 Spacecraft Simulation) is used to provide the necessary data. The underlying infrastructure used to transfer messages between FSW and the hardware models can also be used to monitor, intercept, and inject messages, which has proven to be beneficial for VV of larger missions such as James Webb Space Telescope (JWST). As hardware is procured, drivers can be added to the environment to enable hardware-in-the-loop (HWIL) testing. When strict time synchronization is not vital, any number of combinations of hardware components and software-based models can be tested. The open-source operator interface used in NOS3 is COSMOS from Ball Aerospace. For testing, plug-ins are implemented in COSMOS to control the NOS3 simulations, while the command and telemetry tools available in COSMOS are used to communicate with FSW. NOS3 is actively being used for FSW development and component testing of the Simulation-to-Flight 1 (STF-1) CubeSat. As NOS3 matures, hardware models have been added for common CubeSat components such as Novatel GPS receivers, ClydeSpace electrical power systems and batteries, ISISpace antenna systems, etc. In the future, NASA IVV plans to distribute NOS3 to other CubeSat developers and release the suite to the open-source community.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits.

PubMed

Baig, Hasan; Madsen, Jan

2017-01-15

Simulation and behavioral analysis of genetic circuits is a standard approach of functional verification prior to their physical implementation. Many software tools have been developed to perform in silico analysis for this purpose, but none of them allow users to interact with the model during runtime. The runtime interaction gives the user a feeling of being in the lab performing a real world experiment. In this work, we present a user-friendly software tool named D-VASim (Dynamic Virtual Analyzer and Simulator), which provides a virtual laboratory environment to simulate and analyze the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools by being able to extract and validate the Boolean logic from the SBML model. D-VASim is also capable of analyzing the threshold value and propagation delay of a genetic circuit model. D-VASim is available for Windows and Mac OS and can be downloaded from bda.compute.dtu.dk/downloads/. haba@dtu.dk, jama@dtu.dk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

SAMPA: A free software tool for skin and membrane permeation data analysis.

PubMed

Bezrouk, Aleš; Fiala, Zdeněk; Kotingová, Lenka; Krulichová, Iva Selke; Kopečná, Monika; Vávrová, Kateřina

2017-10-01

Skin and membrane permeation experiments comprise an important step in the development of a transdermal or topical formulation or toxicological risk assessment. The standard method for analyzing these data relies on the linear part of a permeation profile. However, it is difficult to objectively determine when the profile becomes linear, or the experiment duration may be insufficient to reach a maximum or steady state. Here, we present a software tool for Skin And Membrane Permeation data Analysis, SAMPA, that is easy to use and overcomes several of these difficulties. The SAMPA method and software have been validated on in vitro and in vivo permeation data on human, pig and rat skin and model stratum corneum lipid membranes using compounds that range from highly lipophilic polycyclic aromatic hydrocarbons to highly hydrophilic antiviral drug, with and without two permeation enhancers. The SAMPA performance was compared with the standard method using a linear part of the permeation profile and a complex mathematical model. SAMPA is a user-friendly, open-source software tool for analyzing the data obtained from skin and membrane permeation experiments. It runs on a Microsoft Windows platform and is freely available as a Supporting file to this article. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessing ergonomic risks of software: Development of the SEAT.

PubMed

Peres, S Camille; Mehta, Ranjana K; Ritchey, Paul

2017-03-01

Software utilizing interaction designs that require extensive dragging or clicking of icons may increase users' risks for upper extremity cumulative trauma disorders. The purpose of this research is to develop a Self-report Ergonomic Assessment Tool (SEAT) for assessing the risks of software interaction designs and facilitate mitigation of those risks. A 28-item self-report measure was developed by combining and modifying items from existing industrial ergonomic tools. Data were collected from 166 participants after they completed four different tasks that varied by method of input (touch or keyboard and mouse) and type of task (selecting or typing). Principal component analysis found distinct factors associated with stress (i.e., demands) and strain (i.e., response). Repeated measures analyses of variance showed that participants could discriminate the different strain induced by the input methods and tasks. However, participants' ability to discriminate between the stressors associated with that strain was mixed. Further validation of the SEAT is necessary but these results indicate that the SEAT may be a viable method of assessing ergonomics risks presented by software design. Copyright © 2016 Elsevier Ltd. All rights reserved.

Field Validity of Heart Rate Variability Metrics Produced by QRSTool and CMetX

ERIC Educational Resources Information Center

Hibbert, Anita S.; Weinberg, Anna; Klonsky, E. David

2012-01-01

Interest in heart rate variability (HRV) metrics as markers of physiological and psychological health continues to grow beyond those with psychophysiological expertise, increasing the importance of developing suitable tools for researchers new to the field. Allen, Chambers, and Towers (2007) developed QRSTool and CMetX software as simple,…

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.

PubMed

Bray, Mark-Anthony; Carpenter, Anne E

2015-11-04

Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows convenient assessment of track quality, especially for researchers tuning tracking parameters for high-content time-lapse experiments. This makes quality assessment and algorithm adjustment a substantial challenge, particularly when dealing with hundreds of time-lapse movies collected in a high-throughput manner. We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package. Tracer allows multi-parametric morphological data to be visualized on object tracks, providing visualizations that have already been validated within the scientific community for time-lapse experiments, and combining them with simple graph-based measures for highlighting possible tracking artifacts. CellProfiler Tracer is a useful, free tool for inspection and quality control of object tracking data, available from http://www.cellprofiler.org/tracer/.

CrossTalk: The Journal of Defense Software Engineering. Volume 26, Number 6, November/December 2013

DTIC Science & Technology

2013-12-01

requirements during sprint planning. Automated scanning, which includes automated code-review tools, allows the expert to monitor the system... sprint . This enables the validator to leverage the test results for formal validation and verification, and perform a shortened “hybrid” style of IV&V...per SPRINT (1-4 weeks) 1 week 1 Month Up to four months Ø Deliverable product to user Ø Security posture assessed Ø Accredited to field/operate

An Investigation of Software Scaffolds Supporting Modeling Practices

NASA Astrophysics Data System (ADS)

Fretz, Eric B.; Wu, Hsin-Kai; Zhang, Baohui; Davis, Elizabeth A.; Krajcik, Joseph S.; Soloway, Elliot

2002-08-01

Modeling of complex systems and phenomena is of value in science learning and is increasingly emphasised as an important component of science teaching and learning. Modeling engages learners in desired pedagogical activities. These activities include practices such as planning, building, testing, analysing, and critiquing. Designing realistic models is a difficult task. Computer environments allow the creation of dynamic and even more complex models. One way of bringing the design of models within reach is through the use of scaffolds. Scaffolds are intentional assistance provided to learners from a variety of sources, allowing them to complete tasks that would otherwise be out of reach. Currently, our understanding of how scaffolds in software tools assist learners is incomplete. In this paper the scaffolds designed into a dynamic modeling software tool called Model-It are assessed in terms of their ability to support learners' use of modeling practices. Four pairs of middle school students were video-taped as they used the modeling software for three hours, spread over a two week time frame. Detailed analysis of coded videotape transcripts provided evidence of the importance of scaffolds in supporting the use of modeling practices. Learners used a variety of modeling practices, the majority of which occurred in conjunction with scaffolds. The use of three tool scaffolds was assessed as directly as possible, and these scaffolds were seen to support a variety of modeling practices. An argument is made for the continued empirical validation of types and instances of tool scaffolds, and further investigation of the important role of teacher and peer scaffolding in the use of scaffolded tools.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

PubMed Central

2011-01-01

Background Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology. Result We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site. This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser. Conclusions Targeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in http://tools.proteomecenter.org/ATAQS/ATAQS.html PMID:21414234

Detailed requirements document for the integrated structural analysis system, phase B

NASA Technical Reports Server (NTRS)

Rainey, J. A.

1976-01-01

The requirements are defined for a software system entitled integrated Structural Analysis System (ISAS) Phase B which is being developed to provide the user with a tool by which a complete and detailed analysis of a complex structural system can be performed. This software system will allow for automated interface with numerous structural analysis batch programs and for user interaction in the creation, selection, and validation of data. This system will include modifications to the 4 functions developed for ISAS, and the development of 25 new functions. The new functions are described.

Presenting an evaluation model of the trauma registry software.

PubMed

Asadi, Farkhondeh; Paydar, Somayeh

2018-04-01

Trauma is a major cause of 10% death in the worldwide and is considered as a global concern. This problem has made healthcare policy makers and managers to adopt a basic strategy in this context. Trauma registry has an important and basic role in decreasing the mortality and the disabilities due to injuries resulted from trauma. Today, different software are designed for trauma registry. Evaluation of this software improves management, increases efficiency and effectiveness of these systems. Therefore, the aim of this study is to present an evaluation model for trauma registry software. The present study is an applied research. In this study, general and specific criteria of trauma registry software were identified by reviewing literature including books, articles, scientific documents, valid websites and related software in this domain. According to general and specific criteria and related software, a model for evaluating trauma registry software was proposed. Based on the proposed model, a checklist designed and its validity and reliability evaluated. Mentioned model by using of the Delphi technique presented to 12 experts and specialists. To analyze the results, an agreed coefficient of %75 was determined in order to apply changes. Finally, when the model was approved by the experts and professionals, the final version of the evaluation model for the trauma registry software was presented. For evaluating of criteria of trauma registry software, two groups were presented: 1- General criteria, 2- Specific criteria. General criteria of trauma registry software were classified into four main categories including: 1- usability, 2- security, 3- maintainability, and 4-interoperability. Specific criteria were divided into four main categories including: 1- data submission and entry, 2- reporting, 3- quality control, 4- decision and research support. The presented model in this research has introduced important general and specific criteria of trauma registry software and sub criteria related to each main criteria separately. This model was validated by experts in this field. Therefore, this model can be used as a comprehensive model and a standard evaluation tool for measuring efficiency and effectiveness and performance improvement of trauma registry software. Copyright © 2018 Elsevier B.V. All rights reserved.

A Deep Space Orbit Determination Software: Overview and Event Prediction Capability

NASA Astrophysics Data System (ADS)

Kim, Youngkwang; Park, Sang-Young; Lee, Eunji; Kim, Minsik

2017-06-01

This paper presents an overview of deep space orbit determination software (DSODS), as well as validation and verification results on its event prediction capabilities. DSODS was developed in the MATLAB object-oriented programming environment to support the Korea Pathfinder Lunar Orbiter (KPLO) mission. DSODS has three major capabilities: celestial event prediction for spacecraft, orbit determination with deep space network (DSN) tracking data, and DSN tracking data simulation. To achieve its functionality requirements, DSODS consists of four modules: orbit propagation (OP), event prediction (EP), data simulation (DS), and orbit determination (OD) modules. This paper explains the highest-level data flows between modules in event prediction, orbit determination, and tracking data simulation processes. Furthermore, to address the event prediction capability of DSODS, this paper introduces OP and EP modules. The role of the OP module is to handle time and coordinate system conversions, to propagate spacecraft trajectories, and to handle the ephemerides of spacecraft and celestial bodies. Currently, the OP module utilizes the General Mission Analysis Tool (GMAT) as a third-party software component for highfidelity deep space propagation, as well as time and coordinate system conversions. The role of the EP module is to predict celestial events, including eclipses, and ground station visibilities, and this paper presents the functionality requirements of the EP module. The validation and verification results show that, for most cases, event prediction errors were less than 10 millisec when compared with flight proven mission analysis tools such as GMAT and Systems Tool Kit (STK). Thus, we conclude that DSODS is capable of predicting events for the KPLO in real mission applications.

Knowledge-based system verification and validation

NASA Technical Reports Server (NTRS)

Johnson, Sally C.

1990-01-01

The objective of this task is to develop and evaluate a methodology for verification and validation (V&V) of knowledge-based systems (KBS) for space station applications with high reliability requirements. The approach consists of three interrelated tasks. The first task is to evaluate the effectiveness of various validation methods for space station applications. The second task is to recommend requirements for KBS V&V for Space Station Freedom (SSF). The third task is to recommend modifications to the SSF to support the development of KBS using effectiveness software engineering and validation techniques. To accomplish the first task, three complementary techniques will be evaluated: (1) Sensitivity Analysis (Worchester Polytechnic Institute); (2) Formal Verification of Safety Properties (SRI International); and (3) Consistency and Completeness Checking (Lockheed AI Center). During FY89 and FY90, each contractor will independently demonstrate the user of his technique on the fault detection, isolation, and reconfiguration (FDIR) KBS or the manned maneuvering unit (MMU), a rule-based system implemented in LISP. During FY91, the application of each of the techniques to other knowledge representations and KBS architectures will be addressed. After evaluation of the results of the first task and examination of Space Station Freedom V&V requirements for conventional software, a comprehensive KBS V&V methodology will be developed and documented. Development of highly reliable KBS's cannot be accomplished without effective software engineering methods. Using the results of current in-house research to develop and assess software engineering methods for KBS's as well as assessment of techniques being developed elsewhere, an effective software engineering methodology for space station KBS's will be developed, and modification of the SSF to support these tools and methods will be addressed.

An Innovative Software Tool Suite for Power Plant Model Validation and Parameter Calibration using PMU Measurements

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

Li, Yuanyuan; Diao, Ruisheng; Huang, Renke

Maintaining good quality of power plant stability models is of critical importance to ensure the secure and economic operation and planning of today’s power grid with its increasing stochastic and dynamic behavior. According to North American Electric Reliability (NERC) standards, all generators in North America with capacities larger than 10 MVA are required to validate their models every five years. Validation is quite costly and can significantly affect the revenue of generator owners, because the traditional staged testing requires generators to be taken offline. Over the past few years, validating and calibrating parameters using online measurements including phasor measurement unitsmore » (PMUs) and digital fault recorders (DFRs) has been proven to be a cost-effective approach. In this paper, an innovative open-source tool suite is presented for validating power plant models using PPMV tool, identifying bad parameters with trajectory sensitivity analysis, and finally calibrating parameters using an ensemble Kalman filter (EnKF) based algorithm. The architectural design and the detailed procedures to run the tool suite are presented, with results of test on a realistic hydro power plant using PMU measurements for 12 different events. The calibrated parameters of machine, exciter, governor and PSS models demonstrate much better performance than the original models for all the events and show the robustness of the proposed calibration algorithm.« less

Graphics processing unit (GPU) real-time infrared scene generation

NASA Astrophysics Data System (ADS)

Christie, Chad L.; Gouthas, Efthimios (Themie); Williams, Owen M.

2007-04-01

VIRSuite, the GPU-based suite of software tools developed at DSTO for real-time infrared scene generation, is described. The tools include the painting of scene objects with radiometrically-associated colours, translucent object generation, polar plot validation and versatile scene generation. Special features include radiometric scaling within the GPU and the presence of zoom anti-aliasing at the core of VIRSuite. Extension of the zoom anti-aliasing construct to cover target embedding and the treatment of translucent objects is described.

ASDC Advances in the Utilization of Microservices and Hybrid Cloud Environments

NASA Astrophysics Data System (ADS)

Baskin, W. E.; Herbert, A.; Mazaika, A.; Walter, J.

2017-12-01

The Atmospheric Science Data Center (ASDC) is transitioning many of its software tools and applications to standalone microservices deployable in a hybrid cloud, offering benefits such as scalability and efficient environment management. This presentation features several projects the ASDC staff have implemented leveraging the OpenShift Container Application Platform and OpenStack Hybrid Cloud Environment focusing on key tools and techniques applied to: Earth Science data processing Spatial-Temporal metadata generation, validation, repair, and curation Archived Data discovery, visualization, and access

Intelligent Medical Systems for Aerospace Emergency Medical Services

NASA Technical Reports Server (NTRS)

Epler, John; Zimmer, Gary

2004-01-01

The purpose of this project is to develop a portable, hands free device for emergency medical decision support to be used in remote or confined settings by non-physician providers. Phase I of the project will entail the development of a voice-activated device that will utilize an intelligent algorithm to provide guidance in establishing an airway in an emergency situation. The interactive, hands free software will process requests for assistance based on verbal prompts and algorithmic decision-making. The device will allow the CMO to attend to the patient while receiving verbal instruction. The software will also feature graphic representations where it is felt helpful in aiding in procedures. We will also develop a training program to orient users to the algorithmic approach, the use of the hardware and specific procedural considerations. We will validate the efficacy of this mode of technology application by testing in the Johns Hopkins Department of Emergency Medicine. Phase I of the project will focus on the validation of the proposed algorithm, testing and validation of the decision making tool and modifications of medical equipment. In Phase 11, we will produce the first generation software for hands-free, interactive medical decision making for use in acute care environments.

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

NASA Astrophysics Data System (ADS)

Pascal, Bruce D.; Willis, Scooter; Lauer, Janelle L.; Landgraf, Rachelle R.; West, Graham M.; Marciano, David; Novick, Scott; Goswami, Devrishi; Chalmers, Michael J.; Griffin, Patrick R.

2012-09-01

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu.

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

PubMed Central

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

2006-01-01

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

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

PubMed

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

2006-10-13

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

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.

Integration and validation of a data grid software

NASA Astrophysics Data System (ADS)

Carenton-Madiec, Nicolas; Berger, Katharina; Cofino, Antonio

2014-05-01

The Earth System Grid Federation (ESGF) Peer-to-Peer (P2P) is a software infrastructure for the management, dissemination, and analysis of model output and observational data. The ESGF grid is composed with several types of nodes which have different roles. About 40 data nodes host model outputs and datasets using thredds catalogs. About 25 compute nodes offer remote visualization and analysis tools. About 15 index nodes crawl data nodes catalogs and implement faceted and federated search in a web interface. About 15 Identity providers nodes manage accounts, authentication and authorization. Here we will present an actual size test federation spread across different institutes in different countries and a python test suite that were started in December 2013. The first objective of the test suite is to provide a simple tool that helps to test and validate a single data node and its closest index, compute and identity provider peer. The next objective will be to run this test suite on every data node of the federation and therefore test and validate every single node of the whole federation. The suite already implements nosetests, requests, myproxy-logon, subprocess, selenium and fabric python libraries in order to test both web front ends, back ends and security services. The goal of this project is to improve the quality of deliverable in a small developers team context. Developers are widely spread around the world working collaboratively and without hierarchy. This kind of working organization context en-lighted the need of a federated integration test and validation process.

The expert explorer: a tool for hospital data visualization and adverse drug event rules validation.

PubMed

Băceanu, Adrian; Atasiei, Ionuţ; Chazard, Emmanuel; Leroy, Nicolas

2009-01-01

An important part of adverse drug events (ADEs) detection is the validation of the clinical cases and the assessment of the decision rules to detect ADEs. For that purpose, a software called "Expert Explorer" has been designed by Ideea Advertising. Anonymized datasets have been extracted from hospitals into a common repository. The tool has 3 main features. (1) It can display hospital stays in a visual and comprehensive way (diagnoses, drugs, lab results, etc.) using tables and pretty charts. (2) It allows designing and executing dashboards in order to generate knowledge about ADEs. (3) It finally allows uploading decision rules obtained from data mining. Experts can then review the rules, the hospital stays that match the rules, and finally give their advice thanks to specialized forms. Then the rules can be validated, invalidated, or improved (knowledge elicitation phase).

CoRoTlog

NASA Astrophysics Data System (ADS)

Plasson, Ph.

2006-11-01

LESIA, in close cooperation with CNES, DLR and IWF, is responsible for the tests and validation of the CoRoT instrument digital process unit which is made up of the BEX and DPU assembly. The main part of the work has consisted in validating the DPU software and in testing the BEX/DPU coupling. This work took more than two years due to the central role of the software tested and its technical complexity. The first task, in the validation process, was to carry out the acceptance tests of the DPU software. These tests consisted in checking each of the 325 requirements identified in the URD (User Requirements Document) and were played in a configuration using the DPU coupled to a BEX simulator. During the acceptance tests, all the transversal functionalities of the DPU software, like the TC/TM management, the state machine management, the BEX driving, the system monitoring or the maintenance functionalities were checked in depth. The functionalities associated with the seismology and exoplanetology processing, like the loading of window and mask descriptors or the configuration of the service execution parameters, were also exhaustively tested. After having validated the DPU software against the user requirements using a BEX simulator, the following step consisted in coupling the DPU and the BEX in order to check that the formed unit worked correctly and met the performance requirements. These tests were conducted in two phases: the first one was devoted to the functional aspects and the tests of interface, the second one to the performance aspects. The performance tests were based on the use of the DPU software scientific services and on the use of full images representative of a realistic sky as inputs. These tests were also based on the use of a reference set of windows and parameters, which was provided by the scientific team and was representative, in terms of load and complexity, of the one that could be used during the observation mode of the CoRoT instrument. Theywere played in a configuration using either a BCC simulator or a real BCC coupled to a video simulator, to feed the BEX/DPU unit. The validation of the scientific algorithms was conducted in parallel to the phase of the BEX/DPU coupling tests. The objective of this phase was to check that the algorithms implemented in the scientific services of the DPU software were in good conformity with those specified in the URD and that the obtained numerical precision corresponded to that expected. Forty cases of tests were defined covering the fine and rough angular error measurement processing, the rejection of the brilliant pixels, the subtraction of the offset and the sky background, the photometry algorithms, the SAA handling and reference image management. For each test case, the LESIA scientific team produced, by simulation, using the model instrument, the dynamic data files and the parameter sets allowing to feed the DPU on the one hand, and, on the other hand, a model of the onboard software. These data files correspond to FITS images (black windows, star windows, offset windows) containing more or less disturbances and making it possible to test the DPU software in dynamic mode over durations of up to 48 hours. To perform the test and validation activities of the CoRoT instrument digital process unit, a set of software testing tools was developed by LESIA (Software Ground Support Equipment, hereafter "SGSE"). Thanks to their versatility and modularity, these software testing tools were actually used during all the activities of integration, tests and validation of the instrument and its subsystems CoRoTCase and CoRoTCam. The CoRoT SGSE were specified, designed and developed by LESIA. The objective was to have a software system allowing the users (validation team of the onboard software, instrument integration team, etc.) to remotely control and monitor the whole instrument or only one of the subsystems of the instrument like the DPU coupled to a simulator BEX or the BEX/DPU unit coupled to a BCC simulator. The idea was to be able to interact in real time with the system under test by driving the various EGSE, but also to play test procedures implemented as scripts organized into libraries, to record the telemetries and housekeeping data in a database, and to be able to carry out post-mortem analyses.

A 3D interactive multi-object segmentation tool using local robust statistics driven active contours.

PubMed

Gao, Yi; Kikinis, Ron; Bouix, Sylvain; Shenton, Martha; Tannenbaum, Allen

2012-08-01

Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. In the past, much work has been dedicated only to the algorithmic development. Nevertheless, for clinical end users, a well designed algorithm with an interactive software is necessary for an algorithm to be utilized in their daily work. Furthermore, the software would better be open sourced in order to be used and validated by not only the authors but also the entire community. Therefore, the contribution of the present work is twofolds: first, we propose a new robust statistics based conformal metric and the conformal area driven multiple active contour framework, to simultaneously extract multiple targets from MR and CT medical imagery in 3D. Second, an open source graphically interactive 3D segmentation tool based on the aforementioned contour evolution is implemented and is publicly available for end users on multiple platforms. In using this software for the segmentation task, the process is initiated by the user drawn strokes (seeds) in the target region in the image. Then, the local robust statistics are used to describe the object features, and such features are learned adaptively from the seeds under a non-parametric estimation scheme. Subsequently, several active contours evolve simultaneously with their interactions being motivated by the principles of action and reaction-this not only guarantees mutual exclusiveness among the contours, but also no longer relies upon the assumption that the multiple objects fill the entire image domain, which was tacitly or explicitly assumed in many previous works. In doing so, the contours interact and converge to equilibrium at the desired positions of the desired multiple objects. Furthermore, with the aim of not only validating the algorithm and the software, but also demonstrating how the tool is to be used, we provide the reader reproducible experiments that demonstrate the capability of the proposed segmentation tool on several public available data sets. Copyright © 2012 Elsevier B.V. All rights reserved.

A 3D Interactive Multi-object Segmentation Tool using Local Robust Statistics Driven Active Contours

PubMed Central

Gao, Yi; Kikinis, Ron; Bouix, Sylvain; Shenton, Martha; Tannenbaum, Allen

2012-01-01

Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. In the past, much work has been dedicated only to the algorithmic development. Nevertheless, for clinical end users, a well designed algorithm with an interactive software is necessary for an algorithm to be utilized in their daily work. Furthermore, the software would better be open sourced in order to be used and validated by not only the authors but also the entire community. Therefore, the contribution of the present work is twofolds: First, we propose a new robust statistics based conformal metric and the conformal area driven multiple active contour framework, to simultaneously extract multiple targets from MR and CT medical imagery in 3D. Second, an open source graphically interactive 3D segmentation tool based on the aforementioned contour evolution is implemented and is publicly available for end users on multiple platforms. In using this software for the segmentation task, the process is initiated by the user drawn strokes (seeds) in the target region in the image. Then, the local robust statistics are used to describe the object features, and such features are learned adaptively from the seeds under a non-parametric estimation scheme. Subsequently, several active contours evolve simultaneously with their interactions being motivated by the principles of action and reaction — This not only guarantees mutual exclusiveness among the contours, but also no longer relies upon the assumption that the multiple objects fill the entire image domain, which was tacitly or explicitly assumed in many previous works. In doing so, the contours interact and converge to equilibrium at the desired positions of the desired multiple objects. Furthermore, with the aim of not only validating the algorithm and the software, but also demonstrating how the tool is to be used, we provide the reader reproducible experiments that demonstrate the capability of the proposed segmentation tool on several public available data sets. PMID:22831773

Baseline Assessment and Prioritization Framework for IVHM Integrity Assurance Enabling Capabilities

NASA Technical Reports Server (NTRS)

Cooper, Eric G.; DiVito, Benedetto L.; Jacklin, Stephen A.; Miner, Paul S.

2009-01-01

Fundamental to vehicle health management is the deployment of systems incorporating advanced technologies for predicting and detecting anomalous conditions in highly complex and integrated environments. Integrated structural integrity health monitoring, statistical algorithms for detection, estimation, prediction, and fusion, and diagnosis supporting adaptive control are examples of advanced technologies that present considerable verification and validation challenges. These systems necessitate interactions between physical and software-based systems that are highly networked with sensing and actuation subsystems, and incorporate technologies that are, in many respects, different from those employed in civil aviation today. A formidable barrier to deploying these advanced technologies in civil aviation is the lack of enabling verification and validation tools, methods, and technologies. The development of new verification and validation capabilities will not only enable the fielding of advanced vehicle health management systems, but will also provide new assurance capabilities for verification and validation of current generation aviation software which has been implicated in anomalous in-flight behavior. This paper describes the research focused on enabling capabilities for verification and validation underway within NASA s Integrated Vehicle Health Management project, discusses the state of the art of these capabilities, and includes a framework for prioritizing activities.

A validation framework for brain tumor segmentation.

PubMed

Archip, Neculai; Jolesz, Ferenc A; Warfield, Simon K

2007-10-01

We introduce a validation framework for the segmentation of brain tumors from magnetic resonance (MR) images. A novel unsupervised semiautomatic brain tumor segmentation algorithm is also presented. The proposed framework consists of 1) T1-weighted MR images of patients with brain tumors, 2) segmentation of brain tumors performed by four independent experts, 3) segmentation of brain tumors generated by a semiautomatic algorithm, and 4) a software tool that estimates the performance of segmentation algorithms. We demonstrate the validation of the novel segmentation algorithm within the proposed framework. We show its performance and compare it with existent segmentation. The image datasets and software are available at http://www.brain-tumor-repository.org/. We present an Internet resource that provides access to MR brain tumor image data and segmentation that can be openly used by the research community. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results.

MAIN software for density averaging, model building, structure refinement and validation

PubMed Central

Turk, Dušan

2013-01-01

MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms. PMID:23897458

Engineering Software Suite Validates System Design

NASA Technical Reports Server (NTRS)

2007-01-01

EDAptive Computing Inc.'s (ECI) EDAstar engineering software tool suite, created to capture and validate system design requirements, was significantly funded by NASA's Ames Research Center through five Small Business Innovation Research (SBIR) contracts. These programs specifically developed Syscape, used to capture executable specifications of multi-disciplinary systems, and VectorGen, used to automatically generate tests to ensure system implementations meet specifications. According to the company, the VectorGen tests considerably reduce the time and effort required to validate implementation of components, thereby ensuring their safe and reliable operation. EDASHIELD, an additional product offering from ECI, can be used to diagnose, predict, and correct errors after a system has been deployed using EDASTAR -created models. Initial commercialization for EDASTAR included application by a large prime contractor in a military setting, and customers include various branches within the U.S. Department of Defense, industry giants like the Lockheed Martin Corporation, Science Applications International Corporation, and Ball Aerospace and Technologies Corporation, as well as NASA's Langley and Glenn Research Centers

AirLab: a cloud-based platform to manage and share antibody-based single-cell research.

PubMed

Catena, Raúl; Özcan, Alaz; Jacobs, Andrea; Chevrier, Stephane; Bodenmiller, Bernd

2016-06-29

Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories that employ these methods maintain large repositories of antibodies. These ever-growing collections of antibodies, their multiple conjugates, and the large amounts of data generated in assays using specific antibodies and conditions makes a dedicated software solution necessary. We have developed AirLab, a cloud-based tool with web and mobile interfaces, for the organization of these data. AirLab streamlines the processes of antibody purchase, organization, and storage, antibody panel creation, results logging, and antibody validation data sharing and distribution. Furthermore, AirLab enables inventory of other laboratory stocks, such as primers or clinical samples, through user-controlled customization. Thus, AirLab is a mobile-powered and flexible tool that harnesses the capabilities of mobile tools and cloud-based technology to facilitate inventory and sharing of antibody and sample collections and associated validation data.

Cementitious Barriers Partnership FY2013 End-Year Report

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

Flach, G. P.; Langton, C. A.; Burns, H. H.

2013-11-01

In FY2013, the Cementitious Barriers Partnership (CBP) demonstrated continued tangible progress toward fulfilling the objective of developing a set of software tools to improve understanding and prediction of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. In November 2012, the CBP released “Version 1.0” of the CBP Software Toolbox, a suite of software for simulating reactive transport in cementitious materials and important degradation phenomena. In addition, the CBP completed development of new software for the “Version 2.0” Toolbox to be released in early FY2014 and demonstrated use of the Version 1.0 Toolbox on DOEmore » applications. The current primary software components in both Versions 1.0 and 2.0 are LeachXS/ORCHESTRA, STADIUM, and a GoldSim interface for probabilistic analysis of selected degradation scenarios. The CBP Software Toolbox Version 1.0 supports analysis of external sulfate attack (including damage mechanics), carbonation, and primary constituent leaching. Version 2.0 includes the additional analysis of chloride attack and dual regime flow and contaminant migration in fractured and non-fractured cementitious material. The LeachXS component embodies an extensive material property measurements database along with chemical speciation and reactive mass transport simulation cases with emphasis on leaching of major, trace and radionuclide constituents from cementitious materials used in DOE facilities, such as Saltstone (Savannah River) and Cast Stone (Hanford), tank closure grouts, and barrier concretes. STADIUM focuses on the physical and structural service life of materials and components based on chemical speciation and reactive mass transport of major cement constituents and aggressive species (e.g., chloride, sulfate, etc.). THAMES is a planned future CBP Toolbox component focused on simulation of the microstructure of cementitious materials and calculation of resultant hydraulic and constituent mass transfer parameters needed in modeling. Two CBP software demonstrations were conducted in FY2013, one to support the Saltstone Disposal Facility (SDF) at SRS and the other on a representative Hanford high-level waste tank. The CBP Toolbox demonstration on the SDF provided analysis on the most probable degradation mechanisms to the cementitious vault enclosure caused by sulfate and carbonation ingress. This analysis was documented and resulted in the issuance of a SDF Performance Assessment Special Analysis by Liquid Waste Operations this fiscal year. The two new software tools supporting chloride attack and dual-regime flow will provide additional degradation tools to better evaluate performance of DOE and commercial cementitious barriers. The CBP SRNL experimental program produced two patent applications and field data that will be used in the development and calibration of CBP software tools being developed in FY2014. The CBP software and simulation tools varies from other efforts in that all the tools are based upon specific and relevant experimental research of cementitious materials utilized in DOE applications. The CBP FY2013 program involved continuing research to improve and enhance the simulation tools as well as developing new tools that model other key degradation phenomena not addressed in Version 1.0. Also efforts to continue to verify the various simulation tools through laboratory experiments and analysis of field specimens are ongoing and will continue into FY2014 to quantify and reduce the uncertainty associated with performance assessments. This end-year report summarizes FY2013 software development efforts and the various experimental programs that are providing data for calibration and validation of the CBP developed software.« less

Developing and testing instruments for improving cooperation and patient's participation in mental health care.

PubMed

Latvala, E; Saranto, K; Pekkala, E

2004-10-01

The main purpose of the project was to develop computerized instruments that could be used by nurses and patients to assess their cooperation and mutual contributions to care. This paper presents a part of the project: the reliability and validity testing phase of a process of instrument development. To test the validity and reliability of the instruments, data were collected with questionnaires from nurses (n = 146) and patients (n = 286). The validity evaluated as construct validity and the reliability evaluated as internal consistency of the instruments were quite good. Construct validity was tested by factor analysis, and internal consistency was tested by Cronbach's alpha coefficient, which varied from 0.69 to 0.79. The instruments, which consisted of a software application that can be operated in a www environment, were meant to be used as tools in the psychiatric nursing context for assessing the cooperation between the nurses and patients and the patient's participation in his/her care. Furthermore, the computer programme can be used as a tool for developing and assessing the patient orientation in nursing.

The Earth System Documentation (ES-DOC) Software Process

NASA Astrophysics Data System (ADS)

Greenslade, M. A.; Murphy, S.; Treshansky, A.; DeLuca, C.; Guilyardi, E.; Denvil, S.

2013-12-01

Earth System Documentation (ES-DOC) is an international project supplying high-quality tools & services in support of earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation eco-system that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software, and applies a software development methodology that places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system and currently supporting the following projects: * Coupled Model Inter-comparison Project Phase 5 (CMIP5); * Dynamical Core Model Inter-comparison Project (DCMIP); * National Climate Predictions and Projections Platforms Quantitative Evaluation of Downscaling Workshop. This talk will demonstrate that ES-DOC implements a relatively mature software development process. Taking a pragmatic Agile process as inspiration, ES-DOC: * Iteratively develops and releases working software; * Captures user requirements via a narrative based approach; * Uses online collaboration tools (e.g. Earth System CoG) to manage progress; * Prototypes applications to validate their feasibility; * Leverages meta-programming techniques where appropriate; * Automates testing whenever sensibly feasible; * Streamlines complex deployments to a single command; * Extensively leverages GitHub and Pivotal Tracker; * Enforces strict separation of the UI from underlying API's; * Conducts code reviews.

ETHOWATCHER: validation of a tool for behavioral and video-tracking analysis in laboratory animals.

PubMed

Crispim Junior, Carlos Fernando; Pederiva, Cesar Nonato; Bose, Ricardo Chessini; Garcia, Vitor Augusto; Lino-de-Oliveira, Cilene; Marino-Neto, José

2012-02-01

We present a software (ETHOWATCHER(®)) developed to support ethography, object tracking and extraction of kinematic variables from digital video files of laboratory animals. The tracking module allows controlled segmentation of the target from the background, extracting image attributes used to calculate the distance traveled, orientation, length, area and a path graph of the experimental animal. The ethography module allows recording of catalog-based behaviors from environment or from video files continuously or frame-by-frame. The output reports duration, frequency and latency of each behavior and the sequence of events in a time-segmented format, set by the user. Validation tests were conducted on kinematic measurements and on the detection of known behavioral effects of drugs. This software is freely available at www.ethowatcher.ufsc.br. Copyright © 2011 Elsevier Ltd. All rights reserved.

Computational challenges and human factors influencing the design and use of clinical research participant eligibility pre-screening tools

PubMed Central

2012-01-01

Background Clinical trials are the primary mechanism for advancing clinical care and evidenced-based practice, yet challenges with the recruitment of participants for such trials are widely recognized as a major barrier to these types of studies. Data warehouses (DW) store large amounts of heterogenous clinical data that can be used to enhance recruitment practices, but multiple challenges exist when using a data warehouse for such activities, due to the manner of collection, management, integration, analysis, and dissemination of the data. A critical step in leveraging the DW for recruitment purposes is being able to match trial eligibility criteria to discrete and semi-structured data types in the data warehouse, though trial eligibility criteria tend to be written without concern for their computability. We present the multi-modal evaluation of a web-based tool that can be used for pre-screening patients for clinical trial eligibility and assess the ability of this tool to be practically used for clinical research pre-screening and recruitment. Methods The study used a validation study, usability testing, and a heuristic evaluation to evaluate and characterize the operational characteristics of the software as well as human factors affecting its use. Results Clinical trials from the Division of Cardiology and the Department of Family Medicine were used for this multi-modal evaluation, which included a validation study, usability study, and a heuristic evaluation. From the results of the validation study, the software demonstrated a positive predictive value (PPV) of 54.12% and 0.7%, respectively, and a negative predictive value (NPV) of 73.3% and 87.5%, respectively, for two types of clinical trials. Heuristic principles concerning error prevention and documentation were characterized as the major usability issues during the heuristic evaluation. Conclusions This software is intended to provide an initial list of eligible patients to a clinical study coordinators, which provides a starting point for further eligibility screening by the coordinator. Because this software has a high “rule in” ability, meaning that it is able to remove patients who are not eligible for the study, the use of an automated tool built to leverage an existing enterprise DW can be beneficial to determining eligibility and facilitating clinical trial recruitment through pre-screening. While the results of this study are promising, further refinement and study of this and related approaches to automated eligibility screening, including comparison to other approaches and stakeholder perceptions, are needed and future studies are planned to address these needs. PMID:22646313

Computational challenges and human factors influencing the design and use of clinical research participant eligibility pre-screening tools.

PubMed

Pressler, Taylor R; Yen, Po-Yin; Ding, Jing; Liu, Jianhua; Embi, Peter J; Payne, Philip R O

2012-05-30

Clinical trials are the primary mechanism for advancing clinical care and evidenced-based practice, yet challenges with the recruitment of participants for such trials are widely recognized as a major barrier to these types of studies. Data warehouses (DW) store large amounts of heterogenous clinical data that can be used to enhance recruitment practices, but multiple challenges exist when using a data warehouse for such activities, due to the manner of collection, management, integration, analysis, and dissemination of the data. A critical step in leveraging the DW for recruitment purposes is being able to match trial eligibility criteria to discrete and semi-structured data types in the data warehouse, though trial eligibility criteria tend to be written without concern for their computability. We present the multi-modal evaluation of a web-based tool that can be used for pre-screening patients for clinical trial eligibility and assess the ability of this tool to be practically used for clinical research pre-screening and recruitment. The study used a validation study, usability testing, and a heuristic evaluation to evaluate and characterize the operational characteristics of the software as well as human factors affecting its use. Clinical trials from the Division of Cardiology and the Department of Family Medicine were used for this multi-modal evaluation, which included a validation study, usability study, and a heuristic evaluation. From the results of the validation study, the software demonstrated a positive predictive value (PPV) of 54.12% and 0.7%, respectively, and a negative predictive value (NPV) of 73.3% and 87.5%, respectively, for two types of clinical trials. Heuristic principles concerning error prevention and documentation were characterized as the major usability issues during the heuristic evaluation. This software is intended to provide an initial list of eligible patients to a clinical study coordinators, which provides a starting point for further eligibility screening by the coordinator. Because this software has a high "rule in" ability, meaning that it is able to remove patients who are not eligible for the study, the use of an automated tool built to leverage an existing enterprise DW can be beneficial to determining eligibility and facilitating clinical trial recruitment through pre-screening. While the results of this study are promising, further refinement and study of this and related approaches to automated eligibility screening, including comparison to other approaches and stakeholder perceptions, are needed and future studies are planned to address these needs.

CAMEO-SIM: a physics-based broadband scene simulation tool for assessment of camouflage, concealment, and deception methodologies

NASA Astrophysics Data System (ADS)

Moorhead, Ian R.; Gilmore, Marilyn A.; Houlbrook, Alexander W.; Oxford, David E.; Filbee, David R.; Stroud, Colin A.; Hutchings, G.; Kirk, Albert

2001-09-01

Assessment of camouflage, concealment, and deception (CCD) methodologies is not a trivial problem; conventionally the only method has been to carry out field trials, which are both expensive and subject to the vagaries of the weather. In recent years computing power has increased, such that there are now many research programs using synthetic environments for CCD assessments. Such an approach is attractive; the user has complete control over the environmental parameters and many more scenarios can be investigated. The UK Ministry of Defence is currently developing a synthetic scene generation tool for assessing the effectiveness of air vehicle camouflage schemes. The software is sufficiently flexible to allow it to be used in a broader range of applications, including full CCD assessment. The synthetic scene simulation system (CAMEO- SIM) has been developed, as an extensible system, to provide imagery within the 0.4 to 14 micrometers spectral band with as high a physical fidelity as possible. it consists of a scene design tool, an image generator, that incorporates both radiosity and ray-tracing process, and an experimental trials tool. The scene design tool allows the user to develop a 3D representation of the scenario of interest from a fixed viewpoint. Target(s) of interest can be placed anywhere within this 3D representation and may be either static or moving. Different illumination conditions and effects of the atmosphere can be modeled together with directional reflectance effects. The user has complete control over the level of fidelity of the final image. The output from the rendering tool is a sequence of radiance maps, which may be used by sensor models or for experimental trials in which observers carry out target acquisition tasks. The software also maintains an audit trail of all data selected to generate a particular image, both in terms of material properties used and the rendering options chosen. A range of verification tests has shown that the software computes the correct values for analytically tractable scenarios. Validation test using simple scenes have also been undertaken. More complex validation tests using observer trials are planned. The current version of CAMEO-SIM and how its images are used for camouflage assessment is described. The verification and validation tests undertaken are discussed. In addition, example images will be used to demonstrate the significance of different effects, such as spectral rendering and shadows. Planned developments of CAMEO-SIM are also outlined.

SOAP. A tool for the fast computation of photometry and radial velocity induced by stellar spots

NASA Astrophysics Data System (ADS)

Boisse, I.; Bonfils, X.; Santos, N. C.

2012-09-01

We define and put at the disposal of the community SOAP, Spot Oscillation And Planet, a software tool that simulates the effect of stellar spots and plages on radial velocimetry and photometry. This paper describes the tool release and provides instructions for its use. We present detailed tests with previous computations and real data to assess the code's performance and to validate its suitability. We characterize the variations of the radial velocity, line bisector, and photometric amplitude as a function of the main variables: projected stellar rotational velocity, filling factor of the spot, resolution of the spectrograph, linear limb-darkening coefficient, latitude of the spot, and inclination of the star. Finally, we model the spot distributions on the active stars HD 166435, TW Hya and HD 189733, which reproduce the observations. We show that the software is remarkably fast, allowing several evolutions in its capabilities that could be performed to study the next challenges in the exoplanetary field connected with the stellar variability. The tool is available at http://www.astro.up.pt/soap

Rotorcraft Optimization Tools: Incorporating Rotorcraft Design Codes into Multi-Disciplinary Design, Analysis, and Optimization

NASA Technical Reports Server (NTRS)

Meyn, Larry A.

2018-01-01

One of the goals of NASA's Revolutionary Vertical Lift Technology Project (RVLT) is to provide validated tools for multidisciplinary design, analysis and optimization (MDAO) of vertical lift vehicles. As part of this effort, the software package, RotorCraft Optimization Tools (RCOTOOLS), is being developed to facilitate incorporating key rotorcraft conceptual design codes into optimizations using the OpenMDAO multi-disciplinary optimization framework written in Python. RCOTOOLS, also written in Python, currently supports the incorporation of the NASA Design and Analysis of RotorCraft (NDARC) vehicle sizing tool and the Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics II (CAMRAD II) analysis tool into OpenMDAO-driven optimizations. Both of these tools use detailed, file-based inputs and outputs, so RCOTOOLS provides software wrappers to update input files with new design variable values, execute these codes and then extract specific response variable values from the file outputs. These wrappers are designed to be flexible and easy to use. RCOTOOLS also provides several utilities to aid in optimization model development, including Graphical User Interface (GUI) tools for browsing input and output files in order to identify text strings that are used to identify specific variables as optimization input and response variables. This paper provides an overview of RCOTOOLS and its use

Technical Note: Development and performance of a software tool for quality assurance of online replanning with a conventional Linac or MR-Linac.

PubMed

Chen, Guang-Pei; Ahunbay, Ergun; Li, X Allen

2016-04-01

To develop an integrated quality assurance (QA) software tool for online replanning capable of efficiently and automatically checking radiation treatment (RT) planning parameters and gross plan quality, verifying treatment plan data transfer from treatment planning system (TPS) to record and verify (R&V) system, performing a secondary monitor unit (MU) calculation with or without a presence of a magnetic field from MR-Linac, and validating the delivery record consistency with the plan. The software tool, named ArtQA, was developed to obtain and compare plan and treatment parameters from both the TPS and the R&V system database. The TPS data are accessed via direct file reading and the R&V data are retrieved via open database connectivity and structured query language. Plan quality is evaluated with both the logical consistency of planning parameters and the achieved dose-volume histograms. Beams in between the TPS and R&V system are matched based on geometry configurations. To consider the effect of a 1.5 T transverse magnetic field from MR-Linac in the secondary MU calculation, a method based on modified Clarkson integration algorithm was developed and tested for a series of clinical situations. ArtQA has been used in their clinic and can quickly detect inconsistencies and deviations in the entire RT planning process. With the use of the ArtQA tool, the efficiency for plan check including plan quality, data transfer, and delivery check can be improved by at least 60%. The newly developed independent MU calculation tool for MR-Linac reduces the difference between the plan and calculated MUs by 10%. The software tool ArtQA can be used to perform a comprehensive QA check from planning to delivery with conventional Linac or MR-Linac and is an essential tool for online replanning where the QA check needs to be performed rapidly.

Technical Note: Development and performance of a software tool for quality assurance of online replanning with a conventional Linac or MR-Linac

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

Chen, Guang-Pei, E-mail: gpchen@mcw.edu; Ahunbay, Ergun; Li, X. Allen

Purpose: To develop an integrated quality assurance (QA) software tool for online replanning capable of efficiently and automatically checking radiation treatment (RT) planning parameters and gross plan quality, verifying treatment plan data transfer from treatment planning system (TPS) to record and verify (R&V) system, performing a secondary monitor unit (MU) calculation with or without a presence of a magnetic field from MR-Linac, and validating the delivery record consistency with the plan. Methods: The software tool, named ArtQA, was developed to obtain and compare plan and treatment parameters from both the TPS and the R&V system database. The TPS data aremore » accessed via direct file reading and the R&V data are retrieved via open database connectivity and structured query language. Plan quality is evaluated with both the logical consistency of planning parameters and the achieved dose–volume histograms. Beams in between the TPS and R&V system are matched based on geometry configurations. To consider the effect of a 1.5 T transverse magnetic field from MR-Linac in the secondary MU calculation, a method based on modified Clarkson integration algorithm was developed and tested for a series of clinical situations. Results: ArtQA has been used in their clinic and can quickly detect inconsistencies and deviations in the entire RT planning process. With the use of the ArtQA tool, the efficiency for plan check including plan quality, data transfer, and delivery check can be improved by at least 60%. The newly developed independent MU calculation tool for MR-Linac reduces the difference between the plan and calculated MUs by 10%. Conclusions: The software tool ArtQA can be used to perform a comprehensive QA check from planning to delivery with conventional Linac or MR-Linac and is an essential tool for online replanning where the QA check needs to be performed rapidly.« less

Software platform for simulation of a prototype proton CT scanner.

PubMed

Giacometti, Valentina; Bashkirov, Vladimir A; Piersimoni, Pierluigi; Guatelli, Susanna; Plautz, Tia E; Sadrozinski, Hartmut F-W; Johnson, Robert P; Zatserklyaniy, Andriy; Tessonnier, Thomas; Parodi, Katia; Rosenfeld, Anatoly B; Schulte, Reinhard W

2017-03-01

Proton computed tomography (pCT) is a promising imaging technique to substitute or at least complement x-ray CT for more accurate proton therapy treatment planning as it allows calculating directly proton relative stopping power from proton energy loss measurements. A proton CT scanner with a silicon-based particle tracking system and a five-stage scintillating energy detector has been completed. In parallel a modular software platform was developed to characterize the performance of the proposed pCT. The modular pCT software platform consists of (1) a Geant4-based simulation modeling the Loma Linda proton therapy beam line and the prototype proton CT scanner, (2) water equivalent path length (WEPL) calibration of the scintillating energy detector, and (3) image reconstruction algorithm for the reconstruction of the relative stopping power (RSP) of the scanned object. In this work, each component of the modular pCT software platform is described and validated with respect to experimental data and benchmarked against theoretical predictions. In particular, the RSP reconstruction was validated with both experimental scans, water column measurements, and theoretical calculations. The results show that the pCT software platform accurately reproduces the performance of the existing prototype pCT scanner with a RSP agreement between experimental and simulated values to better than 1.5%. The validated platform is a versatile tool for clinical proton CT performance and application studies in a virtual setting. The platform is flexible and can be modified to simulate not yet existing versions of pCT scanners and higher proton energies than those currently clinically available. © 2017 American Association of Physicists in Medicine.

Uncertainty Modeling for Robustness Analysis of Control Upset Prevention and Recovery Systems

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Khong, Thuan H.; Shin, Jong-Yeob; Kwatny, Harry; Chang, Bor-Chin; Balas, Gary J.

2005-01-01

Formal robustness analysis of aircraft control upset prevention and recovery systems could play an important role in their validation and ultimate certification. Such systems (developed for failure detection, identification, and reconfiguration, as well as upset recovery) need to be evaluated over broad regions of the flight envelope and under extreme flight conditions, and should include various sources of uncertainty. However, formulation of linear fractional transformation (LFT) models for representing system uncertainty can be very difficult for complex parameter-dependent systems. This paper describes a preliminary LFT modeling software tool which uses a matrix-based computational approach that can be directly applied to parametric uncertainty problems involving multivariate matrix polynomial dependencies. Several examples are presented (including an F-16 at an extreme flight condition, a missile model, and a generic example with numerous crossproduct terms), and comparisons are given with other LFT modeling tools that are currently available. The LFT modeling method and preliminary software tool presented in this paper are shown to compare favorably with these methods.

Advanced data management system architectures testbed

NASA Technical Reports Server (NTRS)

Grant, Terry

1990-01-01

The objective of the Architecture and Tools Testbed is to provide a working, experimental focus to the evolving automation applications for the Space Station Freedom data management system. Emphasis is on defining and refining real-world applications including the following: the validation of user needs; understanding system requirements and capabilities; and extending capabilities. The approach is to provide an open, distributed system of high performance workstations representing both the standard data processors and networks and advanced RISC-based processors and multiprocessor systems. The system provides a base from which to develop and evaluate new performance and risk management concepts and for sharing the results. Participants are given a common view of requirements and capability via: remote login to the testbed; standard, natural user interfaces to simulations and emulations; special attention to user manuals for all software tools; and E-mail communication. The testbed elements which instantiate the approach are briefly described including the workstations, the software simulation and monitoring tools, and performance and fault tolerance experiments.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

OpenComet: An automated tool for comet assay image analysis

PubMed Central

Gyori, Benjamin M.; Venkatachalam, Gireedhar; Thiagarajan, P.S.; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time. PMID:24624335

OpenComet: an automated tool for comet assay image analysis.

PubMed

Gyori, Benjamin M; Venkatachalam, Gireedhar; Thiagarajan, P S; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

A Summary of Revisions Applied to a Turbulence Response Analysis Method for Flexible Aircraft Configurations

NASA Technical Reports Server (NTRS)

Funk, Christie J.; Perry, Boyd, III; Silva, Walter A.; Newman, Brett

2014-01-01

A software program and associated methodology to study gust loading on aircraft exists for a classification of geometrically simplified flexible configurations. This program consists of a simple aircraft response model with two rigid and three flexible symmetric degrees-of - freedom and allows for the calculation of various airplane responses due to a discrete one-minus- cosine gust as well as continuous turbulence. Simplifications, assumptions, and opportunities for potential improvements pertaining to the existing software program are first identified, then a revised version of the original software tool is developed with improved methodology to include more complex geometries, additional excitation cases, and additional output data so as to provide a more useful and precise tool for gust load analysis. In order to improve the original software program to enhance usefulness, a wing control surface and horizontal tail control surface is added, an extended application of the discrete one-minus-cosine gust input is employed, a supplemental continuous turbulence spectrum is implemented, and a capability to animate the total vehicle deformation response to gust inputs is included. These revisions and enhancements are implemented and an analysis of the results is used to validate the modifications.

Designing and encoding models for synthetic biology.

PubMed

Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

2009-08-06

A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.

Spacecraft Avionics Software Development Then and Now: Different but the Same

NASA Technical Reports Server (NTRS)

Mangieri, Mark L.; Garman, John (Jack); Vice, Jason

2012-01-01

NASA has always been in the business of balancing new technologies and techniques to achieve human space travel objectives. NASA s historic Software Production Facility (SPF) was developed to serve complex avionics software solutions during an era dominated by mainframes, tape drives, and lower level programming languages. These systems have proven themselves resilient enough to serve the Shuttle Orbiter Avionics life cycle for decades. The SPF and its predecessor the Software Development Lab (SDL) at NASA s Johnson Space Center (JSC) hosted flight software (FSW) engineering, development, simulation, and test. It was active from the beginning of Shuttle Orbiter development in 1972 through the end of the shuttle program in the summer of 2011 almost 40 years. NASA s Kedalion engineering analysis lab is on the forefront of validating and using many contemporary avionics HW/SW development and integration techniques, which represent new paradigms to NASA s heritage culture in avionics software engineering. Kedalion has validated many of the Orion project s HW/SW engineering techniques borrowed from the adjacent commercial aircraft avionics environment, inserting new techniques and skills into the Multi-Purpose Crew Vehicle (MPCV) Orion program. Using contemporary agile techniques, COTS products, early rapid prototyping, in-house expertise and tools, and customer collaboration, NASA has adopted a cost effective paradigm that is currently serving Orion effectively. This paper will explore and contrast differences in technology employed over the years of NASA s space program, due largely to technological advances in hardware and software systems, while acknowledging that the basic software engineering and integration paradigms share many similarities.

SU-E-T-50: Automatic Validation of Megavoltage Beams Modeled for Clinical Use in Radiation Therapy

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

Melchior, M; Salinas Aranda, F; 21st Century Oncology, Ft. Myers, FL

2014-06-01

Purpose: To automatically validate megavoltage beams modeled in XiO™ 4.50 (Elekta, Stockholm, Sweden) and Varian Eclipse™ Treatment Planning Systems (TPS) (Varian Associates, Palo Alto, CA, USA), reducing validation time before beam-on for clinical use. Methods: A software application that can automatically read and analyze DICOM RT Dose and W2CAD files was developed using MatLab integrated development environment.TPS calculated dose distributions, in DICOM RT Dose format, and dose values measured in different Varian Clinac beams, in W2CAD format, were compared. Experimental beam data used were those acquired for beam commissioning, collected on a water phantom with a 2D automatic beam scanningmore » system.Two methods were chosen to evaluate dose distributions fitting: gamma analysis and point tests described in Appendix E of IAEA TECDOC-1583. Depth dose curves and beam profiles were evaluated for both open and wedged beams. Tolerance parameters chosen for gamma analysis are 3% and 3 mm dose and distance, respectively.Absolute dose was measured independently at points proposed in Appendix E of TECDOC-1583 to validate software results. Results: TPS calculated depth dose distributions agree with measured beam data under fixed precision values at all depths analyzed. Measured beam dose profiles match TPS calculated doses with high accuracy in both open and wedged beams. Depth and profile dose distributions fitting analysis show gamma values < 1. Relative errors at points proposed in Appendix E of TECDOC-1583 meet therein recommended tolerances.Independent absolute dose measurements at points proposed in Appendix E of TECDOC-1583 confirm software results. Conclusion: Automatic validation of megavoltage beams modeled for their use in the clinic was accomplished. The software tool developed proved efficient, giving users a convenient and reliable environment to decide whether to accept or not a beam model for clinical use. Validation time before beam-on for clinical use was reduced to a few hours.« less

mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.

PubMed

Strohalm, Martin; Kavan, Daniel; Novák, Petr; Volný, Michael; Havlícek, Vladimír

2010-06-01

While tools for the automated analysis of MS and LC-MS/MS data are continuously improving, it is still often the case that at the end of an experiment, the mass spectrometrist will spend time carefully examining individual spectra. Current software support is mostly provided only by the instrument vendors, and the available software tools are often instrument-dependent. Here we present a new generation of mMass, a cross-platform environment for the precise analysis of individual mass spectra. The software covers a wide range of processing tasks such as import from various data formats, smoothing, baseline correction, peak picking, deisotoping, charge determination, and recalibration. Functions presented in the earlier versions such as in silico digestion and fragmentation were redesigned and improved. In addition to Mascot, an interface for ProFound has been implemented. A specific tool is available for isotopic pattern modeling to enable precise data validation. The largest available lipid database (from the LIPID MAPS Consortium) has been incorporated and together with the new compound search tool lipids can be rapidly identified. In addition, the user can define custom libraries of compounds and use them analogously. The new version of mMass is based on a stand-alone Python library, which provides the basic functionality for data processing and interpretation. This library can serve as a good starting point for other developers in their projects. Binary distributions of mMass, its source code, a detailed user's guide, and video tutorials are freely available from www.mmass.org .

Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN.

PubMed

Jug, Gregor; Anderluh, Marko; Tomašič, Tihomir

2015-06-01

Five docking tools, namely AutoDock, FRED, CDOCKER, FlexX and GOLD, have been critically examined, with the aim of selecting those most appropriate for use as docking tools for docking molecules to the lectin dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN). This lectin has been selected for its rather non-druggable binding site, which enables complex interactions that guide the binding of the core monosaccharide. Since optimal orientation is crucial for forming coordination bonds, it was important to assess whether the selected docking tools could reproduce the optimal binding conformation for several oligosaccharides that are known to bind DC-SIGN. Our results show that even widely used docking programs have certain limitations when faced with a rather shallow and featureless binding site, as is the case of DC-SIGN. The FRED docking software (OpenEye Scientific Software, Inc.) was found to score as the best tool for docking ligands to DC-SIGN. The performance of FRED was further assessed on another lectin, Langerin. We have demonstrated that this validated docking protocol could be used for docking to other lectins similar to DC-SIGN.

Validation, reliability, and specificity of CliniCom™ Psychiatric Assessment Software.

PubMed

Handal, Nelson; LePage, James; Dayley, Philip; Baldwin, Barbara; Roeser, Amellia; Kay, Joni; Theobald, Heather Ann; Nellamattathil, Michael; Drotar, Scott; Weir, Connor; Tindell, Neil; Tice, Kevin

2018-07-01

The purpose of this study was to determine the specificity and reproducibility of CliniCom™ Psychiatric Assessment Software to appropriately diagnose five prevalent mental health disorders. This online assessment tool incorporates proprietary algorithms for its propensity assessment. Unlike other questionnaires, which require a survey per specific mental disorder, CliniCom can simultaneously assess multiple mental disorders for an individual. CliniCom was concordant with other commonly used assessment tools in diagnosing five prevalent disorders including: Attention Deficit and Hyperactivity Disorder, Generalized Anxiety Disorder, Major Depressive Disorder, Obsessive Compulsive Disorder, and Social Phobia. The online tool was overall 78% concordant in diagnosing the same disorder during a test-retest analysis. When subjects exhibited two, three, or four disorders, the tool was less consistent in diagnosing the same set of disorders during the test-retest analysis (53% concordant). However, if evaluated as individual disorders within subjects, the more persistent disorders had a higher rate of concordance: MDD (83.3%), ADHD (81.0%), and OCD (68.4%). This study proposes CliniCom as an online assessment tool that demonstrates specificity in identifying specific psychiatric conditions and shows reproducibility over multiple administrations. Copyright © 2018 Elsevier B.V. All rights reserved.

The Software Architecture of the Upgraded ESA DRAMA Software Suite

NASA Astrophysics Data System (ADS)

Kebschull, Christopher; Flegel, Sven; Gelhaus, Johannes; Mockel, Marek; Braun, Vitali; Radtke, Jonas; Wiedemann, Carsten; Vorsmann, Peter; Sanchez-Ortiz, Noelia; Krag, Holger

2013-08-01

In the beginnings of man's space flight activities there was the belief that space is so big that everybody could use it without any repercussions. However during the last six decades the increasing use of Earth's orbits has lead to a rapid growth in the space debris environment, which has a big influence on current and future space missions. For this reason ESA issued the "Requirements on Space Debris Mitigation for ESA Projects" [1] in 2008, which apply to all ESA missions henceforth. The DRAMA (Debris Risk Assessment and Mitigation Analysis) software suite had been developed to support the planning of space missions to comply with these requirements. During the last year the DRAMA software suite has been upgraded under ESA contract by TUBS and DEIMOS to include additional tools and increase the performance of existing ones. This paper describes the overall software architecture of the ESA DRAMA software suite. Specifically the new graphical user interface, which manages the five main tools ARES (Assessment of Risk Event Statistics), MIDAS (MASTER-based Impact Flux and Damage Assessment Software), OSCAR (Orbital Spacecraft Active Removal), CROC (Cross Section of Complex Bodies) and SARA (Re-entry Survival and Risk Analysis) is being discussed. The advancements are highlighted as well as the challenges that arise from the integration of the five tool interfaces. A framework had been developed at the ILR and was used for MASTER-2009 and PROOF-2009. The Java based GUI framework, enables the cross-platform deployment, and its underlying model-view-presenter (MVP) software pattern, meet strict design requirements necessary to ensure a robust and reliable method of operation in an environment where the GUI is separated from the processing back-end. While the GUI framework evolved with each project, allowing an increasing degree of integration of services like validators for input fields, it has also increased in complexity. The paper will conclude with an outlook on the future development of the GUI framework, where the potential for advancements will be shown.

Psychometric Properties of Korean Version of the Second Victim Experience and Support Tool (K-SVEST).

PubMed

Kim, Eun-Mi; Kim, Sun-Aee; Lee, Ju-Ry; Burlison, Jonathan D; Oh, Eui Geum

2018-02-13

"Second victims" are defined as healthcare professionals whose wellness is influenced by adverse clinical events. The Second Victim Experience and Support Tool (SVEST) was used to measure the second-victim experience and quality of support resources. Although the reliability and validity of the original SVEST have been validated, those for the Korean tool have not been validated. The aim of the study was to evaluate the psychometric properties of the Korean version of the SVEST. The study included 305 clinical nurses as participants. The SVEST was translated into Korean via back translation. Content validity was assessed by seven experts, and test-retest reliability was evaluated by 30 clinicians. Internal consistency and construct validity were assessed via confirmatory factor analysis. The analyses were performed using SPSS 23.0 and STATA 13.0 software. The content validity index value demonstrated validity; item- and scale-level content validity index values were both 0.95. Test-retest reliability and internal consistency reliability were satisfactory: the intraclass consistent coefficient was 0.71, and Cronbach α values ranged from 0.59 to 0.87. The CFA showed a significantly good fit for an eight-factor structure (χ = 578.21, df = 303, comparative fit index = 0.92, Tucker-Lewis index = 0.90, root mean square error of approximation = 0.05). The K-SVEST demonstrated good psychometric properties and adequate validity and reliability. The results showed that the Korean version of SVEST demonstrated the extent of second victimhood and support resources in Korean healthcare workers and could aid in the development of support programs and evaluation of their effectiveness.

Lessons Learned from Optical Payload for Lasercomm Science (OPALS) Mission Operations

NASA Technical Reports Server (NTRS)

Sindiy, Oleg V.; Abrahamson, Matthew J.; Biswas, Abhijit; Wright, Malcolm W.; Padams, Jordan H.; Konyha, Alexander L.

2015-01-01

This paper provides an overview of Optical Payload for Lasercomm Science (OPALS) activities and lessons learned during mission operations. Activities described cover the periods of commissioning, prime, and extended mission operations, during which primary and secondary mission objectives were achieved for demonstrating space-to-ground optical communications. Lessons learned cover Mission Operations System topics in areas of: architecture verification and validation, staffing, mission support area, workstations, workstation tools, interfaces with support services, supporting ground stations, team training, procedures, flight software upgrades, post-processing tools, and public outreach.

Object oriented fault diagnosis system for space shuttle main engine redlines

NASA Technical Reports Server (NTRS)

Rogers, John S.; Mohapatra, Saroj Kumar

1990-01-01

A great deal of attention has recently been given to Artificial Intelligence research in the area of computer aided diagnostics. Due to the dynamic and complex nature of space shuttle red-line parameters, a research effort is under way to develop a real time diagnostic tool that will employ historical and engineering rulebases as well as a sensor validity checking. The capability of AI software development tools (KEE and G2) will be explored by applying object oriented programming techniques in accomplishing the diagnostic evaluation.

Spacecraft Internal Acoustic Environment Modeling

NASA Technical Reports Server (NTRS)

Allen, Christopher; Chu, S. Reynold

2008-01-01

The objective of the project is to develop an acoustic modeling capability, based on commercial off-the-shelf software, to be used as a tool for oversight of the future manned Constellation vehicles to ensure compliance with acoustic requirements and thus provide a safe and habitable acoustic environment for the crews, and to validate developed models via building physical mockups and conducting acoustic measurements.

Code Sharing and Collaboration: Experiences from the Scientist's Expert Assistant Project and their Relevance to the Virtual Observatory

NASA Technical Reports Server (NTRS)

Jones, Jeremy; Grosvenor, Sandy; Wolf, Karl; Li, Connie; Koratkar, Anuradha; Powers, Edward I. (Technical Monitor)

2001-01-01

In the Virtual Observatory (VO), software tools will perform the functions that have traditionally been performed by physical observatories and their instruments. These tools will not be adjuncts to VO functionality but will make up the very core of the VO. Consequently, the tradition of observatory and system independent tools serving a small user base is not valid for the VO. For the VO to succeed, we must improve software collaboration and code sharing between projects and groups. A significant goal of the Scientist's Expert Assistant (SEA) project has been promoting effective collaboration and code sharing between groups. During the past three years, the SEA project has been developing prototypes for new observation planning software tools and strategies. Initially funded by the Next Generation Space Telescope, parts of the SEA code have since been adopted by the Space Telescope Science Institute. SEA has also supplied code for SOFIA, the SIRTF planning tools, and the JSky Open Source Java library. The potential benefits of sharing code are clear. The recipient gains functionality for considerably less cost. The provider gains additional developers working with their code. If enough users groups adopt a set of common code and tools, defacto standards can emerge (as demonstrated by the success of the FITS standard). Code sharing also raises a number of challenges related to the management of the code. In this talk, we will review our experiences with SEA - both successes and failures - and offer some lessons learned that may promote further successes in collaboration and re-use.

Code Sharing and Collaboration: Experiences From the Scientist's Expert Assistant Project and Their Relevance to the Virtual Observatory

NASA Technical Reports Server (NTRS)

Korathkar, Anuradha; Grosvenor, Sandy; Jones, Jeremy; Li, Connie; Mackey, Jennifer; Neher, Ken; Obenschain, Arthur F. (Technical Monitor)

2001-01-01

In the Virtual Observatory (VO), software tools will perform the functions that have traditionally been performed by physical observatories and their instruments. These tools will not be adjuncts to VO functionality but will make up the very core of the VO. Consequently, the tradition of observatory and system independent tools serving a small user base is not valid for the VO. For the VO to succeed, we must improve software collaboration and code sharing between projects and groups. A significant goal of the Scientist's Expert Assistant (SEA) project has been promoting effective collaboration and code sharing among groups. During the past three years, the SEA project has been developing prototypes for new observation planning software tools and strategies. Initially funded by the Next Generation Space Telescope, parts of the SEA code have since been adopted by the Space Telescope Science Institute. SEA has also supplied code for the SIRTF (Space Infrared Telescope Facility) planning tools, and the JSky Open Source Java library. The potential benefits of sharing code are clear. The recipient gains functionality for considerably less cost. The provider gains additional developers working with their code. If enough users groups adopt a set of common code and tools, de facto standards can emerge (as demonstrated by the success of the FITS standard). Code sharing also raises a number of challenges related to the management of the code. In this talk, we will review our experiences with SEA--both successes and failures, and offer some lessons learned that might promote further successes in collaboration and re-use.

GiA Roots: software for the high throughput analysis of plant root system architecture.

PubMed

Galkovskyi, Taras; Mileyko, Yuriy; Bucksch, Alexander; Moore, Brad; Symonova, Olga; Price, Charles A; Topp, Christopher N; Iyer-Pascuzzi, Anjali S; Zurek, Paul R; Fang, Suqin; Harer, John; Benfey, Philip N; Weitz, Joshua S

2012-07-26

Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks. We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user. We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.

Increasing rigor in NMR-based metabolomics through validated and open source tools

PubMed Central

Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

2016-01-01

The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism’s phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. PMID:27643760

Increasing rigor in NMR-based metabolomics through validated and open source tools.

PubMed

Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

2017-02-01

The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. Copyright © 2016. Published by Elsevier Ltd.

The SCEC Broadband Platform: Open-Source Software for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Goulet, C. A.; Maechling, P. J.; Callaghan, S.; Jordan, T. H.

2016-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100 Hz) ground motions for earthquakes at regional scales. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The BBP scientific software modules implement kinematic rupture generation, low- and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, several ground motion intensity measure calculations, and various ground motion goodness-of-fit tools. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground-motion seismograms, using multiple alternative ground motion simulation methods, and software utilities to generate tables, plots, and maps. The BBP has been developed over the last five years in a collaborative project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The SCEC BBP software released in 2016 can be compiled and run on recent Linux and Mac OS X systems with GNU compilers. It includes five simulation methods, seven simulation regions covering California, Japan, and Eastern North America, and the ability to compare simulation results against empirical ground motion models (aka GMPEs). The latest version includes updated ground motion simulation methods, a suite of new validation metrics and a simplified command line user interface.

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.

PubMed

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M; Montelione, Gaetano T

2013-08-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

PDBStat: A Universal Restraint Converter and Restraint Analysis Software Package for Protein NMR

PubMed Central

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M.; Montelione, Gaetano T

2013-01-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data. PMID:23897031

Implementation of the validation testing in MPPG 5.a "Commissioning and QA of treatment planning dose calculations-megavoltage photon and electron beams".

PubMed

Jacqmin, Dustin J; Bredfeldt, Jeremy S; Frigo, Sean P; Smilowitz, Jennifer B

2017-01-01

The AAPM Medical Physics Practice Guideline (MPPG) 5.a provides concise guidance on the commissioning and QA of beam modeling and dose calculation in radiotherapy treatment planning systems. This work discusses the implementation of the validation testing recommended in MPPG 5.a at two institutions. The two institutions worked collaboratively to create a common set of treatment fields and analysis tools to deliver and analyze the validation tests. This included the development of a novel, open-source software tool to compare scanning water tank measurements to 3D DICOM-RT Dose distributions. Dose calculation algorithms in both Pinnacle and Eclipse were tested with MPPG 5.a to validate the modeling of Varian TrueBeam linear accelerators. The validation process resulted in more than 200 water tank scans and more than 50 point measurements per institution, each of which was compared to a dose calculation from the institution's treatment planning system (TPS). Overall, the validation testing recommended in MPPG 5.a took approximately 79 person-hours for a machine with four photon and five electron energies for a single TPS. Of the 79 person-hours, 26 person-hours required time on the machine, and the remainder involved preparation and analysis. The basic photon, electron, and heterogeneity correction tests were evaluated with the tolerances in MPPG 5.a, and the tolerances were met for all tests. The MPPG 5.a evaluation criteria were used to assess the small field and IMRT/VMAT validation tests. Both institutions found the use of MPPG 5.a to be a valuable resource during the commissioning process. The validation testing in MPPG 5.a showed the strengths and limitations of the TPS models. In addition, the data collected during the validation testing is useful for routine QA of the TPS, validation of software upgrades, and commissioning of new algorithms. © 2016 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Validation of a general practice audit and data extraction tool.

PubMed

Peiris, David; Agaliotis, Maria; Patel, Bindu; Patel, Anushka

2013-11-01

We assessed how accurately a common general practitioner (GP) audit tool extracts data from two software systems. First, pathology test codes were audited at 33 practices covering nine companies. Second, a manual audit of chronic disease data from 200 random patient records at two practices was compared with audit tool data. Pathology review: all companies assigned correct codes for cholesterol, creatinine and glycated haemoglobin; four companies assigned incorrect codes for albuminuria tests, precluding accurate detection with the audit tool. Case record review: there was strong agreement between the manual audit and the tool for all variables except chronic kidney disease diagnoses, which was due to a tool-related programming error. The audit tool accurately detected most chronic disease data in two GP record systems. The one exception, however, highlights the importance of surveillance systems to promptly identify errors. This will maximise potential for audit tools to improve healthcare quality.

ETICS: the international software engineering service for the grid

NASA Astrophysics Data System (ADS)

Meglio, A. D.; Bégin, M.-E.; Couvares, P.; Ronchieri, E.; Takacs, E.

2008-07-01

The ETICS system is a distributed software configuration, build and test system designed to fulfil the needs of improving the quality, reliability and interoperability of distributed software in general and grid software in particular. The ETICS project is a consortium of five partners (CERN, INFN, Engineering Ingegneria Informatica, 4D Soft and the University of Wisconsin-Madison). The ETICS service consists of a build and test job execution system based on the Metronome software and an integrated set of web services and software engineering tools to design, maintain and control build and test scenarios. The ETICS system allows taking into account complex dependencies among applications and middleware components and provides a rich environment to perform static and dynamic analysis of the software and execute deployment, system and interoperability tests. This paper gives an overview of the system architecture and functionality set and then describes how the EC-funded EGEE, DILIGENT and OMII-Europe projects are using the software engineering services to build, validate and distribute their software. Finally a number of significant use and test cases will be described to show how ETICS can be used in particular to perform interoperability tests of grid middleware using the grid itself.

LICA AstroCalc, a software to analyze the impact of artificial light: Extracting parameters from the spectra of street and indoor lamps

NASA Astrophysics Data System (ADS)

Ayuga, Carlos Eugenio Tapia; Zamorano, Jaime

2018-07-01

The night sky spectra of light-polluted areas is the result of the artificial light scattered back from the atmosphere and the reemission of the light after reflections in painted surfaces. This emission comes mainly from street and decorative lamps. We have built an extensive database of lamps spectra covering from UV to near IR and the software needed to analyze them. We describe the LICA-AstroCalc free software that is a user friendly GUI tool to extract information from our database spectra or any other user provided spectrum. The software also includes the complete color database of paints from NCS comprising 1950 types. This helps to evaluate how different colors modify the reflected spectra from different lamps. All spectroscopic measurements have been validated with recommendations from CIELAB and ISO from NCS database.

Precise and Scalable Static Program Analysis of NASA Flight Software

NASA Technical Reports Server (NTRS)

Brat, G.; Venet, A.

2005-01-01

Recent NASA mission failures (e.g., Mars Polar Lander and Mars Orbiter) illustrate the importance of having an efficient verification and validation process for such systems. One software error, as simple as it may be, can cause the loss of an expensive mission, or lead to budget overruns and crunched schedules. Unfortunately, traditional verification methods cannot guarantee the absence of errors in software systems. Therefore, we have developed the CGS static program analysis tool, which can exhaustively analyze large C programs. CGS analyzes the source code and identifies statements in which arrays are accessed out of bounds, or, pointers are used outside the memory region they should address. This paper gives a high-level description of CGS and its theoretical foundations. It also reports on the use of CGS on real NASA software systems used in Mars missions (from Mars PathFinder to Mars Exploration Rover) and on the International Space Station.

45 CFR 153.350 - Risk adjustment data validation standards.

Code of Federal Regulations, 2012 CFR

2012-10-01

... implementation of any risk adjustment software and ensure proper validation of a statistically valid sample of... respect to implementation of risk adjustment software or as a result of data validation conducted pursuant... implementation of risk adjustment software or data validation. ...

Comparison of quality control software tools for diffusion tensor imaging.

PubMed

Liu, Bilan; Zhu, Tong; Zhong, Jianhui

2015-04-01

Image quality of diffusion tensor imaging (DTI) is critical for image interpretation, diagnostic accuracy and efficiency. However, DTI is susceptible to numerous detrimental artifacts that may impair the reliability and validity of the obtained data. Although many quality control (QC) software tools are being developed and are widely used and each has its different tradeoffs, there is still no general agreement on an image quality control routine for DTIs, and the practical impact of these tradeoffs is not well studied. An objective comparison that identifies the pros and cons of each of the QC tools will be helpful for the users to make the best choice among tools for specific DTI applications. This study aims to quantitatively compare the effectiveness of three popular QC tools including DTI studio (Johns Hopkins University), DTIprep (University of North Carolina at Chapel Hill, University of Iowa and University of Utah) and TORTOISE (National Institute of Health). Both synthetic and in vivo human brain data were used to quantify adverse effects of major DTI artifacts to tensor calculation as well as the effectiveness of different QC tools in identifying and correcting these artifacts. The technical basis of each tool was discussed, and the ways in which particular techniques affect the output of each of the tools were analyzed. The different functions and I/O formats that three QC tools provide for building a general DTI processing pipeline and integration with other popular image processing tools were also discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

MPST Software: grl_pef_check

NASA Technical Reports Server (NTRS)

Call, Jared A.; Kwok, John H.; Fisher, Forest W.

2013-01-01

This innovation is a tool used to verify and validate spacecraft sequences at the predicted events file (PEF) level for the GRAIL (Gravity Recovery and Interior Laboratory, see http://www.nasa. gov/mission_pages/grail/main/index. html) mission as part of the Multi-Mission Planning and Sequencing Team (MPST) operations process to reduce the possibility for errors. This tool is used to catch any sequence related errors or issues immediately after the seqgen modeling to streamline downstream processes. This script verifies and validates the seqgen modeling for the GRAIL MPST process. A PEF is provided as input, and dozens of checks are performed on it to verify and validate the command products including command content, command ordering, flight-rule violations, modeling boundary consistency, resource limits, and ground commanding consistency. By performing as many checks as early in the process as possible, grl_pef_check streamlines the MPST task of generating GRAIL command and modeled products on an aggressive schedule. By enumerating each check being performed, and clearly stating the criteria and assumptions made at each step, grl_pef_check can be used as a manual checklist as well as an automated tool. This helper script was written with a focus on enabling the user with the information they need in order to evaluate a sequence quickly and efficiently, while still keeping them informed and active in the overall sequencing process. grl_pef_check verifies and validates the modeling and sequence content prior to investing any more effort into the build. There are dozens of various items in the modeling run that need to be checked, which is a time-consuming and errorprone task. Currently, no software exists that provides this functionality. Compared to a manual process, this script reduces human error and saves considerable man-hours by automating and streamlining the mission planning and sequencing task for the GRAIL mission.

An open tool for input function estimation and quantification of dynamic PET FDG brain scans.

PubMed

Bertrán, Martín; Martínez, Natalia; Carbajal, Guillermo; Fernández, Alicia; Gómez, Álvaro

2016-08-01

Positron emission tomography (PET) analysis of clinical studies is mostly restricted to qualitative evaluation. Quantitative analysis of PET studies is highly desirable to be able to compute an objective measurement of the process of interest in order to evaluate treatment response and/or compare patient data. But implementation of quantitative analysis generally requires the determination of the input function: the arterial blood or plasma activity which indicates how much tracer is available for uptake in the brain. The purpose of our work was to share with the community an open software tool that can assist in the estimation of this input function, and the derivation of a quantitative map from the dynamic PET study. Arterial blood sampling during the PET study is the gold standard method to get the input function, but is uncomfortable and risky for the patient so it is rarely used in routine studies. To overcome the lack of a direct input function, different alternatives have been devised and are available in the literature. These alternatives derive the input function from the PET image itself (image-derived input function) or from data gathered from previous similar studies (population-based input function). In this article, we present ongoing work that includes the development of a software tool that integrates several methods with novel strategies for the segmentation of blood pools and parameter estimation. The tool is available as an extension to the 3D Slicer software. Tests on phantoms were conducted in order to validate the implemented methods. We evaluated the segmentation algorithms over a range of acquisition conditions and vasculature size. Input function estimation algorithms were evaluated against ground truth of the phantoms, as well as on their impact over the final quantification map. End-to-end use of the tool yields quantification maps with [Formula: see text] relative error in the estimated influx versus ground truth on phantoms. The main contribution of this article is the development of an open-source, free to use tool that encapsulates several well-known methods for the estimation of the input function and the quantification of dynamic PET FDG studies. Some alternative strategies are also proposed and implemented in the tool for the segmentation of blood pools and parameter estimation. The tool was tested on phantoms with encouraging results that suggest that even bloodless estimators could provide a viable alternative to blood sampling for quantification using graphical analysis. The open tool is a promising opportunity for collaboration among investigators and further validation on real studies.

Update: Advancement of Contact Dynamics Modeling for Human Spaceflight Simulation Applications

NASA Technical Reports Server (NTRS)

Brain, Thomas A.; Kovel, Erik B.; MacLean, John R.; Quiocho, Leslie J.

2017-01-01

Pong is a new software tool developed at the NASA Johnson Space Center that advances interference-based geometric contact dynamics based on 3D graphics models. The Pong software consists of three parts: a set of scripts to extract geometric data from 3D graphics models, a contact dynamics engine that provides collision detection and force calculations based on the extracted geometric data, and a set of scripts for visualizing the dynamics response with the 3D graphics models. The contact dynamics engine can be linked with an external multibody dynamics engine to provide an integrated multibody contact dynamics simulation. This paper provides a detailed overview of Pong including the overall approach and modeling capabilities, which encompasses force generation from contact primitives and friction to computational performance. Two specific Pong-based examples of International Space Station applications are discussed, and the related verification and validation using this new tool are also addressed.

ClusCo: clustering and comparison of protein models.

PubMed

Jamroz, Michal; Kolinski, Andrzej

2013-02-22

The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline. Clusco is fast and easy-to-use software for high-throughput comparison of protein models with different similarity measures (cRMSD, dRMSD, GDT_TS, TM-Score, MaxSub, Contact Map Overlap) and clustering of the comparison results with standard methods: K-means Clustering or Hierarchical Agglomerative Clustering. The application was highly optimized and written in C/C++, including the code for parallel execution on CPU and GPU, which resulted in a significant speedup over similar clustering and scoring computation programs.

extrap: Software to assist the selection of extrapolation methods for moving-boat ADCP streamflow measurements

USGS Publications Warehouse

Mueller, David S.

2013-01-01

profiles from the entire cross section and multiple transects to determine a mean profile for the measurement. The use of an exponent derived from normalized data from the entire cross section is shown to be valid for application of the power velocity distribution law in the computation of the unmeasured discharge in a cross section. Selected statistics are combined with empirically derived criteria to automatically select the appropriate extrapolation methods. A graphical user interface (GUI) provides the user tools to visually evaluate the automatically selected extrapolation methods and manually change them, as necessary. The sensitivity of the total discharge to available extrapolation methods is presented in the GUI. Use of extrap by field hydrographers has demonstrated that extrap is a more accurate and efficient method of determining the appropriate extrapolation methods compared with tools currently (2012) provided in the ADCP manufacturers’ software.

Design and Control of Compliant Tensegrity Robots Through Simulation and Hardware Validation

NASA Technical Reports Server (NTRS)

Caluwaerts, Ken; Despraz, Jeremie; Iscen, Atil; Sabelhaus, Andrew P.; Bruce, Jonathan; Schrauwen, Benjamin; Sunspiral, Vytas

2014-01-01

To better understand the role of tensegrity structures in biological systems and their application to robotics, the Dynamic Tensegrity Robotics Lab at NASA Ames Research Center has developed and validated two different software environments for the analysis, simulation, and design of tensegrity robots. These tools, along with new control methodologies and the modular hardware components developed to validate them, are presented as a system for the design of actuated tensegrity structures. As evidenced from their appearance in many biological systems, tensegrity ("tensile-integrity") structures have unique physical properties which make them ideal for interaction with uncertain environments. Yet these characteristics, such as variable structural compliance, and global multi-path load distribution through the tension network, make design and control of bio-inspired tensegrity robots extremely challenging. This work presents the progress in using these two tools in tackling the design and control challenges. The results of this analysis includes multiple novel control approaches for mobility and terrain interaction of spherical tensegrity structures. The current hardware prototype of a six-bar tensegrity, code-named ReCTeR, is presented in the context of this validation.

Impact of computer-based treatment planning software on clinical judgment of dental students for planning prosthodontic rehabilitation

PubMed Central

Deshpande, Saee; Chahande, Jayashree

2014-01-01

Purpose Successful prosthodontic rehabilitation involves making many interrelated clinical decisions which have an impact on each other. Self-directed computer-based training has been shown to be a very useful tool to develop synthetic and analytical problem-solving skills among students. Thus, a computer-based case study and treatment planning (CSTP) software program was developed which would allow students to work through the process of comprehensive, multidisciplinary treatment planning for patients in a structured and logical manner. The present study was aimed at assessing the effect of this CSTP software on the clinical judgment of dental students while planning prosthodontic rehabilitation and to assess the students’ perceptions about using the program for its intended use. Methods A CSTP software program was developed and validated. The impact of this program on the clinical decision making skills of dental graduates was evaluated by real life patient encounters, using a modified and validated mini-CEX. Students’ perceptions about the program were obtained by a pre-validated feedback questionnaire. Results The faculty assessment scores of clinical judgment improved significantly after the use of this program. The majority of students felt it was an informative, useful, and innovative way of learning and they strongly felt that they had learnt the logical progression of planning, the insight into decision making, and the need for flexibility in treatment planning after using this program. Conclusion CSTP software was well received by the students. There was significant improvement in students’ clinical judgment after using this program. It should thus be envisaged fundamentally as an adjunct to conventional teaching techniques to improve students’ decision making skills and confidence. PMID:25170288

The Advanced Human Eye Model (AHEM): a personal binocular eye modeling system inclusive of refraction, diffraction, and scatter.

PubMed

Donnelly, William

2008-11-01

To present a commercially available software tool for creating eye models to assist the development of ophthalmic optics and instrumentation, simulate ailments or surgery-induced changes, explore vision research questions, and provide assistance to clinicians in planning treatment or analyzing clinical outcomes. A commercially available eye modeling system was developed, the Advanced Human Eye Model (AHEM). Two mainstream optical software engines, ZEMAX (ZEMAX Development Corp) and ASAP (Breault Research Organization), were used to construct a similar software eye model and compared. The method of using the AHEM is described and various eye modeling scenarios are created. These scenarios consist of retinal imaging of targets and sources; optimization capability; spectacles, contact lens, and intraocular lens insertion and correction; Zernike surface deformation on the cornea; cataract simulation and scattering; a gradient index lens; a binocular mode; a retinal implant; system import/export; and ray path exploration. Similarity of the two different optical software engines showed validity to the mechanism of the AHEM. Metrics and graphical data are generated from the various modeling scenarios particular to their input specifications. The AHEM is a user-friendly commercially available software tool from Breault Research Organization, which can assist the design of ophthalmic optics and instrumentation, simulate ailments or refractive surgery-induced changes, answer vision research questions, or assist clinicians in planning treatment or analyzing clinical outcomes.

Seaworthy Quantum Key Distribution Design and Validation (SEAKEY)

DTIC Science & Technology

2014-10-30

to single photon detection, at comparable detection efficiencies. On the other hand, error-correction codes are better developed for small-alphabet...protocol is several orders of magnitude better than the Shapiro protocol, which needs entangled states. The bits/mode performance achieved by our...putting together a software tool implemented in MATLAB , which talks to the MODTRAN database via an intermediate numerical dump of transmission data

The Activities of the European Consortium on Nuclear Data Development and Analysis for Fusion

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

Fischer, U., E-mail: ulrich.fischer@kit.edu; Avrigeanu, M.; Avrigeanu, V.

This paper presents an overview of the activities of the European Consortium on Nuclear Data Development and Analysis for Fusion. The Consortium combines available European expertise to provide services for the generation, maintenance, and validation of nuclear data evaluations and data files relevant for ITER, IFMIF and DEMO, as well as codes and software tools required for related nuclear calculations.

Spacecraft Internal Acoustic Environment Modeling

NASA Technical Reports Server (NTRS)

Chu, S. Reynold; Allen, Chris

2009-01-01

The objective of the project is to develop an acoustic modeling capability, based on commercial off-the-shelf software, to be used as a tool for oversight of the future manned Constellation vehicles. The use of such a model will help ensure compliance with acoustic requirements. Also, this project includes modeling validation and development feedback via building physical mockups and conducting acoustic measurements to compare with the predictions.

Data Visualization and Analysis Tools for the Global Precipitation Measurement (GPM) Validation Network

NASA Technical Reports Server (NTRS)

Morris, Kenneth R.; Schwaller, Mathew

2010-01-01

The Validation Network (VN) prototype for the Global Precipitation Measurement (GPM) Mission compares data from the Tropical Rainfall Measuring Mission (TRMM) satellite Precipitation Radar (PR) to similar measurements from U.S. and international operational weather radars. This prototype is a major component of the GPM Ground Validation System (GVS). The VN provides a means for the precipitation measurement community to identify and resolve significant discrepancies between the ground radar (GR) observations and similar satellite observations. The VN prototype is based on research results and computer code described by Anagnostou et al. (2001), Bolen and Chandrasekar (2000), and Liao et al. (2001), and has previously been described by Morris, et al. (2007). Morris and Schwaller (2009) describe the PR-GR volume-matching algorithm used to create the VN match-up data set used for the comparisons. This paper describes software tools that have been developed for visualization and statistical analysis of the original and volume matched PR and GR data.

ESA's tools for internal charging

NASA Astrophysics Data System (ADS)

Sorensen, J.; Rodgers, D. J.; Ryden, K. A.; Latham, P. M.; Wrenn, G. L.; Levy, L.; Panabiere, G.

2000-06-01

Electrostatic discharges, caused by bulk charging of spacecraft insulating materials, are a major cause of satellite anomalies. A quantitative knowledge of the charge build-up is essential in order to eliminate these problems in the design stage. This is a presentation of ESA's tools to assess whether a given structure is liable to experience electrostatic discharges or not. A study has been made of the physical phenomenon, and an engineering specification has been created to be used to assess a structure for potential discharge problems. The specification has been implemented in a new software DICTAT. The implementation of tests in dedicated facilities is an important part of the specification, and tests have been performed to validate the new tool.

Verification and Validation of the General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Qureshi, Rizwan H.; Cooley, D. Steven; Parker, Joel J. K.; Grubb, Thomas G.

2014-01-01

This paper describes the processes and results of Verification and Validation (V&V) efforts for the General Mission Analysis Tool (GMAT). We describe the test program and environments, the tools used for independent test data, and comparison results. The V&V effort produced approximately 13,000 test scripts that are run as part of the nightly buildtest process. In addition, we created approximately 3000 automated GUI tests that are run every two weeks. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results in most areas, and detailed test results for key areas. The final product of the V&V effort presented in this paper was GMAT version R2013a, the first Gold release of the software with completely updated documentation and greatly improved quality. Release R2013a was the staging release for flight qualification performed at Goddard Space Flight Center (GSFC) ultimately resulting in GMAT version R2013b.

Computer-Aided Nodule Assessment and Risk Yield Risk Management of Adenocarcinoma: The Future of Imaging?

PubMed

Foley, Finbar; Rajagopalan, Srinivasan; Raghunath, Sushravya M; Boland, Jennifer M; Karwoski, Ronald A; Maldonado, Fabien; Bartholmai, Brian J; Peikert, Tobias

2016-01-01

Increased clinical use of chest high-resolution computed tomography results in increased identification of lung adenocarcinomas and persistent subsolid opacities. However, these lesions range from very indolent to extremely aggressive tumors. Clinically relevant diagnostic tools to noninvasively risk stratify and guide individualized management of these lesions are lacking. Research efforts investigating semiquantitative measures to decrease interrater and intrarater variability are emerging, and in some cases steps have been taken to automate this process. However, many such methods currently are still suboptimal, require validation and are not yet clinically applicable. The computer-aided nodule assessment and risk yield software application represents a validated tool for the automated, quantitative, and noninvasive tool for risk stratification of adenocarcinoma lung nodules. Computer-aided nodule assessment and risk yield correlates well with consensus histology and postsurgical patient outcomes, and therefore may help to guide individualized patient management, for example, in identification of nodules amenable to radiological surveillance, or in need of adjunctive therapy. Copyright © 2016 Elsevier Inc. All rights reserved.

CANARY Risk Management of Adenocarcinoma: The Future of Imaging?

PubMed Central

Foley, Finbar; Rajagopalan, Srinivasan; Raghunath, Sushravya M; Boland, Jennifer M; Karwoski, Ronald A.; Maldonado, Fabien; Bartholmai, Brian J; Peikert, Tobias

2016-01-01

Increased clinical utilization of chest high resolution computed tomography results in increased identification of lung adenocarcinomas and persistent sub-solid opacities. However, these lesions range from very indolent to extremely aggressive tumors. Clinically relevant diagnostic tools to non-invasively risk stratify and guide individualized management of these lesions are lacking. Research efforts investigating semi-quantitative measures to decrease inter- and intra-rater variability are emerging, and in some cases steps have been taken to automate this process. However, many such methods currently are still sub-optimal, require validation and are not yet clinically applicable. The Computer-Aided Nodule Assessment and Risk Yield (CANARY) software application represents a validated tool for the automated, quantitative, non-invasive tool for risk stratification of adenocarcinoma lung nodules. CANARY correlates well with consensus histology and post-surgical patient outcomes and therefore may help to guide individualized patient management e.g. in identification of nodules amenable to radiological surveillance, or in need of adjunctive therapy. PMID:27568149

From data to the decision: A software architecture to integrate predictive modelling in clinical settings.

PubMed

Martinez-Millana, A; Fernandez-Llatas, C; Sacchi, L; Segagni, D; Guillen, S; Bellazzi, R; Traver, V

2015-08-01

The application of statistics and mathematics over large amounts of data is providing healthcare systems with new tools for screening and managing multiple diseases. Nonetheless, these tools have many technical and clinical limitations as they are based on datasets with concrete characteristics. This proposition paper describes a novel architecture focused on providing a validation framework for discrimination and prediction models in the screening of Type 2 diabetes. For that, the architecture has been designed to gather different data sources under a common data structure and, furthermore, to be controlled by a centralized component (Orchestrator) in charge of directing the interaction flows among data sources, models and graphical user interfaces. This innovative approach aims to overcome the data-dependency of the models by providing a validation framework for the models as they are used within clinical settings.

Validation of Alternative In Vitro Methods to Animal Testing: Concepts, Challenges, Processes and Tools.

PubMed

Griesinger, Claudius; Desprez, Bertrand; Coecke, Sandra; Casey, Warren; Zuang, Valérie

This chapter explores the concepts, processes, tools and challenges relating to the validation of alternative methods for toxicity and safety testing. In general terms, validation is the process of assessing the appropriateness and usefulness of a tool for its intended purpose. Validation is routinely used in various contexts in science, technology, the manufacturing and services sectors. It serves to assess the fitness-for-purpose of devices, systems, software up to entire methodologies. In the area of toxicity testing, validation plays an indispensable role: "alternative approaches" are increasingly replacing animal models as predictive tools and it needs to be demonstrated that these novel methods are fit for purpose. Alternative approaches include in vitro test methods, non-testing approaches such as predictive computer models up to entire testing and assessment strategies composed of method suites, data sources and decision-aiding tools. Data generated with alternative approaches are ultimately used for decision-making on public health and the protection of the environment. It is therefore essential that the underlying methods and methodologies are thoroughly characterised, assessed and transparently documented through validation studies involving impartial actors. Importantly, validation serves as a filter to ensure that only test methods able to produce data that help to address legislative requirements (e.g. EU's REACH legislation) are accepted as official testing tools and, owing to the globalisation of markets, recognised on international level (e.g. through inclusion in OECD test guidelines). Since validation creates a credible and transparent evidence base on test methods, it provides a quality stamp, supporting companies developing and marketing alternative methods and creating considerable business opportunities. Validation of alternative methods is conducted through scientific studies assessing two key hypotheses, reliability and relevance of the test method for a given purpose. Relevance encapsulates the scientific basis of the test method, its capacity to predict adverse effects in the "target system" (i.e. human health or the environment) as well as its applicability for the intended purpose. In this chapter we focus on the validation of non-animal in vitro alternative testing methods and review the concepts, challenges, processes and tools fundamental to the validation of in vitro methods intended for hazard testing of chemicals. We explore major challenges and peculiarities of validation in this area. Based on the notion that validation per se is a scientific endeavour that needs to adhere to key scientific principles, namely objectivity and appropriate choice of methodology, we examine basic aspects of study design and management, and provide illustrations of statistical approaches to describe predictive performance of validated test methods as well as their reliability.

PIRATE: pediatric imaging response assessment and targeting environment

NASA Astrophysics Data System (ADS)

Glenn, Russell; Zhang, Yong; Krasin, Matthew; Hua, Chiaho

2010-02-01

By combining the strengths of various imaging modalities, the multimodality imaging approach has potential to improve tumor staging, delineation of tumor boundaries, chemo-radiotherapy regime design, and treatment response assessment in cancer management. To address the urgent needs for efficient tools to analyze large-scale clinical trial data, we have developed an integrated multimodality, functional and anatomical imaging analysis software package for target definition and therapy response assessment in pediatric radiotherapy (RT) patients. Our software provides quantitative tools for automated image segmentation, region-of-interest (ROI) histogram analysis, spatial volume-of-interest (VOI) analysis, and voxel-wise correlation across modalities. To demonstrate the clinical applicability of this software, histogram analyses were performed on baseline and follow-up 18F-fluorodeoxyglucose (18F-FDG) PET images of nine patients with rhabdomyosarcoma enrolled in an institutional clinical trial at St. Jude Children's Research Hospital. In addition, we combined 18F-FDG PET, dynamic-contrast-enhanced (DCE) MR, and anatomical MR data to visualize the heterogeneity in tumor pathophysiology with the ultimate goal of adaptive targeting of regions with high tumor burden. Our software is able to simultaneously analyze multimodality images across multiple time points, which could greatly speed up the analysis of large-scale clinical trial data and validation of potential imaging biomarkers.

Federal Emergency Management Information System (FEMIS) system administration guide. Version 1.4

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

Arp, J.A.; Burnett, R.A.; Downing, T.R.

The Federal Emergency Management Information System (FEMIS) is an emergency management planning and analysis tool that was developed by the Pacific Northwest National Laboratory (PNNL) under the direction of the US Army Chemical Biological Defense Command. The FEMIS System Administration Guide defines FEMIS hardware and software requirements and gives instructions for installing the FEMIS software package. This document also contains information on the following: software installation for the FEMIS data servers, communication server, mail server, and the emergency management workstations; distribution media loading and FEMIS installation validation and troubleshooting; and system management of FEMIS users, login privileges, and usage. Themore » system administration utilities (tools), available in the FEMIS client software, are described for user accounts and site profile. This document also describes the installation and use of system and database administration utilities that will assist in keeping the FEMIS system running in an operational environment. The FEMIS system is designed for a single Chemical Stockpile Emergency Preparedness Program (CSEPP) site that has multiple Emergency Operations Centers (EOCs). Each EOC has personal computers (PCs) that emergency planners and operations personnel use to do their jobs. These PCs are connected via a local area network (LAN) to servers that provide EOC-wide services. Each EOC is interconnected to other EOCs via telecommunications links.« less

An Overview of Modifications Applied to a Turbulence Response Analysis Method for Flexible Aircraft Configurations

NASA Technical Reports Server (NTRS)

Funk, Christie J.

2013-01-01

A software program and associated methodology to study gust loading on aircraft exists for a classification of geometrically simplified flexible configurations. This program consists of a simple aircraft response model with two rigid and three flexible symmetric degrees of freedom and allows for the calculation of various airplane responses due to a discrete one-minus-cosine gust as well as continuous turbulence. Simplifications, assumptions, and opportunities for potential improvements pertaining to the existing software program are first identified, then a revised version of the original software tool is developed with improved methodology to include more complex geometries, additional excitation cases, and output data so as to provide a more useful and accurate tool for gust load analysis. Revisions are made in the categories of aircraft geometry, computation of aerodynamic forces and moments, and implementation of horizontal tail mode shapes. In order to improve the original software program to enhance usefulness, a wing control surface and horizontal tail control surface is added, an extended application of the discrete one-minus-cosine gust input is employed, a supplemental continuous turbulence spectrum is implemented, and a capability to animate the total vehicle deformation response to gust inputs in included. These revisions and enhancements are implemented and an analysis of the results is used to validate the modifications.

Automating Risk Analysis of Software Design Models

PubMed Central

Ruiz, Guifré; Heymann, Elisa; César, Eduardo; Miller, Barton P.

2014-01-01

The growth of the internet and networked systems has exposed software to an increased amount of security threats. One of the responses from software developers to these threats is the introduction of security activities in the software development lifecycle. This paper describes an approach to reduce the need for costly human expertise to perform risk analysis in software, which is common in secure development methodologies, by automating threat modeling. Reducing the dependency on security experts aims at reducing the cost of secure development by allowing non-security-aware developers to apply secure development with little to no additional cost, making secure development more accessible. To automate threat modeling two data structures are introduced, identification trees and mitigation trees, to identify threats in software designs and advise mitigation techniques, while taking into account specification requirements and cost concerns. These are the components of our model for automated threat modeling, AutSEC. We validated AutSEC by implementing it in a tool based on data flow diagrams, from the Microsoft security development methodology, and applying it to VOMS, a grid middleware component, to evaluate our model's performance. PMID:25136688

Automating risk analysis of software design models.

PubMed

Frydman, Maxime; Ruiz, Guifré; Heymann, Elisa; César, Eduardo; Miller, Barton P

2014-01-01

The growth of the internet and networked systems has exposed software to an increased amount of security threats. One of the responses from software developers to these threats is the introduction of security activities in the software development lifecycle. This paper describes an approach to reduce the need for costly human expertise to perform risk analysis in software, which is common in secure development methodologies, by automating threat modeling. Reducing the dependency on security experts aims at reducing the cost of secure development by allowing non-security-aware developers to apply secure development with little to no additional cost, making secure development more accessible. To automate threat modeling two data structures are introduced, identification trees and mitigation trees, to identify threats in software designs and advise mitigation techniques, while taking into account specification requirements and cost concerns. These are the components of our model for automated threat modeling, AutSEC. We validated AutSEC by implementing it in a tool based on data flow diagrams, from the Microsoft security development methodology, and applying it to VOMS, a grid middleware component, to evaluate our model's performance.

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.

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

NASA Technical Reports Server (NTRS)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy; Kim, Youngkwang; Conway, Claire; Conway, Darrel J.

2017-01-01

This paper describes the processes and results of Verification and Validation (VV) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The VV effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

NASA Technical Reports Server (NTRS)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy (Compiler); Kim, Youngkwang; Conway, Claire (Compiler); Conway, Darrel

2017-01-01

This paper describes the processes and results of Verification and Validation (V&V) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The V&V effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

The Validation by Measurement Theory of Proposed Object-Oriented Software Metrics

NASA Technical Reports Server (NTRS)

Neal, Ralph D.

1996-01-01

Moving software development into the engineering arena requires controllability, and to control a process, it must be measurable. Measuring the process does no good if the product is not also measured, i.e., being the best at producing an inferior product does not define a quality process. Also, not every number extracted from software development is a valid measurement. A valid measurement only results when we are able to verify that the number is representative of the attribute that we wish to measure. Many proposed software metrics are used by practitioners without these metrics ever having been validated, leading to costly but often useless calculations. Several researchers have bemoaned the lack of scientific precision in much of the published software measurement work and have called for validation of software metrics by measurement theory. This dissertation applies measurement theory to validate fifty proposed object-oriented software metrics.

Development of a video-simulation instrument for assessing cognition in older adults.

PubMed

Ip, Edward H; Barnard, Ryan; Marshall, Sarah A; Lu, Lingyi; Sink, Kaycee; Wilson, Valerie; Chamberlain, Dana; Rapp, Stephen R

2017-12-06

Commonly used methods to assess cognition, such as direct observation, self-report, or neuropsychological testing, have significant limitations. Therefore, a novel tablet computer-based video simulation was created with the goal of being valid, reliable, and easy to administer. The design and implementation of the SIMBAC (Simulation-Based Assessment of Cognition) instrument is described in detail, as well as informatics "lessons learned" during development. The software emulates 5 common instrumental activities of daily living (IADLs) and scores participants' performance. The modules were chosen by a panel of geriatricians based on relevance to daily functioning and ability to be modeled electronically, and included facial recognition, pairing faces with the correct names, filling a pillbox, using an automated teller machine (ATM), and automatic renewal of a prescription using a telephone. Software development included three phases 1) a period of initial design and testing (alpha version), 2) pilot study with 10 cognitively normal and 10 cognitively impaired adults over the age of 60 (beta version), and 3) larger validation study with 162 older adults of mixed cognitive status (release version). Results of the pilot study are discussed in the context of refining the instrument; full results of the validation study are reported in a separate article. In both studies, SIMBAC reliably differentiated controls from persons with cognitive impairment, and performance was highly correlated with Mini Mental Status Examination (MMSE) score. Several informatics challenges emerged during software development, which are broadly relevant to the design and use of electronic assessment tools. Solutions to these issues, such as protection of subject privacy and safeguarding against data loss, are discussed in depth. Collection of fine-grained data (highly detailed information such as time spent reading directions and the number of taps on screen) is also considered. SIMBAC provides clinicians direct insight into whether subjects can successfully perform selected cognitively intensive activities essential for independent living and advances the field of cognitive assessment. Insight gained from the development process could inform other researchers who seek to develop software tools in health care.

Survey of Verification and Validation Techniques for Small Satellite Software Development

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.

2015-01-01

The purpose of this paper is to provide an overview of the current trends and practices in small-satellite software verification and validation. This document is not intended to promote a specific software assurance method. Rather, it seeks to present an unbiased survey of software assurance methods used to verify and validate small satellite software and to make mention of the benefits and value of each approach. These methods include simulation and testing, verification and validation with model-based design, formal methods, and fault-tolerant software design with run-time monitoring. Although the literature reveals that simulation and testing has by far the longest legacy, model-based design methods are proving to be useful for software verification and validation. Some work in formal methods, though not widely used for any satellites, may offer new ways to improve small satellite software verification and validation. These methods need to be further advanced to deal with the state explosion problem and to make them more usable by small-satellite software engineers to be regularly applied to software verification. Last, it is explained how run-time monitoring, combined with fault-tolerant software design methods, provides an important means to detect and correct software errors that escape the verification process or those errors that are produced after launch through the effects of ionizing radiation.

Proceedings Second Annual Cyber Security and Information Infrastructure Research Workshop

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

Sheldon, Frederick T; Krings, Axel; Yoo, Seong-Moo

2006-01-01

The workshop theme is Cyber Security: Beyond the Maginot Line Recently the FBI reported that computer crime has skyrocketed costing over $67 billion in 2005 alone and affecting 2.8M+ businesses and organizations. Attack sophistication is unprecedented along with availability of open source concomitant tools. Private, academic, and public sectors invest significant resources in cyber security. Industry primarily performs cyber security research as an investment in future products and services. While the public sector also funds cyber security R&D, the majority of this activity focuses on the specific mission(s) of the funding agency. Thus, broad areas of cyber security remain neglectedmore » or underdeveloped. Consequently, this workshop endeavors to explore issues involving cyber security and related technologies toward strengthening such areas and enabling the development of new tools and methods for securing our information infrastructure critical assets. We aim to assemble new ideas and proposals about robust models on which we can build the architecture of a secure cyberspace including but not limited to: * Knowledge discovery and management * Critical infrastructure protection * De-obfuscating tools for the validation and verification of tamper-proofed software * Computer network defense technologies * Scalable information assurance strategies * Assessment-driven design for trust * Security metrics and testing methodologies * Validation of security and survivability properties * Threat assessment and risk analysis * Early accurate detection of the insider threat * Security hardened sensor networks and ubiquitous computing environments * Mobile software authentication protocols * A new "model" of the threat to replace the "Maginot Line" model and more . . .« less

PSG-EXPERT. An expert system for the diagnosis of sleep disorders.

PubMed

Fred, A; Filipe, J; Partinen, M; Paiva, T

2000-01-01

This paper describes PSG-EXPERT, an expert system in the domain of sleep disorders exploring polysomnographic data. The developed software tool is addressed from two points of view: (1)--as an integrated environment for the development of diagnosis-oriented expert systems; (2)--as an auxiliary diagnosis tool in the particular domain of sleep disorders. Developed over a Windows platform, this software tool extends one of the most popular shells--CLIPS (C Language Integrated Production System) with the following features: backward chaining engine; graph-based explanation facilities; knowledge editor including a fuzzy fact editor and a rules editor, with facts-rules integrity checking; belief revision mechanism; built-in case generator and validation module. It therefore provides graphical support for knowledge acquisition, edition, explanation and validation. From an application domain point of view, PSG-Expert is an auxiliary diagnosis system for sleep disorders based on polysomnographic data, that aims at assisting the medical expert in his diagnosis task by providing automatic analysis of polysomnographic data, summarising the results of this analysis in terms of a report of major findings and possible diagnosis consistent with the polysomnographic data. Sleep disorders classification follows the International Classification of Sleep Disorders. Major features of the system include: browsing on patients data records; structured navigation on Sleep Disorders descriptions according to ASDA definitions; internet links to related pages; diagnosis consistent with polysomnographic data; graphical user-interface including graph-based explanatory facilities; uncertainty modelling and belief revision; production of reports; connection to remote databases.

Microstructure Modeling of Third Generation Disk Alloys

NASA Technical Reports Server (NTRS)

Jou, Herng-Jeng

2010-01-01

The objective of this program was to model, validate, and predict the precipitation microstructure evolution, using PrecipiCalc (QuesTek Innovations LLC) software, for 3rd generation Ni-based gas turbine disc superalloys during processing and service, with a set of logical and consistent experiments and characterizations. Furthermore, within this program, the originally research-oriented microstructure simulation tool was to be further improved and implemented to be a useful and user-friendly engineering tool. In this report, the key accomplishments achieved during the third year (2009) of the program are summarized. The activities of this year included: Further development of multistep precipitation simulation framework for gamma prime microstructure evolution during heat treatment; Calibration and validation of gamma prime microstructure modeling with supersolvus heat treated LSHR; Modeling of the microstructure evolution of the minor phases, particularly carbides, during isothermal aging, representing the long term microstructure stability during thermal exposure; and the implementation of software tools. During the research and development efforts to extend the precipitation microstructure modeling and prediction capability in this 3-year program, we identified a hurdle, related to slow gamma prime coarsening rate, with no satisfactory scientific explanation currently available. It is desirable to raise this issue to the Ni-based superalloys research community, with hope that in future there will be a mechanistic understanding and physics-based treatment to overcome the hurdle. In the mean time, an empirical correction factor was developed in this modeling effort to capture the experimental observations.

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

Science.gov Websites

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

Method for Pre-Conditioning a Measured Surface Height Map for Model Validation

NASA Technical Reports Server (NTRS)

Sidick, Erkin

2012-01-01

This software allows one to up-sample or down-sample a measured surface map for model validation, not only without introducing any re-sampling errors, but also eliminating the existing measurement noise and measurement errors. Because the re-sampling of a surface map is accomplished based on the analytical expressions of Zernike-polynomials and a power spectral density model, such re-sampling does not introduce any aliasing and interpolation errors as is done by the conventional interpolation and FFT-based (fast-Fourier-transform-based) spatial-filtering method. Also, this new method automatically eliminates the measurement noise and other measurement errors such as artificial discontinuity. The developmental cycle of an optical system, such as a space telescope, includes, but is not limited to, the following two steps: (1) deriving requirements or specs on the optical quality of individual optics before they are fabricated through optical modeling and simulations, and (2) validating the optical model using the measured surface height maps after all optics are fabricated. There are a number of computational issues related to model validation, one of which is the "pre-conditioning" or pre-processing of the measured surface maps before using them in a model validation software tool. This software addresses the following issues: (1) up- or down-sampling a measured surface map to match it with the gridded data format of a model validation tool, and (2) eliminating the surface measurement noise or measurement errors such that the resulted surface height map is continuous or smoothly-varying. So far, the preferred method used for re-sampling a surface map is two-dimensional interpolation. The main problem of this method is that the same pixel can take different values when the method of interpolation is changed among the different methods such as the "nearest," "linear," "cubic," and "spline" fitting in Matlab. The conventional, FFT-based spatial filtering method used to eliminate the surface measurement noise or measurement errors can also suffer from aliasing effects. During re-sampling of a surface map, this software preserves the low spatial-frequency characteristic of a given surface map through the use of Zernike-polynomial fit coefficients, and maintains mid- and high-spatial-frequency characteristics of the given surface map by the use of a PSD model derived from the two-dimensional PSD data of the mid- and high-spatial-frequency components of the original surface map. Because this new method creates the new surface map in the desired sampling format from analytical expressions only, it does not encounter any aliasing effects and does not cause any discontinuity in the resultant surface map.

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

Navarro, Carmen; Martínez, Victor; Blanco, Armando; Cano, Carlos

2017-12-01

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data. We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization. ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality. © The Authors 2017. Published by Oxford University Press.

Computer-assisted teaching of skin flap surgery: validation of a mobile platform software for medical students.

PubMed

de Sena, David P; Fabricio, Daniela D; Lopes, Maria Helena I; da Silva, Vinicius D

2013-01-01

The purpose of this study was to develop and validate a multimedia software application for mobile platforms to assist in the teaching and learning process of design and construction of a skin flap. Traditional training in surgery is based on learning by doing. Initially, the use of cadavers and animal models appeared to be a valid alternative for training. However, many conflicts with these training models prompted progression to synthetic and virtual reality models. Fifty volunteer fifth- and sixth-year medical students completed a pretest and were randomly allocated into two groups of 25 students each. The control group was exposed for 5 minutes to a standard text-based print article, while the test group used multimedia software describing how to fashion a rhomboid flap. Each group then performed a cutaneous flap on a training bench model while being evaluated by three blinded BSPS (Brazilian Society of Plastic Surgery) board-certified surgeons using the OSATS (Objective Structured Assessment of Technical Skill) protocol and answered a post-test. The text-based group was then tested again using the software. The computer-assisted learning (CAL) group had superior performance as confirmed by checklist scores (p<0.002), overall global assessment (p = 0.017) and post-test results (p<0.001). All participants ranked the multimedia method as the best study tool. CAL learners exhibited better subjective and objective performance when fashioning rhomboid flaps as compared to those taught with standard print material. These findings indicate that students preferred to learn using the multimedia method.

VALIDATING the Accuracy of Sighten's Automated Shading Tool

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

Solar companies - including installers, financiers, and distributors - leverage Sighten software to deliver accurate shading calculations and solar proposals. Sighten recently partnered with Google Project Sunroof to provide automated remote shading analysis directly within the Sighten platform. The National Renewable Energy Laboratory (NREL), in partnership with Sighten, independently verified the accuracy of Sighten's remote-shading solar access values (SAVs) on an annual basis for locations in Los Angeles, California, and Denver, Colorado.

The microcomputer scientific software series 9: user's guide to Geo-CLM: geostatistical interpolation of the historical climatic record in the Lake States.

Treesearch

Margaret R. Holdaway

1994-01-01

Describes Geo-CLM, a computer application (for Mac or DOS) whose primary aim is to perform multiple kriging runs to interpolate the historic climatic record at research plots in the Lake States. It is an exploration and analysis tool. Addition capabilities include climatic databases, a flexible test mode, cross validation, lat/long conversion, English/metric units,...

15 CFR 995.27 - Format validation software testing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 3 2013-01-01 2013-01-01 false Format validation software testing... of NOAA ENC Products § 995.27 Format validation software testing. Tests shall be performed verifying, as far as reasonable and practicable, that CEVAD's data testing software performs the checks, as...

15 CFR 995.27 - Format validation software testing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 3 2014-01-01 2014-01-01 false Format validation software testing... of NOAA ENC Products § 995.27 Format validation software testing. Tests shall be performed verifying, as far as reasonable and practicable, that CEVAD's data testing software performs the checks, as...

15 CFR 995.27 - Format validation software testing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 15 Commerce and Foreign Trade 3 2012-01-01 2012-01-01 false Format validation software testing... of NOAA ENC Products § 995.27 Format validation software testing. Tests shall be performed verifying, as far as reasonable and practicable, that CEVAD's data testing software performs the checks, as...

15 CFR 995.27 - Format validation software testing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 3 2011-01-01 2011-01-01 false Format validation software testing... of NOAA ENC Products § 995.27 Format validation software testing. Tests shall be performed verifying, as far as reasonable and practicable, that CEVAD's data testing software performs the checks, as...

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Beckman, Carol S.; Benzinger, Leonora; Beshers, George; Hammerslag, David; Kimball, John; Kirslis, Peter A.; Render, Hal; Richards, Paul; Terwilliger, Robert

1985-01-01

The SAGA system is a software environment that is designed to support most of the software development activities that occur in a software lifecycle. The system can be configured to support specific software development applications using given programming languages, tools, and methodologies. Meta-tools are provided to ease configuration. The SAGA system consists of a small number of software components that are adapted by the meta-tools into specific tools for use in the software development application. The modules are design so that the meta-tools can construct an environment which is both integrated and flexible. The SAGA project is documented in several papers which are presented.

Debugging and Performance Analysis Software Tools for Peregrine System |

Science.gov Websites

High-Performance Computing | NREL Debugging and Performance Analysis Software Tools for Peregrine System Debugging and Performance Analysis Software Tools for Peregrine System Learn about debugging and performance analysis software tools available to use with the Peregrine system. Allinea

Performance Assessment of the Commercial CFD Software for the Prediction of the Reactor Internal Flow

NASA Astrophysics Data System (ADS)

Lee, Gong Hee; Bang, Young Seok; Woo, Sweng Woong; Kim, Do Hyeong; Kang, Min Ku

2014-06-01

As the computer hardware technology develops the license applicants for nuclear power plant use the commercial CFD software with the aim of reducing the excessive conservatism associated with using simplified and conservative analysis tools. Even if some of CFD software developer and its user think that a state of the art CFD software can be used to solve reasonably at least the single-phase nuclear reactor problems, there is still limitation and uncertainty in the calculation result. From a regulatory perspective, Korea Institute of Nuclear Safety (KINS) is presently conducting the performance assessment of the commercial CFD software for nuclear reactor problems. In this study, in order to examine the validity of the results of 1/5 scaled APR+ (Advanced Power Reactor Plus) flow distribution tests and the applicability of CFD in the analysis of reactor internal flow, the simulation was conducted with the two commercial CFD software (ANSYS CFX V.14 and FLUENT V.14) among the numerous commercial CFD software and was compared with the measurement. In addition, what needs to be improved in CFD for the accurate simulation of reactor core inlet flow was discussed.

A GPU Simulation Tool for Training and Optimisation in 2D Digital X-Ray Imaging.

PubMed

Gallio, Elena; Rampado, Osvaldo; Gianaria, Elena; Bianchi, Silvio Diego; Ropolo, Roberto

2015-01-01

Conventional radiology is performed by means of digital detectors, with various types of technology and different performance in terms of efficiency and image quality. Following the arrival of a new digital detector in a radiology department, all the staff involved should adapt the procedure parameters to the properties of the detector, in order to achieve an optimal result in terms of correct diagnostic information and minimum radiation risks for the patient. The aim of this study was to develop and validate a software capable of simulating a digital X-ray imaging system, using graphics processing unit computing. All radiological image components were implemented in this application: an X-ray tube with primary beam, a virtual patient, noise, scatter radiation, a grid and a digital detector. Three different digital detectors (two digital radiography and a computed radiography systems) were implemented. In order to validate the software, we carried out a quantitative comparison of geometrical and anthropomorphic phantom simulated images with those acquired. In terms of average pixel values, the maximum differences were below 15%, while the noise values were in agreement with a maximum difference of 20%. The relative trends of contrast to noise ratio versus beam energy and intensity were well simulated. Total calculation times were below 3 seconds for clinical images with pixel size of actual dimensions less than 0.2 mm. The application proved to be efficient and realistic. Short calculation times and the accuracy of the results obtained make this software a useful tool for training operators and dose optimisation studies.

GiNA, an Efficient and High-Throughput Software for Horticultural Phenotyping

PubMed Central

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

2016-01-01

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables. PMID:27529547

GiNA, an Efficient and High-Throughput Software for Horticultural Phenotyping.

PubMed

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

2016-01-01

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables.

The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

PubMed

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Development of a comprehensive software engineering environment

NASA Technical Reports Server (NTRS)

Hartrum, Thomas C.; Lamont, Gary B.

1987-01-01

The generation of a set of tools for software lifecycle is a recurring theme in the software engineering literature. The development of such tools and their integration into a software development environment is a difficult task because of the magnitude (number of variables) and the complexity (combinatorics) of the software lifecycle process. An initial development of a global approach was initiated in 1982 as the Software Development Workbench (SDW). Continuing efforts focus on tool development, tool integration, human interfacing, data dictionaries, and testing algorithms. Current efforts are emphasizing natural language interfaces, expert system software development associates and distributed environments with Ada as the target language. The current implementation of the SDW is on a VAX-11/780. Other software development tools are being networked through engineering workstations.

A new possibility in thoracoscopic virtual reality simulation training: development and testing of a novel virtual reality simulator for video-assisted thoracoscopic surgery lobectomy.

PubMed

Jensen, Katrine; Bjerrum, Flemming; Hansen, Henrik Jessen; Petersen, René Horsleben; Pedersen, Jesper Holst; Konge, Lars

2015-10-01

The aims of this study were to develop virtual reality simulation software for video-assisted thoracic surgery (VATS) lobectomy, to explore the opinions of thoracic surgeons concerning the VATS lobectomy simulator and to test the validity of the simulator metrics. Experienced VATS surgeons worked with computer specialists to develop a VATS lobectomy software for a virtual reality simulator. Thoracic surgeons with different degrees of experience in VATS were enrolled at the 22nd meeting of the European Society of Thoracic Surgeons (ESTS) held in Copenhagen in June 2014. The surgeons were divided according to the number of performed VATS lobectomies: novices (0 VATS lobectomies), intermediates (1-49 VATS lobectomies) and experienced (>50 VATS lobectomies). The participants all performed a lobectomy of a right upper lobe on the simulator and answered a questionnaire regarding content validity. Metrics were compared between the three groups. We succeeded in developing the first version of a virtual reality VATS lobectomy simulator. A total of 103 thoracic surgeons completed the simulated lobectomy and were distributed as follows: novices n = 32, intermediates n = 45 and experienced n = 26. All groups rated the overall user realism of the VATS lobectomy scenario to a median of 5 on a scale 1-7, with 7 being the best score. The experienced surgeons found the graphics and movements realistic and rated the scenario high in terms of usefulness as a training tool for novice and intermediate experienced thoracic surgeons, but not very useful as a training tool for experienced surgeons. The metric scores were not statistically significant between groups. This is the first study to describe a commercially available virtual reality simulator for a VATS lobectomy. More than 100 thoracic surgeons found the simulator realistic, and hence it showed good content validity. However, none of the built-in simulator metrics could significantly distinguish between novice, intermediate experienced and experienced surgeons, and further development of the simulator software is necessary to develop valid metrics. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

TU-A-17A-02: In Memoriam of Ben Galkin: Virtual Tools for Validation of X-Ray Breast Imaging Systems

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

Myers, K; Bakic, P; Abbey, C

2014-06-15

This symposium will explore simulation methods for the preclinical evaluation of novel 3D and 4D x-ray breast imaging systems – the subject of AAPM taskgroup TG234. Given the complex design of modern imaging systems, simulations offer significant advantages over long and costly clinical studies in terms of reproducibility, reduced radiation exposures, a known reference standard, and the capability for studying patient and disease subpopulations through appropriate choice of simulation parameters. Our focus will be on testing the realism of software anthropomorphic phantoms and virtual clinical trials tools developed for the optimization and validation of breast imaging systems. The symposium willmore » review the stateof- the-science, as well as the advantages and limitations of various approaches to testing realism of phantoms and simulated breast images. Approaches based upon the visual assessment of synthetic breast images by expert observers will be contrasted with approaches based upon comparing statistical properties between synthetic and clinical images. The role of observer models in the assessment of realism will be considered. Finally, an industry perspective will be presented, summarizing the role and importance of virtual tools and simulation methods in product development. The challenges and conditions that must be satisfied in order for computational modeling and simulation to play a significantly increased role in the design and evaluation of novel breast imaging systems will be addressed. Learning Objectives: Review the state-of-the science in testing realism of software anthropomorphic phantoms and virtual clinical trials tools; Compare approaches based upon the visual assessment by expert observers vs. the analysis of statistical properties of synthetic images; Discuss the role of observer models in the assessment of realism; Summarize the industry perspective to virtual methods for breast imaging.« less

Objective breast symmetry analysis with the breast analyzing tool (BAT): improved tool for clinical trials.

PubMed

Krois, Wilfried; Romar, Alexander Ken; Wild, Thomas; Dubsky, Peter; Exner, Ruth; Panhofer, Peter; Jakesz, Raimund; Gnant, Michael; Fitzal, Florian

2017-07-01

Objective cosmetic analysis is important to evaluate the cosmetic outcome after breast surgery or breast radiotherapy. For this purpose, we aimed to improve our recently developed objective scoring software, the Breast Analyzing Tool (BAT ® ). A questionnaire about important factors for breast symmetry was handed out to ten experts (surgeons) and eight non-experts (students). Using these factors, the first-generation BAT ® software formula has been modified and the breast symmetry index (BSI) from 129 women after breast surgery has been calculated by the first author with this new BAT ® formula. The resulting BSI values of these 129 breast cancer patients were then correlated with subjective symmetry scores from the 18 observers using the Harris scale. The BSI of ten images was also calculated from five observers different from the first author to calculate inter-rater reliability. In a second phase, the new BAT ® formula was validated and correlated with subjective scores of additional 50 women after breast surgery. The inter-rater reliability analysis of the objective evaluation by the BAT ® from five individuals showed an ICC of 0.992 with almost no difference between different observers. All subjective scores of 50 patients correlated with the modified BSI score with a high Pearson correlation coefficient of 0.909 (p < .001) which was better compared to the old software (r = 0.769; p < .001). The modified BAT ® software improves the correlation between subjective and objective BSI values, and may be a new standard for trials evaluating breast symmetry.

Distributed and Collaborative Software Analysis

NASA Astrophysics Data System (ADS)

Ghezzi, Giacomo; Gall, Harald C.

Throughout the years software engineers have come up with a myriad of specialized tools and techniques that focus on a certain type of software analysissoftware analysis such as source code analysis, co-change analysis or bug prediction. However, easy and straight forward synergies between these analyses and tools rarely exist because of their stand-alone nature, their platform dependence, their different input and output formats and the variety of data to analyze. As a consequence, distributed and collaborative software analysiscollaborative software analysis scenarios and in particular interoperability are severely limited. We describe a distributed and collaborative software analysis platform that allows for a seamless interoperability of software analysis tools across platform, geographical and organizational boundaries. We realize software analysis tools as services that can be accessed and composed over the Internet. These distributed analysis services shall be widely accessible in our incrementally augmented Software Analysis Broker software analysis broker where organizations and tool providers can register and share their tools. To allow (semi-) automatic use and composition of these tools, they are classified and mapped into a software analysis taxonomy and adhere to specific meta-models and ontologiesontologies for their category of analysis.

Evolving software reengineering technology for the emerging innovative-competitive era

NASA Technical Reports Server (NTRS)

Hwang, Phillip Q.; Lock, Evan; Prywes, Noah

1994-01-01

This paper reports on a multi-tool commercial/military environment combining software Domain Analysis techniques with Reusable Software and Reengineering of Legacy Software. It is based on the development of a military version for the Department of Defense (DOD). The integrated tools in the military version are: Software Specification Assistant (SSA) and Software Reengineering Environment (SRE), developed by Computer Command and Control Company (CCCC) for Naval Surface Warfare Center (NSWC) and Joint Logistics Commanders (JLC), and the Advanced Research Project Agency (ARPA) STARS Software Engineering Environment (SEE) developed by Boeing for NAVAIR PMA 205. The paper describes transitioning these integrated tools to commercial use. There is a critical need for the transition for the following reasons: First, to date, 70 percent of programmers' time is applied to software maintenance. The work of these users has not been facilitated by existing tools. The addition of Software Reengineering will also facilitate software maintenance and upgrading. In fact, the integrated tools will support the entire software life cycle. Second, the integrated tools are essential to Business Process Reengineering, which seeks radical process innovations to achieve breakthrough results. Done well, process reengineering delivers extraordinary gains in process speed, productivity and profitability. Most importantly, it discovers new opportunities for products and services in collaboration with other organizations. Legacy computer software must be changed rapidly to support innovative business processes. The integrated tools will provide commercial organizations important competitive advantages. This, in turn, will increase employment by creating new business opportunities. Third, the integrated system will produce much higher quality software than use of the tools separately. The reason for this is that producing or upgrading software requires keen understanding of extremely complex applications which is facilitated by the integrated tools. The radical savings in the time and cost associated with software, due to use of CASE tools that support combined Reuse of Software and Reengineering of Legacy Code, will add an important impetus to improving the automation of enterprises. This will be reflected in continuing operations, as well as in innovating new business processes. The proposed multi-tool software development is based on state of the art technology, which will be further advanced through the use of open systems for adding new tools and experience in their use.

High-throughput neuroimaging-genetics computational infrastructure

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D.; Franco, Joseph; Toga, Arthur W.

2014-01-01

Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer's and Parkinson's data, we provide several examples of translational applications using this infrastructure1. PMID:24795619

The validation by measurement theory of proposed object-oriented software metrics

NASA Technical Reports Server (NTRS)

Neal, Ralph D.

1994-01-01

Moving software development into the engineering arena requires controllability, and to control a process, it must be measurable. Measuring the process does no good if the product is not also measured, i.e., being the best at producing an inferior product does not define a quality process. Also, not every number extracted from software development is a valid measurement. A valid measurement only results when we are able to verify that the number is representative of the attribute that we wish to measure. Many proposed software metrics are used by practitioners without these metrics ever having been validated, leading to costly but often useless calculations. Several researchers have bemoaned the lack of scientific precision in much of the published software measurement work and have called for validation of software metrics by measurement theory. This dissertation applies measurement theory to validate fifty proposed object-oriented software metrics (Li and Henry, 1993; Chidamber and Kemerrer, 1994; Lorenz and Kidd, 1994).

Validation of Medical Tourism Service Quality Questionnaire (MTSQQ) for Iranian Hospitals.

PubMed

Qolipour, Mohammad; Torabipour, Amin; Khiavi, Farzad Faraji; Malehi, Amal Saki

2017-03-01

Assessing service quality is one of the basic requirements to develop the medical tourism industry. There is no valid and reliable tool to measure service quality of medical tourism. This study aimed to determine the reliability and validity of a Persian version of medical tourism service quality questionnaire for Iranian hospitals. To validate the medical tourism service quality questionnaire (MTSQQ), a cross-sectional study was conducted on 250 Iraqi patients referred to hospitals in Ahvaz (Iran) from 2015. To design a questionnaire and determine its content validity, the Delphi Technique (3 rounds) with the participation of 20 medical tourism experts was used. Construct validity of the questionnaire was assessed through exploratory and confirmatory factor analysis. Reliability was assessed using Cronbach's alpha coefficient. Data were analyzed by Excel 2007, SPSS version18, and Lisrel l8.0 software. The content validity of the questionnaire with CVI=0.775 was confirmed. According to exploratory factor analysis, the MTSQQ included 31 items and 8 dimensions (tangibility, reliability, responsiveness, assurance, empathy, exchange and travel facilities, technical and infrastructure facilities and safety and security). Construct validity of the questionnaire was confirmed, based on the goodness of fit quantities of model (RMSEA=0.032, CFI= 0.98, GFI=0.88). Cronbach's alpha coefficient was 0.837 and 0.919 for expectation and perception questionnaire. The results of the study showed that the medical tourism SERVQUAL questionnaire with 31 items and 8 dimensions was a valid and reliable tool to measure service quality of medical tourism in Iranian hospitals.

Bioinformatics approach for choosing the correct reference genes when studying gene expression in human keratinocytes.

PubMed

Beer, Lucian; Mlitz, Veronika; Gschwandtner, Maria; Berger, Tanja; Narzt, Marie-Sophie; Gruber, Florian; Brunner, Patrick M; Tschachler, Erwin; Mildner, Michael

2015-10-01

Reverse transcription polymerase chain reaction (qRT-PCR) has become a mainstay in many areas of skin research. To enable quantitative analysis, it is necessary to analyse expression of reference genes (RGs) for normalization of target gene expression. The selection of reliable RGs therefore has an important impact on the experimental outcome. In this study, we aimed to identify and validate the best suited RGs for qRT-PCR in human primary keratinocytes (KCs) over a broad range of experimental conditions using the novel bioinformatics tool 'RefGenes', which is based on a manually curated database of published microarray data. Expression of 6 RGs identified by RefGenes software and 12 commonly used RGs were validated by qRT-PCR. We assessed whether these 18 markers fulfilled the requirements for a valid RG by the comprehensive ranking of four bioinformatics tools and the coefficient of variation (CV). In an overall ranking, we found GUSB to be the most stably expressed RG, whereas the expression values of the commonly used RGs, GAPDH and B2M were significantly affected by varying experimental conditions. Our results identify RefGenes as a powerful tool for the identification of valid RGs and suggest GUSB as the most reliable RG for KCs. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Fault Tree Analysis Application for Safety and Reliability

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

Many commercial software tools exist for fault tree analysis (FTA), an accepted method for mitigating risk in systems. The method embedded in the tools identifies a root as use in system components, but when software is identified as a root cause, it does not build trees into the software component. No commercial software tools have been built specifically for development and analysis of software fault trees. Research indicates that the methods of FTA could be applied to software, but the method is not practical without automated tool support. With appropriate automated tool support, software fault tree analysis (SFTA) may be a practical technique for identifying the underlying cause of software faults that may lead to critical system failures. We strive to demonstrate that existing commercial tools for FTA can be adapted for use with SFTA, and that applied to a safety-critical system, SFTA can be used to identify serious potential problems long before integrator and system testing.

Hierarchical Ada robot programming system (HARPS)- A complete and working telerobot control system based on the NASREM model

NASA Technical Reports Server (NTRS)

Leake, Stephen; Green, Tom; Cofer, Sue; Sauerwein, Tim

1989-01-01

HARPS is a telerobot control system that can perform some simple but useful tasks. This capability is demonstrated by performing the ORU exchange demonstration. HARPS is based on NASREM (NASA Standard Reference Model). All software is developed in Ada, and the project incorporates a number of different CASE (computer-aided software engineering) tools. NASREM was found to be a valid and useful model for building a telerobot control system. Its hierarchical and distributed structure creates a natural and logical flow for implementing large complex robust control systems. The ability of Ada to create and enforce abstraction enhanced the implementation of such control systems.

Design and Experimental Validation of a USBL Underwater Acoustic Positioning System.

PubMed

Reis, Joel; Morgado, Marco; Batista, Pedro; Oliveira, Paulo; Silvestre, Carlos

2016-09-14

This paper presents the steps for developing a low-cost POrtableNavigation Tool for Underwater Scenarios (PONTUS) to be used as a localization device for subsea targets. PONTUS consists of an integrated ultra-short baseline acoustic positioning system aided by an inertial navigation system. Built on a practical design, it can be mounted on an underwater robotic vehicle or be operated by a scuba diver. It also features a graphical user interface that provides information on the tracking of the designated target, in addition to some details on the physical properties inside PONTUS. A full disclosure of the architecture of the tool is first presented, followed by thorough technical descriptions of the hardware components ensemble and the software development process. A series of experiments was carried out to validate the developed prototype, and the results are presented herein, which allow assessing its overall performance.

Development of a Three-Dimensional, Unstructured Material Response Design Tool

NASA Technical Reports Server (NTRS)

Schulz, Joseph C.; Stern, Eric C.; Muppidi, Suman; Palmer, Grant E.; Schroeder, Olivia

2017-01-01

A preliminary verification and validation of a new material response model is presented. This model, Icarus, is intended to serve as a design tool for the thermal protection systems of re-entry vehicles. Currently, the capability of the model is limited to simulating the pyrolysis of a material as a result of the radiative and convective surface heating imposed on the material from the surrounding high enthalpy gas. Since the major focus behind the development of Icarus has been model extensibility, the hope is that additional physics can be quickly added. This extensibility is critical since thermal protection systems are becoming increasing complex, e.g. woven carbon polymers. Additionally, as a three-dimensional, unstructured, finite-volume model, Icarus is capable of modeling complex geometries. In this paper, the mathematical and numerical formulation is presented followed by a discussion of the software architecture and some preliminary verification and validation studies.

Design and Experimental Validation of a USBL Underwater Acoustic Positioning System

PubMed Central

Reis, Joel; Morgado, Marco; Batista, Pedro; Oliveira, Paulo; Silvestre, Carlos

2016-01-01

This paper presents the steps for developing a low-cost POrtableNavigation Tool for Underwater Scenarios (PONTUS) to be used as a localization device for subsea targets. PONTUS consists of an integrated ultra-short baseline acoustic positioning system aided by an inertial navigation system. Built on a practical design, it can be mounted on an underwater robotic vehicle or be operated by a scuba diver. It also features a graphical user interface that provides information on the tracking of the designated target, in addition to some details on the physical properties inside PONTUS. A full disclosure of the architecture of the tool is first presented, followed by thorough technical descriptions of the hardware components ensemble and the software development process. A series of experiments was carried out to validate the developed prototype, and the results are presented herein, which allow assessing its overall performance. PMID:27649181

Registration of in vivo MR to histology of rodent brains using blockface imaging

NASA Astrophysics Data System (ADS)

Uberti, Mariano; Liu, Yutong; Dou, Huanyu; Mosley, R. Lee; Gendelman, Howard E.; Boska, Michael

2009-02-01

Registration of MRI to histopathological sections can enhance bioimaging validation for use in pathobiologic, diagnostic, and therapeutic evaluations. However, commonly used registration methods fall short of this goal due to tissue shrinkage and tearing after brain extraction and preparation. In attempts to overcome these limitations we developed a software toolbox using 3D blockface imaging as the common space of reference. This toolbox includes a semi-automatic brain extraction technique using constraint level sets (CLS), 3D reconstruction methods for the blockface and MR volume, and a 2D warping technique using thin-plate splines with landmark optimization. Using this toolbox, the rodent brain volume is first extracted from the whole head MRI using CLS. The blockface volume is reconstructed followed by 3D brain MRI registration to the blockface volume to correct the global deformations due to brain extraction and fixation. Finally, registered MRI and histological slices are warped to corresponding blockface images to correct slice specific deformations. The CLS brain extraction technique was validated by comparing manual results showing 94% overlap. The image warping technique was validated by calculating target registration error (TRE). Results showed a registration accuracy of a TRE < 1 pixel. Lastly, the registration method and the software tools developed were used to validate cell migration in murine human immunodeficiency virus type one encephalitis.

AeroADL: applying the integration of the Suomi-NPP science algorithms with the Algorithm Development Library to the calibration and validation task

NASA Astrophysics Data System (ADS)

Houchin, J. S.

2014-09-01

A common problem for the off-line validation of the calibration algorithms and algorithm coefficients is being able to run science data through the exact same software used for on-line calibration of that data. The Joint Polar Satellite System (JPSS) program solved part of this problem by making the Algorithm Development Library (ADL) available, which allows the operational algorithm code to be compiled and run on a desktop Linux workstation using flat file input and output. However, this solved only part of the problem, as the toolkit and methods to initiate the processing of data through the algorithms were geared specifically toward the algorithm developer, not the calibration analyst. In algorithm development mode, a limited number of sets of test data are staged for the algorithm once, and then run through the algorithm over and over as the software is developed and debugged. In calibration analyst mode, we are continually running new data sets through the algorithm, which requires significant effort to stage each of those data sets for the algorithm without additional tools. AeroADL solves this second problem by providing a set of scripts that wrap the ADL tools, providing both efficient means to stage and process an input data set, to override static calibration coefficient look-up-tables (LUT) with experimental versions of those tables, and to manage a library containing multiple versions of each of the static LUT files in such a way that the correct set of LUTs required for each algorithm are automatically provided to the algorithm without analyst effort. Using AeroADL, The Aerospace Corporation's analyst team has demonstrated the ability to quickly and efficiently perform analysis tasks for both the VIIRS and OMPS sensors with minimal training on the software tools.

COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA

PubMed Central

Wenger, Craig D.; Phanstiel, Douglas H.; Lee, M. Violet; Bailey, Derek J.; Coon, Joshua J.

2011-01-01

Here we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. We detail a synergistic set of tools for protein database generation, spectral reduction, peptide false discovery rate analysis, peptide quantitation via isobaric labeling, protein parsimony and protein false discovery rate analysis, and protein quantitation. We strive for maximum ease of use, utilizing graphical user interfaces and working with data files in the original instrument vendor format. Results are stored in plain text comma-separated values files, which are easy to view and manipulate with a text editor or spreadsheet program. We illustrate the operation and efficacy of COMPASS through the use of two LC–MS/MS datasets. The first is a dataset of a highly annotated mixture of standard proteins and manually validated contaminants that exhibits the identification workflow. The second is a dataset of yeast peptides, labeled with isobaric stable isotope tags and mixed in known ratios, to demonstrate the quantitative workflow. For these two datasets, COMPASS performs equivalently or better than the current de facto standard, the Trans-Proteomic Pipeline. PMID:21298793

Optimum-AIV: A planning and scheduling system for spacecraft AIV

NASA Technical Reports Server (NTRS)

Arentoft, M. M.; Fuchs, Jens J.; Parrod, Y.; Gasquet, Andre; Stader, J.; Stokes, I.; Vadon, H.

1991-01-01

A project undertaken for the European Space Agency (ESA) is presented. The project is developing a knowledge based software system for planning and scheduling of activities for spacecraft assembly, integration, and verification (AIV). The system extends into the monitoring of plan execution and the plan repair phase. The objectives are to develop an operational kernel of a planning, scheduling, and plan repair tool, called OPTIMUM-AIV, and to provide facilities which will allow individual projects to customize the kernel to suit its specific needs. The kernel shall consist of a set of software functionalities for assistance in initial specification of the AIV plan, in verification and generation of valid plans and schedules for the AIV activities, and in interactive monitoring and execution problem recovery for the detailed AIV plans. Embedded in OPTIMUM-AIV are external interfaces which allow integration with alternative scheduling systems and project databases. The current status of the OPTIMUM-AIV project, as of Jan. 1991, is that a further analysis of the AIV domain has taken place through interviews with satellite AIV experts, a software requirement document (SRD) for the full operational tool was approved, and an architectural design document (ADD) for the kernel excluding external interfaces is ready for review.

Shielded-Twisted-Pair Cable Model for Chafe Fault Detection via Time-Domain Reflectometry

NASA Technical Reports Server (NTRS)

Schuet, Stefan R.; Timucin, Dogan A.; Wheeler, Kevin R.

2012-01-01

This report details the development, verification, and validation of an innovative physics-based model of electrical signal propagation through shielded-twisted-pair cable, which is commonly found on aircraft and offers an ideal proving ground for detection of small holes in a shield well before catastrophic damage occurs. The accuracy of this model is verified through numerical electromagnetic simulations using a commercially available software tool. The model is shown to be representative of more realistic (analytically intractable) cable configurations as well. A probabilistic framework is developed for validating the model accuracy with reflectometry data obtained from real aircraft-grade cables chafed in the laboratory.

Developing smartphone apps for behavioural studies: The AlcoRisk app case study.

PubMed

Smith, Anthony; de Salas, Kristy; Lewis, Ian; Schüz, Benjamin

2017-08-01

Smartphone apps have emerged as valuable research tools to sample human behaviours at their time of occurrence within natural environments. Human behaviour sampling methods, such as Ecological Momentary Assessment (EMA), aim to facilitate research that is situated in ecologically valid real world environments rather than laboratory environments. Researchers have trialled a range of EMA smartphone apps to sample human behaviours such as dieting, physical activity and smoking. Software development processes for EMA smartphones apps, however, are not widely documented with little guidance provided for the integration of complex multidisciplinary behavioural and technical fields. In this paper, the AlcoRisk app for studying alcohol consumption and risk taking tendencies is presented alongside a software development process that integrates these multidisciplinary fields. The software development process consists of three stages including requirements analysis, feature and interface design followed by app implementation. Results from a preliminary feasibility study support the efficacy of the AlcoRisk app's software development process. Copyright © 2017 Elsevier Inc. All rights reserved.

Design and control of compliant tensegrity robots through simulation and hardware validation

PubMed Central

Caluwaerts, Ken; Despraz, Jérémie; Işçen, Atıl; Sabelhaus, Andrew P.; Bruce, Jonathan; Schrauwen, Benjamin; SunSpiral, Vytas

2014-01-01

To better understand the role of tensegrity structures in biological systems and their application to robotics, the Dynamic Tensegrity Robotics Lab at NASA Ames Research Center, Moffett Field, CA, USA, has developed and validated two software environments for the analysis, simulation and design of tensegrity robots. These tools, along with new control methodologies and the modular hardware components developed to validate them, are presented as a system for the design of actuated tensegrity structures. As evidenced from their appearance in many biological systems, tensegrity (‘tensile–integrity’) structures have unique physical properties that make them ideal for interaction with uncertain environments. Yet, these characteristics make design and control of bioinspired tensegrity robots extremely challenging. This work presents the progress our tools have made in tackling the design and control challenges of spherical tensegrity structures. We focus on this shape since it lends itself to rolling locomotion. The results of our analyses include multiple novel control approaches for mobility and terrain interaction of spherical tensegrity structures that have been tested in simulation. A hardware prototype of a spherical six-bar tensegrity, the Reservoir Compliant Tensegrity Robot, is used to empirically validate the accuracy of simulation. PMID:24990292

Application of Novel Software Algorithms to Spectral-Domain Optical Coherence Tomography for Automated Detection of Diabetic Retinopathy.

PubMed

Adhi, Mehreen; Semy, Salim K; Stein, David W; Potter, Daniel M; Kuklinski, Walter S; Sleeper, Harry A; Duker, Jay S; Waheed, Nadia K

2016-05-01

To present novel software algorithms applied to spectral-domain optical coherence tomography (SD-OCT) for automated detection of diabetic retinopathy (DR). Thirty-one diabetic patients (44 eyes) and 18 healthy, nondiabetic controls (20 eyes) who underwent volumetric SD-OCT imaging and fundus photography were retrospectively identified. A retina specialist independently graded DR stage. Trained automated software generated a retinal thickness score signifying macular edema and a cluster score signifying microaneurysms and/or hard exudates for each volumetric SD-OCT. Of 44 diabetic eyes, 38 had DR and six eyes did not have DR. Leave-one-out cross-validation using a linear discriminant at missed detection/false alarm ratio of 3.00 computed software sensitivity and specificity of 92% and 69%, respectively, for DR detection when compared to clinical assessment. Novel software algorithms applied to commercially available SD-OCT can successfully detect DR and may have potential as a viable screening tool for DR in future. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:410-417.]. Copyright 2016, SLACK Incorporated.

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

PubMed

Bieri, Michael; d'Auvergne, Edward J; Gooley, Paul R

2011-06-01

Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

Development of a computer-assisted forensic radiographic identification method using the lateral cervical and lumbar spine.

PubMed

Derrick, Sharon M; Raxter, Michelle H; Hipp, John A; Goel, Priya; Chan, Elaine F; Love, Jennifer C; Wiersema, Jason M; Akella, N Shastry

2015-01-01

Medical examiners and coroners (ME/C) in the United States hold statutory responsibility to identify deceased individuals who fall under their jurisdiction. The computer-assisted decedent identification (CADI) project was designed to modify software used in diagnosis and treatment of spinal injuries into a mathematically validated tool for ME/C identification of fleshed decedents. CADI software analyzes the shapes of targeted vertebral bodies imaged in an array of standard radiographs and quantifies the likelihood that any two of the radiographs contain matching vertebral bodies. Six validation tests measured the repeatability, reliability, and sensitivity of the method, and the effects of age, sex, and number of radiographs in array composition. CADI returned a 92-100% success rate in identifying the true matching pair of vertebrae within arrays of five to 30 radiographs. Further development of CADI is expected to produce a novel identification method for use in ME/C offices that is reliable, timely, and cost-effective. © 2014 American Academy of Forensic Sciences.

Simulation Assessment Validation Environment (SAVE). Software User’s Manual

DTIC Science & Technology

2000-09-01

requirements and decisions are made. The integration is leveraging work from other DoD organizations so that high -end results are attainable much faster than...planning through the modeling and simulation data capture and visualization process. The planners can complete the manufacturing process plan with a high ...technologies. This tool is also used to perform “ high level” factory process simulation prior to full CAD model development and help define feasible

Ada Programming Support Environment (APSE) Evaluation and Validation (E&V) Team

DTIC Science & Technology

1991-12-31

standards. The purpose of the team was to assist the project in several ways. Raymond Szymanski of Wright Research Iand Development Center (WRDC, now...debuggers, program library systems, and compiler diagnostics. The test suite does not include explicit tests for the existence of language features . The...support software is a set of tools and procedures which assist in preparing and executing the test suite, in extracting data from the results of

Development of a patient-specific surgical simulator for pediatric laparoscopic procedures.

PubMed

Saber, Nikoo R; Menon, Vinay; St-Pierre, Jean C; Looi, Thomas; Drake, James M; Cyril, Xavier

2014-01-01

The purpose of this study is to develop and evaluate a pediatric patient-specific surgical simulator for the planning, practice, and validation of laparoscopic surgical procedures prior to intervention, initially focusing on the choledochal cyst resection and reconstruction scenario. The simulator is comprised of software elements including a deformable body physics engine, virtual surgical tools, and abdominal organs. Hardware components such as haptics-enabled hand controllers and a representative endoscopic tool have also been integrated. The prototype is able to perform a number of surgical tasks and further development work is under way to simulate the complete procedure with acceptable fidelity and accuracy.

A Brief Tool to Assess Image-Based Dietary Records and Guide Nutrition Counselling Among Pregnant Women: An Evaluation

PubMed Central

Ashman, Amy M; Collins, Clare E; Brown, Leanne J; Rae, Kym M

2016-01-01

Background Dietitians ideally should provide personally tailored nutrition advice to pregnant women. Provision is hampered by a lack of appropriate tools for nutrition assessment and counselling in practice settings. Smartphone technology, through the use of image-based dietary records, can address limitations of traditional methods of recording dietary intake. Feedback on these records can then be provided by the dietitian via smartphone. Efficacy and validity of these methods requires examination. Objective The aims of the Australian Diet Bytes and Baby Bumps study, which used image-based dietary records and a purpose-built brief Selected Nutrient and Diet Quality (SNaQ) tool to provide tailored nutrition advice to pregnant women, were to assess relative validity of the SNaQ tool for analyzing dietary intake compared with nutrient analysis software, to describe the nutritional intake adequacy of pregnant participants, and to assess acceptability of dietary feedback via smartphone. Methods Eligible women used a smartphone app to record everything they consumed over 3 nonconsecutive days. Records consisted of an image of the food or drink item placed next to a fiducial marker, with a voice or text description, or both, providing additional detail. We used the SNaQ tool to analyze participants’ intake of daily food group servings and selected key micronutrients for pregnancy relative to Australian guideline recommendations. A visual reference guide consisting of images of foods and drinks in standard serving sizes assisted the dietitian with quantification. Feedback on participants’ diets was provided via 2 methods: (1) a short video summary sent to participants’ smartphones, and (2) a follow-up telephone consultation with a dietitian. Agreement between dietary intake assessment using the SNaQ tool and nutrient analysis software was evaluated using Spearman rank correlation and Cohen kappa. Results We enrolled 27 women (median age 28.8 years, 8 Indigenous Australians, 15 primiparas), of whom 25 completed the image-based dietary record. Median intakes of grains, vegetables, fruit, meat, and dairy were below recommendations. Median (interquartile range) intake of energy-dense, nutrient-poor foods was 3.5 (2.4-3.9) servings/day and exceeded recommendations (0-2.5 servings/day). Positive correlations between the SNaQ tool and nutrient analysis software were observed for energy (ρ=.898, P<.001) and all selected micronutrients (iron, calcium, zinc, folate, and iodine, ρ range .510-.955, all P<.05), both with and without vitamin and mineral supplements included in the analysis. Cohen kappa showed moderate to substantial agreement for selected micronutrients when supplements were included (kappa range .488-.803, all P ≤.001) and for calcium, iodine, and zinc when excluded (kappa range .554-.632, all P<.001). A total of 17 women reported changing their diet as a result of the personalized nutrition advice. Conclusions The SNaQ tool demonstrated acceptable validity for assessing adequacy of key pregnancy nutrient intakes and preliminary evidence of utility to support dietitians in providing women with personalized advice to optimize nutrition during pregnancy. PMID:27815234

Integration and validation testing for PhEDEx, DBS and DAS with the PhEDEx LifeCycle agent

NASA Astrophysics Data System (ADS)

Boeser, C.; Chwalek, T.; Giffels, M.; Kuznetsov, V.; Wildish, T.

2014-06-01

The ever-increasing amount of data handled by the CMS dataflow and workflow management tools poses new challenges for cross-validation among different systems within CMS experiment at LHC. To approach this problem we developed an integration test suite based on the LifeCycle agent, a tool originally conceived for stress-testing new releases of PhEDEx, the CMS data-placement tool. The LifeCycle agent provides a framework for customising the test workflow in arbitrary ways, and can scale to levels of activity well beyond those seen in normal running. This means we can run realistic performance tests at scales not likely to be seen by the experiment for some years, or with custom topologies to examine particular situations that may cause concern some time in the future. The LifeCycle agent has recently been enhanced to become a general purpose integration and validation testing tool for major CMS services. It allows cross-system integration tests of all three components to be performed in controlled environments, without interfering with production services. In this paper we discuss the design and implementation of the LifeCycle agent. We describe how it is used for small-scale debugging and validation tests, and how we extend that to large-scale tests of whole groups of sub-systems. We show how the LifeCycle agent can emulate the action of operators, physicists, or software agents external to the system under test, and how it can be scaled to large and complex systems.

A Methodology for the Design of Application-Specific Cyber-Physical Social Sensing Co-Simulators.

PubMed

Sánchez, Borja Bordel; Alcarria, Ramón; Sánchez-Picot, Álvaro; Sánchez-de-Rivera, Diego

2017-09-22

Cyber-Physical Social Sensing (CPSS) is a new trend in the context of pervasive sensing. In these new systems, various domains coexist in time, evolve together and influence each other. Thus, application-specific tools are necessary for specifying and validating designs and simulating systems. However, nowadays, different tools are employed to simulate each domain independently. Mainly, the cause of the lack of co-simulation instruments to simulate all domains together is the extreme difficulty of combining and synchronizing various tools. In order to reduce that difficulty, an adequate architecture for the final co-simulator must be selected. Therefore, in this paper the authors investigate and propose a methodology for the design of CPSS co-simulation tools. The paper describes the four steps that software architects should follow in order to design the most adequate co-simulator for a certain application, considering the final users' needs and requirements and various additional factors such as the development team's experience. Moreover, the first practical use case of the proposed methodology is provided. An experimental validation is also included in order to evaluate the performing of the proposed co-simulator and to determine the correctness of the proposal.

A Methodology for the Design of Application-Specific Cyber-Physical Social Sensing Co-Simulators

PubMed Central

Sánchez-Picot, Álvaro

2017-01-01

Cyber-Physical Social Sensing (CPSS) is a new trend in the context of pervasive sensing. In these new systems, various domains coexist in time, evolve together and influence each other. Thus, application-specific tools are necessary for specifying and validating designs and simulating systems. However, nowadays, different tools are employed to simulate each domain independently. Mainly, the cause of the lack of co-simulation instruments to simulate all domains together is the extreme difficulty of combining and synchronizing various tools. In order to reduce that difficulty, an adequate architecture for the final co-simulator must be selected. Therefore, in this paper the authors investigate and propose a methodology for the design of CPSS co-simulation tools. The paper describes the four steps that software architects should follow in order to design the most adequate co-simulator for a certain application, considering the final users’ needs and requirements and various additional factors such as the development team’s experience. Moreover, the first practical use case of the proposed methodology is provided. An experimental validation is also included in order to evaluate the performing of the proposed co-simulator and to determine the correctness of the proposal. PMID:28937610

78 FR 1162 - Cardiovascular Devices; Reclassification of External Cardiac Compressor

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-08

... safety and electromagnetic compatibility; For devices containing software, software verification... electromagnetic compatibility; For devices containing software, software verification, validation, and hazard... electrical components, appropriate analysis and testing must validate electrical safety and electromagnetic...

IPMP Global Fit - A one-step direct data analysis tool for predictive microbiology.

PubMed

Huang, Lihan

2017-12-04

The objective of this work is to develop and validate a unified optimization algorithm for performing one-step global regression analysis of isothermal growth and survival curves for determination of kinetic parameters in predictive microbiology. The algorithm is incorporated with user-friendly graphical interfaces (GUIs) to develop a data analysis tool, the USDA IPMP-Global Fit. The GUIs are designed to guide the users to easily navigate through the data analysis process and properly select the initial parameters for different combinations of mathematical models. The software is developed for one-step kinetic analysis to directly construct tertiary models by minimizing the global error between the experimental observations and mathematical models. The current version of the software is specifically designed for constructing tertiary models with time and temperature as the independent model parameters in the package. The software is tested with a total of 9 different combinations of primary and secondary models for growth and survival of various microorganisms. The results of data analysis show that this software provides accurate estimates of kinetic parameters. In addition, it can be used to improve the experimental design and data collection for more accurate estimation of kinetic parameters. IPMP-Global Fit can be used in combination with the regular USDA-IPMP for solving the inverse problems and developing tertiary models in predictive microbiology. Published by Elsevier B.V.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

A Validation Study of Merging and Spacing Techniques in a NAS-Wide Simulation

NASA Technical Reports Server (NTRS)

Glaab, Patricia C.

2011-01-01

In November 2010, Intelligent Automation, Inc. (IAI) delivered an M&S software tool to that allows system level studies of the complex terminal airspace with the ACES simulation. The software was evaluated against current day arrivals in the Atlanta TRACON using Atlanta's Hartsfield-Jackson International Airport (KATL) arrival schedules. Results of this validation effort are presented describing data sets, traffic flow assumptions and techniques, and arrival rate comparisons between reported landings at Atlanta versus simulated arrivals using the same traffic sets in ACES equipped with M&S. Initial results showed the simulated system capacity to be significantly below arrival capacity seen at KATL. Data was gathered for Atlanta using commercial airport and flight tracking websites (like FlightAware.com), and analyzed to insure compatible techniques were used for result reporting and comparison. TFM operators for Atlanta were consulted for tuning final simulation parameters and for guidance in flow management techniques during high volume operations. Using these modified parameters and incorporating TFM guidance for efficiencies in flowing aircraft, arrival capacity for KATL was matched for the simulation. Following this validation effort, a sensitivity study was conducted to measure the impact of variations in system parameters on the Atlanta airport arrival capacity.

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-30

information that are returned from the tools to the human user, and the forms in which these outputs are presented. Page 2 of 4 STAGE OF DEVELOPMENT: What... AUTOMIATED SOFTWARE TOOL MONITORING SYSTEM APPENDIX 2 2-1 INTRODUCTION This document and Automated Software Tool Monitoring Program (Appendix 1) are...t Output Output features provide links from the tool to both the human user and the target machine (where applicable). They describe the types

Performance evaluation of automated segmentation software on optical coherence tomography volume data

PubMed Central

Tian, Jing; Varga, Boglarka; Tatrai, Erika; Fanni, Palya; Somfai, Gabor Mark; Smiddy, William E.

2016-01-01

Over the past two decades a significant number of OCT segmentation approaches have been proposed in the literature. Each methodology has been conceived for and/or evaluated using specific datasets that do not reflect the complexities of the majority of widely available retinal features observed in clinical settings. In addition, there does not exist an appropriate OCT dataset with ground truth that reflects the realities of everyday retinal features observed in clinical settings. While the need for unbiased performance evaluation of automated segmentation algorithms is obvious, the validation process of segmentation algorithms have been usually performed by comparing with manual labelings from each study and there has been a lack of common ground truth. Therefore, a performance comparison of different algorithms using the same ground truth has never been performed. This paper reviews research-oriented tools for automated segmentation of the retinal tissue on OCT images. It also evaluates and compares the performance of these software tools with a common ground truth. PMID:27159849

NOTE: Development of modified voxel phantoms for the numerical dosimetric reconstruction of radiological accidents involving external sources: implementation in SESAME tool

NASA Astrophysics Data System (ADS)

Courageot, Estelle; Sayah, Rima; Huet, Christelle

2010-05-01

Estimating the dose distribution in a victim's body is a relevant indicator in assessing biological damage from exposure in the event of a radiological accident caused by an external source. When the dose distribution is evaluated with a numerical anthropomorphic model, the posture and morphology of the victim have to be reproduced as realistically as possible. Several years ago, IRSN developed a specific software application, called the simulation of external source accident with medical images (SESAME), for the dosimetric reconstruction of radiological accidents by numerical simulation. This tool combines voxel geometry and the MCNP(X) Monte Carlo computer code for radiation-material interaction. This note presents a new functionality in this software that enables the modelling of a victim's posture and morphology based on non-uniform rational B-spline (NURBS) surfaces. The procedure for constructing the modified voxel phantoms is described, along with a numerical validation of this new functionality using a voxel phantom of the RANDO tissue-equivalent physical model.

Development of modified voxel phantoms for the numerical dosimetric reconstruction of radiological accidents involving external sources: implementation in SESAME tool.

PubMed

Courageot, Estelle; Sayah, Rima; Huet, Christelle

2010-05-07

Estimating the dose distribution in a victim's body is a relevant indicator in assessing biological damage from exposure in the event of a radiological accident caused by an external source. When the dose distribution is evaluated with a numerical anthropomorphic model, the posture and morphology of the victim have to be reproduced as realistically as possible. Several years ago, IRSN developed a specific software application, called the simulation of external source accident with medical images (SESAME), for the dosimetric reconstruction of radiological accidents by numerical simulation. This tool combines voxel geometry and the MCNP(X) Monte Carlo computer code for radiation-material interaction. This note presents a new functionality in this software that enables the modelling of a victim's posture and morphology based on non-uniform rational B-spline (NURBS) surfaces. The procedure for constructing the modified voxel phantoms is described, along with a numerical validation of this new functionality using a voxel phantom of the RANDO tissue-equivalent physical model.

Near-Earth object intercept trajectory design for planetary defense

NASA Astrophysics Data System (ADS)

Vardaxis, George; Wie, Bong

2014-08-01

Tracking the orbit of asteroids and planning for asteroid missions have ceased to be a simple exercise, and become more of a necessity, as the number of identified potentially hazardous near-Earth asteroids increases. Several software tools such as Mystic, MALTO, Copernicus, SNAP, OTIS, and GMAT have been developed by NASA for spacecraft trajectory optimization and mission design. However, this paper further expands upon the development and validation of an Asteroid Mission Design Software Tool (AMiDST), through the use of approach and post-encounter orbital variations and analytic keyhole theory. Combining these new capabilities with that of a high-precision orbit propagator, this paper describes fictional mission trajectory design examples of using AMiDST as applied to a fictitious asteroid 2013 PDC-E. During the 2013 IAA Planetary Defense Conference, the asteroid 2013 PDC-E was used for an exercise where participants simulated the decision-making process for developing deflection and civil defense responses to a hypothetical asteroid threat.

Development and preliminary validation of an index for indicating the risks of the design of working hours to health and wellbeing.

PubMed

Schomann, Carsten; Giebel, Ole; Nachreiner, Friedhelm

2006-01-01

BASS 4, a computer program for the design and evaluation of workings hours, is an example of an ergonomics-based software tool that can be used by safety practitioners at the shop floor with regard to legal, ergonomic, and economic criteria. Based on experiences with this computer program, a less sophisticated Working-Hours-Risk Index for assessing the quality of work schedules (including flexible work hours) to indicate risks to health and wellbeing has been developed to provide a quick and easy applicable tool for legally required risk assessments. The results of a validation study show that this risk index seems to be a promising indicator for predicting risks of health complaints and wellbeing. The purpose of the Risk Index is to simplify the evaluation process at the shop floor and provide some more general information about the quality of a work schedule that can be used for triggering preventive interventions. Such a risk index complies with practitioners' expectations and requests for easy, useful, and valid instruments.

Automated diabetic retinopathy detection in smartphone-based fundus photography using artificial intelligence.

PubMed

Rajalakshmi, Ramachandran; Subashini, Radhakrishnan; Anjana, Ranjit Mohan; Mohan, Viswanathan

2018-06-01

To assess the role of artificial intelligence (AI)-based automated software for detection of diabetic retinopathy (DR) and sight-threatening DR (STDR) by fundus photography taken using a smartphone-based device and validate it against ophthalmologist's grading. Three hundred and one patients with type 2 diabetes underwent retinal photography with Remidio 'Fundus on phone' (FOP), a smartphone-based device, at a tertiary care diabetes centre in India. Grading of DR was performed by the ophthalmologists using International Clinical DR (ICDR) classification scale. STDR was defined by the presence of severe non-proliferative DR, proliferative DR or diabetic macular oedema (DME). The retinal photographs were graded using a validated AI DR screening software (EyeArt TM ) designed to identify DR, referable DR (moderate non-proliferative DR or worse and/or DME) or STDR. The sensitivity and specificity of automated grading were assessed and validated against the ophthalmologists' grading. Retinal images of 296 patients were graded. DR was detected by the ophthalmologists in 191 (64.5%) and by the AI software in 203 (68.6%) patients while STDR was detected in 112 (37.8%) and 146 (49.3%) patients, respectively. The AI software showed 95.8% (95% CI 92.9-98.7) sensitivity and 80.2% (95% CI 72.6-87.8) specificity for detecting any DR and 99.1% (95% CI 95.1-99.9) sensitivity and 80.4% (95% CI 73.9-85.9) specificity in detecting STDR with a kappa agreement of k = 0.78 (p < 0.001) and k = 0.75 (p < 0.001), respectively. Automated AI analysis of FOP smartphone retinal imaging has very high sensitivity for detecting DR and STDR and thus can be an initial tool for mass retinal screening in people with diabetes.

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

PubMed

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters

PubMed Central

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software − ‘RED’ (RNA Editing sites Detector) − for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector. PMID:26930599

Software Engineering Laboratory (SEL) compendium of tools, revision 1

NASA Technical Reports Server (NTRS)

1982-01-01

A set of programs used to aid software product development is listed. Known as software tools, such programs include requirements analyzers, design languages, precompilers, code auditors, code analyzers, and software librarians. Abstracts, resource requirements, documentation, processing summaries, and availability are indicated for most tools.

Data flow modeling techniques

NASA Technical Reports Server (NTRS)

Kavi, K. M.

1984-01-01

There have been a number of simulation packages developed for the purpose of designing, testing and validating computer systems, digital systems and software systems. Complex analytical tools based on Markov and semi-Markov processes have been designed to estimate the reliability and performance of simulated systems. Petri nets have received wide acceptance for modeling complex and highly parallel computers. In this research data flow models for computer systems are investigated. Data flow models can be used to simulate both software and hardware in a uniform manner. Data flow simulation techniques provide the computer systems designer with a CAD environment which enables highly parallel complex systems to be defined, evaluated at all levels and finally implemented in either hardware or software. Inherent in data flow concept is the hierarchical handling of complex systems. In this paper we will describe how data flow can be used to model computer system.

A Monte Carlo software for the 1-dimensional simulation of IBIC experiments

NASA Astrophysics Data System (ADS)

Forneris, J.; Jakšić, M.; Pastuović, Ž.; Vittone, E.

2014-08-01

The ion beam induced charge (IBIC) microscopy is a valuable tool for the analysis of the electronic properties of semiconductors. In this work, a recently developed Monte Carlo approach for the simulation of IBIC experiments is presented along with a self-standing software equipped with graphical user interface. The method is based on the probabilistic interpretation of the excess charge carrier continuity equations and it offers to the end-user the full control not only of the physical properties ruling the induced charge formation mechanism (i.e., mobility, lifetime, electrostatics, device's geometry), but also of the relevant experimental conditions (ionization profiles, beam dispersion, electronic noise) affecting the measurement of the IBIC pulses. Moreover, the software implements a novel model for the quantitative evaluation of the radiation damage effects on the charge collection efficiency degradation of ion-beam-irradiated devices. The reliability of the model implementation is then validated against a benchmark IBIC experiment.

An integrated user-oriented laboratory for verification of digital flight control systems: Features and capabilities

NASA Technical Reports Server (NTRS)

Defeo, P.; Doane, D.; Saito, J.

1982-01-01

A Digital Flight Control Systems Verification Laboratory (DFCSVL) has been established at NASA Ames Research Center. This report describes the major elements of the laboratory, the research activities that can be supported in the area of verification and validation of digital flight control systems (DFCS), and the operating scenarios within which these activities can be carried out. The DFCSVL consists of a palletized dual-dual flight-control system linked to a dedicated PDP-11/60 processor. Major software support programs are hosted in a remotely located UNIVAC 1100 accessible from the PDP-11/60 through a modem link. Important features of the DFCSVL include extensive hardware and software fault insertion capabilities, a real-time closed loop environment to exercise the DFCS, an integrated set of software verification tools, and a user-oriented interface to all the resources and capabilities.

Spectrum analysis on quality requirements consideration in software design documents.

PubMed

Kaiya, Haruhiko; Umemura, Masahiro; Ogata, Shinpei; Kaijiri, Kenji

2013-12-01

Software quality requirements defined in the requirements analysis stage should be implemented in the final products, such as source codes and system deployment. To guarantee this meta-requirement, quality requirements should be considered in the intermediate stages, such as the design stage or the architectural definition stage. We propose a novel method for checking whether quality requirements are considered in the design stage. In this method, a technique called "spectrum analysis for quality requirements" is applied not only to requirements specifications but also to design documents. The technique enables us to derive the spectrum of a document, and quality requirements considerations in the document are numerically represented in the spectrum. We can thus objectively identify whether the considerations of quality requirements in a requirements document are adapted to its design document. To validate the method, we applied it to commercial software systems with the help of a supporting tool, and we confirmed that the method worked well.

Building the European Seismological Research Infrastructure: results from 4 years NERIES EC project

NASA Astrophysics Data System (ADS)

van Eck, T.; Giardini, D.

2010-12-01

The EC Research Infrastructure (RI) project, Network of Research Infrastructures for European Seismology (NERIES), implemented a comprehensive European integrated RI for earthquake seismological data that is scalable and sustainable. NERIES opened a significant amount of additional seismological data, integrated different distributed data archives, implemented and produced advanced analysis tools and advanced software packages and tools. A single seismic data portal provides a single access point and overview for European seismological data available for the earth science research community. Additional data access tools and sites have been implemented to meet user and robustness requirements, notably those at the EMSC and ORFEUS. The datasets compiled in NERIES and available through the portal include among others: - The expanded Virtual European Broadband Seismic Network (VEBSN) with real-time access to more then 500 stations from > 53 observatories. This data is continuously monitored, quality controlled and archived in the European Integrated Distributed waveform Archive (EIDA). - A unique integration of acceleration datasets from seven networks in seven European or associated countries centrally accessible in a homogeneous format, thus forming the core comprehensive European acceleration database. Standardized parameter analysis and actual software are included in the database. - A Distributed Archive of Historical Earthquake Data (AHEAD) for research purposes, containing among others a comprehensive European Macroseismic Database and Earthquake Catalogue (1000 - 1963, M ≥5.8), including analysis tools. - Data from 3 one year OBS deployments at three sites, Atlantic, Ionian and Ligurian Sea within the general SEED format, thus creating the core integrated data base for ocean, sea and land based seismological observatories. Tools to facilitate analysis and data mining of the RI datasets are: - A comprehensive set of European seismological velocity reference model including a standardized model description with several visualisation tools currently adapted on a global scale. - An integrated approach to seismic hazard modelling and forecasting, a community accepted forecasting testing and model validation approach and the core hazard portal developed along the same technologies as the NERIES data portal. - Implemented homogeneous shakemap estimation tools at several large European observatories and a complementary new loss estimation software tool. - A comprehensive set of new techniques for geotechnical site characterization with relevant software packages documented and maintained (www.geopsy.org). - A set of software packages for data mining, data reduction, data exchange and information management in seismology as research and observatory analysis tools NERIES has a long-term impact and is coordinated with related US initiatives IRIS and EarthScope. The follow-up EC project of NERIES, NERA (2010 - 2014), is funded and will integrate the seismological and the earthquake engineering infrastructures. NERIES further provided the proof of concept for the ESFRI2008 initiative: the European Plate Observing System (EPOS). Its preparatory phase (2010 - 2014) is also funded by the EC.

Technical note on the validation of a semi-automated image analysis software application for estrogen and progesterone receptor detection in breast cancer.

PubMed

Krecsák, László; Micsik, Tamás; Kiszler, Gábor; Krenács, Tibor; Szabó, Dániel; Jónás, Viktor; Császár, Gergely; Czuni, László; Gurzó, Péter; Ficsor, Levente; Molnár, Béla

2011-01-18

The immunohistochemical detection of estrogen (ER) and progesterone (PR) receptors in breast cancer is routinely used for prognostic and predictive testing. Whole slide digitalization supported by dedicated software tools allows quantization of the image objects (e.g. cell membrane, nuclei) and an unbiased analysis of immunostaining results. Validation studies of image analysis applications for the detection of ER and PR in breast cancer specimens provided strong concordance between the pathologist's manual assessment of slides and scoring performed using different software applications. The effectiveness of two connected semi-automated image analysis software (NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14) for determination of ER and PR status in formalin-fixed paraffin embedded breast cancer specimens immunostained with the automated Leica Bond Max system was studied. First the detection algorithm was calibrated to the scores provided an independent assessors (pathologist), using selected areas from 38 small digital slides (created from 16 cases) containing a mean number of 195 cells. Each cell was manually marked and scored according to the Allred-system combining frequency and intensity scores. The performance of the calibrated algorithm was tested on 16 cases (14 invasive ductal carcinoma, 2 invasive lobular carcinoma) against the pathologist's manual scoring of digital slides. The detection was calibrated to 87 percent object detection agreement and almost perfect Total Score agreement (Cohen's kappa 0.859, quadratic weighted kappa 0.986) from slight or moderate agreement at the start of the study, using the un-calibrated algorithm. The performance of the application was tested against the pathologist's manual scoring of digital slides on 53 regions of interest of 16 ER and PR slides covering all positivity ranges, and the quadratic weighted kappa provided almost perfect agreement (κ = 0.981) among the two scoring schemes. NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14 software application proved to be a reliable image analysis tool for pathologists testing ER and PR status in breast cancer.

15 CFR 995.27 - Format validation software testing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Format validation software testing... CERTIFICATION REQUIREMENTS FOR NOAA HYDROGRAPHIC PRODUCTS AND SERVICES CERTIFICATION REQUIREMENTS FOR... of NOAA ENC Products § 995.27 Format validation software testing. Tests shall be performed verifying...

Integrating Testing into Software Engineering Courses Supported by a Collaborative Learning Environment

ERIC Educational Resources Information Center

Clarke, Peter J.; Davis, Debra; King, Tariq M.; Pava, Jairo; Jones, Edward L.

2014-01-01

As software becomes more ubiquitous and complex, the cost of software bugs continues to grow at a staggering rate. To remedy this situation, there needs to be major improvement in the knowledge and application of software validation techniques. Although there are several software validation techniques, software testing continues to be one of the…

Automated support for experience-based software management

NASA Technical Reports Server (NTRS)

Valett, Jon D.

1992-01-01

To effectively manage a software development project, the software manager must have access to key information concerning a project's status. This information includes not only data relating to the project of interest, but also, the experience of past development efforts within the environment. This paper describes the concepts and functionality of a software management tool designed to provide this information. This tool, called the Software Management Environment (SME), enables the software manager to compare an ongoing development effort with previous efforts and with models of the 'typical' project within the environment, to predict future project status, to analyze a project's strengths and weaknesses, and to assess the project's quality. In order to provide these functions the tool utilizes a vast corporate memory that includes a data base of software metrics, a set of models and relationships that describe the software development environment, and a set of rules that capture other knowledge and experience of software managers within the environment. Integrating these major concepts into one software management tool, the SME is a model of the type of management tool needed for all software development organizations.

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

PubMed Central

Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

2016-01-01

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection. PMID:26799713

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding.

PubMed

Fan, Wei; Zong, Jie; Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

2016-01-01

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.

Visualization tool for three-dimensional plasma velocity distributions (ISEE_3D) as a plug-in for SPEDAS

NASA Astrophysics Data System (ADS)

Keika, Kunihiro; Miyoshi, Yoshizumi; Machida, Shinobu; Ieda, Akimasa; Seki, Kanako; Hori, Tomoaki; Miyashita, Yukinaga; Shoji, Masafumi; Shinohara, Iku; Angelopoulos, Vassilis; Lewis, Jim W.; Flores, Aaron

2017-12-01

This paper introduces ISEE_3D, an interactive visualization tool for three-dimensional plasma velocity distribution functions, developed by the Institute for Space-Earth Environmental Research, Nagoya University, Japan. The tool provides a variety of methods to visualize the distribution function of space plasma: scatter, volume, and isosurface modes. The tool also has a wide range of functions, such as displaying magnetic field vectors and two-dimensional slices of distributions to facilitate extensive analysis. The coordinate transformation to the magnetic field coordinates is also implemented in the tool. The source codes of the tool are written as scripts of a widely used data analysis software language, Interactive Data Language, which has been widespread in the field of space physics and solar physics. The current version of the tool can be used for data files of the plasma distribution function from the Geotail satellite mission, which are publicly accessible through the Data Archives and Transmission System of the Institute of Space and Astronautical Science (ISAS)/Japan Aerospace Exploration Agency (JAXA). The tool is also available in the Space Physics Environment Data Analysis Software to visualize plasma data from the Magnetospheric Multiscale and the Time History of Events and Macroscale Interactions during Substorms missions. The tool is planned to be applied to data from other missions, such as Arase (ERG) and Van Allen Probes after replacing or adding data loading plug-ins. This visualization tool helps scientists understand the dynamics of space plasma better, particularly in the regions where the magnetohydrodynamic approximation is not valid, for example, the Earth's inner magnetosphere, magnetopause, bow shock, and plasma sheet.

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.

Software project management tools in global software development: a systematic mapping study.

PubMed

Chadli, Saad Yasser; Idri, Ali; Ros, Joaquín Nicolás; Fernández-Alemán, José Luis; de Gea, Juan M Carrillo; Toval, Ambrosio

2016-01-01

Global software development (GSD) which is a growing trend in the software industry is characterized by a highly distributed environment. Performing software project management (SPM) in such conditions implies the need to overcome new limitations resulting from cultural, temporal and geographic separation. The aim of this research is to discover and classify the various tools mentioned in literature that provide GSD project managers with support and to identify in what way they support group interaction. A systematic mapping study has been performed by means of automatic searches in five sources. We have then synthesized the data extracted and presented the results of this study. A total of 102 tools were identified as being used in SPM activities in GSD. We have classified these tools, according to the software life cycle process on which they focus and how they support the 3C collaboration model (communication, coordination and cooperation). The majority of the tools found are standalone tools (77%). A small number of platforms (8%) also offer a set of interacting tools that cover the software development lifecycle. Results also indicate that SPM areas in GSD are not adequately supported by corresponding tools and deserve more attention from tool builders.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

Verification, Validation and Sensitivity Studies in Computational Biomechanics

PubMed Central

Anderson, Andrew E.; Ellis, Benjamin J.; Weiss, Jeffrey A.

2012-01-01

Computational techniques and software for the analysis of problems in mechanics have naturally moved from their origins in the traditional engineering disciplines to the study of cell, tissue and organ biomechanics. Increasingly complex models have been developed to describe and predict the mechanical behavior of such biological systems. While the availability of advanced computational tools has led to exciting research advances in the field, the utility of these models is often the subject of criticism due to inadequate model verification and validation. The objective of this review is to present the concepts of verification, validation and sensitivity studies with regard to the construction, analysis and interpretation of models in computational biomechanics. Specific examples from the field are discussed. It is hoped that this review will serve as a guide to the use of verification and validation principles in the field of computational biomechanics, thereby improving the peer acceptance of studies that use computational modeling techniques. PMID:17558646

aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

PubMed Central

Niedworok, Christian J.; Brown, Alexander P. Y.; Jorge Cardoso, M.; Osten, Pavel; Ourselin, Sebastien; Modat, Marc; Margrie, Troy W.

2016-01-01

The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain. PMID:27384127

Online Remote Sensing Interface

NASA Technical Reports Server (NTRS)

Lawhead, Joel

2007-01-01

BasinTools Module 1 processes remotely sensed raster data, including multi- and hyper-spectral data products, via a Web site with no downloads and no plug-ins required. The interface provides standardized algorithms designed so that a user with little or no remote-sensing experience can use the site. This Web-based approach reduces the amount of software, hardware, and computing power necessary to perform the specified analyses. Access to imagery and derived products is enterprise-level and controlled. Because the user never takes possession of the imagery, the licensing of the data is greatly simplified. BasinTools takes the "just-in-time" inventory control model from commercial manufacturing and applies it to remotely-sensed data. Products are created and delivered on-the-fly with no human intervention, even for casual users. Well-defined procedures can be combined in different ways to extend verified and validated methods in order to derive new remote-sensing products, which improves efficiency in any well-defined geospatial domain. Remote-sensing products produced in BasinTools are self-documenting, allowing procedures to be independently verified or peer-reviewed. The software can be used enterprise-wide to conduct low-level remote sensing, viewing, sharing, and manipulating of image data without the need for desktop applications.

Metabolomic Analysis and Visualization Engine for LC–MS Data

PubMed Central

Melamud, Eugene; Vastag, Livia; Rabinowitz, Joshua D.

2017-01-01

Metabolomic analysis by liquid chromatography–high-resolution mass spectrometry results in data sets with thousands of features arising from metabolites, fragments, isotopes, and adducts. Here we describe a software package, Metabolomic Analysis and Visualization ENgine (MAVEN), designed for efficient interactive analysis of LC–MS data, including in the presence of isotope labeling. The software contains tools for all aspects of the data analysis process, from feature extraction to pathway-based graphical data display. To facilitate data validation, a machine learning algorithm automatically assesses peak quality. Users interact with raw data primarily in the form of extracted ion chromatograms, which are displayed with overlaid circles indicating peak quality, and bar graphs of peak intensities for both unlabeled and isotope-labeled metabolite forms. Click-based navigation leads to additional information, such as raw data for specific isotopic forms or for metabolites changing significantly between conditions. Fast data processing algorithms result in nearly delay-free browsing. Drop-down menus provide tools for the overlay of data onto pathway maps. These tools enable animating series of pathway graphs, e.g., to show propagation of labeled forms through a metabolic network. MAVEN is released under an open source license at http://maven.princeton.edu. PMID:21049934

Integrating and Managing Bim in GIS, Software Review

NASA Astrophysics Data System (ADS)

El Meouche, R.; Rezoug, M.; Hijazi, I.

2013-08-01

Since the advent of Computer-Aided Design (CAD) and Geographical Information System (GIS) tools, project participants have been increasingly leveraging these tools throughout the different phases of a civil infrastructure project. In recent years the number of GIS software that provides tools to enable the integration of Building information in geo context has risen sharply. More and more GIS software are added tools for this purposes and other software projects are regularly extending these tools. However, each software has its different strength and weakness and its purpose of use. This paper provides a thorough review to investigate the software capabilities and clarify its purpose. For this study, Autodesk Revit 2012 i.e. BIM editor software was used to create BIMs. In the first step, three building models were created, the resulted models were converted to BIM format and then the software was used to integrate it. For the evaluation of the software, general characteristics was studied such as the user interface, what formats are supported (import/export), and the way building information are imported.

A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

PubMed Central

Ross, James D.; Cullen, D. Kacy; Harris, James P.; LaPlaca, Michelle C.; DeWeerth, Stephen P.

2015-01-01

Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identification of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classifying features in 2-D and merging these classifications into 3-D objects; the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the platform provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological complexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥95%. We demonstrated the robustness of these algorithms in a more complex arena through the automated segmentation of neural cells in ex vivo brain slices. These novel methods surpass previous techniques by improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. PMID:26257609

Architectures and Evaluation for Adjustable Control Autonomy for Space-Based Life Support Systems

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Schreckenghost, Debra K.

2001-01-01

In the past five years, a number of automation applications for control of crew life support systems have been developed and evaluated in the Adjustable Autonomy Testbed at NASA's Johnson Space Center. This paper surveys progress on an adjustable autonomous control architecture for situations where software and human operators work together to manage anomalies and other system problems. When problems occur, the level of control autonomy can be adjusted, so that operators and software agents can work together on diagnosis and recovery. In 1997 adjustable autonomy software was developed to manage gas transfer and storage in a closed life support test. Four crewmembers lived and worked in a chamber for 91 days, with both air and water recycling. CO2 was converted to O2 by gas processing systems and wheat crops. With the automation software, significantly fewer hours were spent monitoring operations. System-level validation testing of the software by interactive hybrid simulation revealed problems both in software requirements and implementation. Since that time, we have been developing multi-agent approaches for automation software and human operators, to cooperatively control systems and manage problems. Each new capability has been tested and demonstrated in realistic dynamic anomaly scenarios, using the hybrid simulation tool.

SU-E-T-103: Development and Implementation of Web Based Quality Control Software

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

Studinski, R; Taylor, R; Angers, C

Purpose: Historically many radiation medicine programs have maintained their Quality Control (QC) test results in paper records or Microsoft Excel worksheets. Both these approaches represent significant logistical challenges, and are not predisposed to data review and approval. It has been our group's aim to develop and implement web based software designed not just to record and store QC data in a centralized database, but to provide scheduling and data review tools to help manage a radiation therapy clinics Equipment Quality control program. Methods: The software was written in the Python programming language using the Django web framework. In order tomore » promote collaboration and validation from other centres the code was made open source and is freely available to the public via an online source code repository. The code was written to provide a common user interface for data entry, formalize the review and approval process, and offer automated data trending and process control analysis of test results. Results: As of February 2014, our installation of QAtrack+ has 180 tests defined in its database and has collected ∼22 000 test results, all of which have been reviewed and approved by a physicist via QATrack+'s review tools. These results include records for quality control of Elekta accelerators, CT simulators, our brachytherapy programme, TomoTherapy and Cyberknife units. Currently at least 5 other centres are known to be running QAtrack+ clinically, forming the start of an international user community. Conclusion: QAtrack+ has proven to be an effective tool for collecting radiation therapy QC data, allowing for rapid review and trending of data for a wide variety of treatment units. As free and open source software, all source code, documentation and a bug tracker are available to the public at https://bitbucket.org/tohccmedphys/qatrackplus/.« less

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

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.

Software attribute visualization for high integrity software

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

Pollock, G.M.

1998-03-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

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

PubMed

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

2009-12-17

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

Validation of Medical Tourism Service Quality Questionnaire (MTSQQ) for Iranian Hospitals

PubMed Central

Qolipour, Mohammad; Torabipour, Amin; Khiavi, Farzad Faraji; Malehi, Amal Saki

2017-01-01

Introduction Assessing service quality is one of the basic requirements to develop the medical tourism industry. There is no valid and reliable tool to measure service quality of medical tourism. This study aimed to determine the reliability and validity of a Persian version of medical tourism service quality questionnaire for Iranian hospitals. Methods To validate the medical tourism service quality questionnaire (MTSQQ), a cross-sectional study was conducted on 250 Iraqi patients referred to hospitals in Ahvaz (Iran) from 2015. To design a questionnaire and determine its content validity, the Delphi Technique (3 rounds) with the participation of 20 medical tourism experts was used. Construct validity of the questionnaire was assessed through exploratory and confirmatory factor analysis. Reliability was assessed using Cronbach’s alpha coefficient. Data were analyzed by Excel 2007, SPSS version18, and Lisrel l8.0 software. Results The content validity of the questionnaire with CVI=0.775 was confirmed. According to exploratory factor analysis, the MTSQQ included 31 items and 8 dimensions (tangibility, reliability, responsiveness, assurance, empathy, exchange and travel facilities, technical and infrastructure facilities and safety and security). Construct validity of the questionnaire was confirmed, based on the goodness of fit quantities of model (RMSEA=0.032, CFI= 0.98, GFI=0.88). Cronbach’s alpha coefficient was 0.837 and 0.919 for expectation and perception questionnaire. Conclusion The results of the study showed that the medical tourism SERVQUAL questionnaire with 31 items and 8 dimensions was a valid and reliable tool to measure service quality of medical tourism in Iranian hospitals. PMID:28461863

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

FILTSoft: A computational tool for microstrip planar filter design

NASA Astrophysics Data System (ADS)

Elsayed, M. H.; Abidin, Z. Z.; Dahlan, S. H.; Cholan N., A.; Ngu, Xavier T. I.; Majid, H. A.

2017-09-01

Filters are key component of any communication system to control spectrum and suppress interferences. Designing a filter involves long process as well as good understanding of the basic hardware technology. Hence this paper introduces an automated design tool based on Matlab-GUI, called the FILTSoft (acronym for Filter Design Software) to ease the process. FILTSoft is a user friendly filter design tool to aid, guide and expedite calculations from lumped elements level to microstrip structure. Users just have to provide the required filter specifications as well as the material description. FILTSoft will calculate and display the lumped element details, the planar filter structure, and the expected filter's response. An example of a lowpass filter design was calculated using FILTSoft and the results were validated through prototype measurement for comparison purposes.

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

PubMed

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

2018-05-22

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

Software Engineering for Scientific Computer Simulations

NASA Astrophysics Data System (ADS)

Post, Douglass E.; Henderson, Dale B.; Kendall, Richard P.; Whitney, Earl M.

2004-11-01

Computer simulation is becoming a very powerful tool for analyzing and predicting the performance of fusion experiments. Simulation efforts are evolving from including only a few effects to many effects, from small teams with a few people to large teams, and from workstations and small processor count parallel computers to massively parallel platforms. Successfully making this transition requires attention to software engineering issues. We report on the conclusions drawn from a number of case studies of large scale scientific computing projects within DOE, academia and the DoD. The major lessons learned include attention to sound project management including setting reasonable and achievable requirements, building a good code team, enforcing customer focus, carrying out verification and validation and selecting the optimum computational mathematics approaches.

Imperial College near infrared spectroscopy neuroimaging analysis framework.

PubMed

Orihuela-Espina, Felipe; Leff, Daniel R; James, David R C; Darzi, Ara W; Yang, Guang-Zhong

2018-01-01

This paper describes the Imperial College near infrared spectroscopy neuroimaging analysis (ICNNA) software tool for functional near infrared spectroscopy neuroimaging data. ICNNA is a MATLAB-based object-oriented framework encompassing an application programming interface and a graphical user interface. ICNNA incorporates reconstruction based on the modified Beer-Lambert law and basic processing and data validation capabilities. Emphasis is placed on the full experiment rather than individual neuroimages as the central element of analysis. The software offers three types of analyses including classical statistical methods based on comparison of changes in relative concentrations of hemoglobin between the task and baseline periods, graph theory-based metrics of connectivity and, distinctively, an analysis approach based on manifold embedding. This paper presents the different capabilities of ICNNA in its current version.

Mixed-Dimensionality VLSI-Type Configurable Tools for Virtual Prototyping of Biomicrofluidic Devices and Integrated Systems

NASA Astrophysics Data System (ADS)

Makhijani, Vinod B.; Przekwas, Andrzej J.

2002-10-01

This report presents results of a DARPA/MTO Composite CAD Project aimed to develop a comprehensive microsystem CAD environment, CFD-ACE+ Multiphysics, for bio and microfluidic devices and complete microsystems. The project began in July 1998, and was a three-year team effort between CFD Research Corporation, California Institute of Technology (CalTech), University of California, Berkeley (UCB), and Tanner Research, with Mr. Don Verlee from Abbott Labs participating as a consultant on the project. The overall objective of this project was to develop, validate and demonstrate several applications of a user-configurable VLSI-type mixed-dimensionality software tool for design of biomicrofluidics devices and integrated systems. The developed tool would provide high fidelity 3-D multiphysics modeling capability, l-D fluidic circuits modeling, and SPICE interface for system level simulations, and mixed-dimensionality design. It would combine tools for layouts and process fabrication, geometric modeling, and automated grid generation, and interfaces to EDA tools (e.g. Cadence) and MCAD tools (e.g. ProE).

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

NASA Technical Reports Server (NTRS)

Maul, William A.; Fulton, Christopher E.

2011-01-01

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

Adaptation of G-TAG Software for Validating Touch-and-Go Comet Surface Sampling Design Methodology

NASA Technical Reports Server (NTRS)

Mandic, Milan; Acikmese, Behcet; Blackmore, Lars

2011-01-01

The G-TAG software tool was developed under the R&TD on Integrated Autonomous Guidance, Navigation, and Control for Comet Sample Return, and represents a novel, multi-body dynamics simulation software tool for studying TAG sampling. The G-TAG multi-body simulation tool provides a simulation environment in which a Touch-and-Go (TAG) sampling event can be extensively tested. TAG sampling requires the spacecraft to descend to the surface, contact the surface with a sampling collection device, and then to ascend to a safe altitude. The TAG event lasts only a few seconds but is mission-critical with potentially high risk. Consequently, there is a need for the TAG event to be well characterized and studied by simulation and analysis in order for the proposal teams to converge on a reliable spacecraft design. This adaptation of the G-TAG tool was developed to support the Comet Odyssey proposal effort, and is specifically focused to address comet sample return missions. In this application, the spacecraft descends to and samples from the surface of a comet. Performance of the spacecraft during TAG is assessed based on survivability and sample collection performance. For the adaptation of the G-TAG simulation tool to comet scenarios, models are developed that accurately describe the properties of the spacecraft, approach trajectories, and descent velocities, as well as the models of the external forces and torques acting on the spacecraft. The adapted models of the spacecraft, descent profiles, and external sampling forces/torques were more sophisticated and customized for comets than those available in the basic G-TAG simulation tool. Scenarios implemented include the study of variations in requirements, spacecraft design (size, locations, etc. of the spacecraft components), and the environment (surface properties, slope, disturbances, etc.). The simulations, along with their visual representations using G-View, contributed to the Comet Odyssey New Frontiers proposal effort by indicating problems and/or benefits of different approaches and designs.

The LINDSAY Virtual Human Project: an immersive approach to anatomy and physiology.

PubMed

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

2013-01-01

The increasing number of digital anatomy teaching software packages challenges anatomy educators on how to best integrate these tools for teaching and learning. Realistically, there exists a complex interplay of design, implementation, politics, and learning needs in the development and integration of software for education, each of which may be further amplified by the somewhat siloed roles of programmers, faculty, and students. LINDSAY Presenter is newly designed software that permits faculty and students to model and manipulate three-dimensional anatomy presentations and images, while including embedded quizzes, links, and text-based content. A validated tool measuring impact across pedagogy, resources, interactivity, freedom, granularity, and factors outside the immediate learning event was used in conjunction with observation, field notes, and focus groups to critically examine the impact of attitudes and perceptions of all stakeholders in the early implementation of LINDSAY Presenter before and after a three-week trial period with the software. Results demonstrate that external, personal media usage, along with students' awareness of the need to apply anatomy to clinical professional situations drove expectations of LINDSAY Presenter. A focus on the software over learning, which can be expected during initial orientation, surprisingly remained after three weeks of use. The time-intensive investment required to create learning content is a detractor from user-generated content and may reflect the consumption nature of other forms of digital learning. Early excitement over new technologies needs to be tempered with clear understanding of what learning is afforded, and how these constructively support future application and integration into professional practice. Copyright © 2012 American Association of Anatomists.

Generating DEM from LIDAR data - comparison of available software tools

NASA Astrophysics Data System (ADS)

Korzeniowska, K.; Lacka, M.

2011-12-01

In recent years many software tools and applications have appeared that offer procedures, scripts and algorithms to process and visualize ALS data. This variety of software tools and of "point cloud" processing methods contributed to the aim of this study: to assess algorithms available in various software tools that are used to classify LIDAR "point cloud" data, through a careful examination of Digital Elevation Models (DEMs) generated from LIDAR data on a base of these algorithms. The works focused on the most important available software tools: both commercial and open source ones. Two sites in a mountain area were selected for the study. The area of each site is 0.645 sq km. DEMs generated with analysed software tools ware compared with a reference dataset, generated using manual methods to eliminate non ground points. Surfaces were analysed using raster analysis. Minimum, maximum and mean differences between reference DEM and DEMs generated with analysed software tools were calculated, together with Root Mean Square Error. Differences between DEMs were also examined visually using transects along the grid axes in the test sites.

Software validation applied to spreadsheets used in laboratories working under ISO/IEC 17025

NASA Astrophysics Data System (ADS)

Banegas, J. M.; Orué, M. W.

2016-07-01

Several documents deal with software validation. Nevertheless, more are too complex to be applied to validate spreadsheets - surely the most used software in laboratories working under ISO/IEC 17025. The method proposed in this work is intended to be directly applied to validate spreadsheets. It includes a systematic way to document requirements, operational aspects regarding to validation, and a simple method to keep records of validation results and modifications history. This method is actually being used in an accredited calibration laboratory, showing to be practical and efficient.

Lessons learned in deploying software estimation technology and tools

NASA Technical Reports Server (NTRS)

Panlilio-Yap, Nikki; Ho, Danny

1994-01-01

Developing a software product involves estimating various project parameters. This is typically done in the planning stages of the project when there is much uncertainty and very little information. Coming up with accurate estimates of effort, cost, schedule, and reliability is a critical problem faced by all software project managers. The use of estimation models and commercially available tools in conjunction with the best bottom-up estimates of software-development experts enhances the ability of a product development group to derive reasonable estimates of important project parameters. This paper describes the experience of the IBM Software Solutions (SWS) Toronto Laboratory in selecting software estimation models and tools and deploying their use to the laboratory's product development groups. It introduces the SLIM and COSTAR products, the software estimation tools selected for deployment to the product areas, and discusses the rationale for their selection. The paper also describes the mechanisms used for technology injection and tool deployment, and concludes with a discussion of important lessons learned in the technology and tool insertion process.

Validation of ICDPIC software injury severity scores using a large regional trauma registry.

PubMed

Greene, Nathaniel H; Kernic, Mary A; Vavilala, Monica S; Rivara, Frederick P

2015-10-01

Administrative or quality improvement registries may or may not contain the elements needed for investigations by trauma researchers. International Classification of Diseases Program for Injury Categorisation (ICDPIC), a statistical program available through Stata, is a powerful tool that can extract injury severity scores from ICD-9-CM codes. We conducted a validation study for use of the ICDPIC in trauma research. We conducted a retrospective cohort validation study of 40,418 patients with injury using a large regional trauma registry. ICDPIC-generated AIS scores for each body region were compared with trauma registry AIS scores (gold standard) in adult and paediatric populations. A separate analysis was conducted among patients with traumatic brain injury (TBI) comparing the ICDPIC tool with ICD-9-CM embedded severity codes. Performance in characterising overall injury severity, by the ISS, was also assessed. The ICDPIC tool generated substantial correlations in thoracic and abdominal trauma (weighted κ 0.87-0.92), and in head and neck trauma (weighted κ 0.76-0.83). The ICDPIC tool captured TBI severity better than ICD-9-CM code embedded severity and offered the advantage of generating a severity value for every patient (rather than having missing data). Its ability to produce an accurate severity score was consistent within each body region as well as overall. The ICDPIC tool performs well in classifying injury severity and is superior to ICD-9-CM embedded severity for TBI. Use of ICDPIC demonstrates substantial efficiency and may be a preferred tool in determining injury severity for large trauma datasets, provided researchers understand its limitations and take caution when examining smaller trauma datasets. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Evaluation of the efficiency and reliability of software generated by code generators

NASA Technical Reports Server (NTRS)

Schreur, Barbara

1994-01-01

There are numerous studies which show that CASE Tools greatly facilitate software development. As a result of these advantages, an increasing amount of software development is done with CASE Tools. As more software engineers become proficient with these tools, their experience and feedback lead to further development with the tools themselves. What has not been widely studied, however, is the reliability and efficiency of the actual code produced by the CASE Tools. This investigation considered these matters. Three segments of code generated by MATRIXx, one of many commercially available CASE Tools, were chosen for analysis: ETOFLIGHT, a portion of the Earth to Orbit Flight software, and ECLSS and PFMC, modules for Environmental Control and Life Support System and Pump Fan Motor Control, respectively.

Evaluation of the BreastSimulator software platform for breast tomography

NASA Astrophysics Data System (ADS)

Mettivier, G.; Bliznakova, K.; Sechopoulos, I.; Boone, J. M.; Di Lillo, F.; Sarno, A.; Castriconi, R.; Russo, P.

2017-08-01

The aim of this work was the evaluation of the software BreastSimulator, a breast x-ray imaging simulation software, as a tool for the creation of 3D uncompressed breast digital models and for the simulation and the optimization of computed tomography (CT) scanners dedicated to the breast. Eight 3D digital breast phantoms were created with glandular fractions in the range 10%-35%. The models are characterised by different sizes and modelled realistic anatomical features. X-ray CT projections were simulated for a dedicated cone-beam CT scanner and reconstructed with the FDK algorithm. X-ray projection images were simulated for 5 mono-energetic (27, 32, 35, 43 and 51 keV) and 3 poly-energetic x-ray spectra typically employed in current CT scanners dedicated to the breast (49, 60, or 80 kVp). Clinical CT images acquired from two different clinical breast CT scanners were used for comparison purposes. The quantitative evaluation included calculation of the power-law exponent, β, from simulated and real breast tomograms, based on the power spectrum fitted with a function of the spatial frequency, f, of the form S(f)  =  α/f   β . The breast models were validated by comparison against clinical breast CT and published data. We found that the calculated β coefficients were close to that of clinical CT data from a dedicated breast CT scanner and reported data in the literature. In evaluating the software package BreastSimulator to generate breast models suitable for use with breast CT imaging, we found that the breast phantoms produced with the software tool can reproduce the anatomical structure of real breasts, as evaluated by calculating the β exponent from the power spectral analysis of simulated images. As such, this research tool might contribute considerably to the further development, testing and optimisation of breast CT imaging techniques.

WinHPC System Software | High-Performance Computing | NREL

Science.gov Websites

Software WinHPC System Software Learn about the software applications, tools, toolchains, and for industrial applications. Intel Compilers Development Tool, Toolchain Suite featuring an industry

The development of AR book for computer learning

NASA Astrophysics Data System (ADS)

Phadung, Muneeroh; Wani, Najela; Tongmnee, Nur-aiynee

2017-08-01

Educators need to provide the alternative educational tools to foster learning outcomes of students. By using AR technology to create exciting edutainment experiences, this paper presents how augmented reality (AR) can be applied in the education. This study aims to develop the AR book for tenth grade students (age 15-16) and evaluate its quality. The AR book was developed based on ADDIE framework processes to provide computer learning on software computer knowledge. The content was accorded with the current Thai education curriculum. The AR book had 10 pages in three topics (the first was "Introduction," the second was "System Software" and the third was "Application Software"). Each page contained markers that placed virtual objects (2D animation and video clip). The obtained data were analyzed in terms of average and standard deviation. The validity of multimedia design of the AR book was assessed by three experts in multimedia design. A five-point Likert scale was used and the values were X¯ =4 .84 , S.D. = 1.27 which referred to very high. Moreover, three content experts, who specialize in computer teaching, evaluated the AR book's validity. The values determined by the experts were X¯ =4 .69 , S.D. = 0.29 which referred to very high. Implications for future study and education are discussed.

EpiTools, A software suite for presurgical brain mapping in epilepsy: Intracerebral EEG.

PubMed

Medina Villalon, S; Paz, R; Roehri, N; Lagarde, S; Pizzo, F; Colombet, B; Bartolomei, F; Carron, R; Bénar, C-G

2018-06-01

In pharmacoresistant epilepsy, exploration with depth electrodes can be needed to precisely define the epileptogenic zone. Accurate location of these electrodes is thus essential for the interpretation of Stereotaxic EEG (SEEG) signals. As SEEG analysis increasingly relies on signal processing, it is crucial to make a link between these results and patient's anatomy. Our aims were thus to develop a suite of software tools, called "EpiTools", able to i) precisely and automatically localize the position of each SEEG contact and ii) display the results of signal analysis in each patient's anatomy. The first tool, GARDEL (GUI for Automatic Registration and Depth Electrode Localization), is able to automatically localize SEEG contacts and to label each contact according to a pre-specified nomenclature (for instance that of FreeSurfer or MarsAtlas). The second tool, 3Dviewer, enables to visualize in the 3D anatomy of the patient the origin of signal processing results such as rate of biomarkers, connectivity graphs or Epileptogenicity Index. GARDEL was validated in 30 patients by clinicians and proved to be highly reliable to determine within the patient's individual anatomy the actual location of contacts. GARDEL is a fully automatic electrode localization tool needing limited user interaction (only for electrode naming or contact correction). The 3Dviewer is able to read signal processing results and to display them in link with patient's anatomy. EpiTools can help speeding up the interpretation of SEEG data and improving its precision. Copyright © 2018 Elsevier B.V. All rights reserved.

Installing and Setting Up the Git Software Tool on OS X | High-Performance

Science.gov Websites

Computing | NREL the Git Software Tool on OS X Installing and Setting Up the Git Software Tool on OS X Learn how to install the Git software tool on OS X for use with the Peregrine system. You can . Binary Installer for OS X - Easiest! You can download the latest version of git from http://git-scm.com

NASA's Approach to Software Assurance

NASA Technical Reports Server (NTRS)

Wetherholt, Martha

2015-01-01

NASA defines software assurance as: the planned and systematic set of activities that ensure conformance of software life cycle processes and products to requirements, standards, and procedures via quality, safety, reliability, and independent verification and validation. NASA's implementation of this approach to the quality, safety, reliability, security and verification and validation of software is brought together in one discipline, software assurance. Organizationally, NASA has software assurance at each NASA center, a Software Assurance Manager at NASA Headquarters, a Software Assurance Technical Fellow (currently the same person as the SA Manager), and an Independent Verification and Validation Organization with its own facility. An umbrella risk mitigation strategy for safety and mission success assurance of NASA's software, software assurance covers a wide area and is better structured to address the dynamic changes in how software is developed, used, and managed, as well as it's increasingly complex functionality. Being flexible, risk based, and prepared for challenges in software at NASA is essential, especially as much of our software is unique for each mission.

VDA, a Method of Choosing a Better Algorithm with Fewer Validations

PubMed Central

Kluger, Yuval

2011-01-01

The multitude of bioinformatics algorithms designed for performing a particular computational task presents end-users with the problem of selecting the most appropriate computational tool for analyzing their biological data. The choice of the best available method is often based on expensive experimental validation of the results. We propose an approach to design validation sets for method comparison and performance assessment that are effective in terms of cost and discrimination power. Validation Discriminant Analysis (VDA) is a method for designing a minimal validation dataset to allow reliable comparisons between the performances of different algorithms. Implementation of our VDA approach achieves this reduction by selecting predictions that maximize the minimum Hamming distance between algorithmic predictions in the validation set. We show that VDA can be used to correctly rank algorithms according to their performances. These results are further supported by simulations and by realistic algorithmic comparisons in silico. VDA is a novel, cost-efficient method for minimizing the number of validation experiments necessary for reliable performance estimation and fair comparison between algorithms. Our VDA software is available at http://sourceforge.net/projects/klugerlab/files/VDA/ PMID:22046256

Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

PubMed

Chakrabortty, S; Sen, M; Pal, P

2014-03-01

A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

Applying CASE Tools for On-Board Software Development

NASA Astrophysics Data System (ADS)

Brammer, U.; Hönle, A.

For many space projects the software development is facing great pressure with respect to quality, costs and schedule. One way to cope with these challenges is the application of CASE tools for automatic generation of code and documentation. This paper describes two CASE tools: Rhapsody (I-Logix) featuring UML and ISG (BSSE) that provides modeling of finite state machines. Both tools have been used at Kayser-Threde in different space projects for the development of on-board software. The tools are discussed with regard to the full software development cycle.

Software for predictive microbiology and risk assessment: a description and comparison of tools presented at the ICPMF8 Software Fair.

PubMed

Tenenhaus-Aziza, Fanny; Ellouze, Mariem

2015-02-01

The 8th International Conference on Predictive Modelling in Food was held in Paris, France in September 2013. One of the major topics of this conference was the transfer of knowledge and tools between academics and stakeholders of the food sector. During the conference, a "Software Fair" was held to provide information and demonstrations of predictive microbiology and risk assessment software. This article presents an overall description of the 16 software tools demonstrated at the session and provides a comparison based on several criteria such as the modeling approach, the different modules available (e.g. databases, predictors, fitting tools, risk assessment tools), the studied environmental factors (temperature, pH, aw, etc.), the type of media (broth or food) and the number and type of the provided micro-organisms (pathogens and spoilers). The present study is a guide to help users select the software tools which are most suitable to their specific needs, before they test and explore the tool(s) in more depth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Introduction of software tools for epidemiological surveillance in infection control in Colombia

PubMed Central

Motoa, Gabriel; Vallejo, Marta; Blanco, Víctor M; Correa, Adriana; de la Cadena, Elsa; Villegas, María Virginia

2015-01-01

Introduction: Healthcare-Associated Infections (HAI) are a challenge for patient safety in the hospitals. Infection control committees (ICC) should follow CDC definitions when monitoring HAI. The handmade method of epidemiological surveillance (ES) may affect the sensitivity and specificity of the monitoring system, while electronic surveillance can improve the performance, quality and traceability of recorded information. Objective: To assess the implementation of a strategy for electronic surveillance of HAI, Bacterial Resistance and Antimicrobial Consumption by the ICC of 23 high-complexity clinics and hospitals in Colombia, during the period 2012-2013. Methods: An observational study evaluating the introduction of electronic tools in the ICC was performed; we evaluated the structure and operation of the ICC, the degree of incorporation of the software HAI Solutions and the adherence to record the required information. Results: Thirty-eight percent of hospitals (8/23) had active surveillance strategies with standard criteria of the CDC, and 87% of institutions adhered to the module of identification of cases using the HAI Solutions software. In contrast, compliance with the diligence of the risk factors for device-associated HAIs was 33%. Conclusions: The introduction of ES could achieve greater adherence to a model of active surveillance, standardized and prospective, helping to improve the validity and quality of the recorded information. PMID:26309340

Introduction of software tools for epidemiological surveillance in infection control in Colombia.

PubMed

Hernández-Gómez, Cristhian; Motoa, Gabriel; Vallejo, Marta; Blanco, Víctor M; Correa, Adriana; de la Cadena, Elsa; Villegas, María Virginia

2015-01-01

Healthcare-Associated Infections (HAI) are a challenge for patient safety in the hospitals. Infection control committees (ICC) should follow CDC definitions when monitoring HAI. The handmade method of epidemiological surveillance (ES) may affect the sensitivity and specificity of the monitoring system, while electronic surveillance can improve the performance, quality and traceability of recorded information. To assess the implementation of a strategy for electronic surveillance of HAI, Bacterial Resistance and Antimicrobial Consumption by the ICC of 23 high-complexity clinics and hospitals in Colombia, during the period 2012-2013. An observational study evaluating the introduction of electronic tools in the ICC was performed; we evaluated the structure and operation of the ICC, the degree of incorporation of the software HAI Solutions and the adherence to record the required information. Thirty-eight percent of hospitals (8/23) had active surveillance strategies with standard criteria of the CDC, and 87% of institutions adhered to the module of identification of cases using the HAI Solutions software. In contrast, compliance with the diligence of the risk factors for device-associated HAIs was 33%. The introduction of ES could achieve greater adherence to a model of active surveillance, standardized and prospective, helping to improve the validity and quality of the recorded information.

Standards for the user interface - Developing a user consensus. [for Space Station Information System

NASA Technical Reports Server (NTRS)

Moe, Karen L.; Perkins, Dorothy C.; Szczur, Martha R.

1987-01-01

The user support environment (USE) which is a set of software tools for a flexible standard interactive user interface to the Space Station systems, platforms, and payloads is described in detail. Included in the USE concept are a user interface language, a run time environment and user interface management system, support tools, and standards for human interaction methods. The goals and challenges of the USE are discussed as well as a methodology based on prototype demonstrations for involving users in the process of validating the USE concepts. By prototyping the key concepts and salient features of the proposed user interface standards, the user's ability to respond is greatly enhanced.

Utility of an emulation and simulation computer model for air revitalization system hardware design, development, and test

NASA Technical Reports Server (NTRS)

Yanosy, J. L.; Rowell, L. F.

1985-01-01

Efforts to make increasingly use of suitable computer programs in the design of hardware have the potential to reduce expenditures. In this context, NASA has evaluated the benefits provided by software tools through an application to the Environmental Control and Life Support (ECLS) system. The present paper is concerned with the benefits obtained by an employment of simulation tools in the case of the Air Revitalization System (ARS) of a Space Station life support system. Attention is given to the ARS functions and components, a computer program overview, a SAND (solid amine water desorbed) bed model description, a model validation, and details regarding the simulation benefits.

Toolpack mathematical software development environment

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

Osterweil, L.

1982-07-21

The purpose of this research project was to produce a well integrated set of tools for the support of numerical computation. The project entailed the specification, design and implementation of both a diversity of tools and an innovative tool integration mechanism. This large configuration of tightly integrated tools comprises an environment for numerical software development, and has been named Toolpack/IST (Integrated System of Tools). Following the creation of this environment in prototype form, the environment software was readied for widespread distribution by transitioning it to a development organization for systematization, documentation and distribution. It is expected that public release ofmore » Toolpack/IST will begin imminently and will provide a basis for evaluation of the innovative software approaches taken as well as a uniform set of development tools for the numerical software community.« less

Software development environments: Status and trends

NASA Technical Reports Server (NTRS)

Duffel, Larry E.

1988-01-01

Currently software engineers are the essential integrating factors tying several components together. The components consist of process, methods, computers, tools, support environments, and software engineers. The engineers today empower the tools versus the tools empowering the engineers. Some of the issues in software engineering are quality, managing the software engineering process, and productivity. A strategy to accomplish this is to promote the evolution of software engineering from an ad hoc, labor intensive activity to a managed, technology supported discipline. This strategy may be implemented by putting the process under management control, adopting appropriate methods, inserting the technology that provides automated support for the process and methods, collecting automated tools into an integrated environment and educating the personnel.

Design and control of compliant tensegrity robots through simulation and hardware validation.

PubMed

Caluwaerts, Ken; Despraz, Jérémie; Işçen, Atıl; Sabelhaus, Andrew P; Bruce, Jonathan; Schrauwen, Benjamin; SunSpiral, Vytas

2014-09-06

To better understand the role of tensegrity structures in biological systems and their application to robotics, the Dynamic Tensegrity Robotics Lab at NASA Ames Research Center, Moffett Field, CA, USA, has developed and validated two software environments for the analysis, simulation and design of tensegrity robots. These tools, along with new control methodologies and the modular hardware components developed to validate them, are presented as a system for the design of actuated tensegrity structures. As evidenced from their appearance in many biological systems, tensegrity ('tensile-integrity') structures have unique physical properties that make them ideal for interaction with uncertain environments. Yet, these characteristics make design and control of bioinspired tensegrity robots extremely challenging. This work presents the progress our tools have made in tackling the design and control challenges of spherical tensegrity structures. We focus on this shape since it lends itself to rolling locomotion. The results of our analyses include multiple novel control approaches for mobility and terrain interaction of spherical tensegrity structures that have been tested in simulation. A hardware prototype of a spherical six-bar tensegrity, the Reservoir Compliant Tensegrity Robot, is used to empirically validate the accuracy of simulation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Interprofessional partnerships in chronic illness care: a conceptual model for measuring partnership effectiveness

PubMed Central

Butt, Gail; Markle-Reid, Maureen; Browne, Gina

2008-01-01

Introduction Interprofessional health and social service partnerships (IHSSP) are internationally acknowledged as integral for comprehensive chronic illness care. However, the evidence-base for partnership effectiveness is lacking. This paper aims to clarify partnership measurement issues, conceptualize IHSSP at the front-line staff level, and identify tools valid for group process measurement. Theory and methods A systematic literature review utilizing three interrelated searches was conducted. Thematic analysis techniques were supported by NVivo 7 software. Complexity theory was used to guide the analysis, ground the new conceptualization and validate the selected measures. Other properties of the measures were critiqued using established criteria. Results There is a need for a convergent view of what constitutes a partnership and its measurement. The salient attributes of IHSSP and their interorganizational context were described and grounded within complexity theory. Two measures were selected and validated for measurement of proximal group outcomes. Conclusion This paper depicts a novel complexity theory-based conceptual model for IHSSP of front-line staff who provide chronic illness care. The conceptualization provides the underpinnings for a comprehensive evaluative framework for partnerships. Two partnership process measurement tools, the PSAT and TCI are valid for IHSSP process measurement with consideration of their strengths and limitations. PMID:18493591

PHM for Ground Support Systems Case Study: From Requirements to Integration

NASA Technical Reports Server (NTRS)

Teubert, Chris

2015-01-01

This session will detail the experience of members of the NASA Ames Prognostic Center of Excellence (PCoE) producing PHM tools for NASA Advanced Ground Support Systems, including the challenges in applying their research in a production environment. Specifically, we will 1) go over the systems engineering and review process used; 2) Discuss the challenges and pitfalls in this process; 3) discuss software architecting, documentation, verification and validation activities and 4) discuss challenges in communicating the benefits and limitations of PHM Technologies.

Multi-Scale Homogenization for 3D Multiphase Composites: Development of Robust Software Tools for Material/Structural Characterization Across Length Scales

DTIC Science & Technology

2013-11-01

person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number...position‐dependent  [ ]. Thanks  to  this  relation, eqs.  (1)  can be reduced to a single ( vectorial ) equation for the displacement  :     ⋅ 0. (3

77 FR 50723 - Verification, Validation, Reviews, and Audits for Digital Computer Software Used in Safety...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... Digital Computer Software Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear Regulatory..., ``Verification, Validation, Reviews, and Audits for Digital Computer Software used in Safety Systems of Nuclear... NRC regulations promoting the development of, and compliance with, software verification and...

NASA's Advanced Multimission Operations System: A Case Study in Formalizing Software Architecture Evolution

NASA Technical Reports Server (NTRS)

Barnes, Jeffrey M.

2011-01-01

All software systems of significant size and longevity eventually undergo changes to their basic architectural structure. Such changes may be prompted by evolving requirements, changing technology, or other reasons. Whatever the cause, software architecture evolution is commonplace in real world software projects. Recently, software architecture researchers have begun to study this phenomenon in depth. However, this work has suffered from problems of validation; research in this area has tended to make heavy use of toy examples and hypothetical scenarios and has not been well supported by real world examples. To help address this problem, I describe an ongoing effort at the Jet Propulsion Laboratory to re-architect the Advanced Multimission Operations System (AMMOS), which is used to operate NASA's deep-space and astrophysics missions. Based on examination of project documents and interviews with project personnel, I describe the goals and approach of this evolution effort and then present models that capture some of the key architectural changes. Finally, I demonstrate how approaches and formal methods from my previous research in architecture evolution may be applied to this evolution, while using languages and tools already in place at the Jet Propulsion Laboratory.

A framework for assessing the adequacy and effectiveness of software development methodologies

NASA Technical Reports Server (NTRS)

Arthur, James D.; Nance, Richard E.

1990-01-01

Tools, techniques, environments, and methodologies dominate the software engineering literature, but relatively little research in the evaluation of methodologies is evident. This work reports an initial attempt to develop a procedural approach to evaluating software development methodologies. Prominent in this approach are: (1) an explication of the role of a methodology in the software development process; (2) the development of a procedure based on linkages among objectives, principles, and attributes; and (3) the establishment of a basis for reduction of the subjective nature of the evaluation through the introduction of properties. An application of the evaluation procedure to two Navy methodologies has provided consistent results that demonstrate the utility and versatility of the evaluation procedure. Current research efforts focus on the continued refinement of the evaluation procedure through the identification and integration of product quality indicators reflective of attribute presence, and the validation of metrics supporting the measure of those indicators. The consequent refinement of the evaluation procedure offers promise of a flexible approach that admits to change as the field of knowledge matures. In conclusion, the procedural approach presented in this paper represents a promising path toward the end goal of objectively evaluating software engineering methodologies.

Development and Validation of a Portable and Inexpensive Tool to Measure the Drop Vertical Jump Using the Microsoft Kinect V2.

PubMed

Gray, Aaron D; Willis, Brad W; Skubic, Marjorie; Huo, Zhiyu; Razu, Swithin; Sherman, Seth L; Guess, Trent M; Jahandar, Amirhossein; Gulbrandsen, Trevor R; Miller, Scott; Siesener, Nathan J

Noncontact anterior cruciate ligament (ACL) injury in adolescent female athletes is an increasing problem. The knee-ankle separation ratio (KASR), calculated at initial contact (IC) and peak flexion (PF) during the drop vertical jump (DVJ), is a measure of dynamic knee valgus. The Microsoft Kinect V2 has shown promise as a reliable and valid marker-less motion capture device. The Kinect V2 will demonstrate good to excellent correlation between KASR results at IC and PF during the DVJ, as compared with a "gold standard" Vicon motion analysis system. Descriptive laboratory study. Level 2. Thirty-eight healthy volunteer subjects (20 male, 18 female) performed 5 DVJ trials, simultaneously measured by a Vicon MX-T40S system, 2 AMTI force platforms, and a Kinect V2 with customized software. A total of 190 jumps were completed. The KASR was calculated at IC and PF during the DVJ. The intraclass correlation coefficient (ICC) assessed the degree of KASR agreement between the Kinect and Vicon systems. The ICCs of the Kinect V2 and Vicon KASR at IC and PF were 0.84 and 0.95, respectively, showing excellent agreement between the 2 measures. The Kinect V2 successfully identified the KASR at PF and IC frames in 182 of 190 trials, demonstrating 95.8% reliability. The Kinect V2 demonstrated excellent ICC of the KASR at IC and PF during the DVJ when compared with the Vicon system. A customized Kinect V2 software program demonstrated good reliability in identifying the KASR at IC and PF during the DVJ. Reliable, valid, inexpensive, and efficient screening tools may improve the accessibility of motion analysis assessment of adolescent female athletes.

Validation of an Open-Source Tool for Measuring Carotid Lumen Diameter and Intima-Media Thickness.

PubMed

Manterola, Hugo Luis; Lo Vercio, Lucas; Díaz, Alejandro; Del Fresno, Mariana; Larrabide, Ignacio

2018-05-14

In low- and middle-income regions, a relatively large number of deaths occur from cardiovascular disease or stroke. Carotid intima-media thickness (cIMT) and carotid lumen diameter (cLD) are strong indicators of cardiovascular event risk and stenosis severity, respectively. The interactive open-source software described here, Cimtool, is based on active contours for measuring these indicators in clinical practice and thus helping in preventive diagnosis and treatment. Cimtool was validated using carotid phantoms and real images obtained using ultrasound. Expert users measured cIMT and cLD in regular practice and also with Cimtool. The results obtained with Cimtool were then compared with the results for the manual approach in terms of measurement agreement, time spent on the measurements and usability. Intra-observer variability when using Cimtool was also analyzed. Statistical analysis revealed strong agreement between the manual method and Cimtool (p > 0.01 for cIMT and cLD). The correlation coefficient for both cIMT and cLD measurements was r > 0.9. Moreover, this software allowed the users to spend considerably less time on each measurement (3.5 min per study versus 50 s with Cimtool on average). An open-source, interactive, validated tool for measuring cIMT and cLD clinically was thus developed. Compared with the manual approach, Cimtool's straightforward measurement flow allows the user to spend less time per measurement and has less standard deviation. The coefficients of variation for measurements and intra-observer variability were lower than those reported for recent automated approaches, even with low-quality images. Copyright © 2018 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

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

PubMed Central

2015-01-01

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

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

PubMed

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

2014-09-22

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

Building Energy Simulation Test for Existing Homes (BESTEST-EX) (Presentation)

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

Judkoff, R.; Neymark, J.; Polly, B.

2011-12-01

This presentation discusses the goals of NREL Analysis Accuracy R&D; BESTEST-EX goals; what BESTEST-EX is; how it works; 'Building Physics' cases; 'Building Physics' reference results; 'utility bill calibration' cases; limitations and potential future work. Goals of NREL Analysis Accuracy R&D are: (1) Provide industry with the tools and technical information needed to improve the accuracy and consistency of analysis methods; (2) Reduce the risks associated with purchasing, financing, and selling energy efficiency upgrades; and (3) Enhance software and input collection methods considering impacts on accuracy, cost, and time of energy assessments. BESTEST-EX Goals are: (1) Test software predictions of retrofitmore » energy savings in existing homes; (2) Ensure building physics calculations and utility bill calibration procedures perform up to a minimum standard; and (3) Quantify impact of uncertainties in input audit data and occupant behavior. BESTEST-EX is a repeatable procedure that tests how well audit software predictions compare to the current state of the art in building energy simulation. There is no direct truth standard. However, reference software have been subjected to validation testing, including comparisons with empirical data.« less

Benefits of an automated GLP final report preparation software solution.

PubMed

Elvebak, Larry E

2011-07-01

The final product of analytical laboratories performing US FDA-regulated (or GLP) method validation and bioanalysis studies is the final report. Although there are commercial-off-the-shelf (COTS) software/instrument systems available to laboratory managers to automate and manage almost every aspect of the instrumental and sample-handling processes of GLP studies, there are few software systems available to fully manage the GLP final report preparation process. This lack of appropriate COTS tools results in the implementation of rather Byzantine and manual processes to cobble together all the information needed to generate a GLP final report. The manual nature of these processes results in the need for several iterative quality control and quality assurance events to ensure data accuracy and report formatting. The industry is in need of a COTS solution that gives laboratory managers and study directors the ability to manage as many portions as possible of the GLP final report writing process and the ability to generate a GLP final report with the click of a button. This article describes the COTS software features needed to give laboratory managers and study directors such a solution.

Validation of software for calculating the likelihood ratio for parentage and kinship.

PubMed

Drábek, J

2009-03-01

Although the likelihood ratio is a well-known statistical technique, commercial off-the-shelf (COTS) software products for its calculation are not sufficiently validated to suit general requirements for the competence of testing and calibration laboratories (EN/ISO/IEC 17025:2005 norm) per se. The software in question can be considered critical as it directly weighs the forensic evidence allowing judges to decide on guilt or innocence or to identify person or kin (i.e.: in mass fatalities). For these reasons, accredited laboratories shall validate likelihood ratio software in accordance with the above norm. To validate software for calculating the likelihood ratio in parentage/kinship scenarios I assessed available vendors, chose two programs (Paternity Index and familias) for testing, and finally validated them using tests derived from elaboration of the available guidelines for the field of forensics, biomedicine, and software engineering. MS Excel calculation using known likelihood ratio formulas or peer-reviewed results of difficult paternity cases were used as a reference. Using seven testing cases, it was found that both programs satisfied the requirements for basic paternity cases. However, only a combination of two software programs fulfills the criteria needed for our purpose in the whole spectrum of functions under validation with the exceptions of providing algebraic formulas in cases of mutation and/or silent allele.

An open source automatic quality assurance (OSAQA) tool for the ACR MRI phantom.

PubMed

Sun, Jidi; Barnes, Michael; Dowling, Jason; Menk, Fred; Stanwell, Peter; Greer, Peter B

2015-03-01

Routine quality assurance (QA) is necessary and essential to ensure MR scanner performance. This includes geometric distortion, slice positioning and thickness accuracy, high contrast spatial resolution, intensity uniformity, ghosting artefact and low contrast object detectability. However, this manual process can be very time consuming. This paper describes the development and validation of an open source tool to automate the MR QA process, which aims to increase physicist efficiency, and improve the consistency of QA results by reducing human error. The OSAQA software was developed in Matlab and the source code is available for download from http://jidisun.wix.com/osaqa-project/. During program execution QA results are logged for immediate review and are also exported to a spreadsheet for long-term machine performance reporting. For the automatic contrast QA test, a user specific contrast evaluation was designed to improve accuracy for individuals on different display monitors. American College of Radiology QA images were acquired over a period of 2 months to compare manual QA and the results from the proposed OSAQA software. OSAQA was found to significantly reduce the QA time from approximately 45 to 2 min. Both the manual and OSAQA results were found to agree with regard to the recommended criteria and the differences were insignificant compared to the criteria. The intensity homogeneity filter is necessary to obtain an image with acceptable quality and at the same time keeps the high contrast spatial resolution within the recommended criterion. The OSAQA tool has been validated on scanners with different field strengths and manufacturers. A number of suggestions have been made to improve both the phantom design and QA protocol in the future.

Using SysML for verification and validation planning on the Large Synoptic Survey Telescope (LSST)

NASA Astrophysics Data System (ADS)

Selvy, Brian M.; Claver, Charles; Angeli, George

2014-08-01

This paper provides an overview of the tool, language, and methodology used for Verification and Validation Planning on the Large Synoptic Survey Telescope (LSST) Project. LSST has implemented a Model Based Systems Engineering (MBSE) approach as a means of defining all systems engineering planning and definition activities that have historically been captured in paper documents. Specifically, LSST has adopted the Systems Modeling Language (SysML) standard and is utilizing a software tool called Enterprise Architect, developed by Sparx Systems. Much of the historical use of SysML has focused on the early phases of the project life cycle. Our approach is to extend the advantages of MBSE into later stages of the construction project. This paper details the methodology employed to use the tool to document the verification planning phases, including the extension of the language to accommodate the project's needs. The process includes defining the Verification Plan for each requirement, which in turn consists of a Verification Requirement, Success Criteria, Verification Method(s), Verification Level, and Verification Owner. Each Verification Method for each Requirement is defined as a Verification Activity and mapped into Verification Events, which are collections of activities that can be executed concurrently in an efficient and complementary way. Verification Event dependency and sequences are modeled using Activity Diagrams. The methodology employed also ties in to the Project Management Control System (PMCS), which utilizes Primavera P6 software, mapping each Verification Activity as a step in a planned activity. This approach leads to full traceability from initial Requirement to scheduled, costed, and resource loaded PMCS task-based activities, ensuring all requirements will be verified.

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

PubMed Central

Stephens, Zachary D.; Hudson, Matthew E.; Mainzer, Liudmila S.; Taschuk, Morgan; Weber, Matthew R.; Iyer, Ravishankar K.

2016-01-01

An obstacle to validating and benchmarking methods for genome analysis is that there are few reference datasets available for which the “ground truth” about the mutational landscape of the sample genome is known and fully validated. Additionally, the free and public availability of real human genome datasets is incompatible with the preservation of donor privacy. In order to better analyze and understand genomic data, we need test datasets that model all variants, reflecting known biology as well as sequencing artifacts. Read simulators can fulfill this requirement, but are often criticized for limited resemblance to true data and overall inflexibility. We present NEAT (NExt-generation sequencing Analysis Toolkit), a set of tools that not only includes an easy-to-use read simulator, but also scripts to facilitate variant comparison and tool evaluation. NEAT has a wide variety of tunable parameters which can be set manually on the default model or parameterized using real datasets. The software is freely available at github.com/zstephens/neat-genreads. PMID:27893777

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.

PubMed

Pauthenier, Cyrille; Faulon, Jean-Loup

2014-07-01

PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as for DNA libraries creation of DNA shuffling experiments and to have the simplest interface possible. It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools. We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters. All primer pairs efficiently amplified their target without any optimization of the PCR conditions. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hyper-X Stage Separation Trajectory Validation Studies

NASA Technical Reports Server (NTRS)

Tartabini, Paul V.; Bose, David M.; McMinn, John D.; Martin, John G.; Strovers, Brian K.

2003-01-01

An independent twelve degree-of-freedom simulation of the X-43A separation trajectory was created with the Program to Optimize Simulated trajectories (POST II). This simulation modeled the multi-body dynamics of the X-43A and its booster and included the effect of two pyrotechnically actuated pistons used to push the vehicles apart as well as aerodynamic interaction forces and moments between the two vehicles. The simulation was developed to validate trajectory studies conducted with a 14 degree-of-freedom simulation created early in the program using the Automatic Dynamic Analysis of Mechanics Systems (ADAMS) simulation software. The POST simulation was less detailed than the official ADAMS-based simulation used by the Project, but was simpler, more concise and ran faster, while providing similar results. The increase in speed provided by the POST simulation provided the Project with an alternate analysis tool. This tool was ideal for performing separation control logic trade studies that required the running of numerous Monte Carlo trajectories.

Development of an Unstructured, Three-Dimensional Material Response Design Tool

NASA Technical Reports Server (NTRS)

Schulz, Joseph; Stern, Eric; Palmer, Grant; Muppidi, Suman; Schroeder, Olivia

2017-01-01

A preliminary verification and validation of a new material response model is presented. This model, Icarus, is intended to serve as a design tool for the thermal protection systems of re-entry vehicles. Currently, the capability of the model is limited to simulating the pyrolysis of a material as a result of the radiative and convective surface heating imposed on the material from the surrounding high enthalpy gas. Since the major focus behind the development of Icarus has been model extensibility, the hope is that additional physics can be quickly added. The extensibility is critical since thermal protection systems are becoming increasing complex, e.g. woven carbon polymers. Additionally, as a three-dimensional, unstructured, finite-volume model, Icarus is capable of modeling complex geometries as well as multi-dimensional physics, which have been shown to be important in some scenarios and are not captured by one-dimensional models. In this paper, the mathematical and numerical formulation is presented followed by a discussion of the software architecture and some preliminary verification and validation studies.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

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

Software management tools: Lessons learned from use

NASA Technical Reports Server (NTRS)

Reifer, D. J.; Valett, J.; Knight, J.; Wenneson, G.

1985-01-01

Experience in inserting software project planning tools into more than 100 projects producing mission critical software are discussed. The problems the software project manager faces are listed along with methods and tools available to handle them. Experience is reported with the Project Manager's Workstation (PMW) and the SoftCost-R cost estimating package. Finally, the results of a survey, which looked at what could be done in the future to overcome the problems experienced and build a set of truly useful tools, are presented.

Parameter Estimation of the Thermal Network Model of a Machine Tool Spindle by Self-made Bluetooth Temperature Sensor Module

PubMed Central

Lo, Yuan-Chieh; Hu, Yuh-Chung; Chang, Pei-Zen

2018-01-01

Thermal characteristic analysis is essential for machine tool spindles because sudden failures may occur due to unexpected thermal issue. This article presents a lumped-parameter Thermal Network Model (TNM) and its parameter estimation scheme, including hardware and software, in order to characterize both the steady-state and transient thermal behavior of machine tool spindles. For the hardware, the authors develop a Bluetooth Temperature Sensor Module (BTSM) which accompanying with three types of temperature-sensing probes (magnetic, screw, and probe). Its specification, through experimental test, achieves to the precision ±(0.1 + 0.0029|t|) °C, resolution 0.00489 °C, power consumption 7 mW, and size Ø40 mm × 27 mm. For the software, the heat transfer characteristics of the machine tool spindle correlative to rotating speed are derived based on the theory of heat transfer and empirical formula. The predictive TNM of spindles was developed by grey-box estimation and experimental results. Even under such complicated operating conditions as various speeds and different initial conditions, the experiments validate that the present modeling methodology provides a robust and reliable tool for the temperature prediction with normalized mean square error of 99.5% agreement, and the present approach is transferable to the other spindles with a similar structure. For realizing the edge computing in smart manufacturing, a reduced-order TNM is constructed by Model Order Reduction (MOR) technique and implemented into the real-time embedded system. PMID:29473877

Parameter Estimation of the Thermal Network Model of a Machine Tool Spindle by Self-made Bluetooth Temperature Sensor Module.

PubMed

Lo, Yuan-Chieh; Hu, Yuh-Chung; Chang, Pei-Zen

2018-02-23

Thermal characteristic analysis is essential for machine tool spindles because sudden failures may occur due to unexpected thermal issue. This article presents a lumped-parameter Thermal Network Model (TNM) and its parameter estimation scheme, including hardware and software, in order to characterize both the steady-state and transient thermal behavior of machine tool spindles. For the hardware, the authors develop a Bluetooth Temperature Sensor Module (BTSM) which accompanying with three types of temperature-sensing probes (magnetic, screw, and probe). Its specification, through experimental test, achieves to the precision ±(0.1 + 0.0029|t|) °C, resolution 0.00489 °C, power consumption 7 mW, and size Ø40 mm × 27 mm. For the software, the heat transfer characteristics of the machine tool spindle correlative to rotating speed are derived based on the theory of heat transfer and empirical formula. The predictive TNM of spindles was developed by grey-box estimation and experimental results. Even under such complicated operating conditions as various speeds and different initial conditions, the experiments validate that the present modeling methodology provides a robust and reliable tool for the temperature prediction with normalized mean square error of 99.5% agreement, and the present approach is transferable to the other spindles with a similar structure. For realizing the edge computing in smart manufacturing, a reduced-order TNM is constructed by Model Order Reduction (MOR) technique and implemented into the real-time embedded system.

DigBody®: A new 3D modeling tool for nasal virtual surgery.

PubMed

Burgos, M A; Sanmiguel-Rojas, E; Singh, Narinder; Esteban-Ortega, F

2018-07-01

Recent studies have demonstrated that a significant number of surgical procedures for nasal airway obstruction (NAO) have a high rate of surgical failure. In part, this problem is due to the lack of reliable objective clinical parameters to aid surgeons during preoperative planning. Modeling tools that allow virtual surgery to be performed do exist, but all require direct manipulation of computed tomography (CT) or magnetic resonance imaging (MRI) data. Specialists in Rhinology have criticized these tools for their complex user interface, and have requested more intuitive, user-friendly and powerful software to make virtual surgery more accessible and realistic. In this paper we present a new virtual surgery software tool, DigBody ® . This new surgery module is integrated into the computational fluid dynamics (CFD) program MeComLand ® , which was developed exclusively to analyze nasal airflow. DigBody ® works directly with a 3D nasal model that mimics real surgery. Furthermore, this surgery module permits direct assessment of the operated cavity following virtual surgery by CFD simulation. The effectiveness of DigBody ® has been demonstrated by real surgery on two patients based on prior virtual operation results. Both subjects experienced excellent surgical outcomes with no residual nasal obstruction. This tool has great potential to aid surgeons in modeling potential surgical maneuvers, minimizing complications, and being confident that patients will receive optimal postoperative outcomes, validated by personalized CFD testing. Copyright © 2018 Elsevier Ltd. All rights reserved.

Validation of high throughput sequencing and microbial forensics applications

PubMed Central

2014-01-01

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security. PMID:25101166

Validation of high throughput sequencing and microbial forensics applications.

PubMed

Budowle, Bruce; Connell, Nancy D; Bielecka-Oder, Anna; Colwell, Rita R; Corbett, Cindi R; Fletcher, Jacqueline; Forsman, Mats; Kadavy, Dana R; Markotic, Alemka; Morse, Stephen A; Murch, Randall S; Sajantila, Antti; Schmedes, Sarah E; Ternus, Krista L; Turner, Stephen D; Minot, Samuel

2014-01-01

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

Quadratic Blind Linear Unmixing: A Graphical User Interface for Tissue Characterization

PubMed Central

Gutierrez-Navarro, O.; Campos-Delgado, D.U.; Arce-Santana, E. R.; Jo, Javier A.

2016-01-01

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition. PMID:26589467

Quadratic blind linear unmixing: A graphical user interface for tissue characterization.

PubMed

Gutierrez-Navarro, O; Campos-Delgado, D U; Arce-Santana, E R; Jo, Javier A

2016-02-01

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Comparisons of Kinematics and Dynamics Simulation Software Tools

NASA Technical Reports Server (NTRS)

Shiue, Yeu-Sheng Paul

2002-01-01

Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

MFV-class: a multi-faceted visualization tool of object classes.

PubMed

Zhang, Zhi-meng; Pan, Yun-he; Zhuang, Yue-ting

2004-11-01

Classes are key software components in an object-oriented software system. In many industrial OO software systems, there are some classes that have complicated structure and relationships. So in the processes of software maintenance, testing, software reengineering, software reuse and software restructure, it is a challenge for software engineers to understand these classes thoroughly. This paper proposes a class comprehension model based on constructivist learning theory, and implements a software visualization tool (MFV-Class) to help in the comprehension of a class. The tool provides multiple views of class to uncover manifold facets of class contents. It enables visualizing three object-oriented metrics of classes to help users focus on the understanding process. A case study was conducted to evaluate our approach and the toolkit.

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.

Inventory on the dietary assessment tools available and needed in africa: a prerequisite for setting up a common methodological research infrastructure for nutritional surveillance, research, and prevention of diet-related non-communicable diseases.

PubMed

Pisa, Pedro T; Landais, Edwige; Margetts, Barrie; Vorster, Hester H; Friedenreich, Christine M; Huybrechts, Inge; Martin-Prevel, Yves; Branca, Francesco; Lee, Warren T K; Leclercq, Catherine; Jerling, Johann; Zotor, Francis; Amuna, Paul; Al Jawaldeh, Ayoub; Aderibigbe, Olaide Ruth; Amoussa, Waliou Hounkpatin; Anderson, Cheryl A M; Aounallah-Skhiri, Hajer; Atek, Madjid; Benhura, Chakare; Chifamba, Jephat; Covic, Namukolo; Dary, Omar; Delisle, Hélène; El Ati, Jalila; El Hamdouchi, Asmaa; El Rhazi, Karima; Faber, Mieke; Kalimbira, Alexander; Korkalo, Liisa; Kruger, Annamarie; Ledo, James; Machiweni, Tatenda; Mahachi, Carol; Mathe, Nonsikelelo; Mokori, Alex; Mouquet-Rivier, Claire; Mutie, Catherine; Nashandi, Hilde Liisa; Norris, Shane A; Onabanjo, Oluseye Olusegun; Rambeloson, Zo; Saha, Foudjo Brice U; Ubaoji, Kingsley Ikechukwu; Zaghloul, Sahar; Slimani, Nadia

2018-01-02

To carry out an inventory on the availability, challenges, and needs of dietary assessment (DA) methods in Africa as a pre-requisite to provide evidence, and set directions (strategies) for implementing common dietary methods and support web-research infrastructure across countries. The inventory was performed within the framework of the "Africa's Study on Physical Activity and Dietary Assessment Methods" (AS-PADAM) project. It involves international institutional and African networks. An inventory questionnaire was developed and disseminated through the networks. Eighteen countries responded to the dietary inventory questionnaire. Various DA tools were reported in Africa; 24-Hour Dietary Recall and Food Frequency Questionnaire were the most commonly used tools. Few tools were validated and tested for reliability. Face-to-face interview was the common method of administration. No computerized software or other new (web) technologies were reported. No tools were standardized across countries. The lack of comparable DA methods across represented countries is a major obstacle to implement comprehensive and joint nutrition-related programmes for surveillance, programme evaluation, research, and prevention. There is a need to develop new or adapt existing DA methods across countries by employing related research infrastructure that has been validated and standardized in other settings, with the view to standardizing methods for wider use.

Open environments to support systems engineering tool integration: A study using the Portable Common Tool Environment (PCTE)

NASA Technical Reports Server (NTRS)

Eckhardt, Dave E., Jr.; Jipping, Michael J.; Wild, Chris J.; Zeil, Steven J.; Roberts, Cathy C.

1993-01-01

A study of computer engineering tool integration using the Portable Common Tool Environment (PCTE) Public Interface Standard is presented. Over a 10-week time frame, three existing software products were encapsulated to work in the Emeraude environment, an implementation of the PCTE version 1.5 standard. The software products used were a computer-aided software engineering (CASE) design tool, a software reuse tool, and a computer architecture design and analysis tool. The tool set was then demonstrated to work in a coordinated design process in the Emeraude environment. The project and the features of PCTE used are described, experience with the use of Emeraude environment over the project time frame is summarized, and several related areas for future research are summarized.

Advanced Information Processing System (AIPS)-based fault tolerant avionics architecture for launch vehicles

NASA Technical Reports Server (NTRS)

Lala, Jaynarayan H.; Harper, Richard E.; Jaskowiak, Kenneth R.; Rosch, Gene; Alger, Linda S.; Schor, Andrei L.

1990-01-01

An avionics architecture for the advanced launch system (ALS) that uses validated hardware and software building blocks developed under the advanced information processing system program is presented. The AIPS for ALS architecture defined is preliminary, and reliability requirements can be met by the AIPS hardware and software building blocks that are built using the state-of-the-art technology available in the 1992-93 time frame. The level of detail in the architecture definition reflects the level of detail available in the ALS requirements. As the avionics requirements are refined, the architecture can also be refined and defined in greater detail with the help of analysis and simulation tools. A useful methodology is demonstrated for investigating the impact of the avionics suite to the recurring cost of the ALS. It is shown that allowing the vehicle to launch with selected detected failures can potentially reduce the recurring launch costs. A comparative analysis shows that validated fault-tolerant avionics built out of Class B parts can result in lower life-cycle-cost in comparison to simplex avionics built out of Class S parts or other redundant architectures.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M.; Le Novére, Nicolas; Myers, Chris J.; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Waltemath, Dagmar; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528569

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Hoops, Stefan; Keating, Sarah M.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528564

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

PubMed Central

Dinov, Ivo; Lozev, Kamen; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Zamanyan, Alen; Chakrapani, Shruthi; Van Horn, John; Parker, D. Stott; Magsipoc, Rico; Leung, Kelvin; Gutman, Boris; Woods, Roger; Toga, Arthur

2010-01-01

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu. PMID:20927408

WASP (Write a Scientific Paper) using Excel - 1: Data entry and validation.

PubMed

Grech, Victor

2018-02-01

Data collection for the purposes of analysis, after the planning and execution of a research study, commences with data input and validation. The process of data entry and analysis may appear daunting to the uninitiated, but as pointed out in the 1970s in a series of papers by British Medical Journal Deputy Editor TDV Swinscow, modern hardware and software (he was then referring to the availability of hand calculators) permits the performance of statistical testing outside a computer laboratory. In this day and age, modern software, such as the ubiquitous and almost universally familiar Microsoft Excel™ greatly facilitates this process. This first paper comprises the first of a collection of papers which will emulate Swinscow's series, in his own words, "addressed to readers who want to start at the beginning, not to those who are already skilled statisticians." These papers will have less focus on the actual arithmetic, and more emphasis on how to actually implement simple statistics, step by step, using Excel, thereby constituting the equivalent of Swinscow's papers in the personal computer age. Data entry can be facilitated by several underutilised features in Excel. This paper will explain Excel's little-known form function, data validation implementation at input stage, simple coding tips and data cleaning tools. Copyright © 2018 Elsevier B.V. All rights reserved.

A Computational Model for Predicting RNase H Domain of Retrovirus.

PubMed

Wu, Sijia; Zhang, Xinman; Han, Jiuqiang

2016-01-01

RNase H (RNH) is a pivotal domain in retrovirus to cleave the DNA-RNA hybrid for continuing retroviral replication. The crucial role indicates that RNH is a promising drug target for therapeutic intervention. However, annotated RNHs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. In this work, a computational RNH model was proposed to annotate new putative RNHs (np-RNHs) in the retroviruses. It basically predicts RNH domains through recognizing their start and end sites separately with SVM method. The classification accuracy rates are 100%, 99.01% and 97.52% respectively corresponding to jack-knife, 10-fold cross-validation and 5-fold cross-validation test. Subsequently, this model discovered 14,033 np-RNHs after scanning sequences without RNH annotations. All these predicted np-RNHs and annotated RNHs were employed to analyze the length, hydrophobicity and evolutionary relationship of RNH domains. They are all related to retroviral genera, which validates the classification of retroviruses to a certain degree. In the end, a software tool was designed for the application of our prediction model. The software together with datasets involved in this paper can be available for free download at https://sourceforge.net/projects/rhtool/files/?source=navbar.

ToxPredictor: a Toxicity Estimation Software Tool

EPA Science Inventory

The Computational Toxicology Team within the National Risk Management Research Laboratory has developed a software tool that will allow the user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be ac...

Dynamic visualization techniques for high consequence software

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

Pollock, G.M.

1998-02-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification. The prototype tool is described along with the requirements constraint language after a brief literature review is presented. Examples of howmore » the tool can be used are also presented. In conclusion, the most significant advantage of this tool is to provide a first step in evaluating specification completeness, and to provide a more productive method for program comprehension and debugging. The expected payoff is increased software surety confidence, increased program comprehension, and reduced development and debugging time.« less

48 CFR 252.227-7019 - Validation of asserted restrictions-Computer software.

Code of Federal Regulations, 2010 CFR

2010-10-01

... restrictions-Computer software. 252.227-7019 Section 252.227-7019 Federal Acquisition Regulations System...—Computer software. As prescribed in 227.7104(e)(3) or 227.7203-6(c), use the following clause: Validation of Asserted Restrictions—Computer Software (JUN 1995) (a) Definitions. (1) As used in this clause...

48 CFR 252.227-7019 - Validation of asserted restrictions-Computer software.

Code of Federal Regulations, 2011 CFR

2011-10-01

... restrictions-Computer software. 252.227-7019 Section 252.227-7019 Federal Acquisition Regulations System...—Computer software. As prescribed in 227.7104(e)(3) or 227.7203-6(c), use the following clause: Validation of Asserted Restrictions—Computer Software (SEP 2011) (a) Definitions. (1) As used in this clause...

48 CFR 252.227-7019 - Validation of asserted restrictions-Computer software.

Code of Federal Regulations, 2012 CFR

2012-10-01

... restrictions-Computer software. 252.227-7019 Section 252.227-7019 Federal Acquisition Regulations System...—Computer software. As prescribed in 227.7104(e)(3) or 227.7203-6(c), use the following clause: Validation of Asserted Restrictions—Computer Software (SEP 2011) (a) Definitions. (1) As used in this clause...

48 CFR 252.227-7019 - Validation of asserted restrictions-Computer software.

Code of Federal Regulations, 2014 CFR

2014-10-01

... restrictions-Computer software. 252.227-7019 Section 252.227-7019 Federal Acquisition Regulations System...—Computer software. As prescribed in 227.7104(e)(3) or 227.7203-6(c), use the following clause: Validation of Asserted Restrictions—Computer Software (SEP 2011) (a) Definitions. (1) As used in this clause...

48 CFR 252.227-7019 - Validation of asserted restrictions-Computer software.

Code of Federal Regulations, 2013 CFR

2013-10-01

... restrictions-Computer software. 252.227-7019 Section 252.227-7019 Federal Acquisition Regulations System...—Computer software. As prescribed in 227.7104(e)(3) or 227.7203-6(c), use the following clause: Validation of Asserted Restrictions—Computer Software (SEP 2011) (a) Definitions. (1) As used in this clause...

RotCFD Software Validation - Computational and Experimental Data Comparison

NASA Technical Reports Server (NTRS)

Fernandez, Ovidio Montalvo

2014-01-01

RotCFD is a software intended to ease the design of NextGen rotorcraft. Since RotCFD is a new software still in the development process, the results need to be validated to determine the software's accuracy. The purpose of the present document is to explain one of the approaches to accomplish that goal.

Test Analysis Tools to Ensure Higher Quality of On-Board Real Time Software for Space Applications

NASA Astrophysics Data System (ADS)

Boudillet, O.; Mescam, J.-C.; Dalemagne, D.

2008-08-01

EADS Astrium Space Transportation, in its Les Mureaux premises, is responsible for the French M51 nuclear deterrent missile onboard SW. There was also developed over 1 million of line of code, mostly in ADA, for the Automated Transfer Vehicle (ATV) onboard SW and the flight control SW of the ARIANE5 launcher which has put it into orbit. As part of the ATV SW, ASTRIUM ST has developed the first Category A SW ever qualified for a European space application. To ensure that all these embedded SW have been developed with the highest quality and reliability level, specific development tools have been designed to cover the steps of source code verification, automated validation test or complete target instruction coverage verification. Three of such dedicated tools are presented here.

SESAME: a software tool for the numerical dosimetric reconstruction of radiological accidents involving external sources and its application to the accident in Chile in December 2005.

PubMed

Huet, C; Lemosquet, A; Clairand, I; Rioual, J B; Franck, D; de Carlan, L; Aubineau-Lanièce, I; Bottollier-Depois, J F

2009-01-01

Estimating the dose distribution in a victim's body is a relevant indicator in assessing biological damage from exposure in the event of a radiological accident caused by an external source. This dose distribution can be assessed by physical dosimetric reconstruction methods. Physical dosimetric reconstruction can be achieved using experimental or numerical techniques. This article presents the laboratory-developed SESAME--Simulation of External Source Accident with MEdical images--tool specific to dosimetric reconstruction of radiological accidents through numerical simulations which combine voxel geometry and the radiation-material interaction MCNP(X) Monte Carlo computer code. The experimental validation of the tool using a photon field and its application to a radiological accident in Chile in December 2005 are also described.

Bringing your tools to CyVerse Discovery Environment using Docker

PubMed Central

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse’s Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse’s production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use. PMID:27803802

Bringing your tools to CyVerse Discovery Environment using Docker.

PubMed

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use.

A new optimization tool path planning for 3-axis end milling of free-form surfaces based on efficient machining intervals

NASA Astrophysics Data System (ADS)

Vu, Duy-Duc; Monies, Frédéric; Rubio, Walter

2018-05-01

A large number of studies, based on 3-axis end milling of free-form surfaces, seek to optimize tool path planning. Approaches try to optimize the machining time by reducing the total tool path length while respecting the criterion of the maximum scallop height. Theoretically, the tool path trajectories that remove the most material follow the directions in which the machined width is the largest. The free-form surface is often considered as a single machining area. Therefore, the optimization on the entire surface is limited. Indeed, it is difficult to define tool trajectories with optimal feed directions which generate largest machined widths. Another limiting point of previous approaches for effectively reduce machining time is the inadequate choice of the tool. Researchers use generally a spherical tool on the entire surface. However, the gains proposed by these different methods developed with these tools lead to relatively small time savings. Therefore, this study proposes a new method, using toroidal milling tools, for generating toolpaths in different regions on the machining surface. The surface is divided into several regions based on machining intervals. These intervals ensure that the effective radius of the tool, at each cutter-contact points on the surface, is always greater than the radius of the tool in an optimized feed direction. A parallel plane strategy is then used on the sub-surfaces with an optimal specific feed direction for each sub-surface. This method allows one to mill the entire surface with efficiency greater than with the use of a spherical tool. The proposed method is calculated and modeled using Maple software to find optimal regions and feed directions in each region. This new method is tested on a free-form surface. A comparison is made with a spherical cutter to show the significant gains obtained with a toroidal milling cutter. Comparisons with CAM software and experimental validations are also done. The results show the efficiency of the method.

Computer aided manual validation of mass spectrometry-based proteomic data.

PubMed

Curran, Timothy G; Bryson, Bryan D; Reigelhaupt, Michael; Johnson, Hannah; White, Forest M

2013-06-15

Advances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics. Copyright © 2013 Elsevier Inc. All rights reserved.

Full Life-Cycle Defect Management Assessment: Initial Inspection Data Collection Results and Research Questions for Further Study

NASA Technical Reports Server (NTRS)

Shull, Forrest; Feldmann, Raimund; Haingaertner, Ralf; Regardie, Myrna; Seaman, Carolyn

2007-01-01

It is often the case in software projects that when schedule and budget resources are limited, the Verification and Validation (V&V) activities suffer. Fewer V&V activities can be afforded and moreover, short-term challenges can result in V&V activities being scaled back or dropped altogether. As a result, too often the default solution is to save activities for improving software quality until too late in the life-cycle, relying on late-term code inspections followed by thorough testing activities to reduce defect counts to acceptable levels. As many project managers realize, however, this is a resource-intensive way of achieving the required quality for software. The Full Life-cycle Defect Management Assessment Initiative, funded by NASA s Office of Safety and Mission Assurance under the Software Assurance Research Program, aims to address these problems by: Improving the effectiveness of early life-cycle V&V activities to make their benefits more attractive to team leads. Specifically, we focus on software inspection, a proven method that can be applied to any software work product, long before executable code has been developed; Better communicating this effectiveness to software development teams, along with suggestions for parameters to improve in the future to increase effectiveness; Analyzing the impact of early life-cycle V&V on the effectiveness and cost required for late life-cycle V&V activities, such as testing, in order to make the tradeoffs more apparent. This white paper reports on an initial milestone in this work, the development of a preliminary model of inspection effectiveness across multiple NASA Centers. This model contributes toward reaching our project goals by: Allowing an examination of inspection parameters, across different types of projects and different work products, for an analysis of factors that impact defect detection effectiveness. Allowing a comparison of this NASA-specific model to existing recommendations in the literature regarding how to plan effective inspections. Forming a baseline model which can be extended to incorporate factors describing: the numbers and types of defects that are missed by inspections; how such defects flow downstream through software development phases; how effectively they can be caught by testing activities in the late stages of development. The model has been implemented in a prototype web-enabled decision-support tool which allows developers to enter their inspection data and receive feedback based on a comparison against the model. The tool also allows users to access reusable materials (such as checklists) from projects included in the baseline. Both the tool itself and the model underlying it will continue to be extended throughout the remainder of this initiative. As results of analyzing inspection effectiveness for defect containment are determined, they can be shared via the tool and also via updates to existing training courses on metrics and software inspections. Moreover, the tool will help satisfy key CMMI requirements for the NASA Centers, as it will enable NASA to take a global view across peer review results for various types of projects to identify systemic problems. This analysis can result in continuous improvements to the approach to verification.

Proceedings of the Ninth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1984-01-01

Experiences in measurement, utilization, and evaluation of software methodologies, models, and tools are discussed. NASA's involvement in ever larger and more complex systems, like the space station project, provides a motive for the support of software engineering research and the exchange of ideas in such forums. The topics of current SEL research are software error studies, experiments with software development, and software tools.

Software Management Environment (SME): Components and algorithms

NASA Technical Reports Server (NTRS)

Hendrick, Robert; Kistler, David; Valett, Jon

1994-01-01

This document presents the components and algorithms of the Software Management Environment (SME), a management tool developed for the Software Engineering Branch (Code 552) of the Flight Dynamics Division (FDD) of the Goddard Space Flight Center (GSFC). The SME provides an integrated set of visually oriented experienced-based tools that can assist software development managers in managing and planning software development projects. This document describes and illustrates the analysis functions that underlie the SME's project monitoring, estimation, and planning tools. 'SME Components and Algorithms' is a companion reference to 'SME Concepts and Architecture' and 'Software Engineering Laboratory (SEL) Relationships, Models, and Management Rules.'

Multiyear Plan for Validation of EnergyPlus Multi-Zone HVAC System Modeling using ORNL's Flexible Research Platform

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

Im, Piljae; Bhandari, Mahabir S.; New, Joshua Ryan

This document describes the Oak Ridge National Laboratory (ORNL) multiyear experimental plan for validation and uncertainty characterization of whole-building energy simulation for a multi-zone research facility using a traditional rooftop unit (RTU) as a baseline heating, ventilating, and air conditioning (HVAC) system. The project’s overarching objective is to increase the accuracy of energy simulation tools by enabling empirical validation of key inputs and algorithms. Doing so is required to inform the design of increasingly integrated building systems and to enable accountability for performance gaps between design and operation of a building. The project will produce documented data sets that canmore » be used to validate key functionality in different energy simulation tools and to identify errors and inadequate assumptions in simulation engines so that developers can correct them. ASHRAE Standard 140, Method of Test for the Evaluation of Building Energy Analysis Computer Programs (ASHRAE 2004), currently consists primarily of tests to compare different simulation programs with one another. This project will generate sets of measured data to enable empirical validation, incorporate these test data sets in an extended version of Standard 140, and apply these tests to the Department of Energy’s (DOE) EnergyPlus software (EnergyPlus 2016) to initiate the correction of any significant deficiencies. The fitness-for-purpose of the key algorithms in EnergyPlus will be established and demonstrated, and vendors of other simulation programs will be able to demonstrate the validity of their products. The data set will be equally applicable to validation of other simulation engines as well.« less

Analysis of total phenolic, flavonoids, anthocyanins and tannins content in Romanian red wines: prediction of antioxidant activities and classification of wines using artificial neural networks.

PubMed

Hosu, Anamaria; Cristea, Vasile-Mircea; Cimpoiu, Claudia

2014-05-01

Wine is one of the most consumed beverages over the world containing large quantities of polyphenolic compounds. These compounds are responsible for quality of red wines, influencing the antioxidant activity, astringency, bitterness and colour, their composition in wine being influenced by the varieties, the vintage and the wineries. The aim of the present work is to build software instruments intended to work as data-mining tools for predicting valuable properties of wine and for revealing different wine classes. The developed ANNs are able to reveal the relationships between the concentration of total phenolic, flavonoids, anthocyanins, and tannins content, associated to the antioxidant activity, and the wine distinctive classes determined by the wine variety, harvesting year or winery. The presented ANNs proved to be reliable software tools for assessment or validation of the wine essential characteristics and authenticity and may be further used to establish a database of analytical characteristics of wines. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Modular Repository-based Infrastructure for Simulation Model Storage and Execution Support in the Context of In Silico Oncology and In Silico Medicine.

PubMed

Christodoulou, Nikolaos A; Tousert, Nikolaos E; Georgiadi, Eleni Ch; Argyri, Katerina D; Misichroni, Fay D; Stamatakos, Georgios S

2016-01-01

The plethora of available disease prediction models and the ongoing process of their application into clinical practice - following their clinical validation - have created new needs regarding their efficient handling and exploitation. Consolidation of software implementations, descriptive information, and supportive tools in a single place, offering persistent storage as well as proper management of execution results, is a priority, especially with respect to the needs of large healthcare providers. At the same time, modelers should be able to access these storage facilities under special rights, in order to upgrade and maintain their work. In addition, the end users should be provided with all the necessary interfaces for model execution and effortless result retrieval. We therefore propose a software infrastructure, based on a tool, model and data repository that handles the storage of models and pertinent execution-related data, along with functionalities for execution management, communication with third-party applications, user-friendly interfaces to access and use the infrastructure with minimal effort and basic security features.

A Modular Repository-based Infrastructure for Simulation Model Storage and Execution Support in the Context of In Silico Oncology and In Silico Medicine

PubMed Central

Christodoulou, Nikolaos A.; Tousert, Nikolaos E.; Georgiadi, Eleni Ch.; Argyri, Katerina D.; Misichroni, Fay D.; Stamatakos, Georgios S.

2016-01-01

The plethora of available disease prediction models and the ongoing process of their application into clinical practice – following their clinical validation – have created new needs regarding their efficient handling and exploitation. Consolidation of software implementations, descriptive information, and supportive tools in a single place, offering persistent storage as well as proper management of execution results, is a priority, especially with respect to the needs of large healthcare providers. At the same time, modelers should be able to access these storage facilities under special rights, in order to upgrade and maintain their work. In addition, the end users should be provided with all the necessary interfaces for model execution and effortless result retrieval. We therefore propose a software infrastructure, based on a tool, model and data repository that handles the storage of models and pertinent execution-related data, along with functionalities for execution management, communication with third-party applications, user-friendly interfaces to access and use the infrastructure with minimal effort and basic security features. PMID:27812280

Formalizing procedures for operations automation, operator training and spacecraft autonomy

NASA Technical Reports Server (NTRS)

Lecouat, Francois; Desaintvincent, Arnaud

1994-01-01

The generation and validation of operations procedures is a key task of mission preparation that is quite complex and costly. This has motivated the development of software applications providing support for procedures preparation. Several applications have been developed at MATRA MARCONI SPACE (MMS) over the last five years. They are presented in the first section of this paper. The main idea is that if procedures are represented in a formal language, they can be managed more easily with a computer tool and some automatic verifications can be performed. One difficulty is to define a formal language that is easy to use for operators and operations engineers. From the experience of the various procedures management tools developed in the last five years (including the POM, EOA, and CSS projects), MMS has derived OPSMAKER, a generic tool for procedure elaboration and validation. It has been applied to quite different types of missions, ranging from crew procedures (PREVISE system), ground control centers management procedures (PROCSU system), and - most relevant to the present paper - satellite operation procedures (PROCSAT developed for CNES, to support the preparation and verification of SPOT 4 operation procedures, and OPSAT for MMS telecom satellites operation procedures).

Open source posturography.

PubMed

Rey-Martinez, Jorge; Pérez-Fernández, Nicolás

2016-12-01

The proposed validation goal of 0.9 in intra-class correlation coefficient was reached with the results of this study. With the obtained results we consider that the developed software (RombergLab) is a validated balance assessment software. The reliability of this software is dependent of the used force platform technical specifications. Develop and validate a posturography software and share its source code in open source terms. Prospective non-randomized validation study: 20 consecutive adults underwent two balance assessment tests, six condition posturography was performed using a clinical approved software and force platform and the same conditions were measured using the new developed open source software using a low cost force platform. Intra-class correlation index of the sway area obtained from the center of pressure variations in both devices for the six conditions was the main variable used for validation. Excellent concordance between RombergLab and clinical approved force platform was obtained (intra-class correlation coefficient =0.94). A Bland and Altman graphic concordance plot was also obtained. The source code used to develop RombergLab was published in open source terms.

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

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

Marzouk, Youssef; Conrad, Patrick; Bigoni, Daniele

QUEST (\\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a historymore » of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is the MIT Uncertainty Quantification library, called MUQ (\\url{muq.mit.edu}).« less

Closing the Certification Gaps in Adaptive Flight Control Software

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.

2008-01-01

Over the last five decades, extensive research has been performed to design and develop adaptive control systems for aerospace systems and other applications where the capability to change controller behavior at different operating conditions is highly desirable. Although adaptive flight control has been partially implemented through the use of gain-scheduled control, truly adaptive control systems using learning algorithms and on-line system identification methods have not seen commercial deployment. The reason is that the certification process for adaptive flight control software for use in national air space has not yet been decided. The purpose of this paper is to examine the gaps between the state-of-the-art methodologies used to certify conventional (i.e., non-adaptive) flight control system software and what will likely to be needed to satisfy FAA airworthiness requirements. These gaps include the lack of a certification plan or process guide, the need to develop verification and validation tools and methodologies to analyze adaptive controller stability and convergence, as well as the development of metrics to evaluate adaptive controller performance at off-nominal flight conditions. This paper presents the major certification gap areas, a description of the current state of the verification methodologies, and what further research efforts will likely be needed to close the gaps remaining in current certification practices. It is envisioned that closing the gap will require certain advances in simulation methods, comprehensive methods to determine learning algorithm stability and convergence rates, the development of performance metrics for adaptive controllers, the application of formal software assurance methods, the application of on-line software monitoring tools for adaptive controller health assessment, and the development of a certification case for adaptive system safety of flight.

An assessment of space shuttle flight software development processes

NASA Technical Reports Server (NTRS)

1993-01-01

In early 1991, the National Aeronautics and Space Administration's (NASA's) Office of Space Flight commissioned the Aeronautics and Space Engineering Board (ASEB) of the National Research Council (NRC) to investigate the adequacy of the current process by which NASA develops and verifies changes and updates to the Space Shuttle flight software. The Committee for Review of Oversight Mechanisms for Space Shuttle Flight Software Processes was convened in Jan. 1992 to accomplish the following tasks: (1) review the entire flight software development process from the initial requirements definition phase to final implementation, including object code build and final machine loading; (2) review and critique NASA's independent verification and validation process and mechanisms, including NASA's established software development and testing standards; (3) determine the acceptability and adequacy of the complete flight software development process, including the embedded validation and verification processes through comparison with (1) generally accepted industry practices, and (2) generally accepted Department of Defense and/or other government practices (comparing NASA's program with organizations and projects having similar volumes of software development, software maturity, complexity, criticality, lines of code, and national standards); (4) consider whether independent verification and validation should continue. An overview of the study, independent verification and validation of critical software, and the Space Shuttle flight software development process are addressed. Findings and recommendations are presented.

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

ERIC Educational Resources Information Center

Bantz, David A.; And Others

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

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

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

Assistive Software Tools for Secondary-Level Students with Literacy Difficulties

ERIC Educational Resources Information Center

Lange, Alissa A.; McPhillips, Martin; Mulhern, Gerry; Wylie, Judith

2006-01-01

The present study assessed the compensatory effectiveness of four assistive software tools (speech synthesis, spellchecker, homophone tool, and dictionary) on literacy. Secondary-level students (N = 93) with reading difficulties completed computer-based tests of literacy skills. Training on their respective software followed for those assigned to…