Lessons Learned from Application of System and Software Level RAMS Analysis to a Space Control System

NASA Astrophysics Data System (ADS)

Silva, N.; Esper, A.

2012-01-01

The work presented in this article represents the results of applying RAMS analysis to a critical space control system, both at system and software levels. The system level RAMS analysis allowed the assignment of criticalities to the high level components, which was further refined by a tailored software level RAMS analysis. The importance of the software level RAMS analysis in the identification of new failure modes and its impact on the system level RAMS analysis is discussed. Recommendations of changes in the software architecture have also been proposed in order to reduce the criticality of the SW components to an acceptable minimum. The dependability analysis was performed in accordance to ECSS-Q-ST-80, which had to be tailored and complemented in some aspects. This tailoring will also be detailed in the article and lessons learned from the application of this tailoring will be shared, stating the importance to space systems safety evaluations. The paper presents the applied techniques, the relevant results obtained, the effort required for performing the tasks and the planned strategy for ROI estimation, as well as the soft skills required and acquired during these activities.

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

ERIC Educational Resources Information Center

Li, Jian; Lomax, Richard G.

2011-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1982-01-01

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

ACES: Space shuttle flight software analysis expert system

NASA Technical Reports Server (NTRS)

Satterwhite, R. Scott

1990-01-01

The Analysis Criteria Evaluation System (ACES) is a knowledge based expert system that automates the final certification of the Space Shuttle onboard flight software. Guidance, navigation and control of the Space Shuttle through all its flight phases are accomplished by a complex onboard flight software system. This software is reconfigured for each flight to allow thousands of mission-specific parameters to be introduced and must therefore be thoroughly certified prior to each flight. This certification is performed in ground simulations by executing the software in the flight computers. Flight trajectories from liftoff to landing, including abort scenarios, are simulated and the results are stored for analysis. The current methodology of performing this analysis is repetitive and requires many man-hours. The ultimate goals of ACES are to capture the knowledge of the current experts and improve the quality and reduce the manpower required to certify the Space Shuttle onboard flight software.

A methodology for producing reliable software, volume 1

NASA Technical Reports Server (NTRS)

Stucki, L. G.; Moranda, P. B.; Foshee, G.; Kirchoff, M.; Omre, R.

1976-01-01

An investigation into the areas having an impact on producing reliable software including automated verification tools, software modeling, testing techniques, structured programming, and management techniques is presented. This final report contains the results of this investigation, analysis of each technique, and the definition of a methodology for producing reliable software.

Software Systems for Prediction and Immediate Assessment of Emergency Situations on Municipalities Territories

NASA Astrophysics Data System (ADS)

Poluyan, L. V.; Syutkina, E. V.; Guryev, E. S.

2017-11-01

The comparative analysis of key features of the software systems TOXI+Risk and ALOHA is presented. The authors made a comparison of domestic (TOXI+Risk) and foreign (ALOHA) software systems allowing to give the quantitative assessment of impact areas (pressure, thermal, toxic) in case of hypothetical emergencies in potentially hazardous objects of the oil, gas, chemical, petrochemical and oil-processing industry. Both software systems use different mathematical models for assessment of the release rate of a chemically hazardous substance from a storage tank and its evaporation. The comparison of the accuracy of definition of impact areas made by both software systems to verify the examples shows good convergence of both products. The analysis results showed that the ALOHA software can be actively used for forecasting and immediate assessment of emergency situations, assessment of damage as a result of emergencies on the territories of municipalities.

Validating the Effectiveness of Switching the Vancomycin TDM Analysis Software Based on the Predictive Accuracy.

PubMed

Imai, Shungo; Yamada, Takehiro; Ishiguro, Nobuhisa; Miyamoto, Takenori; Kagami, Keisuke; Tomiyama, Naoki; Niinuma, Yusuke; Nagasaki, Daisuke; Suzuki, Koji; Yamagami, Akira; Kasashi, Kumiko; Kobayashi, Masaki; Iseki, Ken

2017-01-01

Based on the predictive performance in our previous study, we switched the therapeutic drug monitoring (TDM) analysis software for dose setting of vancomycin (VCM) from "Vancomycin MEEK TDM analysis software Ver2.0" (MEEK) to "SHIONOGI-VCM-TDM ver.2009" (VCM-TDM) in January 2015. In the present study, our aim was to validate the effectiveness of the changing VCM TDM analysis software in initial dose setting of VCM. The enrolled patients were divided into two groups, each having 162 patients in total, who received VCM with the initial dose set using MEEK (MEEK group) or VCM-TDM (VCM-TDM group). We compared the rates of attaining the therapeutic range (trough value; 10-20 μg/mL) of serum VCM concentration between the groups. Multivariate logistic regression analysis was performed to confirm that changing the VCM TDM analysis software was an independent factor related to attaining the therapeutic range. Switching the VCM TDM analysis software from MEEK to VCM-TDM improved the rate of attaining the therapeutic range by 21.6% (MEEK group: 42.6% vs. VCM-TDM group: 64.2%, p<0.01). Patient age ≥65 years, concomitant medication (furosemide) and the TDM analysis software used VCM-TDM were considered to be independent factors for attaining the therapeutic range. These results demonstrated the effectiveness of switching the VCM TDM analysis software from MEEK to VCM-TDM for initial dose setting of VCM.

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

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

PubMed

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

2010-01-11

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

Dependability modeling and assessment in UML-based software development.

PubMed

Bernardi, Simona; Merseguer, José; Petriu, Dorina C

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results.

Dependability Modeling and Assessment in UML-Based Software Development

PubMed Central

Bernardi, Simona; Merseguer, José; Petriu, Dorina C.

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results. PMID:22988428

Software Reliability Analysis of NASA Space Flight Software: A Practical Experience

PubMed Central

Sukhwani, Harish; Alonso, Javier; Trivedi, Kishor S.; Mcginnis, Issac

2017-01-01

In this paper, we present the software reliability analysis of the flight software of a recently launched space mission. For our analysis, we use the defect reports collected during the flight software development. We find that this software was developed in multiple releases, each release spanning across all software life-cycle phases. We also find that the software releases were developed and tested for four different hardware platforms, spanning from off-the-shelf or emulation hardware to actual flight hardware. For releases that exhibit reliability growth or decay, we fit Software Reliability Growth Models (SRGM); otherwise we fit a distribution function. We find that most releases exhibit reliability growth, with Log-Logistic (NHPP) and S-Shaped (NHPP) as the best-fit SRGMs. For the releases that experience reliability decay, we investigate the causes for the same. We find that such releases were the first software releases to be tested on a new hardware platform, and hence they encountered major hardware integration issues. Also such releases seem to have been developed under time pressure in order to start testing on the new hardware platform sooner. Such releases exhibit poor reliability growth, and hence exhibit high predicted failure rate. Other problems include hardware specification changes and delivery delays from vendors. Thus, our analysis provides critical insights and inputs to the management to improve the software development process. As NASA has moved towards a product line engineering for its flight software development, software for future space missions will be developed in a similar manner and hence the analysis results for this mission can be considered as a baseline for future flight software missions. PMID:29278255

Software Reliability Analysis of NASA Space Flight Software: A Practical Experience.

PubMed

Sukhwani, Harish; Alonso, Javier; Trivedi, Kishor S; Mcginnis, Issac

2016-01-01

In this paper, we present the software reliability analysis of the flight software of a recently launched space mission. For our analysis, we use the defect reports collected during the flight software development. We find that this software was developed in multiple releases, each release spanning across all software life-cycle phases. We also find that the software releases were developed and tested for four different hardware platforms, spanning from off-the-shelf or emulation hardware to actual flight hardware. For releases that exhibit reliability growth or decay, we fit Software Reliability Growth Models (SRGM); otherwise we fit a distribution function. We find that most releases exhibit reliability growth, with Log-Logistic (NHPP) and S-Shaped (NHPP) as the best-fit SRGMs. For the releases that experience reliability decay, we investigate the causes for the same. We find that such releases were the first software releases to be tested on a new hardware platform, and hence they encountered major hardware integration issues. Also such releases seem to have been developed under time pressure in order to start testing on the new hardware platform sooner. Such releases exhibit poor reliability growth, and hence exhibit high predicted failure rate. Other problems include hardware specification changes and delivery delays from vendors. Thus, our analysis provides critical insights and inputs to the management to improve the software development process. As NASA has moved towards a product line engineering for its flight software development, software for future space missions will be developed in a similar manner and hence the analysis results for this mission can be considered as a baseline for future flight software missions.

Performance of Different Analytical Software Packages in Quantification of DNA Methylation by Pyrosequencing.

PubMed

Grasso, Chiara; Trevisan, Morena; Fiano, Valentina; Tarallo, Valentina; De Marco, Laura; Sacerdote, Carlotta; Richiardi, Lorenzo; Merletti, Franco; Gillio-Tos, Anna

2016-01-01

Pyrosequencing has emerged as an alternative method of nucleic acid sequencing, well suited for many applications which aim to characterize single nucleotide polymorphisms, mutations, microbial types and CpG methylation in the target DNA. The commercially available pyrosequencing systems can harbor two different types of software which allow analysis in AQ or CpG mode, respectively, both widely employed for DNA methylation analysis. Aim of the study was to assess the performance for DNA methylation analysis at CpG sites of the two pyrosequencing software which allow analysis in AQ or CpG mode, respectively. Despite CpG mode having been specifically generated for CpG methylation quantification, many investigations on this topic have been carried out with AQ mode. As proof of equivalent performance of the two software for this type of analysis is not available, the focus of this paper was to evaluate if the two modes currently used for CpG methylation assessment by pyrosequencing may give overlapping results. We compared the performance of the two software in quantifying DNA methylation in the promoter of selected genes (GSTP1, MGMT, LINE-1) by testing two case series which include DNA from paraffin embedded prostate cancer tissues (PC study, N = 36) and DNA from blood fractions of healthy people (DD study, N = 28), respectively. We found discrepancy in the two pyrosequencing software-based quality assignment of DNA methylation assays. Compared to the software for analysis in the AQ mode, less permissive criteria are supported by the Pyro Q-CpG software, which enables analysis in CpG mode. CpG mode warns the operators about potential unsatisfactory performance of the assay and ensures a more accurate quantitative evaluation of DNA methylation at CpG sites. The implementation of CpG mode is strongly advisable in order to improve the reliability of the methylation analysis results achievable by pyrosequencing.

Software Technology for Adaptable, Reliable Systems (STARS). Software Architecture Seminar Report: Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1994-01-29

other processes, but that he arrived at his results in a different manner. Batory didn’t start with idioms; he performed a domain analysis and...abstracted idioms. Through domain analysis and domain modeling, new idioms can be found and the form of architecture can be the same. It was also questioned...Programming 5. Consensus Definition of Architecture 6. Inductive Analysis of Current Exemplars 7. VHDL (Bailor) 8. Ontological Structuring 3.3.3

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

PubMed Central

2011-01-01

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

Design and implementation of software for automated quality control and data analysis for a complex LC/MS/MS assay for urine opiates and metabolites.

PubMed

Dickerson, Jane A; Schmeling, Michael; Hoofnagle, Andrew N; Hoffman, Noah G

2013-01-16

Mass spectrometry provides a powerful platform for performing quantitative, multiplexed assays in the clinical laboratory, but at the cost of increased complexity of analysis and quality assurance calculations compared to other methodologies. Here we describe the design and implementation of a software application that performs quality control calculations for a complex, multiplexed, mass spectrometric analysis of opioids and opioid metabolites. The development and implementation of this application improved our data analysis and quality assurance processes in several ways. First, use of the software significantly improved the procedural consistency for performing quality control calculations. Second, it reduced the amount of time technologists spent preparing and reviewing the data, saving on average over four hours per run, and in some cases improving turnaround time by a day. Third, it provides a mechanism for coupling procedural and software changes with the results of each analysis. We describe several key details of the implementation including the use of version control software and automated unit tests. These generally useful software engineering principles should be considered for any software development project in the clinical lab. Copyright © 2012 Elsevier B.V. All rights reserved.

Structural Analysis Using NX Nastran 9.0

NASA Technical Reports Server (NTRS)

Rolewicz, Benjamin M.

2014-01-01

NX Nastran is a powerful Finite Element Analysis (FEA) software package used to solve linear and non-linear models for structural and thermal systems. The software, which consists of both a solver and user interface, breaks down analysis into four files, each of which are important to the end results of the analysis. The software offers capabilities for a variety of types of analysis, and also contains a respectable modeling program. Over the course of ten weeks, I was trained to effectively implement NX Nastran into structural analysis and refinement for parts of two missions at NASA's Kennedy Space Center, the Restore mission and the Orion mission.

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

Mining dynamic noteworthy functions in software execution sequences.

PubMed

Zhang, Bing; Huang, Guoyan; Wang, Yuqian; He, Haitao; Ren, Jiadong

2017-01-01

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely.

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

Teaching meta-analysis using MetaLight.

PubMed

Thomas, James; Graziosi, Sergio; Higgins, Steve; Coe, Robert; Torgerson, Carole; Newman, Mark

2012-10-18

Meta-analysis is a statistical method for combining the results of primary studies. It is often used in systematic reviews and is increasingly a method and topic that appears in student dissertations. MetaLight is a freely available software application that runs simple meta-analyses and contains specific functionality to facilitate the teaching and learning of meta-analysis. While there are many courses and resources for meta-analysis available and numerous software applications to run meta-analyses, there are few pieces of software which are aimed specifically at helping those teaching and learning meta-analysis. Valuable teaching time can be spent learning the mechanics of a new software application, rather than on the principles and practices of meta-analysis. We discuss ways in which the MetaLight tool can be used to present some of the main issues involved in undertaking and interpreting a meta-analysis. While there are many software tools available for conducting meta-analysis, in the context of a teaching programme such software can require expenditure both in terms of money and in terms of the time it takes to learn how to use it. MetaLight was developed specifically as a tool to facilitate the teaching and learning of meta-analysis and we have presented here some of the ways it might be used in a training situation.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.; Olariu, Stephen

1995-01-01

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

Development of new vibration energy flow analysis software and its applications to vehicle systems

NASA Astrophysics Data System (ADS)

Kim, D.-J.; Hong, S.-Y.; Park, Y.-H.

2005-09-01

The Energy flow analysis (EFA) offers very promising results in predicting the noise and vibration responses of system structures in medium-to-high frequency ranges. We have developed the Energy flow finite element method (EFFEM) based software, EFADSC++ R4, for the vibration analysis. The software can analyze the system structures composed of beam, plate, spring-damper, rigid body elements and many other components developed, and has many useful functions in analysis. For convenient use of the software, the main functions of the whole software are modularized into translator, model-converter, and solver. The translator module makes it possible to use finite element (FE) model for the vibration analysis. The model-converter module changes FE model into energy flow finite element (EFFE) model, and generates joint elements to cover the vibrational attenuation in the complex structures composed of various elements and can solve the joint element equations by using the wave tra! nsmission approach very quickly. The solver module supports the various direct and iterative solvers for multi-DOF structures. The predictions of vibration for real vehicles by using the developed software were performed successfully.

Influence analysis of Github repositories.

PubMed

Hu, Yan; Zhang, Jun; Bai, Xiaomei; Yu, Shuo; Yang, Zhuo

2016-01-01

With the support of cloud computing techniques, social coding platforms have changed the style of software development. Github is now the most popular social coding platform and project hosting service. Software developers of various levels keep entering Github, and use Github to save their public and private software projects. The large amounts of software developers and software repositories on Github are posing new challenges to the world of software engineering. This paper tries to tackle one of the important problems: analyzing the importance and influence of Github repositories. We proposed a HITS based influence analysis on graphs that represent the star relationship between Github users and repositories. A weighted version of HITS is applied to the overall star graph, and generates a different set of top influential repositories other than the results from standard version of HITS algorithm. We also conduct the influential analysis on per-month star graph, and study the monthly influence ranking of top repositories.

A Visual Basic simulation software tool for performance analysis of a membrane-based advanced water treatment plant.

PubMed

Pal, P; Kumar, R; Srivastava, N; Chaudhuri, J

2014-02-01

A Visual Basic simulation software (WATTPPA) has been developed to analyse the performance of an advanced wastewater treatment plant. This user-friendly and menu-driven software is based on the dynamic mathematical model for an industrial wastewater treatment scheme that integrates chemical, biological and membrane-based unit operations. The software-predicted results corroborate very well with the experimental findings as indicated in the overall correlation coefficient of the order of 0.99. The software permits pre-analysis and manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. It allows quick performance analysis of the whole system as well as the individual units. 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 hazardous wastewater.

Software forecasting as it is really done: A study of JPL software engineers

NASA Technical Reports Server (NTRS)

Griesel, Martha Ann; Hihn, Jairus M.; Bruno, Kristin J.; Fouser, Thomas J.; Tausworthe, Robert C.

1993-01-01

This paper presents a summary of the results to date of a Jet Propulsion Laboratory internally funded research task to study the costing process and parameters used by internally recognized software cost estimating experts. Protocol Analysis and Markov process modeling were used to capture software engineer's forecasting mental models. While there is significant variation between the mental models that were studied, it was nevertheless possible to identify a core set of cost forecasting activities, and it was also found that the mental models cluster around three forecasting techniques. Further partitioning of the mental models revealed clustering of activities, that is very suggestive of a forecasting lifecycle. The different forecasting methods identified were based on the use of multiple-decomposition steps or multiple forecasting steps. The multiple forecasting steps involved either forecasting software size or an additional effort forecast. Virtually no subject used risk reduction steps in combination. The results of the analysis include: the identification of a core set of well defined costing activities, a proposed software forecasting life cycle, and the identification of several basic software forecasting mental models. The paper concludes with a discussion of the implications of the results for current individual and institutional practices.

New Results in Software Model Checking and Analysis

NASA Technical Reports Server (NTRS)

Pasareanu, Corina S.

2010-01-01

This introductory article surveys new techniques, supported by automated tools, for the analysis of software to ensure reliability and safety. Special focus is on model checking techniques. The article also introduces the five papers that are enclosed in this special journal volume.

ZOOM Lite: next-generation sequencing data mapping and visualization software

PubMed Central

Zhang, Zefeng; Lin, Hao; Ma, Bin

2010-01-01

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/. PMID:20530531

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.

The Evolution of Software Publication in Astronomy

NASA Astrophysics Data System (ADS)

Cantiello, Matteo

2018-01-01

Software is a fundamental component of the scientific research process. As astronomical discoveries increasingly rely on complex numerical calculations and the analysis of big data sets, publishing and documenting software is a fundamental step in ensuring transparency and reproducibility of results. I will briefly discuss the recent history of software publication and highlight the challenges and opportunities ahead.

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

PubMed

Shaikh, Masood Ali

2017-09-01

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

Experience report: Using formal methods for requirements analysis of critical spacecraft software

NASA Technical Reports Server (NTRS)

Lutz, Robyn R.; Ampo, Yoko

1994-01-01

Formal specification and analysis of requirements continues to gain support as a method for producing more reliable software. However, the introduction of formal methods to a large software project is difficult, due in part to the unfamiliarity of the specification languages and the lack of graphics. This paper reports results of an investigation into the effectiveness of formal methods as an aid to the requirements analysis of critical, system-level fault-protection software on a spacecraft currently under development. Our experience indicates that formal specification and analysis can enhance the accuracy of the requirements and add assurance prior to design development in this domain. The work described here is part of a larger, NASA-funded research project whose purpose is to use formal-methods techniques to improve the quality of software in space applications. The demonstration project described here is part of the effort to evaluate experimentally the effectiveness of supplementing traditional engineering approaches to requirements specification with the more rigorous specification and analysis available with formal methods.

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

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

1972-01-01

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

Payload software technology

NASA Technical Reports Server (NTRS)

1976-01-01

A software analysis was performed of known STS sortie payload elements and their associated experiments. This provided basic data for STS payload software characteristics and sizes. A set of technology drivers was identified based on a survey of future technology needs and an assessment of current software technology. The results will be used to evolve a planned approach to software technology development. The purpose of this plan is to ensure that software technology is advanced at a pace and a depth sufficient to fulfill the identified future needs.

Getting started on metrics - Jet Propulsion Laboratory productivity and quality

NASA Technical Reports Server (NTRS)

Bush, M. W.

1990-01-01

A review is presented to describe the effort and difficulties of reconstructing fifteen years of JPL software history. In 1987 the collection and analysis of project data were started with the objective of creating laboratory-wide measures of quality and productivity for software development. As a result of this two-year Software Product Assurance metrics study, a rough measurement foundation for software productivity and software quality, and an order-of-magnitude quantitative baseline for software systems and subsystems are now available.

The software application and classification algorithms for welds radiograms analysis

NASA Astrophysics Data System (ADS)

Sikora, R.; Chady, T.; Baniukiewicz, P.; Grzywacz, B.; Lopato, P.; Misztal, L.; Napierała, L.; Piekarczyk, B.; Pietrusewicz, T.; Psuj, G.

2013-01-01

The paper presents a software implementation of an Intelligent System for Radiogram Analysis (ISAR). The system has to support radiologists in welds quality inspection. The image processing part of software with a graphical user interface and a welds classification part are described with selected classification results. Classification was based on a few algorithms: an artificial neural network, a k-means clustering, a simplified k-means and a rough sets theory.

Source Code Analysis Laboratory (SCALe) for Energy Delivery Systems

DTIC Science & Technology

2010-12-01

the software for reevaluation. Once the ree- valuation process is completed, CERT provides the client a report detailing the software’s con - formance...Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8% Wine...inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with energy system software will help

Parametric Design and Mechanical Analysis of Beams based on SINOVATION

NASA Astrophysics Data System (ADS)

Xu, Z. G.; Shen, W. D.; Yang, D. Y.; Liu, W. M.

2017-07-01

In engineering practice, engineer needs to carry out complicated calculation when the loads on the beam are complex. The processes of analysis and calculation take a lot of time and the results are unreliable. So VS2005 and ADK are used to develop a software for beams design based on the 3D CAD software SINOVATION with C ++ programming language. The software can realize the mechanical analysis and parameterized design of various types of beams and output the report of design in HTML format. Efficiency and reliability of design of beams are improved.

Enhanced cardio vascular image analysis by combined representation of results from dynamic MRI and anatomic CTA

NASA Astrophysics Data System (ADS)

Kuehnel, C.; Hennemuth, A.; Oeltze, S.; Boskamp, T.; Peitgen, H.-O.

2008-03-01

The diagnosis support in the field of coronary artery disease (CAD) is very complex due to the numerous symptoms and performed studies leading to the final diagnosis. CTA and MRI are on their way to replace invasive catheter angiography. Thus, there is a need for sophisticated software tools that present the different analysis results, and correlate the anatomical and dynamic image information. We introduce a new software assistant for the combined result visualization of CTA and MR images, in which a dedicated concept for the structured presentation of original data, segmentation results, and individual findings is realized. Therefore, we define a comprehensive class hierarchy and assign suitable interaction functions. User guidance is coupled as closely as possible with available data, supporting a straightforward workflow design. The analysis results are extracted from two previously developed software assistants, providing coronary artery analysis and measurements, function analysis as well as late enhancement data investigation. As an extension we introduce a finding concept directly relating suspicious positions to the underlying data. An affine registration of CT and MR data in combination with the AHA 17-segment model enables the coupling of local findings to positions in all data sets. Furthermore, sophisticated visualization in 2D and 3D and interactive bull's eye plots facilitate a correlation of coronary stenoses and physiology. The software has been evaluated on 20 patient data sets.

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

Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this softwaremore » 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.« less

WinDAM C earthen embankment internal erosion analysis software

USDA-ARS?s Scientific Manuscript database

Two primary causes of dam failure are overtopping and internal erosion. For the purpose of evaluating dam safety for existing earthen embankment dams and proposed earthen embankment dams, Windows Dam Analysis Modules C (WinDAM C) software will simulate either internal erosion or erosion resulting f...

ESML for Earth Science Data Sets and Analysis

NASA Technical Reports Server (NTRS)

Graves, Sara; Ramachandran, Rahul

2003-01-01

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

Capi text V.1--data analysis software for nailfold skin capillaroscopy.

PubMed

Dobrev, Hristo P

2007-01-01

Nailfold skin capillaroscopy is a simple non-invasive method used to assess conditions of disturbed microcirculation such as Raynaud's phenomenon, acrocyanosis, perniones, connective tissue diseases, psoriasis, diabetes mellitus, neuropathy and vibration disease. To develop data analysis software aimed at assisting the documentation and analysis of a capillaroscopic investigation. SOFTWARE DESCRIPTION: The programme is based on a modular principle. The module "Nomenclatures" includes menus for the patients' data. The module "Examinations" includes menus for all general and specific aspects of the medical examination and capillaroscopic investigations. The modules "Settings" and "Information" include customization menus for the programme. The results of nailfold capillaroscopy can be printed in a short or expanded form. This software allows physicians to perform quick search by using various specified criteria and prepare analyses and reports. This software programme will facilitate any practitioner who performs nailfold skin capillaroscopy.

High-throughput image analysis of tumor spheroids: a user-friendly software application to measure the size of spheroids automatically and accurately.

PubMed

Chen, Wenjin; Wong, Chung; Vosburgh, Evan; Levine, Arnold J; Foran, David J; Xu, Eugenia Y

2014-07-08

The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to large-scale screening formats in every step of a drug screen, including large-scale image analysis. Currently there is no ready-to-use and free image analysis software to meet this large-scale format. Most existing methods involve manually drawing the length and width of the imaged 3D spheroids, which is a tedious and time-consuming process. This study presents a high-throughput image analysis software application - SpheroidSizer, which measures the major and minor axial length of the imaged 3D tumor spheroids automatically and accurately; calculates the volume of each individual 3D tumor spheroid; then outputs the results in two different forms in spreadsheets for easy manipulations in the subsequent data analysis. The main advantage of this software is its powerful image analysis application that is adapted for large numbers of images. It provides high-throughput computation and quality-control workflow. The estimated time to process 1,000 images is about 15 min on a minimally configured laptop, or around 1 min on a multi-core performance workstation. The graphical user interface (GUI) is also designed for easy quality control, and users can manually override the computer results. The key method used in this software is adapted from the active contour algorithm, also known as Snakes, which is especially suitable for images with uneven illumination and noisy background that often plagues automated imaging processing in high-throughput screens. The complimentary "Manual Initialize" and "Hand Draw" tools provide the flexibility to SpheroidSizer in dealing with various types of spheroids and diverse quality images. This high-throughput image analysis software remarkably reduces labor and speeds up the analysis process. Implementing this software is beneficial for 3D tumor spheroids to become a routine in vitro model for drug screens in industry and academia.

Spectral analysis software improves confidence in plant and soil water stable isotope analyses performed by isotope ratio infrared spectroscopy (IRIS).

PubMed

West, A G; Goldsmith, G R; Matimati, I; Dawson, T E

2011-08-30

Previous studies have demonstrated the potential for large errors to occur when analyzing waters containing organic contaminants using isotope ratio infrared spectroscopy (IRIS). In an attempt to address this problem, IRIS manufacturers now provide post-processing spectral analysis software capable of identifying samples with the types of spectral interference that compromises their stable isotope analysis. Here we report two independent tests of this post-processing spectral analysis software on two IRIS systems, OA-ICOS (Los Gatos Research Inc.) and WS-CRDS (Picarro Inc.). Following a similar methodology to a previous study, we cryogenically extracted plant leaf water and soil water and measured the δ(2)H and δ(18)O values of identical samples by isotope ratio mass spectrometry (IRMS) and IRIS. As an additional test, we analyzed plant stem waters and tap waters by IRMS and IRIS in an independent laboratory. For all tests we assumed that the IRMS value represented the "true" value against which we could compare the stable isotope results from the IRIS methods. Samples showing significant deviations from the IRMS value (>2σ) were considered to be contaminated and representative of spectral interference in the IRIS measurement. Over the two studies, 83% of plant species were considered contaminated on OA-ICOS and 58% on WS-CRDS. Post-analysis, spectra were analyzed using the manufacturer's spectral analysis software, in order to see if the software correctly identified contaminated samples. In our tests the software performed well, identifying all the samples with major errors. However, some false negatives indicate that user evaluation and testing of the software are necessary. Repeat sampling of plants showed considerable variation in the discrepancies between IRIS and IRMS. As such, we recommend that spectral analysis of IRIS data must be incorporated into standard post-processing routines. Furthermore, we suggest that the results from spectral analysis be included when reporting stable isotope data from IRIS. Copyright © 2011 John Wiley & Sons, Ltd.

Mining dynamic noteworthy functions in software execution sequences

PubMed Central

Huang, Guoyan; Wang, Yuqian; He, Haitao; Ren, Jiadong

2017-01-01

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely. PMID:28278276

ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

NASA Astrophysics Data System (ADS)

Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments

PubMed Central

Sachs, Christian Carsten; Grünberger, Alexander; Helfrich, Stefan; Probst, Christopher; Wiechert, Wolfgang; Kohlheyer, Dietrich; Nöh, Katharina

2016-01-01

Background Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool. Results We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks. Conclusion Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso. PMID:27661996

Data Capture and Analysis Using the BBC Microcomputer--an Interfacing Project Applied to Enzyme Kinetics.

ERIC Educational Resources Information Center

Jones, Lawrence; Graham, Ian

1986-01-01

Reviews the main principles of interfacing and discusses the software developed to perform kinetic data capture and analysis with a BBC microcomputer linked to a recording spectrophotometer. Focuses on the steps in software development. Includes results of a lactate dehydrogenase assay. (ML)

Development of an automated asbestos counting software based on fluorescence microscopy.

PubMed

Alexandrov, Maxym; Ichida, Etsuko; Nishimura, Tomoki; Aoki, Kousuke; Ishida, Takenori; Hirota, Ryuichi; Ikeda, Takeshi; Kawasaki, Tetsuo; Kuroda, Akio

2015-01-01

An emerging alternative to the commonly used analytical methods for asbestos analysis is fluorescence microscopy (FM), which relies on highly specific asbestos-binding probes to distinguish asbestos from interfering non-asbestos fibers. However, all types of microscopic asbestos analysis require laborious examination of large number of fields of view and are prone to subjective errors and large variability between asbestos counts by different analysts and laboratories. A possible solution to these problems is automated counting of asbestos fibers by image analysis software, which would lower the cost and increase the reliability of asbestos testing. This study seeks to develop a fiber recognition and counting software for FM-based asbestos analysis. We discuss the main features of the developed software and the results of its testing. Software testing showed good correlation between automated and manual counts for the samples with medium and high fiber concentrations. At low fiber concentrations, the automated counts were less accurate, leading us to implement correction mode for automated counts. While the full automation of asbestos analysis would require further improvements in accuracy of fiber identification, the developed software could already assist professional asbestos analysts and record detailed fiber dimensions for the use in epidemiological research.

IFDOTMETER: A New Software Application for Automated Immunofluorescence Analysis.

PubMed

Rodríguez-Arribas, Mario; Pizarro-Estrella, Elisa; Gómez-Sánchez, Rubén; Yakhine-Diop, S M S; Gragera-Hidalgo, Antonio; Cristo, Alejandro; Bravo-San Pedro, Jose M; González-Polo, Rosa A; Fuentes, José M

2016-04-01

Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision of the researcher. Once analysis is complete, the results are stored in a spreadsheet. Using software for high-throughput cell image analysis offers researchers the possibility of performing comprehensive and precise analysis of a high number of images in an automated manner, making this routine task easier. © 2015 Society for Laboratory Automation and Screening.

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Reliability Validation and Improvement Framework

DTIC Science & Technology

2012-11-01

systems . Steps in that direction include the use of the Architec- ture Tradeoff Analysis Method ® (ATAM®) developed at the Carnegie Mellon...embedded software • cyber - physical systems (CPSs) to indicate that the embedded software interacts with, manag - es, and controls a physical system [Lee...the use of formal static analysis methods to increase our confidence in system operation beyond testing. However, analysis results

Real-time development of data acquisition and analysis software for hands-on physiology education in neuroscience: G-PRIME.

PubMed

Lott, Gus K; Johnson, Bruce R; Bonow, Robert H; Land, Bruce R; Hoy, Ronald R

2009-01-01

We report on the real-time creation of an application for hands-on neurophysiology in an advanced undergraduate teaching laboratory. Enabled by the rapid software development tools included in the Matlab technical computing environment (The Mathworks, Natick, MA), a team, consisting of a neurophysiology educator and a biophysicist trained as an electrical engineer, interfaced to a course of approximately 15 students from engineering and biology backgrounds. The result is the powerful freeware data acquisition and analysis environment, "g-PRIME." The software was developed from week to week in response to curriculum demands, and student feedback. The program evolved from a simple software oscilloscope, enabling RC circuit analysis, to a suite of tools supporting analysis of neuronal excitability and synaptic transmission analysis in invertebrate model systems. The program has subsequently expanded in application to university courses, research, and high school projects in the US and abroad as free courseware.

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

PubMed

Desai, Trunil S; Srivastava, Shireesh

2018-01-01

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

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

PubMed Central

Desai, Trunil S.

2018-01-01

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

Analysis-Software for Hyperspectral Algal Reflectance Probes v. 1.0

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

Timlin, Jerilyn A.; Reichardt, Thomas A.; Jenson, Travis J.

This software provides onsite analysis of the hyperspectral reflectance data acquired on an outdoor algal pond by a multichannel, fiber-coupled spectroradiometer. The analysis algorithm is based on numerical inversion of a reflectance model, in which the above-water reflectance is expressed as a function of the single backscattering albedo, which is dependent on the backscatter and absorption coefficients of the algal culture, which are in turn related to the algal biomass and pigment optical activity, respectively. Prior to the development of this software, while raw multichannel data were displayed in real time, analysis required a post-processing procedure to extract the relevantmore » parameters. This software provides the capability to track the temporal variation of such culture parameters in real time, as raw data are being acquired, or can be run in a post processing mode. The software allows the user to select between different algal species, incorporate the appropriate calibration data, and observe the quality of the resulting model inversions.« less

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.

PINT, a New Pulsar Timing Software

NASA Astrophysics Data System (ADS)

Luo, Jing; Jenet, Fredrick A.; Ransom, Scott M.; Demorest, Paul; Van Haasteren, Rutger; Archibald, Anne

2015-01-01

We are presenting a new pulsar timing software PINT. The current pulsar timing group are heavily depending on Tempo/Tempo2, a package for analysis pulsar data. However, for a high accuracy pulsar timing related project, such as pulsar timing for gravitational waves, an alternative software is needed for the purpose of examing the results. We are developing a Tempo independent software with a different structure. Different modules is designed to be more isolated and easier to be expanded. Instead of C, we are using Python as our programming language for the advantage of flexibility and powerful docstring. Here, we are presenting the detailed design and the first result of the software.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Off-the-shelf Control of Data Analysis Software

NASA Astrophysics Data System (ADS)

Wampler, S.

The Gemini Project must provide convenient access to data analysis facilities to a wide user community. The international nature of this community makes the selection of data analysis software particularly interesting, with staunch advocates of systems such as ADAM and IRAF among the users. Additionally, the continuing trends towards increased use of networked systems and distributed processing impose additional complexity. To meet these needs, the Gemini Project is proposing the novel approach of using low-cost, off-the-shelf software to abstract out both the control and distribution of data analysis from the functionality of the data analysis software. For example, the orthogonal nature of control versus function means that users might select analysis routines from both ADAM and IRAF as appropriate, distributing these routines across a network of machines. It is the belief of the Gemini Project that this approach results in a system that is highly flexible, maintainable, and inexpensive to develop. The Khoros visualization system is presented as an example of control software that is currently available for providing the control and distribution within a data analysis system. The visual programming environment provided with Khoros is also discussed as a means to providing convenient access to this control.

CRAX. Cassandra Exoskeleton

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

Robinson, D.G.; Eubanks, L.

1998-03-01

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

Cassandra Exoskeleton

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

Robiinson, David G.

1999-02-20

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

BrightStat.com: free statistics online.

PubMed

Stricker, Daniel

2008-10-01

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

Testing of Safety-Critical Software Embedded in an Artificial Heart

NASA Astrophysics Data System (ADS)

Cha, Sungdeok; Jeong, Sehun; Yoo, Junbeom; Kim, Young-Gab

Software is being used more frequently to control medical devices such as artificial heart or robotic surgery system. While much of software safety issues in such systems are similar to other safety-critical systems (e.g., nuclear power plants), domain-specific properties may warrant development of customized techniques to demonstrate fitness of the system on patients. In this paper, we report results of a preliminary analysis done on software controlling a Hybrid Ventricular Assist Device (H-VAD) developed by Korea Artificial Organ Centre (KAOC). It is a state-of-the-art artificial heart which completed animal testing phase. We performed software testing in in-vitro experiments and animal experiments. An abnormal behaviour, never detected during extensive in-vitro analysis and animal testing, was found.

Research of processes of reception and analysis of dynamic digital medical images in hardware/software complexes used for diagnostics and treatment of cardiovascular diseases

NASA Astrophysics Data System (ADS)

Karmazikov, Y. V.; Fainberg, E. M.

2005-06-01

Work with DICOM compatible equipment integrated into hardware and software systems for medical purposes has been considered. Structures of process of reception and translormation of the data are resulted by the example of digital rentgenography and angiography systems, included in hardware-software complex DIMOL-IK. Algorithms of reception and the analysis of the data are offered. Questions of the further processing and storage of the received data are considered.

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.

Dose-Dependent Thresholds of 10-ns Electric Pulse Induced Plasma Membrane Disruption and Cytotoxicity in Multiple Cell Lines

DTIC Science & Technology

2011-01-01

normalized to parallel controls. Flow Cytometry and Confocal Microscopy Upon exposure to 10-ns EP, aliquots of the cellular suspension were added to a tube...Survival data was processed and plotted using GrapherH software (Golden Software, Golden, Colorado). Flow cytometry results were processed in C6 software...Accuri Cytometers, Inc., Ann Arbor, MI) and FCSExpress software (DeNovo Software, Los Angeles, CA). Final analysis and presentation of flow cytometry

STEM_CELL: a software tool for electron microscopy: part 2--analysis of crystalline materials.

PubMed

Grillo, Vincenzo; Rossi, Francesca

2013-02-01

A new graphical software (STEM_CELL) for analysis of HRTEM and STEM-HAADF images is here introduced in detail. The advantage of the software, beyond its graphic interface, is to put together different analysis algorithms and simulation (described in an associated article) to produce novel analysis methodologies. Different implementations and improvements to state of the art approach are reported in the image analysis, filtering, normalization, background subtraction. In particular two important methodological results are here highlighted: (i) the definition of a procedure for atomic scale quantitative analysis of HAADF images, (ii) the extension of geometric phase analysis to large regions up to potentially 1μm through the use of under sampled images with aliasing effects. Copyright © 2012 Elsevier B.V. All rights reserved.

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 Reference Model for Software and System Inspections. White Paper

NASA Technical Reports Server (NTRS)

He, Lulu; Shull, Forrest

2009-01-01

Software Quality Assurance (SQA) is an important component of the software development process. SQA processes provide assurance that the software products and processes in the project life cycle conform to their specified requirements by planning, enacting, and performing a set of activities to provide adequate confidence that quality is being built into the software. Typical techniques include: (1) Testing (2) Simulation (3) Model checking (4) Symbolic execution (5) Management reviews (6) Technical reviews (7) Inspections (8) Walk-throughs (9) Audits (10) Analysis (complexity analysis, control flow analysis, algorithmic analysis) (11) Formal method Our work over the last few years has resulted in substantial knowledge about SQA techniques, especially the areas of technical reviews and inspections. But can we apply the same QA techniques to the system development process? If yes, what kind of tailoring do we need before applying them in the system engineering context? If not, what types of QA techniques are actually used at system level? And, is there any room for improvement.) After a brief examination of the system engineering literature (especially focused on NASA and DoD guidance) we found that: (1) System and software development process interact with each other at different phases through development life cycle (2) Reviews are emphasized in both system and software development. (Figl.3). For some reviews (e.g. SRR, PDR, CDR), there are both system versions and software versions. (3) Analysis techniques are emphasized (e.g. Fault Tree Analysis, Preliminary Hazard Analysis) and some details are given about how to apply them. (4) Reviews are expected to use the outputs of the analysis techniques. In other words, these particular analyses are usually conducted in preparation for (before) reviews. The goal of our work is to explore the interaction between the Quality Assurance (QA) techniques at the system level and the software level.

Integrating Statistical Visualization Research into the Political Science Classroom

ERIC Educational Resources Information Center

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

2011-01-01

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

Multiple breath washout analysis in infants: quality assessment and recommendations for improvement.

PubMed

Anagnostopoulou, Pinelopi; Egger, Barbara; Lurà, Marco; Usemann, Jakob; Schmidt, Anne; Gorlanova, Olga; Korten, Insa; Roos, Markus; Frey, Urs; Latzin, Philipp

2016-03-01

Infant multiple breath washout (MBW) testing serves as a primary outcome in clinical studies. However, it is still unknown whether current software algorithms allow between-centre comparisons. In this study of healthy infants, we quantified MBW measurement errors and tried to improve data quality by simply changing software settings. We analyzed best quality MBW measurements performed with an ultrasonic flowmeter in 24 infants from two centres in Switzerland with the current software settings. To challenge the robustness of these settings, we also used alternative analysis approaches. Using the current analysis software, the coefficient of variation (CV) for functional residual capacity (FRC) differed significantly between centres (mean  ±  SD (%): 9.8  ±  5.6 and 5.8  ±  2.9, respectively, p  =  0.039). In addition, FRC values calculated during the washout differed between  -25 and  +30% from those of the washin of the same tracing. Results were mainly influenced by analysis settings and temperature recordings. Changing few algorithms resulted in significantly more robust analysis. Non-systematic inter-centre differences can be reduced by using correctly recorded environmental data and simple changes in the software algorithms. We provide implications that greatly improve infant MBW outcomes' quality and can be applied when multicentre trials are conducted.

Dental application of novel finite element analysis software for three-dimensional finite element modeling of a dentulous mandible from its computed tomography images.

PubMed

Nakamura, Keiko; Tajima, Kiyoshi; Chen, Ker-Kong; Nagamatsu, Yuki; Kakigawa, Hiroshi; Masumi, Shin-ich

2013-12-01

This study focused on the application of novel finite-element analysis software for constructing a finite-element model from the computed tomography data of a human dentulous mandible. The finite-element model is necessary for evaluating the mechanical response of the alveolar part of the mandible, resulting from occlusal force applied to the teeth during biting. Commercially available patient-specific general computed tomography-based finite-element analysis software was solely applied to the finite-element analysis for the extraction of computed tomography data. The mandibular bone with teeth was extracted from the original images. Both the enamel and the dentin were extracted after image processing, and the periodontal ligament was created from the segmented dentin. The constructed finite-element model was reasonably accurate using a total of 234,644 nodes and 1,268,784 tetrahedral and 40,665 shell elements. The elastic moduli of the heterogeneous mandibular bone were determined from the bone density data of the computed tomography images. The results suggested that the software applied in this study is both useful and powerful for creating a more accurate three-dimensional finite-element model of a dentulous mandible from the computed tomography data without the need for any other software.

Mal-Xtract: Hidden Code Extraction using Memory Analysis

NASA Astrophysics Data System (ADS)

Lim, Charles; Syailendra Kotualubun, Yohanes; Suryadi; Ramli, Kalamullah

2017-01-01

Software packer has been used effectively to hide the original code inside a binary executable, making it more difficult for existing signature based anti malware software to detect malicious code inside the executable. A new method of written and rewritten memory section is introduced to to detect the exact end time of unpacking routine and extract original code from packed binary executable using Memory Analysis running in an software emulated environment. Our experiment results show that at least 97% of the original code from the various binary executable packed with different software packers could be extracted. The proposed method has also been successfully extracted hidden code from recent malware family samples.

Evaluation of management measures of software development. Volume 1: Analysis summary

NASA Technical Reports Server (NTRS)

Page, J.; Card, D.; Mcgarry, F.

1982-01-01

The conceptual model, the data classification scheme, and the analytic procedures are explained. The analytic results are summarized and specific software measures for collection and monitoring are recommended.

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

Sun, Z. J.; Wells, D.; Green, J.

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switchingmore » the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.« less

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

PubMed

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

2017-12-21

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

Testing Software Development Project Productivity Model

NASA Astrophysics Data System (ADS)

Lipkin, Ilya

Software development is an increasingly influential factor in today's business environment, and a major issue affecting software development is how an organization estimates projects. If the organization underestimates cost, schedule, and quality requirements, the end results will not meet customer needs. On the other hand, if the organization overestimates these criteria, resources that could have been used more profitably will be wasted. There is no accurate model or measure available that can guide an organization in a quest for software development, with existing estimation models often underestimating software development efforts as much as 500 to 600 percent. To address this issue, existing models usually are calibrated using local data with a small sample size, with resulting estimates not offering improved cost analysis. This study presents a conceptual model for accurately estimating software development, based on an extensive literature review and theoretical analysis based on Sociotechnical Systems (STS) theory. The conceptual model serves as a solution to bridge organizational and technological factors and is validated using an empirical dataset provided by the DoD. Practical implications of this study allow for practitioners to concentrate on specific constructs of interest that provide the best value for the least amount of time. This study outlines key contributing constructs that are unique for Software Size E-SLOC, Man-hours Spent, and Quality of the Product, those constructs having the largest contribution to project productivity. This study discusses customer characteristics and provides a framework for a simplified project analysis for source selection evaluation and audit task reviews for the customers and suppliers. Theoretical contributions of this study provide an initial theory-based hypothesized project productivity model that can be used as a generic overall model across several application domains such as IT, Command and Control, Simulation and etc... This research validates findings from previous work concerning software project productivity and leverages said results in this study. The hypothesized project productivity model provides statistical support and validation of expert opinions used by practitioners in the field of software project estimation.

ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

PubMed

Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. Copyright © 2011 Elsevier Inc. All rights reserved.

An overview of STRUCTURE: applications, parameter settings, and supporting software

PubMed Central

Porras-Hurtado, Liliana; Ruiz, Yarimar; Santos, Carla; Phillips, Christopher; Carracedo, Ángel; Lareu, Maria V.

2013-01-01

Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data. PMID:23755071

Information Extraction for System-Software Safety Analysis: Calendar Year 2007 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2008-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis on the models to identify possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations; 4) perform discrete-time-based simulation on the models to investigate scenarios where these paths may play a role in failures and mishaps; and 5) identify resulting candidate scenarios for software integration testing. This paper describes new challenges in a NASA abort system case, and enhancements made to develop the integrated tool set.

Performance evaluation of the RITG148+ set of TomoTherapy quality assurance tools using RTQA2 radiochromic film.

PubMed

Lobb, Eric C

2016-07-08

Version 6.3 of the RITG148+ software package offers eight automated analysis routines for quality assurance of the TomoTherapy platform. A performance evaluation of each routine was performed in order to compare RITG148+ results with traditionally accepted analysis techniques and verify that simulated changes in machine parameters are correctly identified by the software. Reference films were exposed according to AAPM TG-148 methodology for each routine and the RITG148+ results were compared with either alternative software analysis techniques or manual analysis techniques in order to assess baseline agreement. Changes in machine performance were simulated through translational and rotational adjustments to subsequently irradiated films, and these films were analyzed to verify that the applied changes were accurately detected by each of the RITG148+ routines. For the Hounsfield unit routine, an assessment of the "Frame Averaging" functionality and the effects of phantom roll on the routine results are presented. All RITG148+ routines reported acceptable baseline results consistent with alternative analysis techniques, with 9 of the 11 baseline test results showing agreement of 0.1mm/0.1° or better. Simulated changes were correctly identified by the RITG148+ routines within approximately 0.2 mm/0.2° with the exception of the Field Centervs. Jaw Setting routine, which was found to have limited accuracy in cases where field centers were not aligned for all jaw settings due to inaccurate autorotation of the film during analysis. The performance of the RITG148+ software package was found to be acceptable for introduction into our clinical environment as an automated alternative to traditional analysis techniques for routine TomoTherapy quality assurance testing.

Software For Computing Reliability Of Other Software

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Benefits of Software GPS Receivers for Enhanced Signal Processing

DTIC Science & Technology

2000-01-01

1 Published in GPS SOLUTIONS 4(1) Summer, 2000, pages 56-66. Benefits of Software GPS Receivers for Enhanced Signal Processing Alison Brown...Diego, CA 92110-3127 Number of Pages: 24 Number of Figures: 20 ABSTRACT In this paper the architecture of a software GPS receiver is described...and an analysis is included of the performance of a software GPS receiver when tracking the GPS signals in challenging environments. Results are

Source Code Analysis Laboratory (SCALe)

DTIC Science & Technology

2012-04-01

Versus Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8...is inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with software for a particular...servers support a collection of virtual machines (VMs) that can be configured to support analysis in various environments, such as Windows XP and Linux . A

Development of Cross-Platform Software for Well Logging Data Visualization

NASA Astrophysics Data System (ADS)

Akhmadulin, R. K.; Miraev, A. I.

2017-07-01

Well logging data processing is one of the main sources of information in the oil-gas field analysis and is of great importance in the process of its development and operation. Therefore, it is important to have the software which would accurately and clearly provide the user with processed data in the form of well logs. In this work, there have been developed a software product which not only has the basic functionality for this task (loading data from .las files, well log curves display, etc.), but can be run in different operating systems and on different devices. In the article a subject field analysis and task formulation have been performed, and the software design stage has been considered. At the end of the work the resulting software product interface has been described.

Application of software technology to automatic test data analysis

NASA Technical Reports Server (NTRS)

Stagner, J. R.

1991-01-01

The verification process for a major software subsystem was partially automated as part of a feasibility demonstration. The methods employed are generally useful and applicable to other types of subsystems. The effort resulted in substantial savings in test engineer analysis time and offers a method for inclusion of automatic verification as a part of regression testing.

THE VALIDITY OF USING ROC SOFTWARE FOR ANALYSING VISUAL GRADING CHARACTERISTICS DATA: AN INVESTIGATION BASED ON THE NOVEL SOFTWARE VGC ANALYZER.

PubMed

Hansson, Jonny; Månsson, Lars Gunnar; Båth, Magnus

2016-06-01

The purpose of the present work was to investigate the validity of using single-reader-adapted receiver operating characteristics (ROC) software for analysis of visual grading characteristics (VGC) data. VGC data from four published VGC studies on optimisation of X-ray examinations, previously analysed using ROCFIT, were reanalysed using a recently developed software dedicated to VGC analysis (VGC Analyzer), and the outcomes [the mean and 95 % confidence interval (CI) of the area under the VGC curve (AUCVGC) and the p-value] were compared. The studies included both paired and non-paired data and were reanalysed both for the fixed-reader and the random-reader situations. The results showed good agreement between the softwares for the mean AUCVGC For non-paired data, wider CIs were obtained with VGC Analyzer than previously reported, whereas for paired data, the previously reported CIs were similar or even broader. Similar observations were made for the p-values. The results indicate that the use of single-reader-adapted ROC software such as ROCFIT for analysing non-paired VGC data may lead to an increased risk of committing Type I errors, especially in the random-reader situation. On the other hand, the use of ROC software for analysis of paired VGC data may lead to an increased risk of committing Type II errors, especially in the fixed-reader situation. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Reproducibility of dynamic contrast-enhanced MRI and dynamic susceptibility contrast MRI in the study of brain gliomas: a comparison of data obtained using different commercial software.

PubMed

Conte, Gian Marco; Castellano, Antonella; Altabella, Luisa; Iadanza, Antonella; Cadioli, Marcello; Falini, Andrea; Anzalone, Nicoletta

2017-04-01

Dynamic susceptibility contrast MRI (DSC) and dynamic contrast-enhanced MRI (DCE) are useful tools in the diagnosis and follow-up of brain gliomas; nevertheless, both techniques leave the open issue of data reproducibility. We evaluated the reproducibility of data obtained using two different commercial software for perfusion maps calculation and analysis, as one of the potential sources of variability can be the software itself. DSC and DCE analyses from 20 patients with gliomas were tested for both the intrasoftware (as intraobserver and interobserver reproducibility) and the intersoftware reproducibility, as well as the impact of different postprocessing choices [vascular input function (VIF) selection and deconvolution algorithms] on the quantification of perfusion biomarkers plasma volume (Vp), volume transfer constant (K trans ) and rCBV. Data reproducibility was evaluated with the intraclass correlation coefficient (ICC) and Bland-Altman analysis. For all the biomarkers, the intra- and interobserver reproducibility resulted in almost perfect agreement in each software, whereas for the intersoftware reproducibility the value ranged from 0.311 to 0.577, suggesting fair to moderate agreement; Bland-Altman analysis showed high dispersion of data, thus confirming these findings. Comparisons of different VIF estimation methods for DCE biomarkers resulted in ICC of 0.636 for K trans and 0.662 for Vp; comparison of two deconvolution algorithms in DSC resulted in an ICC of 0.999. The use of single software ensures very good intraobserver and interobservers reproducibility. Caution should be taken when comparing data obtained using different software or different postprocessing within the same software, as reproducibility is not guaranteed anymore.

Deuterostome Evolution: Large Data Set Analysis

NASA Technical Reports Server (NTRS)

Janies, Daniel; Wheeler, Ward

2004-01-01

This award allowed us to develop novel hardware for phylogenetics, collect genomic data and produce several phylogenies of deuterostome organisms, communicate the results publicly, release software into the public domain, publish textbooks and papers, and prepare for the next research projects. There are no resulting subject inventions to report. We review these activities in three sections: 1) Hardware and software and development; 2) Evolutionary biology research; 3) Our proposed future direction, predictive analysis of pathogens in support of the NASA mission.

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.

One-Click Data Analysis Software for Science Operations

NASA Astrophysics Data System (ADS)

Navarro, Vicente

2015-12-01

One of the important activities of ESA Science Operations Centre is to provide Data Analysis Software (DAS) to enable users and scientists to process data further to higher levels. During operations and post-operations, Data Analysis Software (DAS) is fully maintained and updated for new OS and library releases. Nonetheless, once a Mission goes into the "legacy" phase, there are very limited funds and long-term preservation becomes more and more difficult. Building on Virtual Machine (VM), Cloud computing and Software as a Service (SaaS) technologies, this project has aimed at providing long-term preservation of Data Analysis Software for the following missions: - PIA for ISO (1995) - SAS for XMM-Newton (1999) - Hipe for Herschel (2009) - EXIA for EXOSAT (1983) Following goals have guided the architecture: - Support for all operations, post-operations and archive/legacy phases. - Support for local (user's computer) and cloud environments (ESAC-Cloud, Amazon - AWS). - Support for expert users, requiring full capabilities. - Provision of a simple web-based interface. This talk describes the architecture, challenges, results and lessons learnt gathered in this project.

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.

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares

PubMed Central

Bonnet, Agnès; Lagarrigue, Sandrine; Liaubet, Laurence; Robert-Granié, Christèle; SanCristobal, Magali; Tosser-Klopp, Gwenola

2009-01-01

Background As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results. Results GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation. Conclusion Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated). PMID:19615111

Software for computerised analysis of cardiotocographic traces.

PubMed

Romano, M; Bifulco, P; Ruffo, M; Improta, G; Clemente, F; Cesarelli, M

2016-02-01

Despite the widespread use of cardiotocography in foetal monitoring, the evaluation of foetal status suffers from a considerable inter and intra-observer variability. In order to overcome the main limitations of visual cardiotocographic assessment, computerised methods to analyse cardiotocographic recordings have been recently developed. In this study, a new software for automated analysis of foetal heart rate is presented. It allows an automatic procedure for measuring the most relevant parameters derivable from cardiotocographic traces. Simulated and real cardiotocographic traces were analysed to test software reliability. In artificial traces, we simulated a set number of events (accelerations, decelerations and contractions) to be recognised. In the case of real signals, instead, results of the computerised analysis were compared with the visual assessment performed by 18 expert clinicians and three performance indexes were computed to gain information about performances of the proposed software. The software showed preliminary performance we judged satisfactory in that the results matched completely the requirements, as proved by tests on artificial signals in which all simulated events were detected from the software. Performance indexes computed in comparison with obstetricians' evaluations are, on the contrary, not so satisfactory; in fact they led to obtain the following values of the statistical parameters: sensitivity equal to 93%, positive predictive value equal to 82% and accuracy equal to 77%. Very probably this arises from the high variability of trace annotation carried out by clinicians. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Statistics of software vulnerability detection in certification testing

NASA Astrophysics Data System (ADS)

Barabanov, A. V.; Markov, A. S.; Tsirlov, V. L.

2018-05-01

The paper discusses practical aspects of introduction of the methods to detect software vulnerability in the day-to-day activities of the accredited testing laboratory. It presents the approval results of the vulnerability detection methods as part of the study of the open source software and the software that is a test object of the certification tests under information security requirements, including software for communication networks. Results of the study showing the allocation of identified vulnerabilities by types of attacks, country of origin, programming languages used in the development, methods for detecting vulnerability, etc. are given. The experience of foreign information security certification systems related to the detection of certified software vulnerabilities is analyzed. The main conclusion based on the study is the need to implement practices for developing secure software in the development life cycle processes. The conclusions and recommendations for the testing laboratories on the implementation of the vulnerability analysis methods are laid down.

A parallel and sensitive software tool for methylation analysis on multicore platforms.

PubMed

Tárraga, Joaquín; Pérez, Mariano; Orduña, Juan M; Duato, José; Medina, Ignacio; Dopazo, Joaquín

2015-10-01

DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads. Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password 'anonymous'). juan.orduna@uv.es or jdopazo@cipf.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

ANTONIA perfusion and stroke. A software tool for the multi-purpose analysis of MR perfusion-weighted datasets and quantitative ischemic stroke assessment.

PubMed

Forkert, N D; Cheng, B; Kemmling, A; Thomalla, G; Fiehler, J

2014-01-01

The objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of additional datasets for the specific purpose of acute ischemic stroke patient dataset evaluation. Three different methods for the analysis of DSC or DCE PWI datasets are currently implemented in ANTONIA, which can be case-specifically selected based on the study protocol. These methods comprise a curve fitting method as well as a deconvolution-based and deconvolution-free method integrating a previously defined arterial input function. The perfusion analysis is extended for the purpose of acute ischemic stroke analysis by additional methods that enable an automatic atlas-based selection of the arterial input function, an analysis of the perfusion-diffusion and DWI-FLAIR mismatch as well as segmentation-based volumetric analyses. For reliability evaluation, the described software tool was used by two observers for quantitative analysis of 15 datasets from acute ischemic stroke patients to extract the acute lesion core volume, FLAIR ratio, perfusion-diffusion mismatch volume with manually as well as automatically selected arterial input functions, and follow-up lesion volume. The results of this evaluation revealed that the described software tool leads to highly reproducible results for all parameters if the automatic arterial input function selection method is used. Due to the broad selection of processing methods that are available in the software tool, ANTONIA is especially helpful to support image-based perfusion and acute ischemic stroke research projects.

Meta-analysis of Odds Ratios: Current Good Practices

PubMed Central

Chang, Bei-Hung; Hoaglin, David C.

2016-01-01

Background Many systematic reviews of randomized clinical trials lead to meta-analyses of odds ratios. The customary methods of estimating an overall odds ratio involve weighted averages of the individual trials’ estimates of the logarithm of the odds ratio. That approach, however, has several shortcomings, arising from assumptions and approximations, that render the results unreliable. Although the problems have been documented in the literature for many years, the conventional methods persist in software and applications. A well-developed alternative approach avoids the approximations by working directly with the numbers of subjects and events in the arms of the individual trials. Objective We aim to raise awareness of methods that avoid the conventional approximations, can be applied with widely available software, and produce more-reliable results. Methods We summarize the fixed-effect and random-effects approaches to meta-analysis; describe conventional, approximate methods and alternative methods; apply the methods in a meta-analysis of 19 randomized trials of endoscopic sclerotherapy in patients with cirrhosis and esophagogastric varices; and compare the results. We demonstrate the use of SAS, Stata, and R software for the analysis. Results In the example, point estimates and confidence intervals for the overall log-odds-ratio differ between the conventional and alternative methods, in ways that can affect inferences. Programming is straightforward in the three software packages; an appendix gives the details. Conclusions The modest additional programming required should not be an obstacle to adoption of the alternative methods. Because their results are unreliable, use of the conventional methods for meta-analysis of odds ratios should be discontinued. PMID:28169977

Using Statistical Analysis Software to Advance Nitro Plasticizer Wettability

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

Shear, Trevor Allan

Statistical analysis in science is an extremely powerful tool that is often underutilized. Additionally, it is frequently the case that data is misinterpreted or not used to its fullest extent. Utilizing the advanced software JMP®, many aspects of experimental design and data analysis can be evaluated and improved. This overview will detail the features of JMP® and how they were used to advance a project, resulting in time and cost savings, as well as the collection of scientifically sound data. The project analyzed in this report addresses the inability of a nitro plasticizer to coat a gold coated quartz crystalmore » sensor used in a quartz crystal microbalance. Through the use of the JMP® software, the wettability of the nitro plasticizer was increased by over 200% using an atmospheric plasma pen, ensuring good sample preparation and reliable results.« less

Modeling and analysis of visual digital impact model for a Chinese human thorax.

PubMed

Zhu, Jin; Wang, Kai-Ming; Li, Shu; Liu, Hai-Yan; Jing, Xiao; Li, Xiao-Fang; Liu, Yi-He

2017-01-01

To establish a three-dimensional finite element model of the human chest for engineering research on individual protection. Computed tomography (CT) scanning data were used for three-dimensional reconstruction with the medical image reconstruction software Mimics. The finite element method (FEM) preprocessing software ANSYS ICEM CFD was used for cell mesh generation, and the relevant material behavior parameters of all of the model's parts were specified. The finite element model was constructed with the FEM software, and the model availability was verified based on previous cadaver experimental data. A finite element model approximating the anatomical structure of the human chest was established, and the model's simulation results conformed to the results of the cadaver experiment overall. Segment data of the human body and specialized software can be utilized for FEM model reconstruction to satisfy the need for numerical analysis of shocks to the human chest in engineering research on body mechanics.

PolyPhred analysis software for mutation detection from fluorescence-based sequence data.

PubMed

Montgomery, Kate T; Iartchouck, Oleg; Li, Li; Loomis, Stephanie; Obourn, Vanessa; Kucherlapati, Raju

2008-10-01

The ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the availability of the sequence of the human genome. Large cohorts of individuals exhibiting certain phenotypes can be studied and candidate genes resequenced. However, the challenge of analyzing sequence data from many individuals with accuracy, speed, and economy is great. This unit describes one set of software tools: Phred, Phrap, PolyPhred, and Consed. Coverage includes the advantages and disadvantages of these analysis tools, details for obtaining and using the software, and the results one may expect. The software is being continually updated to permit further automation of mutation analysis. Currently, however, at least some manual review is required if one wishes to identify 100% of the variants in a sample set.

ATLAS particle detector CSC ROD software design and implementation, and, Addition of K physics to chi-squared analysis of FDQM

NASA Astrophysics Data System (ADS)

Hawkins, Donovan Lee

In this thesis I present a software framework for use on the ATLAS muon CSC readout driver. This C++ framework uses plug-in Decoders incorporating hand-optimized assembly language routines to perform sparsification and data formatting. The software is designed with both flexibility and performance in mind, and runs on a custom 9U VME board using Texas Instruments TMS360C6203 digital signal processors. I describe the requirements of the software, the methods used in its design, and the results of testing the software with simulated data. I also present modifications to a chi-squared analysis of the Standard Model and Four Down Quark Model (FDQM) originally done by Dr. Dennis Silverman. The addition of four new experiments to the analysis has little effect on the Standard Model but provides important new restrictions on the FDQM. The method used to incorporate these new experiments is presented, and the consequences of their addition are reviewed.

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

NASA Technical Reports Server (NTRS)

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

2011-01-01

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

Computerised curve deconvolution of TL/OSL curves using a popular spreadsheet program.

PubMed

Afouxenidis, D; Polymeris, G S; Tsirliganis, N C; Kitis, G

2012-05-01

This paper exploits the possibility of using commercial software for thermoluminescence and optically stimulated luminescence curve deconvolution analysis. The widely used software package Microsoft Excel, with the Solver utility has been used to perform deconvolution analysis to both experimental and reference glow curves resulted from the GLOw Curve ANalysis INtercomparison project. The simple interface of this programme combined with the powerful Solver utility, allows the analysis of complex stimulated luminescence curves into their components and the evaluation of the associated luminescence parameters.

Relation between Alice Software and Programming Learning: A Systematic Review of the Literature and Meta-Analysis

ERIC Educational Resources Information Center

Costa, Joana M.; Miranda, Guilhermina L.

2017-01-01

This paper presents the results of a systematic review of the literature, including a meta-analysis, about the effectiveness of the use of Alice software in programming learning when compared to the use of a conventional programming language. Our research included studies published between the years 2000 and 2014 in the main databases. We gathered…

An Analysis of Mimosa pudica Leaves Movement by Using LoggerPro Software

NASA Astrophysics Data System (ADS)

Sugito; Susilo; Handayani, L.; Marwoto, P.

2016-08-01

The unique phenomena of Mimosa pudica are the closing and opening movements of its leaves when they got a stimulus. By using certain software, these movements can be drawn into graphic that can be analysed. The LoggerPro provides facilities needed to analyse recorded videos of the plant's reaction to stimulus. Then, through the resulted graph, analysis of some variables can be carried out. The result showed that the plant's movement fits an equation of y = mx + c.

The software product assurance metrics study: JPL's software systems quality and productivity

NASA Technical Reports Server (NTRS)

Bush, Marilyn W.

1989-01-01

The findings are reported of the Jet Propulsion Laboratory (JPL)/Software Product Assurance (SPA) Metrics Study, conducted as part of a larger JPL effort to improve software quality and productivity. Until recently, no comprehensive data had been assembled on how JPL manages and develops software-intensive systems. The first objective was to collect data on software development from as many projects and for as many years as possible. Results from five projects are discussed. These results reflect 15 years of JPL software development, representing over 100 data points (systems and subsystems), over a third of a billion dollars, over four million lines of code and 28,000 person months. Analysis of this data provides a benchmark for gauging the effectiveness of past, present and future software development work. In addition, the study is meant to encourage projects to record existing metrics data and to gather future data. The SPA long term goal is to integrate the collection of historical data and ongoing project data with future project estimations.

P-TRAP: a Panicle Trait Phenotyping tool

PubMed Central

2013-01-01

Background In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods. PMID:23987653

Operations analysis (study 2.1): Shuttle upper stage software requirements

NASA Technical Reports Server (NTRS)

Wolfe, R. R.

1974-01-01

An investigation of software costs related to space shuttle upper stage operations with emphasis on the additional costs attributable to space servicing was conducted. The questions and problem areas include the following: (1) the key parameters involved with software costs; (2) historical data for extrapolation of future costs; (3) elements of the basic software development effort that are applicable to servicing functions; (4) effect of multiple servicing on complexity of the operation; and (5) are recurring software costs significant. The results address these questions and provide a foundation for estimating software costs based on the costs of similar programs and a series of empirical factors.

Classification of voting algorithms for N-version software

NASA Astrophysics Data System (ADS)

Tsarev, R. Yu; Durmuş, M. S.; Üstoglu, I.; Morozov, V. A.

2018-05-01

A voting algorithm in N-version software is a crucial component that evaluates the execution of each of the N versions and determines the correct result. Obviously, the result of the voting algorithm determines the outcome of the N-version software in general. Thus, the choice of the voting algorithm is a vital issue. A lot of voting algorithms were already developed and they may be selected for implementation based on the specifics of the analysis of input data. However, the voting algorithms applied in N-version software are not classified. This article presents an overview of classic and recent voting algorithms used in N-version software and the authors' classification of the voting algorithms. Moreover, the steps of the voting algorithms are presented and the distinctive features of the voting algorithms in Nversion software are defined.

Combining analysis with optimization at Langley Research Center. An evolutionary process

NASA Technical Reports Server (NTRS)

Rogers, J. L., Jr.

1982-01-01

The evolutionary process of combining analysis and optimization codes was traced with a view toward providing insight into the long term goal of developing the methodology for an integrated, multidisciplinary software system for the concurrent analysis and optimization of aerospace structures. It was traced along the lines of strength sizing, concurrent strength and flutter sizing, and general optimization to define a near-term goal for combining analysis and optimization codes. Development of a modular software system combining general-purpose, state-of-the-art, production-level analysis computer programs for structures, aerodynamics, and aeroelasticity with a state-of-the-art optimization program is required. Incorporation of a modular and flexible structural optimization software system into a state-of-the-art finite element analysis computer program will facilitate this effort. This effort results in the software system used that is controlled with a special-purpose language, communicates with a data management system, and is easily modified for adding new programs and capabilities. A 337 degree-of-freedom finite element model is used in verifying the accuracy of this system.

Application of a neural network to simulate analysis in an optimization process

NASA Technical Reports Server (NTRS)

Rogers, James L.; Lamarsh, William J., II

1992-01-01

A new experimental software package called NETS/PROSSS aimed at reducing the computing time required to solve a complex design problem is described. The software combines a neural network for simulating the analysis program with an optimization program. The neural network is applied to approximate results of a finite element analysis program to quickly obtain a near-optimal solution. Results of the NETS/PROSSS optimization process can also be used as an initial design in a normal optimization process and make it possible to converge to an optimum solution with significantly fewer iterations.

Optimization of analytical laboratory work using computer networking and databasing

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

Upp, D.L.; Metcalf, R.A.

1996-06-01

The Health Physics Analysis Laboratory (HPAL) performs around 600,000 analyses for radioactive nuclides each year at Los Alamos National Laboratory (LANL). Analysis matrices vary from nasal swipes, air filters, work area swipes, liquids, to the bottoms of shoes and cat litter. HPAL uses 8 liquid scintillation counters, 8 gas proportional counters, and 9 high purity germanium detectors in 5 laboratories to perform these analyses. HPAL has developed a computer network between the labs and software to produce analysis results. The software and hardware package includes barcode sample tracking, log-in, chain of custody, analysis calculations, analysis result printing, and utility programs.more » All data are written to a database, mirrored on a central server, and eventually written to CD-ROM to provide for online historical results. This system has greatly reduced the work required to provide for analysis results as well as improving the quality of the work performed.« less

NMA Analysis Center

NASA Technical Reports Server (NTRS)

Kierulf, Halfdan Pascal; Andersen, Per Helge

2013-01-01

The Norwegian Mapping Authority (NMA) has during the last few years had a close cooperation with Norwegian Defence Research Establishment (FFI) in the analysis of space geodetic data using the GEOSAT software. In 2012 NMA has taken over the full responsibility for the GEOSAT software. This implies that FFI stopped being an IVS Associate Analysis Center in 2012. NMA has been an IVS Associate Analysis Center since 28 October 2010. NMA's contributions to the IVS as an Analysis Centers focus primarily on routine production of session-by-session unconstrained and consistent normal equations by GEOSAT as input to the IVS combined solution. After the recent improvements, we expect that VLBI results produced with GEOSAT will be consistent with results from the other VLBI Analysis Centers to a satisfactory level.

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

NASA Technical Reports Server (NTRS)

Krantz, Timothy L.

2002-01-01

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

Criteria for software modularization

NASA Technical Reports Server (NTRS)

Card, David N.; Page, Gerald T.; Mcgarry, Frank E.

1985-01-01

A central issue in programming practice involves determining the appropriate size and information content of a software module. This study attempted to determine the effectiveness of two widely used criteria for software modularization, strength and size, in reducing fault rate and development cost. Data from 453 FORTRAN modules developed by professional programmers were analyzed. The results indicated that module strength is a good criterion with respect to fault rate, whereas arbitrary module size limitations inhibit programmer productivity. This analysis is a first step toward defining empirically based standards for software modularization.

Estimation and enhancement of real-time software reliability through mutation analysis

NASA Technical Reports Server (NTRS)

Geist, Robert; Offutt, A. J.; Harris, Frederick C., Jr.

1992-01-01

A simulation-based technique for obtaining numerical estimates of the reliability of N-version, real-time software is presented. An extended stochastic Petri net is employed to represent the synchronization structure of N versions of the software, where dependencies among versions are modeled through correlated sampling of module execution times. Test results utilizing specifications for NASA's planetary lander control software indicate that mutation-based testing could hold greater potential for enhancing reliability than the desirable but perhaps unachievable goal of independence among N versions.

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

NASA Technical Reports Server (NTRS)

Kranz, Timothy L.

2002-01-01

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

Software Aids Visualization of Computed Unsteady Flow

NASA Technical Reports Server (NTRS)

Kao, David; Kenwright, David

2003-01-01

Unsteady Flow Analysis Toolkit (UFAT) is a computer program that synthesizes motions of time-dependent flows represented by very large sets of data generated in computational fluid dynamics simulations. Prior to the development of UFAT, it was necessary to rely on static, single-snapshot depictions of time-dependent flows generated by flow-visualization software designed for steady flows. Whereas it typically takes weeks to analyze the results of a largescale unsteady-flow simulation by use of steady-flow visualization software, the analysis time is reduced to hours when UFAT is used. UFAT can be used to generate graphical objects of flow visualization results using multi-block curvilinear grids in the format of a previously developed NASA data-visualization program, PLOT3D. These graphical objects can be rendered using FAST, another popular flow visualization software developed at NASA. Flow-visualization techniques that can be exploited by use of UFAT include time-dependent tracking of particles, detection of vortex cores, extractions of stream ribbons and surfaces, and tetrahedral decomposition for optimal particle tracking. Unique computational features of UFAT include capabilities for automatic (batch) processing, restart, memory mapping, and parallel processing. These capabilities significantly reduce analysis time and storage requirements, relative to those of prior flow-visualization software. UFAT can be executed on a variety of supercomputers.

Progress on the development of automated data analysis algorithms and software for ultrasonic inspection of composites

NASA Astrophysics Data System (ADS)

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

2014-02-01

Progress is presented on the development and implementation of automated data analysis (ADA) software to address the burden in interpreting ultrasonic inspection data for large composite structures. The automated data analysis algorithm is presented in detail, which follows standard procedures for analyzing signals for time-of-flight indications and backwall amplitude dropout. ADA processing results are presented for test specimens that include inserted materials and discontinuities produced under poor manufacturing conditions.

Assessment of Automated Analyses of Cell Migration on Flat and Nanostructured Surfaces

PubMed Central

Grădinaru, Cristian; Łopacińska, Joanna M.; Huth, Johannes; Kestler, Hans A.; Flyvbjerg, Henrik; Mølhave, Kristian

2012-01-01

Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact that the segmentation routines of such programs are often challenged by nanostructured surfaces makes the question more pertinent. Here we illustrate how it is possible to track cells on bright field microscopy images with image analysis routines implemented in an open-source cell tracking program, PACT (Program for Automated Cell Tracking). We compare the automated motility analysis of three cell tracking programs, PACT, Autozell, and TLA, using the same movies as input for all three programs. We find that different programs track overlapping, but different subsets of cells due to different segmentation methods. Unfortunately, population averages based on such different cell populations, differ significantly in some cases. Thus, results obtained with one software package are not necessarily reproducible by other software. PMID:24688640

Tools for Embedded Computing Systems Software

NASA Technical Reports Server (NTRS)

1978-01-01

A workshop was held to assess the state of tools for embedded systems software and to determine directions for tool development. A synopsis of the talk and the key figures of each workshop presentation, together with chairmen summaries, are presented. The presentations covered four major areas: (1) tools and the software environment (development and testing); (2) tools and software requirements, design, and specification; (3) tools and language processors; and (4) tools and verification and validation (analysis and testing). The utility and contribution of existing tools and research results for the development and testing of embedded computing systems software are described and assessed.

SARA: a software environment for the analysis of relaxation data acquired with accordion spectroscopy

PubMed Central

Harden, Bradley J.

2014-01-01

We present SARA (Software for Accordion Relaxation Analysis), an interactive and user-friendly MATLAB software environment designed for analyzing relaxation data obtained with accordion spectroscopy. Accordion spectroscopy can be used to measure nuclear magnetic resonance (NMR) relaxation rates in a fraction of the time required by traditional methods, yet data analysis can be intimidating and no unified software packages are available to assist investigators. Hence, the technique has not achieved widespread use within the NMR community. SARA offers users a selection of analysis protocols spanning those presented in the literature thus far, with modifications permitting a more general application to crowded spectra such as those of proteins. We discuss the advantages and limitations of each fitting method and suggest a protocol combining the strengths of each procedure to achieve optimal results. In the end, SARA provides an environment for facile extraction of relaxation rates and should promote routine application of accordion relaxation spectroscopy. PMID:24408364

POSTMan (POST-translational modification analysis), a software application for PTM discovery.

PubMed

Arntzen, Magnus Ø; Osland, Christoffer Leif; Raa, Christopher Rasch-Olsen; Kopperud, Reidun; Døskeland, Stein-Ove; Lewis, Aurélia E; D'Santos, Clive S

2009-03-01

Post-translationally modified peptides present in low concentrations are often not selected for CID, resulting in no sequence information for these peptides. We have developed a software POSTMan (POST-translational Modification analysis) allowing post-translationally modified peptides to be targeted for fragmentation. The software aligns LC-MS runs (MS(1) data) between individual runs or within a single run and isolates pairs of peptides which differ by a user defined mass difference (post-translationally modified peptides). The method was validated for acetylated peptides and allowed an assessment of even the basal protein phosphorylation of phenylalanine hydroxylase (PHA) in intact cells.

Non-Grey Radiation Modeling using Thermal Desktop/Sindaworks TFAWS06-1009

NASA Technical Reports Server (NTRS)

Anderson, Kevin R.; Paine, Chris

2006-01-01

This paper provides an overview of the non-grey radiation modeling capabilities of Cullimore and Ring's Thermal Desktop(Registered TradeMark) Version 4.8 SindaWorks software. The non-grey radiation analysis theory implemented by Sindaworks and the methodology used by the software are outlined. Representative results from a parametric trade study of a radiation shield comprised of a series of v-grooved shaped deployable panels is used to illustrate the capabilities of the SindaWorks non-grey radiation thermal analysis software using emissivities with temperature and wavelength dependency modeled via a Hagen-Rubens relationship.

Development of image analysis software for quantification of viable cells in microchips.

PubMed

Georg, Maximilian; Fernández-Cabada, Tamara; Bourguignon, Natalia; Karp, Paola; Peñaherrera, Ana B; Helguera, Gustavo; Lerner, Betiana; Pérez, Maximiliano S; Mertelsmann, Roland

2018-01-01

Over the past few years, image analysis has emerged as a powerful tool for analyzing various cell biology parameters in an unprecedented and highly specific manner. The amount of data that is generated requires automated methods for the processing and analysis of all the resulting information. The software available so far are suitable for the processing of fluorescence and phase contrast images, but often do not provide good results from transmission light microscopy images, due to the intrinsic variation of the acquisition of images technique itself (adjustment of brightness / contrast, for instance) and the variability between image acquisition introduced by operators / equipment. In this contribution, it has been presented an image processing software, Python based image analysis for cell growth (PIACG), that is able to calculate the total area of the well occupied by cells with fusiform and rounded morphology in response to different concentrations of fetal bovine serum in microfluidic chips, from microscopy images in transmission light, in a highly efficient way.

Combining Static Analysis and Model Checking for Software Analysis

NASA Technical Reports Server (NTRS)

Brat, Guillaume; Visser, Willem; Clancy, Daniel (Technical Monitor)

2003-01-01

We present an iterative technique in which model checking and static analysis are combined to verify large software systems. The role of the static analysis is to compute partial order information which the model checker uses to reduce the state space. During exploration, the model checker also computes aliasing information that it gives to the static analyzer which can then refine its analysis. The result of this refined analysis is then fed back to the model checker which updates its partial order reduction. At each step of this iterative process, the static analysis computes optimistic information which results in an unsafe reduction of the state space. However we show that the process converges to a fired point at which time the partial order information is safe and the whole state space is explored.

Four applications of a software data collection and analysis methodology

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Selby, Richard W., Jr.

1985-01-01

The evaluation of software technologies suffers because of the lack of quantitative assessment of their effect on software development and modification. A seven-step data collection and analysis methodology couples software technology evaluation with software measurement. Four in-depth applications of the methodology are presented. The four studies represent each of the general categories of analyses on the software product and development process: blocked subject-project studies, replicated project studies, multi-project variation studies, and single project strategies. The four applications are in the areas of, respectively, software testing, cleanroom software development, characteristic software metric sets, and software error analysis.

A Consumer's Guide to Benchmark Dose Models: Results of U.S. EPA Testing of 14 Dichotomous, 8 Continuous, and 6 Developmental Models (Presentation)

EPA Science Inventory

Benchmark dose risk assessment software (BMDS) was designed by EPA to generate dose-response curves and facilitate the analysis, interpretation and synthesis of toxicological data. Partial results of QA/QC testing of the EPA benchmark dose software (BMDS) are presented. BMDS pr...

A streamlined Python framework for AT-TPC data analysis

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Evaluation of automated decisionmaking methodologies and development of an integrated robotic system simulation, volume 2, part 1. Appendix A: Software documentation

NASA Technical Reports Server (NTRS)

Lowrie, J. W.; Fermelia, A. J.; Haley, D. C.; Gremban, K. D.; Vanbaalen, J.; Walsh, R. W.

1982-01-01

Documentation of the preliminary software developed as a framework for a generalized integrated robotic system simulation is presented. The program structure is composed of three major functions controlled by a program executive. The three major functions are: system definition, analysis tools, and post processing. The system definition function handles user input of system parameters and definition of the manipulator configuration. The analysis tools function handles the computational requirements of the program. The post processing function allows for more detailed study of the results of analysis tool function executions. Also documented is the manipulator joint model software to be used as the basis of the manipulator simulation which will be part of the analysis tools capability.

P-TRAP: a Panicle TRAit Phenotyping tool.

PubMed

A L-Tam, Faroq; Adam, Helene; Anjos, António dos; Lorieux, Mathias; Larmande, Pierre; Ghesquière, Alain; Jouannic, Stefan; Shahbazkia, Hamid Reza

2013-08-29

In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.

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.

Effectiveness of an automatic tracking software in underwater motion analysis.

PubMed

Magalhaes, Fabrício A; Sawacha, Zimi; Di Michele, Rocco; Cortesi, Matteo; Gatta, Giorgio; Fantozzi, Silvia

2013-01-01

Tracking of markers placed on anatomical landmarks is a common practice in sports science to perform the kinematic analysis that interests both athletes and coaches. Although different software programs have been developed to automatically track markers and/or features, none of them was specifically designed to analyze underwater motion. Hence, this study aimed to evaluate the effectiveness of a software developed for automatic tracking of underwater movements (DVP), based on the Kanade-Lucas-Tomasi feature tracker. Twenty-one video recordings of different aquatic exercises (n = 2940 markers' positions) were manually tracked to determine the markers' center coordinates. Then, the videos were automatically tracked using DVP and a commercially available software (COM). Since tracking techniques may produce false targets, an operator was instructed to stop the automatic procedure and to correct the position of the cursor when the distance between the calculated marker's coordinate and the reference one was higher than 4 pixels. The proportion of manual interventions required by the software was used as a measure of the degree of automation. Overall, manual interventions were 10.4% lower for DVP (7.4%) than for COM (17.8%). Moreover, when examining the different exercise modes separately, the percentage of manual interventions was 5.6% to 29.3% lower for DVP than for COM. Similar results were observed when analyzing the type of marker rather than the type of exercise, with 9.9% less manual interventions for DVP than for COM. In conclusion, based on these results, the developed automatic tracking software presented can be used as a valid and useful tool for underwater motion analysis. Key PointsThe availability of effective software for automatic tracking would represent a significant advance for the practical use of kinematic analysis in swimming and other aquatic sports.An important feature of automatic tracking software is to require limited human interventions and supervision, thus allowing short processing time.When tracking underwater movements, the degree of automation of the tracking procedure is influenced by the capability of the algorithm to overcome difficulties linked to the small target size, the low image quality and the presence of background clutters.The newly developed feature-tracking algorithm has shown a good automatic tracking effectiveness in underwater motion analysis with significantly smaller percentage of required manual interventions when compared to a commercial software.

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.

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

An experiment in software reliability

NASA Technical Reports Server (NTRS)

Dunham, J. R.; Pierce, J. L.

1986-01-01

The results of a software reliability experiment conducted in a controlled laboratory setting are reported. The experiment was undertaken to gather data on software failures and is one in a series of experiments being pursued by the Fault Tolerant Systems Branch of NASA Langley Research Center to find a means of credibly performing reliability evaluations of flight control software. The experiment tests a small sample of implementations of radar tracking software having ultra-reliability requirements and uses n-version programming for error detection, and repetitive run modeling for failure and fault rate estimation. The experiment results agree with those of Nagel and Skrivan in that the program error rates suggest an approximate log-linear pattern and the individual faults occurred with significantly different error rates. Additional analysis of the experimental data raises new questions concerning the phenomenon of interacting faults. This phenomenon may provide one explanation for software reliability decay.

[Development and practice evaluation of blood acid-base imbalance analysis software].

PubMed

Chen, Bo; Huang, Haiying; Zhou, Qiang; Peng, Shan; Jia, Hongyu; Ji, Tianxing

2014-11-01

To develop a blood gas, acid-base imbalance analysis computer software to diagnose systematically, rapidly, accurately and automatically determine acid-base imbalance type, and evaluate the clinical application. Using VBA programming language, a computer aided diagnostic software for the judgment of acid-base balance was developed. The clinical data of 220 patients admitted to the Second Affiliated Hospital of Guangzhou Medical University were retrospectively analyzed. The arterial blood gas [pH value, HCO(3)(-), arterial partial pressure of carbon dioxide (PaCO₂)] and electrolytes included data (Na⁺ and Cl⁻) were collected. Data were entered into the software for acid-base imbalances judgment. At the same time the data generation was calculated manually by H-H compensation formula for determining the type of acid-base imbalance. The consistency of judgment results from software and manual calculation was evaluated, and the judgment time of two methods was compared. The clinical diagnosis of the types of acid-base imbalance for the 220 patients: 65 cases were normal, 90 cases with simple type, mixed type in 41 cases, and triplex type in 24 cases. The accuracy of the judgment results of the normal and triplex types from computer software compared with which were calculated manually was 100%, the accuracy of the simple type judgment was 98.9% and 78.0% for the mixed type, and the total accuracy was 95.5%. The Kappa value of judgment result from software and manual judgment was 0.935, P=0.000. It was demonstrated that the consistency was very good. The time for software to determine acid-base imbalances was significantly shorter than the manual judgment (seconds:18.14 ± 3.80 vs. 43.79 ± 23.86, t=7.466, P=0.000), so the method of software was much faster than the manual method. Software judgment can replace manual judgment with the characteristics of rapid, accurate and convenient, can improve work efficiency and quality of clinical doctors and has great clinical application promotion value.

Influence of standardization on the precision (reproducibility) of dental cast analysis with virtual 3-dimensional models.

PubMed

Hayashi, Kazuo; Chung, Onejune; Park, Seojung; Lee, Seung-Pyo; Sachdeva, Rohit C L; Mizoguchi, Itaru

2015-03-01

Virtual 3-dimensional (3D) models obtained by scanning of physical casts have become an alternative to conventional dental cast analysis in orthodontic treatment. If the precision (reproducibility) of virtual 3D model analysis can be further improved, digital orthodontics could be even more widely accepted. The purpose of this study was to clarify the influence of "standardization" of the target points for dental cast analysis using virtual 3D models. Physical plaster models were also measured to obtain additional information. Five sets of dental casts were used. The dental casts were scanned with R700 (3Shape, Copenhagen, Denmark) and REXCAN DS2 3D (Solutionix, Seoul, Korea) scanners. In this study, 3 system and software packages were used: SureSmile (OraMetrix, Richardson, Tex), Rapidform (Inus, Seoul, Korea), and I-DEAS (SDRC, Milford, Conn). Without standardization, the maximum differences were observed between the SureSmile software and the Rapidform software (0.39 mm ± 0.07). With standardization, the maximum differences were observed between the SureSmile software and measurements with a digital caliper (0.099 mm ± 0.01), and this difference was significantly greater (P <0.05) than the 2 other mean difference values. Furthermore, the results of this study showed that the mean differences "WITH" standardization were significantly lower than those "WITHOUT" standardization for all systems, software packages, or methods. The results showed that elimination of the influence of usability or habituation is important for improving the reproducibility of dental cast analysis. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

SEURAT: Visual analytics for the integrated analysis of microarray data

PubMed Central

2010-01-01

Background In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. Results We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. Conclusions The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data. PMID:20525257

NEXT GENERATION ANALYSIS SOFTWARE FOR COMPONENT EVALUATION - Results of Rotational Seismometer Evaluation

NASA Astrophysics Data System (ADS)

Hart, D. M.; Merchant, B. J.; Abbott, R. E.

2012-12-01

The Component Evaluation project at Sandia National Laboratories supports the Ground-based Nuclear Explosion Monitoring program by performing testing and evaluation of the components that are used in seismic and infrasound monitoring systems. In order to perform this work, Component Evaluation maintains a testing facility called the FACT (Facility for Acceptance, Calibration, and Testing) site, a variety of test bed equipment, and a suite of software tools for analyzing test data. Recently, Component Evaluation has successfully integrated several improvements to its software analysis tools and test bed equipment that have substantially improved our ability to test and evaluate components. The software tool that is used to analyze test data is called TALENT: Test and AnaLysis EvaluatioN Tool. TALENT is designed to be a single, standard interface to all test configuration, metadata, parameters, waveforms, and results that are generated in the course of testing monitoring systems. It provides traceability by capturing everything about a test in a relational database that is required to reproduce the results of that test. TALENT provides a simple, yet powerful, user interface to quickly acquire, process, and analyze waveform test data. The software tool has also been expanded recently to handle sensors whose output is proportional to rotation angle, or rotation rate. As an example of this new processing capability, we show results from testing the new ATA ARS-16 rotational seismometer. The test data was collected at the USGS ASL. Four datasets were processed: 1) 1 Hz with increasing amplitude, 2) 4 Hz with increasing amplitude, 3) 16 Hz with increasing amplitude and 4) twenty-six discrete frequencies between 0.353 Hz to 64 Hz. The results are compared to manufacture-supplied data sheets.

On the Multilevel Nature of Meta-Analysis: A Tutorial, Comparison of Software Programs, and Discussion of Analytic Choices.

PubMed

Pastor, Dena A; Lazowski, Rory A

2018-01-01

The term "multilevel meta-analysis" is encountered not only in applied research studies, but in multilevel resources comparing traditional meta-analysis to multilevel meta-analysis. In this tutorial, we argue that the term "multilevel meta-analysis" is redundant since all meta-analysis can be formulated as a special kind of multilevel model. To clarify the multilevel nature of meta-analysis the four standard meta-analytic models are presented using multilevel equations and fit to an example data set using four software programs: two specific to meta-analysis (metafor in R and SPSS macros) and two specific to multilevel modeling (PROC MIXED in SAS and HLM). The same parameter estimates are obtained across programs underscoring that all meta-analyses are multilevel in nature. Despite the equivalent results, not all software programs are alike and differences are noted in the output provided and estimators available. This tutorial also recasts distinctions made in the literature between traditional and multilevel meta-analysis as differences between meta-analytic choices, not between meta-analytic models, and provides guidance to inform choices in estimators, significance tests, moderator analyses, and modeling sequence. The extent to which the software programs allow flexibility with respect to these decisions is noted, with metafor emerging as the most favorable program reviewed.

Analysis Software

NASA Technical Reports Server (NTRS)

1994-01-01

General Purpose Boundary Element Solution Technology (GPBEST) software employs the boundary element method of mechanical engineering analysis, as opposed to finite element. It is, according to one of its developers, 10 times faster in data preparation and more accurate than other methods. Its use results in less expensive products because the time between design and manufacturing is shortened. A commercial derivative of a NASA-developed computer code, it is marketed by Best Corporation to solve problems in stress analysis, heat transfer, fluid analysis and yielding and cracking of solids. Other applications include designing tractor and auto parts, household appliances and acoustic analysis.

Multidisciplinary High-Fidelity Analysis and Optimization of Aerospace Vehicles. Part 2; Preliminary Results

NASA Technical Reports Server (NTRS)

Walsh, J. L.; Weston, R. P.; Samareh, J. A.; Mason, B. H.; Green, L. L.; Biedron, R. T.

2000-01-01

An objective of the High Performance Computing and Communication Program at the NASA Langley Research Center is to demonstrate multidisciplinary shape and sizing optimization of a complete aerospace vehicle configuration by using high-fidelity finite-element structural analysis and computational fluid dynamics aerodynamic analysis in a distributed, heterogeneous computing environment that includes high performance parallel computing. A software system has been designed and implemented to integrate a set of existing discipline analysis codes, some of them computationally intensive, into a distributed computational environment for the design of a high-speed civil transport configuration. The paper describes both the preliminary results from implementing and validating the multidisciplinary analysis and the results from an aerodynamic optimization. The discipline codes are integrated by using the Java programming language and a Common Object Request Broker Architecture compliant software product. A companion paper describes the formulation of the multidisciplinary analysis and optimization system.

HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data.

PubMed

Trivedi, Prinal; Edwards, Jode W; Wang, Jelai; Gadbury, Gary L; Srinivasasainagendra, Vinodh; Zakharkin, Stanislav O; Kim, Kyoungmi; Mehta, Tapan; Brand, Jacob P L; Patki, Amit; Page, Grier P; Allison, David B

2005-04-06

Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics) is a software package designed for analysis of high dimensional biology data such as microarray data. It was initially developed for the analysis of microarray gene expression data, but it can also be used for some applications in proteomics and other aspects of genomics. HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing. Results generated from data preprocessing methods, quality control analysis and hypothesis testing methods are output in the form of Excel CSV tables, graphs and an Html report summarizing data analysis. HDBStat! is a platform-independent software that is freely available to academic institutions and non-profit organizations. It can be downloaded from our website http://www.soph.uab.edu/ssg_content.asp?id=1164.

Space station data system analysis/architecture study. Task 3: Trade studies, DR-5, volume 1

NASA Technical Reports Server (NTRS)

1985-01-01

The primary objective of Task 3 is to provide additional analysis and insight necessary to support key design/programmatic decision for options quantification and selection for system definition. This includes: (1) the identification of key trade study topics; (2) the definition of a trade study procedure for each topic (issues to be resolved, key inputs, criteria/weighting, methodology); (3) conduct tradeoff and sensitivity analysis; and (4) the review/verification of results within the context of evolving system design and definition. The trade study topics addressed in this volume include space autonomy and function automation, software transportability, system network topology, communications standardization, onboard local area networking, distributed operating system, software configuration management, and the software development environment facility.

Integrated Optical Design Analysis (IODA): New Test Data and Modeling Features

NASA Technical Reports Server (NTRS)

Moore, Jim; Troy, Ed; Patrick, Brian

2003-01-01

A general overview of the capabilities of the IODA ("Integrated Optical Design Analysis") exchange of data and modeling results between thermal, structures, optical design, and testing engineering disciplines. This presentation focuses on new features added to the software that allow measured test data to be imported into the IODA environment for post processing or comparisons with pretest model predictions. software is presented. IODA promotes efficient

IUE Data Analysis Software for Personal Computers

NASA Technical Reports Server (NTRS)

Thompson, R.; Caplinger, J.; Taylor, L.; Lawton , P.

1996-01-01

This report summarizes the work performed for the program titled, "IUE Data Analysis Software for Personal Computers" awarded under Astrophysics Data Program NRA 92-OSSA-15. The work performed was completed over a 2-year period starting in April 1994. As a result of the project, 450 IDL routines and eight database tables are now available for distribution for Power Macintosh computers and Personal Computers running Windows 3.1.

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

A Scalable Analysis Toolkit

NASA Technical Reports Server (NTRS)

Aiken, Alexander

2001-01-01

The Scalable Analysis Toolkit (SAT) project aimed to demonstrate that it is feasible and useful to statically detect software bugs in very large systems. The technical focus of the project was on a relatively new class of constraint-based techniques for analysis software, where the desired facts about programs (e.g., the presence of a particular bug) are phrased as constraint problems to be solved. At the beginning of this project, the most successful forms of formal software analysis were limited forms of automatic theorem proving (as exemplified by the analyses used in language type systems and optimizing compilers), semi-automatic theorem proving for full verification, and model checking. With a few notable exceptions these approaches had not been demonstrated to scale to software systems of even 50,000 lines of code. Realistic approaches to large-scale software analysis cannot hope to make every conceivable formal method scale. Thus, the SAT approach is to mix different methods in one application by using coarse and fast but still adequate methods at the largest scales, and reserving the use of more precise but also more expensive methods at smaller scales for critical aspects (that is, aspects critical to the analysis problem under consideration) of a software system. The principled method proposed for combining a heterogeneous collection of formal systems with different scalability characteristics is mixed constraints. This idea had been used previously in small-scale applications with encouraging results: using mostly coarse methods and narrowly targeted precise methods, useful information (meaning the discovery of bugs in real programs) was obtained with excellent scalability.

Unified Software Solution for Efficient SPR Data Analysis in Drug Research

PubMed Central

Dahl, Göran; Steigele, Stephan; Hillertz, Per; Tigerström, Anna; Egnéus, Anders; Mehrle, Alexander; Ginkel, Martin; Edfeldt, Fredrik; Holdgate, Geoff; O’Connell, Nichole; Kappler, Bernd; Brodte, Annette; Rawlins, Philip B.; Davies, Gareth; Westberg, Eva-Lotta; Folmer, Rutger H. A.; Heyse, Stephan

2016-01-01

Surface plasmon resonance (SPR) is a powerful method for obtaining detailed molecular interaction parameters. Modern instrumentation with its increased throughput has enabled routine screening by SPR in hit-to-lead and lead optimization programs, and SPR has become a mainstream drug discovery technology. However, the processing and reporting of SPR data in drug discovery are typically performed manually, which is both time-consuming and tedious. Here, we present the workflow concept, design and experiences with a software module relying on a single, browser-based software platform for the processing, analysis, and reporting of SPR data. The efficiency of this concept lies in the immediate availability of end results: data are processed and analyzed upon loading the raw data file, allowing the user to immediately quality control the results. Once completed, the user can automatically report those results to data repositories for corporate access and quickly generate printed reports or documents. The software module has resulted in a very efficient and effective workflow through saved time and improved quality control. We discuss these benefits and show how this process defines a new benchmark in the drug discovery industry for the handling, interpretation, visualization, and sharing of SPR data. PMID:27789754

Ground Systems Development Environment (GSDE) interface requirements analysis

NASA Technical Reports Server (NTRS)

Church, Victor E.; Philips, John; Hartenstein, Ray; Bassman, Mitchell; Ruskin, Leslie; Perez-Davila, Alfredo

1991-01-01

A set of procedural and functional requirements are presented for the interface between software development environments and software integration and test systems used for space station ground systems software. The requirements focus on the need for centralized configuration management of software as it is transitioned from development to formal, target based testing. This concludes the GSDE Interface Requirements study. A summary is presented of findings concerning the interface itself, possible interface and prototyping directions for further study, and results of the investigation of the Cronus distributed applications environment.

Error Free Software

NASA Technical Reports Server (NTRS)

1985-01-01

A mathematical theory for development of "higher order" software to catch computer mistakes resulted from a Johnson Space Center contract for Apollo spacecraft navigation. Two women who were involved in the project formed Higher Order Software, Inc. to develop and market the system of error analysis and correction. They designed software which is logically error-free, which, in one instance, was found to increase productivity by 600%. USE.IT defines its objectives using AXES -- a user can write in English and the system converts to computer languages. It is employed by several large corporations.

Spreadsheets for Analyzing and Optimizing Space Missions

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Agrawal, Anil K.; Czikmantory, Akos J.; Weisbin, Charles R.; Hua, Hook; Neff, Jon M.; Cowdin, Mark A.; Lewis, Brian S.; Iroz, Juana; Ross, Rick

2009-01-01

XCALIBR (XML Capability Analysis LIBRary) is a set of Extensible Markup Language (XML) database and spreadsheet- based analysis software tools designed to assist in technology-return-on-investment analysis and optimization of technology portfolios pertaining to outer-space missions. XCALIBR is also being examined for use in planning, tracking, and documentation of projects. An XCALIBR database contains information on mission requirements and technological capabilities, which are related by use of an XML taxonomy. XCALIBR incorporates a standardized interface for exporting data and analysis templates to an Excel spreadsheet. Unique features of XCALIBR include the following: It is inherently hierarchical by virtue of its XML basis. The XML taxonomy codifies a comprehensive data structure and data dictionary that includes performance metrics for spacecraft, sensors, and spacecraft systems other than sensors. The taxonomy contains >700 nodes representing all levels, from system through subsystem to individual parts. All entries are searchable and machine readable. There is an intuitive Web-based user interface. The software automatically matches technologies to mission requirements. The software automatically generates, and makes the required entries in, an Excel return-on-investment analysis software tool. The results of an analysis are presented in both tabular and graphical displays.

Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

NASA Astrophysics Data System (ADS)

Fisher, Ward

2014-05-01

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

A Practical Approach to Modified Condition/Decision Coverage

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.; Veerhusem, Dan S.

2001-01-01

Testing of software intended for safety-critical applications in commercial transport aircraft must achieve modified condition/decision coverage (MC/DC) of the software structure. This requirement causes anxiety for many within the aviation software community. Results of a survey of the aviation software industry indicate that many developers believe that meeting the MC/DC requirement is difficult, and the cost is exorbitant. Some of the difficulties stem, no doubt, from the scant information available on the subject. This paper provides a practical 5-step approach for assessing MC/DC for aviation software products, and an analysis of some types of errors expected to be caught when MC/DC is achieved1.

PAnalyzer: A software tool for protein inference in shotgun proteomics

PubMed Central

2012-01-01

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool. PMID:23126499

Rosetta CONSERT operations and data analysis preparation: simulation software tools.

NASA Astrophysics Data System (ADS)

Rogez, Yves; Hérique, Alain; Cardiet, Maël; Zine, Sonia; Westphal, Mathieu; Micallef, Mickael; Berquin, Yann; Kofman, Wlodek

2014-05-01

The CONSERT experiment onboard Rosetta and Philae will perform the tomography of the 67P/CG comet nucleus by measuring radio waves transmission from the Rosetta S/C to the Philae Lander. The accurate analysis of travel time measurements will deliver unique knowledge of the nucleus interior dielectric properties. The challenging complexity of CONSERT operations requirements, combining both Rosetta and Philae, allows only a few set of opportunities to acquire data. Thus, we need a fine analysis of the impact of Rosetta trajectory, Philae position and comet shape on CONSERT measurements, in order to take optimal decisions in a short time. The integration of simulation results and mission parameters provides synthetic information to evaluate performances and risks for each opportunity. The preparation of CONSERT measurements before space operations is a key to achieve the best science return of the experiment. In addition, during Rosetta space operations, these software tools will allow a "real-time" first analysis of the latest measurements to improve the next acquisition sequences. The software tools themselves are built around a 3D electromagnetic radio wave simulation, taking into account the signal polarization. It is based on ray-tracing algorithms specifically designed for quick orbit analysis and radar signal generation. This allows computation on big domains relatively to the wavelength. The extensive use of 3D visualization tools provides comprehensive and synthetic views of the results. The software suite is designed to be extended, after Rosetta operations, to the full 3D measurement data analysis using inversion methods.

Fusing Symbolic and Numerical Diagnostic Computations

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

X-2000 Anomaly Detection Language denotes a developmental computing language, and the software that establishes and utilizes the language, for fusing two diagnostic computer programs, one implementing a numerical analysis method, the other implementing a symbolic analysis method into a unified event-based decision analysis software system for realtime detection of events (e.g., failures) in a spacecraft, aircraft, or other complex engineering system. The numerical analysis method is performed by beacon-based exception analysis for multi-missions (BEAMs), which has been discussed in several previous NASA Tech Briefs articles. The symbolic analysis method is, more specifically, an artificial-intelligence method of the knowledge-based, inference engine type, and its implementation is exemplified by the Spacecraft Health Inference Engine (SHINE) software. The goal in developing the capability to fuse numerical and symbolic diagnostic components is to increase the depth of analysis beyond that previously attainable, thereby increasing the degree of confidence in the computed results. In practical terms, the sought improvement is to enable detection of all or most events, with no or few false alarms.

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

PubMed Central

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-01-01

Background It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. Results This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. Conclusion SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes. PMID:18706080

Critical Thinking Skills of Students through Mathematics Learning with ASSURE Model Assisted by Software Autograph

NASA Astrophysics Data System (ADS)

Kristianti, Y.; Prabawanto, S.; Suhendra, S.

2017-09-01

This study aims to examine the ability of critical thinking and students who attain learning mathematics with learning model ASSURE assisted Autograph software. The design of this study was experimental group with pre-test and post-test control group. The experimental group obtained a mathematics learning with ASSURE-assisted model Autograph software and the control group acquired the mathematics learning with the conventional model. The data are obtained from the research results through critical thinking skills tests. This research was conducted at junior high school level with research population in one of junior high school student in Subang Regency of Lesson Year 2016/2017 and research sample of class VIII student in one of junior high school in Subang Regency for 2 classes. Analysis of research data is administered quantitatively. Quantitative data analysis was performed on the normalized gain level between the two sample groups using a one-way anova test. The results show that mathematics learning with ASSURE assisted model Autograph software can improve the critical thinking ability of junior high school students. Mathematical learning using ASSURE-assisted model Autograph software is significantly better in improving the critical thinking skills of junior high school students compared with conventional models.

Bone histomorphometry using free and commonly available software

PubMed Central

Egan, Kevin P.; Brennan, Tracy A.; Pignolo, Robert J.

2012-01-01

Aims Histomorphometric analysis is a widely used technique to assess changes in tissue structure and function. Commercially-available programs that measure histomorphometric parameters can be cost prohibitive. In this study, we compared an inexpensive method of histomorphometry to a current proprietary software program. Methods and results Image J and Adobe Photoshop® were used to measure static and kinetic bone histomorphometric parameters. Photomicrographs of Goldner’s Trichrome stained femurs were used to generate black and white image masks, representing bone and non-bone tissue, respectively, in Adobe Photoshop®. The masks were used to quantify histomorphometric parameters (bone volume, tissue volume, osteoid volume, mineralizing surface, and interlabel width) in Image J. The resultant values obtained using Image J and the proprietary software were compared and found to be statistically non-significant. Conclusions The wide ranging use of histomorphometric analysis for assessing the basic morphology of tissue components makes it important to have affordable and accurate measurement options that are available for a diverse range of applications. Here we have developed and validated an approach to histomorphometry using commonly and freely available software that is comparable to a much more costly, commercially-available software program. PMID:22882309

Data analysis software for the autoradiographic enhancement process. Volumes 1, 2, and 3, and appendix

NASA Technical Reports Server (NTRS)

Singh, S. P.

1979-01-01

The computer software developed to set up a method for Wiener spectrum analysis of photographic films is presented. This method is used for the quantitative analysis of the autoradiographic enhancement process. The software requirements and design for the autoradiographic enhancement process are given along with the program listings and the users manual. A software description and program listings modification of the data analysis software are included.

Scientific Software - the role of best practices and recommendations

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Infusing Reliability Techniques into Software Safety Analysis

NASA Technical Reports Server (NTRS)

Shi, Ying

2015-01-01

Software safety analysis for a large software intensive system is always a challenge. Software safety practitioners need to ensure that software related hazards are completely identified, controlled, and tracked. This paper discusses in detail how to incorporate the traditional reliability techniques into the entire software safety analysis process. In addition, this paper addresses how information can be effectively shared between the various practitioners involved in the software safety analyses. The author has successfully applied the approach to several aerospace applications. Examples are provided to illustrate the key steps of the proposed approach.

Information Extraction for System-Software Safety Analysis: Calendar Year 2008 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2009-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

Software Process Assessment (SPA)

NASA Technical Reports Server (NTRS)

Rosenberg, Linda H.; Sheppard, Sylvia B.; Butler, Scott A.

1994-01-01

NASA's environment mirrors the changes taking place in the nation at large, i.e. workers are being asked to do more work with fewer resources. For software developers at NASA's Goddard Space Flight Center (GSFC), the effects of this change are that we must continue to produce quality code that is maintainable and reusable, but we must learn to produce it more efficiently and less expensively. To accomplish this goal, the Data Systems Technology Division (DSTD) at GSFC is trying a variety of both proven and state-of-the-art techniques for software development (e.g., object-oriented design, prototyping, designing for reuse, etc.). In order to evaluate the effectiveness of these techniques, the Software Process Assessment (SPA) program was initiated. SPA was begun under the assumption that the effects of different software development processes, techniques, and tools, on the resulting product must be evaluated in an objective manner in order to assess any benefits that may have accrued. SPA involves the collection and analysis of software product and process data. These data include metrics such as effort, code changes, size, complexity, and code readability. This paper describes the SPA data collection and analysis methodology and presents examples of benefits realized thus far by DSTD's software developers and managers.

A new background subtraction method for Western blot densitometry band quantification through image analysis software.

PubMed

Gallo-Oller, Gabriel; Ordoñez, Raquel; Dotor, Javier

2018-06-01

Since its first description, Western blot has been widely used in molecular labs. It constitutes a multistep method that allows the detection and/or quantification of proteins from simple to complex protein mixtures. Western blot quantification method constitutes a critical step in order to obtain accurate and reproducible results. Due to the technical knowledge required for densitometry analysis together with the resources availability, standard office scanners are often used for the imaging acquisition of developed Western blot films. Furthermore, the use of semi-quantitative software as ImageJ (Java-based image-processing and analysis software) is clearly increasing in different scientific fields. In this work, we describe the use of office scanner coupled with the ImageJ software together with a new image background subtraction method for accurate Western blot quantification. The proposed method represents an affordable, accurate and reproducible approximation that could be used in the presence of limited resources availability. Copyright © 2018 Elsevier B.V. All rights reserved.

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

PubMed

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

2012-08-01

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

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat.

PubMed

Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

2017-01-01

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat ( Triticum aestivum ) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way. Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases.

OSPAR standard method and software for statistical analysis of beach litter data.

PubMed

Schulz, Marcus; van Loon, Willem; Fleet, David M; Baggelaar, Paul; van der Meulen, Eit

2017-09-15

The aim of this study is to develop standard statistical methods and software for the analysis of beach litter data. The optimal ensemble of statistical methods comprises the Mann-Kendall trend test, the Theil-Sen slope estimation, the Wilcoxon step trend test and basic descriptive statistics. The application of Litter Analyst, a tailor-made software for analysing the results of beach litter surveys, to OSPAR beach litter data from seven beaches bordering on the south-eastern North Sea, revealed 23 significant trends in the abundances of beach litter types for the period 2009-2014. Litter Analyst revealed a large variation in the abundance of litter types between beaches. To reduce the effects of spatial variation, trend analysis of beach litter data can most effectively be performed at the beach or national level. Spatial aggregation of beach litter data within a region is possible, but resulted in a considerable reduction in the number of significant trends. Copyright © 2017 Elsevier Ltd. All rights reserved.

MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.

PubMed

Muth, Thilo; Kohrs, Fabian; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Reichl, Udo; Martens, Lennart; Renard, Bernhard Y

2018-01-02

Metaproteomics, the mass spectrometry-based analysis of proteins from multispecies samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce the MetaProteomeAnalyzer (MPA) Portable software. In contrast to the original server-based MPA application, this newly developed tool no longer requires computational expertise for installation and is now independent of any relational database system. In addition, MPA Portable now supports state-of-the-art database search engines and a convenient command line interface for high-performance data processing tasks. While search engine results can easily be combined to increase the protein identification yield, an additional two-step workflow is implemented to provide sufficient analysis resolution for further postprocessing steps, such as protein grouping as well as taxonomic and functional annotation. Our new application has been developed with a focus on intuitive usability, adherence to data standards, and adaptation to Web-based workflow platforms. The open source software package can be found at https://github.com/compomics/meta-proteome-analyzer .

Studies of regional and global tectonics and the rotation of the earth using very-long baseline interferometry

NASA Technical Reports Server (NTRS)

Shapiro, Irwin I.

1989-01-01

Progress in the areas of data analysis, atmospheric delay calibration and software conversion is reported. Over 800 very long baseline interferometry (VLBI) experiments were analyzed in the last 6 months. Reprocessing of the Mark III VLBI data set is almost completed. Results of analysis of the water-vapor radiometer (WVR) data were submitted and a preprint of a related paper is attached. Work on conversion of the VLBI analysis software from HP1000 to Unix based workstations is continuing.

Status and Plans for the Vienna VLBI and Satellite Software (VieVS 3.0)

NASA Astrophysics Data System (ADS)

Gruber, Jakob; Böhm, Johannes; Böhm, Sigrid; Girdiuk, Anastasiia; Hellerschmied, Andreas; Hofmeister, Armin; Krásná, Hana; Kwak, Younghee; Landskron, Daniel; Madzak, Matthias; Mayer, David; McCallum, Jamie; Plank, Lucia; Schartner, Matthias; Shabala, Stas; Teke, Kamil; Sun, Jing

2017-04-01

The Vienna VLBI and Satellite Software (VieVS) is a geodetic analysis software developed and maintained at Technische Universität Wien (TU Wien) with contributions from groups all over the world. It is used for both academic purposes in university courses as well as for providing Very Long Baseline Interferometry (VLBI) analysis results to the geodetic community. Written in a modular structure in Matlab, VieVS offers easy access to the source code and the possibility to adapt the programs for particular purposes. The new version 3.0, released in early 2017, includes several new features, e.g., improved scheduling capabilities for observing quasars and satellites. This poster gives an overview of all VLBI-related activities in Vienna and provides an outlook to future plans concerning the Vienna VLBI and Satellite Software (VieVS).

ISS Propulsion Module Crew Systems Interface Analysis in the Intelligent Synthesis Environment

NASA Technical Reports Server (NTRS)

Chen, Di-Wen

1999-01-01

ERGO, a human modeling software for ergonomic assessment and task analysis, was used for the crew systems interface analysis of the International Space Station (ISS) Propulsion Module (PM). The objective of analysis was to alleviate passageway size concerns. Three basic passageway configuration concepts: (1) 45" clear passageway without centerline offset (2) 50" clear passageway, 12" centerline offset, (3) 50" clear passageway, no centerline offset, and were reviewed. 95 percentile male and female models which were provided by the software performed crew system analysis from an anthropometric point of view. Four scenarios in which the crew floats in microgravity through a 50" no-offset passageway as they carry a 16" x 20" x 30" avionics box were simulated in the 10-weeks of intensive study. From the results of the analysis, concept (3) was the preferred option. A full scale, three-dimensional virtual model of the ISS Propulsion Module was created to experience the sense of the Intelligent Synthesis Environment and to evaluate the usability and applicability of the software.

The software analysis project for the Office of Human Resources

NASA Technical Reports Server (NTRS)

Tureman, Robert L., Jr.

1994-01-01

There were two major sections of the project for the Office of Human Resources (OHR). The first section was to conduct a planning study to analyze software use with the goal of recommending software purchases and determining whether the need exists for a file server. The second section was analysis and distribution planning for retirement planning computer program entitled VISION provided by NASA Headquarters. The software planning study was developed to help OHR analyze the current administrative desktop computing environment and make decisions regarding software acquisition and implementation. There were three major areas addressed by the study: current environment new software requirements, and strategies regarding the implementation of a server in the Office. To gather data on current environment, employees were surveyed and an inventory of computers were produced. The surveys were compiled and analyzed by the ASEE fellow with interpretation help by OHR staff. New software requirements represented a compilation and analysis of the surveyed requests of OHR personnel. Finally, the information on the use of a server represents research done by the ASEE fellow and analysis of survey data to determine software requirements for a server. This included selection of a methodology to estimate the number of copies of each software program required given current use and estimated growth. The report presents the results of the computing survey, a description of the current computing environment, recommenations for changes in the computing environment, current software needs, management advantages of using a server, and management considerations in the implementation of a server. In addition, detailed specifications were presented for the hardware and software recommendations to offer a complete picture to OHR management. The retirement planning computer program available to NASA employees will aid in long-range retirement planning. The intended audience is the NASA civil service employee with several years until retirement. The employee enters current salary and savings information as well as goals concerning salary at retirement, assumptions on inflation, and the return on investments. The program produces a picture of the employee's retirement income from all sources based on the assumptions entered. A session showing features of the program was conducted for key personnel at the Center. After analysis, it was decided to offer the program through the Learning Center starting in August 1994.

Demonstration of a Safety Analysis on a Complex System

NASA Technical Reports Server (NTRS)

Leveson, Nancy; Alfaro, Liliana; Alvarado, Christine; Brown, Molly; Hunt, Earl B.; Jaffe, Matt; Joslyn, Susan; Pinnell, Denise; Reese, Jon; Samarziya, Jeffrey;

Software reliability experiments data analysis and investigation

NASA Technical Reports Server (NTRS)

Walker, J. Leslie; Caglayan, Alper K.

1991-01-01

The objectives are to investigate the fundamental reasons which cause independently developed software programs to fail dependently, and to examine fault tolerant software structures which maximize reliability gain in the presence of such dependent failure behavior. The authors used 20 redundant programs from a software reliability experiment to analyze the software errors causing coincident failures, to compare the reliability of N-version and recovery block structures composed of these programs, and to examine the impact of diversity on software reliability using subpopulations of these programs. The results indicate that both conceptually related and unrelated errors can cause coincident failures and that recovery block structures offer more reliability gain than N-version structures if acceptance checks that fail independently from the software components are available. The authors present a theory of general program checkers that have potential application for acceptance tests.

Comparative exploration of multidimensional flow cytometry software: a model approach evaluating T cell polyfunctional behavior.

PubMed

Spear, Timothy T; Nishimura, Michael I; Simms, Patricia E

2017-08-01

Advancement in flow cytometry reagents and instrumentation has allowed for simultaneous analysis of large numbers of lineage/functional immune cell markers. Highly complex datasets generated by polychromatic flow cytometry require proper analytical software to answer investigators' questions. A problem among many investigators and flow cytometry Shared Resource Laboratories (SRLs), including our own, is a lack of access to a flow cytometry-knowledgeable bioinformatics team, making it difficult to learn and choose appropriate analysis tool(s). Here, we comparatively assess various multidimensional flow cytometry software packages for their ability to answer a specific biologic question and provide graphical representation output suitable for publication, as well as their ease of use and cost. We assessed polyfunctional potential of TCR-transduced T cells, serving as a model evaluation, using multidimensional flow cytometry to analyze 6 intracellular cytokines and degranulation on a per-cell basis. Analysis of 7 parameters resulted in 128 possible combinations of positivity/negativity, far too complex for basic flow cytometry software to analyze fully. Various software packages were used, analysis methods used in each described, and representative output displayed. Of the tools investigated, automated classification of cellular expression by nonlinear stochastic embedding (ACCENSE) and coupled analysis in Pestle/simplified presentation of incredibly complex evaluations (SPICE) provided the most user-friendly manipulations and readable output, evaluating effects of altered antigen-specific stimulation on T cell polyfunctionality. This detailed approach may serve as a model for other investigators/SRLs in selecting the most appropriate software to analyze complex flow cytometry datasets. Further development and awareness of available tools will help guide proper data analysis to answer difficult biologic questions arising from incredibly complex datasets. © Society for Leukocyte Biology.

3D echocardiographic analysis of aortic annulus for transcatheter aortic valve replacement using novel aortic valve quantification software: Comparison with computed tomography.

PubMed

Mediratta, Anuj; Addetia, Karima; Medvedofsky, Diego; Schneider, Robert J; Kruse, Eric; Shah, Atman P; Nathan, Sandeep; Paul, Jonathan D; Blair, John E; Ota, Takeyoshi; Balkhy, Husam H; Patel, Amit R; Mor-Avi, Victor; Lang, Roberto M

2017-05-01

With the increasing use of transcatheter aortic valve replacement (TAVR) in patients with aortic stenosis (AS), computed tomography (CT) remains the standard for annulus sizing. However, 3D transesophageal echocardiography (TEE) has been an alternative in patients with contraindications to CT. We sought to (1) test the feasibility, accuracy, and reproducibility of prototype 3DTEE analysis software (Philips) for aortic annular measurements and (2) compare the new approach to the existing echocardiographic techniques. We prospectively studied 52 patients who underwent gated contrast CT, procedural 3DTEE, and TAVR. 3DTEE images were analyzed using novel semi-automated software designed for 3D measurements of the aortic root, which uses multiplanar reconstruction, similar to CT analysis. Aortic annulus measurements included area, perimeter, and diameter calculations from these measurements. The results were compared to CT-derived values. Additionally, 3D echocardiographic measurements (3D planimetry and mitral valve analysis software adapted for the aortic valve) were also compared to the CT reference values. 3DTEE image quality was sufficient in 90% of patients for aortic annulus measurements using the new software, which were in good agreement with CT (r-values: .89-.91) and small (<4%) inter-modality nonsignificant biases. Repeated measurements showed <10% measurements variability. The new 3D analysis was the more accurate and reproducible of the existing echocardiographic techniques. Novel semi-automated 3DTEE analysis software can accurately measure aortic annulus in patients with severe AS undergoing TAVR, in better agreement with CT than the existing methodology. Accordingly, intra-procedural TEE could potentially replace CT in patients where CT carries significant risk. © 2017, Wiley Periodicals, Inc.

Publishing Platform for Scientific Software - Lessons Learned

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin; Fritzsch, Bernadette; Reusser, Dominik; Brembs, Björn; Deinzer, Gernot; Loewe, Peter; Fenner, Martin; van Edig, Xenia; Bertelmann, Roland; Pampel, Heinz; Klump, Jens; Wächter, Joachim

2015-04-01

Scientific software has become an indispensable commodity for the production, processing and analysis of empirical data but also for modelling and simulation of complex processes. Software has a significant influence on the quality of research results. For strengthening the recognition of the academic performance of scientific software development, for increasing its visibility and for promoting the reproducibility of research results, concepts for the publication of scientific software have to be developed, tested, evaluated, and then transferred into operations. For this, the publication and citability of scientific software have to fulfil scientific criteria by means of defined processes and the use of persistent identifiers, similar to data publications. The SciForge project is addressing these challenges. Based on interviews a blueprint for a scientific software publishing platform and a systematic implementation plan has been designed. In addition, the potential of journals, software repositories and persistent identifiers have been evaluated to improve the publication and dissemination of reusable software solutions. It is important that procedures for publishing software as well as methods and tools for software engineering are reflected in the architecture of the platform, in order to improve the quality of the software and the results of research. In addition, it is necessary to work continuously on improving specific conditions that promote the adoption and sustainable utilization of scientific software publications. Among others, this would include policies for the development and publication of scientific software in the institutions but also policies for establishing the necessary competencies and skills of scientists and IT personnel. To implement the concepts developed in SciForge a combined bottom-up / top-down approach is considered that will be implemented in parallel in different scientific domains, e.g. in earth sciences, climate research and the life sciences. Based on the developed blueprints a scientific software publishing platform will be iteratively implemented, tested, and evaluated. Thus the platform should be developed continuously on the basis of gained experiences and results. The platform services will be extended one by one corresponding to the requirements of the communities. Thus the implemented platform for the publication of scientific software can be improved and stabilized incrementally as a tool with software, science, publishing, and user oriented features.

Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software.

PubMed

Nakano, Shogo; Asano, Yasuhisa

2015-02-03

Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software

NASA Astrophysics Data System (ADS)

Nakano, Shogo; Asano, Yasuhisa

2015-02-01

Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

Earth Science Markup Language: Transitioning From Design to Application

NASA Technical Reports Server (NTRS)

Moe, Karen; Graves, Sara; Ramachandran, Rahul

2002-01-01

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

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.

The effects of GeoGebra software on pre-service mathematics teachers' attitudes and views toward proof and proving

NASA Astrophysics Data System (ADS)

Zengin, Yılmaz

2017-11-01

The purpose of this study is to determine the effect of GeoGebra software on pre-service mathematics teachers' attitudes towards proof and proving and to determine pre-service teachers' pre- and post-views regarding proof. The study lasted nine weeks and the participants of the study consisted of 24 pre-service mathematics teachers. The study used the 'Attitude Scale Towards Proof and Proving' and an open-ended questionnaire that were administered before and after the intervention as data collection tools. Paired samples t-test analysis was used for the analysis of quantitative data and content and descriptive analyses were utilized for the analysis of qualitative data. As a result of the data analysis, it was determined that GeoGebra software was an effective tool in increasing pre-service teachers' attitudes towards proof and proving.

Inertial Upper Stage (IUS) software analysis

NASA Technical Reports Server (NTRS)

Grayson, W. L.; Nickel, C. E.; Rose, P. L.; Singh, R. P.

1979-01-01

The Inertial Upper Stage (IUS) System, an extension of the Space Transportation System (STS) operating regime to include higher orbits, orbital plane changes, geosynchronous orbits, and interplanetary trajectories is presented. The IUS software design, the IUS software interfaces with other systems, and the cost effectiveness in software verification are described. Tasks of the IUS discussed include: (1) design analysis; (2) validation requirements analysis; (3) interface analysis; and (4) requirements analysis.

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

Evaluation of Visualization Software

NASA Technical Reports Server (NTRS)

Globus, Al; Uselton, Sam

1995-01-01

Visualization software is widely used in scientific and engineering research. But computed visualizations can be very misleading, and the errors are easy to miss. We feel that the software producing the visualizations must be thoroughly evaluated and the evaluation process as well as the results must be made available. Testing and evaluation of visualization software is not a trivial problem. Several methods used in testing other software are helpful, but these methods are (apparently) often not used. When they are used, the description and results are generally not available to the end user. Additional evaluation methods specific to visualization must also be developed. We present several useful approaches to evaluation, ranging from numerical analysis of mathematical portions of algorithms to measurement of human performance while using visualization systems. Along with this brief survey, we present arguments for the importance of evaluations and discussions of appropriate use of some methods.

Software Framework for Development of Web-GIS Systems for Analysis of Georeferenced Geophysical Data

NASA Astrophysics Data System (ADS)

Okladnikov, I.; Gordov, E. P.; Titov, A. G.

2011-12-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, remote sensing products, etc.) are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated software framework for rapid development of providing such support information-computational systems based on Web-GIS technologies has been created. The software framework consists of 3 basic parts: computational kernel developed using ITTVIS Interactive Data Language (IDL), a set of PHP-controllers run within specialized web portal, and JavaScript class library for development of typical components of web mapping application graphical user interface (GUI) based on AJAX technology. Computational kernel comprise of number of modules for datasets access, mathematical and statistical data analysis and visualization of results. Specialized web-portal consists of web-server Apache, complying OGC standards Geoserver software which is used as a base for presenting cartographical information over the Web, and a set of PHP-controllers implementing web-mapping application logic and governing computational kernel. JavaScript library aiming at graphical user interface development is based on GeoExt library combining ExtJS Framework and OpenLayers software. Based on the software framework an information-computational system for complex analysis of large georeferenced data archives was developed. Structured environmental datasets available for processing now include two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, meteorological observational data for the territory of the former USSR for the 20th century, and others. Current version of the system is already involved into a scientific research process. Particularly, recently the system was successfully used for analysis of Siberia climate changes and its impact in the region. The software framework presented allows rapid development of Web-GIS systems for geophysical data analysis thus providing specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. This work is partially supported by RFBR grants #10-07-00547, #11-05-01190, and SB RAS projects 4.31.1.5, 4.31.2.7, 4, 8, 9, 50 and 66.

Advanced Software for Analysis of High-Speed Rolling-Element Bearings

NASA Technical Reports Server (NTRS)

Poplawski, J. V.; Rumbarger, J. H.; Peters, S. M.; Galatis, H.; Flower, R.

2003-01-01

COBRA-AHS is a package of advanced software for analysis of rigid or flexible shaft systems supported by rolling-element bearings operating at high speeds under complex mechanical and thermal loads. These loads can include centrifugal and thermal loads generated by motions of bearing components. COBRA-AHS offers several improvements over prior commercial bearing-analysis programs: It includes innovative probabilistic fatigue-life-estimating software that provides for computation of three-dimensional stress fields and incorporates stress-based (in contradistinction to prior load-based) mathematical models of fatigue life. It interacts automatically with the ANSYS finite-element code to generate finite-element models for estimating distributions of temperature and temperature-induced changes in dimensions in iterative thermal/dimensional analyses: thus, for example, it can be used to predict changes in clearances and thermal lockup. COBRA-AHS provides an improved graphical user interface that facilitates the iterative cycle of analysis and design by providing analysis results quickly in graphical form, enabling the user to control interactive runs without leaving the program environment, and facilitating transfer of plots and printed results for inclusion in design reports. Additional features include roller-edge stress prediction and influence of shaft and housing distortion on bearing performance.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Liebetreu, John; Moore, Michael S.; Price, Jeremy C.; Abbott, Ben

2005-01-01

This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Moore, Michael S.; Price, Jeremy C.; Abbott, Ben; Liebetreu, John; Reinhart, Richard C.; Kacpura, Thomas J.

2007-01-01

This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

[Finite Element Analysis of Intravascular Stent Based on ANSYS Software].

PubMed

Shi, Gengqiang; Song, Xiaobing

2015-10-01

This paper adopted UG8.0 to bulid the stent and blood vessel models. The models were then imported into the finite element analysis software ANSYS. The simulation results of ANSYS software showed that after endothelial stent implantation, the velocity of the blood was slow and the fluctuation of velocity was small, which meant the flow was relatively stable. When blood flowed through the endothelial stent, the pressure gradually became smaller, and the range of the pressure was not wide. The endothelial shear stress basically unchanged. In general, it can be concluded that the endothelial stents have little impact on the flow of blood and can fully realize its function.

Collaboration, Communication and Co-ordination in Agile Software Development Practice

NASA Astrophysics Data System (ADS)

Robinson, Hugh; Sharp, Helen

This chapter analyses the results of a series of observational studies of agile software developmentagile software development teams, identifying commonalities in collaboration, co-ordination and communication activities. Pairing and customer collaborationcustomer collaboration are focussed on to illustrate the nature of collaboration and communication, as are two simple physical artefacts that emerged through analysis as being an information-rich focal point for the co-ordination of collaboration and communication activities. The analysis shows that pairingpairing has common characteristics across all teams, while customer collaboration differs between the teams depending on the application and organisational context of development.

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.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.

1992-01-01

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

Spatio-temporally resolved spectral measurements of laser-produced plasma and semiautomated spectral measurement-control and analysis software

NASA Astrophysics Data System (ADS)

Cao, S. Q.; Su, M. G.; Min, Q.; Sun, D. X.; O'Sullivan, G.; Dong, C. Z.

2018-02-01

A spatio-temporally resolved spectral measurement system of highly charged ions from laser-produced plasmas is presented. Corresponding semiautomated computer software for measurement control and spectral analysis has been written to achieve the best synchronicity possible among the instruments. This avoids the tedious comparative processes between experimental and theoretical results. To demonstrate the capabilities of this system, a series of spatio-temporally resolved experiments of laser-produced Al plasmas have been performed and applied to benchmark the software. The system is a useful tool for studying the spectral structures of highly charged ions and for evaluating the spatio-temporal evolution of laser-produced plasmas.

Influence of Smartphones and Software on Acoustic Voice Measures

PubMed Central

GRILLO, ELIZABETH U.; BROSIOUS, JENNA N.; SORRELL, STACI L.; ANAND, SUPRAJA

2016-01-01

This study assessed the within-subject variability of voice measures captured using different recording devices (i.e., smartphones and head mounted microphone) and software programs (i.e., Analysis of Dysphonia in Speech and Voice (ADSV), Multi-dimensional Voice Program (MDVP), and Praat). Correlations between the software programs that calculated the voice measures were also analyzed. Results demonstrated no significant within-subject variability across devices and software and that some of the measures were highly correlated across software programs. The study suggests that certain smartphones may be appropriate to record daily voice measures representing the effects of vocal loading within individuals. In addition, even though different algorithms are used to compute voice measures across software programs, some of the programs and measures share a similar relationship. PMID:28775797

CoLiTec software - detection of the near-zero apparent motion

NASA Astrophysics Data System (ADS)

Khlamov, Sergii V.; Savanevych, Vadym E.; Briukhovetskyi, Olexandr B.; Pohorelov, Artem V.

2017-06-01

In this article we described CoLiTec software for full automated frames processing. CoLiTec software allows processing the Big Data of observation results as well as processing of data that is continuously formed during observation. The scope of solving tasks includes frames brightness equalization, moving objects detection, astrometry, photometry, etc. Along with the high efficiency of Big Data processing CoLiTec software also ensures high accuracy of data measurements. A comparative analysis of the functional characteristics and positional accuracy was performed between CoLiTec and Astrometrica software. The benefits of CoLiTec used with wide field and low quality frames were observed. The efficiency of the CoLiTec software was proved by about 700.000 observations and over 1.500 preliminary discoveries.

Demonstrating High-Accuracy Orbital Access Using Open-Source Tools

NASA Technical Reports Server (NTRS)

Gilbertson, Christian; Welch, Bryan

2017-01-01

Orbit propagation is fundamental to almost every space-based analysis. Currently, many system analysts use commercial software to predict the future positions of orbiting satellites. This is one of many capabilities that can replicated, with great accuracy, without using expensive, proprietary software. NASAs SCaN (Space Communication and Navigation) Center for Engineering, Networks, Integration, and Communications (SCENIC) project plans to provide its analysis capabilities using a combination of internal and open-source software, allowing for a much greater measure of customization and flexibility, while reducing recurring software license costs. MATLAB and the open-source Orbit Determination Toolbox created by Goddard Space Flight Center (GSFC) were utilized to develop tools with the capability to propagate orbits, perform line-of-sight (LOS) availability analyses, and visualize the results. The developed programs are modular and can be applied for mission planning and viability analysis in a variety of Solar System applications. The tools can perform 2 and N-body orbit propagation, find inter-satellite and satellite to ground station LOS access (accounting for intermediate oblate spheroid body blocking, geometric restrictions of the antenna field-of-view (FOV), and relativistic corrections), and create animations of planetary movement, satellite orbits, and LOS accesses. The code is the basis for SCENICs broad analysis capabilities including dynamic link analysis, dilution-of-precision navigation analysis, and orbital availability calculations.

A regional land use survey based on remote sensing and other data: A report on a LANDSAT and computer mapping project, volume 1. [Arizona, Colorado, Montana, New Mexico, Utah, and Wyoming

NASA Technical Reports Server (NTRS)

Nez, G. (Principal Investigator); Mutter, D.

1977-01-01

The author has identified the following significant results. New LANDSAT analysis software and linkages with other computer mapping software were developed. Significant results were also achieved in training, communication, and identification of needs for developing the LANDSAT/computer mapping technologies into operational tools for use by decision makers.

Semi-automatic computerized approach to radiological quantification in rheumatoid arthritis

NASA Astrophysics Data System (ADS)

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

2004-04-01

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

The spectra program library: A PC based system for gamma-ray spectra analysis and INAA data reduction

USGS Publications Warehouse

Baedecker, P.A.; Grossman, J.N.

1995-01-01

A PC based system has been developed for the analysis of gamma-ray spectra and for the complete reduction of data from INAA experiments, including software to average the results from mulitple lines and multiple countings and to produce a final report of analysis. Graphics algorithms may be called for the analysis of complex spectral features, to compare the data from alternate photopeaks and to evaluate detector performance during a given counting cycle. A database of results for control samples can be used to prepare quality control charts to evaluate long term precision and to search for systemic variations in data on reference samples as a function of time. The entire software library can be accessed through a user-friendly menu interface with internal help.

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

Kim, Hang Bae

A reliability testing was performed for the software of Shutdown(SDS) Computers for Wolsong Nuclear Power Plants Units 2, 3 and 4. profiles to the SDS Computers and compared the outputs with the predicted results generated by the oracle. Test softwares were written to execute the test automatically. Random test profiles were generated using analysis code. 11 refs., 1 fig.

Using software security analysis to verify the secure socket layer (SSL) protocol

NASA Technical Reports Server (NTRS)

Powell, John D.

2004-01-01

nal Aeronautics and Space Administration (NASA) have tens of thousands of networked computer systems and applications. Software Security vulnerabilities present risks such as lost or corrupted data, information the3, and unavailability of critical systems. These risks represent potentially enormous costs to NASA. The NASA Code Q research initiative 'Reducing Software Security Risk (RSSR) Trough an Integrated Approach '' offers, among its capabilities, formal verification of software security properties, through the use of model based verification (MBV) to address software security risks. [1,2,3,4,5,6] MBV is a formal approach to software assurance that combines analysis of software, via abstract models, with technology, such as model checkers, that provide automation of the mechanical portions of the analysis process. This paper will discuss: The need for formal analysis to assure software systems with respect to software and why testing alone cannot provide it. The means by which MBV with a Flexible Modeling Framework (FMF) accomplishes the necessary analysis task. An example of FMF style MBV in the verification of properties over the Secure Socket Layer (SSL) communication protocol as a demonstration.

Development of Automated Image Analysis Software for Suspended Marine Particle Classification

DTIC Science & Technology

2003-09-30

Development of Automated Image Analysis Software for Suspended Marine Particle Classification Scott Samson Center for Ocean Technology...REPORT TYPE 3. DATES COVERED 00-00-2003 to 00-00-2003 4. TITLE AND SUBTITLE Development of Automated Image Analysis Software for Suspended...objective is to develop automated image analysis software to reduce the effort and time required for manual identification of plankton images. Automated

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

ERIC Educational Resources Information Center

Harwell, Michael

2018-01-01

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

PAnalyzer: a software tool for protein inference in shotgun proteomics.

PubMed

Prieto, Gorka; Aloria, Kerman; Osinalde, Nerea; Fullaondo, Asier; Arizmendi, Jesus M; Matthiesen, Rune

2012-11-05

Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

A Study of the NASS-CDS System for Injury/Fatality Rates of Occupants in Various Restraints and A Discussion of Alternative Presentation Methods

PubMed Central

Stucki, Sheldon Lee; Biss, David J.

2000-01-01

An analysis was performed using the National Automotive Sampling System Crashworthiness Data System (NASS-CDS) database to compare the injury/fatality rates of variously restrained driver occupants as compared to unrestrained driver occupants in the total database of drivers/frontals, and also by Delta-V. A structured search of the NASS-CDS was done using the SAS® statistical analysis software to extract the data for this analysis and the SUDAAN software package was used to arrive at statistical significance indicators. In addition, this paper goes on to investigate different methods for presenting results of accident database searches including significance results; a risk versus Delta-V format for specific exposures; and, a percent cumulative injury versus Delta-V format to characterize injury trends. These alternative analysis presentation methods are then discussed by example using the present study results. PMID:11558105

Tools to minimize interlaboratory variability in vitellogenin gene expression monitoring programs

USGS Publications Warehouse

Jastrow, Aaron; Gordon, Denise A.; Auger, Kasie M.; Punska, Elizabeth C.; Arcaro, Kathleen F.; Keteles, Kristen; Winkelman, Dana L.; Lattier, David; Biales, Adam; Lazorchak, James M.

2017-01-01

The egg yolk precursor protein vitellogenin is widely used as a biomarker of estrogen exposure in male fish. However, standardized methodology is lacking and little is known regarding the reproducibility of results among laboratories using different equipment, reagents, protocols, and data analysis programs. To address this data gap we tested the reproducibility across laboratories to evaluate vitellogenin gene (vtg) expression and assessed the value of using a freely available software data analysis program. Samples collected from studies of male fathead minnows (Pimephales promelas) exposed to 17α-ethinylestradiol (EE2) and minnows exposed to processed wastewater effluent were evaluated for vtg expression in 4 laboratories. Our results indicate reasonable consistency among laboratories if the free software for expression analysis LinRegPCR is used, with 3 of 4 laboratories detecting vtg in fish exposed to 5 ng/L EE2 (n = 5). All 4 laboratories detected significantly increased vtg levels in 15 male fish exposed to wastewater effluent compared with 15 male fish held in a control stream. Finally, we were able to determine that the source of high interlaboratory variability from complementary deoxyribonucleic acid (cDNA) to quantitative polymerase chain reaction (qPCR) analyses was the expression analysis software unique to each real-time qPCR machine. We successfully eliminated the interlaboratory variability by reanalyzing raw fluorescence data with independent freeware, which yielded cycle thresholds and polymerase chain reaction (PCR) efficiencies that calculated results independently of proprietary software. Our results suggest that laboratories engaged in monitoring programs should validate their PCR protocols and analyze their gene expression data following the guidelines established in the present study for all gene expression biomarkers. 

Comparison between a new computer program and the reference software for gray-scale median analysis of atherosclerotic carotid plaques.

PubMed

Casella, Ivan Benaduce; Fukushima, Rodrigo Bono; Marques, Anita Battistini de Azevedo; Cury, Marcus Vinícius Martins; Presti, Calógero

2015-03-01

To compare a new dedicated software program and Adobe Photoshop for gray-scale median (GSM) analysis of B-mode images of carotid plaques. A series of 42 carotid plaques generating ≥50% diameter stenosis was evaluated by a single observer. The best segment for visualization of internal carotid artery plaque was identified on a single longitudinal view and images were recorded in JPEG format. Plaque analysis was performed by both programs. After normalization of image intensity (blood = 0, adventitial layer = 190), histograms were obtained after manual delineation of plaque. Results were compared with nonparametric Wilcoxon signed rank test and Kendall tau-b correlation analysis. GSM ranged from 00 to 100 with Adobe Photoshop and from 00 to 96 with IMTPC, with a high grade of similarity between image pairs, and a highly significant correlation (R = 0.94, p < .0001). IMTPC software appears suitable for the GSM analysis of carotid plaques. © 2014 Wiley Periodicals, Inc.

PHASTpep: Analysis Software for Discovery of Cell-Selective Peptides via Phage Display and Next-Generation Sequencing

PubMed Central

Dasa, Siva Sai Krishna; Kelly, Kimberly A.

2016-01-01

Next-generation sequencing has enhanced the phage display process, allowing for the quantification of millions of sequences resulting from the biopanning process. In response, many valuable analysis programs focused on specificity and finding targeted motifs or consensus sequences were developed. For targeted drug delivery and molecular imaging, it is also necessary to find peptides that are selective—targeting only the cell type or tissue of interest. We present a new analysis strategy and accompanying software, PHage Analysis for Selective Targeted PEPtides (PHASTpep), which identifies highly specific and selective peptides. Using this process, we discovered and validated, both in vitro and in vivo in mice, two sequences (HTTIPKV and APPIMSV) targeted to pancreatic cancer-associated fibroblasts that escaped identification using previously existing software. Our selectivity analysis makes it possible to discover peptides that target a specific cell type and avoid other cell types, enhancing clinical translatability by circumventing complications with systemic use. PMID:27186887

SpotMetrics: An Open-Source Image-Analysis Software Plugin for Automatic Chromatophore Detection and Measurement.

PubMed

Hadjisolomou, Stavros P; El-Haddad, George

2017-01-01

Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented chromatophore organs and reflecting cells. Therefore, a lot can be learned about the cephalopod coloration system by video recording and analyzing the activation of individual chromatophores in time. The fact that adult cephalopods have small chromatophores, up to several hundred thousand in number, makes measurement and analysis over several seconds a difficult task. However, current advancements in videography enable high-resolution and high framerate recording, which can be used to record chromatophore activity in more detail and accuracy in both space and time domains. In turn, the additional pixel information and extra frames per video from such recordings result in large video files of several gigabytes, even when the recording spans only few minutes. We created a software plugin, "SpotMetrics," that can automatically analyze high resolution, high framerate video of chromatophore organ activation in time. This image analysis software can track hundreds of individual chromatophores over several hundred frames to provide measurements of size and color. This software may also be used to measure differences in chromatophore activation during different behaviors which will contribute to our understanding of the cephalopod sensorimotor integration system. In addition, this software can potentially be utilized to detect numbers of round objects and size changes in time, such as eye pupil size or number of bacteria in a sample. Thus, we are making this software plugin freely available as open-source because we believe it will be of benefit to other colleagues both in the cephalopod biology field and also within other disciplines.

The Research of Software Engineering Curriculum Reform

NASA Astrophysics Data System (ADS)

Kuang, Li-Qun; Han, Xie

With the problem that software engineering training can't meet the needs of the community, this paper analysis some outstanding reasons in software engineering curriculum teaching, such as old teaching contents, weak in practice and low quality of teachers etc. We propose the methods of teaching reform as guided by market demand, update the teaching content, optimize the teaching methods, reform the teaching practice, strengthen the teacher-student exchange and promote teachers and students together. We carried out the reform and explore positive and achieved the desired results.

Theoretical and experimental analysis of the impacts of removable storage media and antivirus software on viral spread

NASA Astrophysics Data System (ADS)

Gan, Chenquan; Yang, Xiaofan

2015-05-01

In this paper, a new computer virus propagation model, which incorporates the effects of removable storage media and antivirus software, is proposed and analyzed. The global stability of the unique equilibrium of the model is independent of system parameters. Numerical simulations not only verify this result, but also illustrate the influences of removable storage media and antivirus software on viral spread. On this basis, some applicable measures for suppressing virus prevalence are suggested.

Developing tools for digital radar image data evaluation

NASA Technical Reports Server (NTRS)

Domik, G.; Leberl, F.; Raggam, J.

1986-01-01

The refinement of radar image analysis methods has led to a need for a systems approach to radar image processing software. Developments stimulated through satellite radar are combined with standard image processing techniques to create a user environment to manipulate and analyze airborne and satellite radar images. One aim is to create radar products for the user from the original data to enhance the ease of understanding the contents. The results are called secondary image products and derive from the original digital images. Another aim is to support interactive SAR image analysis. Software methods permit use of a digital height model to create ortho images, synthetic images, stereo-ortho images, radar maps or color combinations of different component products. Efforts are ongoing to integrate individual tools into a combined hardware/software environment for interactive radar image analysis.

Conservative Allowables Determined by a Tsai-Hill Equivalent Criterion for Design of Satellite Composite Parts

NASA Astrophysics Data System (ADS)

Pommatau, Gilles

2014-06-01

The present paper deals with the industrial application, via a software developed by Thales Alenia Space, of a new failure criterion named "Tsai-Hill equivalent criterion" for composite structural parts of satellites. The first part of the paper briefly describes the main hypothesis and the possibilities in terms of failure analysis of the software. The second parts reminds the quadratic and conservative nature of the new failure criterion, already presented in ESA conference in a previous paper. The third part presents the statistical calculation possibilities of the software, and the associated sensitivity analysis, via results obtained on different composites. Then a methodology, proposed to customers and agencies, is presented with its limitations and advantages. It is then conclude that this methodology is an efficient industrial way to perform mechanical analysis on quasi-isotropic composite parts.

Comparison of two freely available software packages for mass spectrometry imaging data analysis using brains from morphine addicted rats.

PubMed

Bodzon-Kulakowska, Anna; Marszalek-Grabska, Marta; Antolak, Anna; Drabik, Anna; Kotlinska, Jolanta H; Suder, Piotr

Data analysis from mass spectrometry imaging (MSI) imaging experiments is a very complex task. Most of the software packages devoted to this purpose are designed by the mass spectrometer manufacturers and, thus, are not freely available. Laboratories developing their own MS-imaging sources usually do not have access to the commercial software, and they must rely on the freely available programs. The most recognized ones are BioMap, developed by Novartis under Interactive Data Language (IDL), and Datacube, developed by the Dutch Foundation for Fundamental Research of Matter (FOM-Amolf). These two systems were used here for the analysis of images received from rat brain tissues subjected to morphine influence and their capabilities were compared in terms of ease of use and the quality of obtained results.

FEBio: finite elements for biomechanics.

PubMed

Maas, Steve A; Ellis, Benjamin J; Ateshian, Gerard A; Weiss, Jeffrey A

2012-01-01

In the field of computational biomechanics, investigators have primarily used commercial software that is neither geared toward biological applications nor sufficiently flexible to follow the latest developments in the field. This lack of a tailored software environment has hampered research progress, as well as dissemination of models and results. To address these issues, we developed the FEBio software suite (http://mrl.sci.utah.edu/software/febio), a nonlinear implicit finite element (FE) framework, designed specifically for analysis in computational solid biomechanics. This paper provides an overview of the theoretical basis of FEBio and its main features. FEBio offers modeling scenarios, constitutive models, and boundary conditions, which are relevant to numerous applications in biomechanics. The open-source FEBio software is written in C++, with particular attention to scalar and parallel performance on modern computer architectures. Software verification is a large part of the development and maintenance of FEBio, and to demonstrate the general approach, the description and results of several problems from the FEBio Verification Suite are presented and compared to analytical solutions or results from other established and verified FE codes. An additional simulation is described that illustrates the application of FEBio to a research problem in biomechanics. Together with the pre- and postprocessing software PREVIEW and POSTVIEW, FEBio provides a tailored solution for research and development in computational biomechanics.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)

PubMed Central

2013-01-01

Background The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. Results We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Conclusions Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools. PMID:24209455

Voxel Datacubes for 3D Visualization in Blender

NASA Astrophysics Data System (ADS)

Gárate, Matías

2017-05-01

The growth of computational astrophysics and the complexity of multi-dimensional data sets evidences the need for new versatile visualization tools for both the analysis and presentation of the data. In this work, we show how to use the open-source software Blender as a three-dimensional (3D) visualization tool to study and visualize numerical simulation results, focusing on astrophysical hydrodynamic experiments. With a datacube as input, the software can generate a volume rendering of the 3D data, show the evolution of a simulation in time, and do a fly-around camera animation to highlight the points of interest. We explain the process to import simulation outputs into Blender using the voxel data format, and how to set up a visualization scene in the software interface. This method allows scientists to perform a complementary visual analysis of their data and display their results in an appealing way, both for outreach and science presentations.

metAlignID: a high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data.

PubMed

Lommen, Arjen; van der Kamp, Henk J; Kools, Harrie J; van der Lee, Martijn K; van der Weg, Guido; Mol, Hans G J

2012-11-09

A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has been developed for and tested on LECO data. The software is developed to run multi-threaded (one thread per processor core) on a standard PC (personal computer) under different operating systems and is as such capable of processing multiple data sets simultaneously. Raw data files are converted into netCDF (network Common Data Form) format using a fast conversion tool. They are then preprocessed using previously developed algorithms originating from metAlign software. Next, the resulting reduced data files are searched against a user-composed library (derived from user or commercial NIST-compatible libraries) (NIST=National Institute of Standards and Technology) and the identified compounds, including an indicative concentration, are reported in Excel format. Data can be processed batch wise. The overall time needed for conversion together with processing and searching of 30 raw data sets for 560 compounds is routinely within an hour. The screening performance is evaluated for detection of pesticides and contaminants in raw data obtained after analysis of soil and plant samples. Results are compared to the existing data-handling routine based on proprietary software (LECO, ChromaTOF). The developed software tool set, which is freely downloadable at www.metalign.nl, greatly accelerates data-analysis and offers more options for fine-tuning automated identification toward specific application needs. The quality of the results obtained is slightly better than the standard processing and also adds a quantitative estimate. The software tool set in combination with two-dimensional gas chromatography coupled to time-of-flight mass spectrometry shows great potential as a highly-automated and fast multi-residue instrumental screening method. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Analysis of direct punch velocity in professional defence

NASA Astrophysics Data System (ADS)

Lapkova, Dora; Adamek, Milan

2016-06-01

This paper is focused on analysis of a direct punch. Nowadays, professional defence is basic part of effective protection of people and property. There are many striking techniques and the goal of this research was to analyze the direct punch. The analysis is aimed to measure the velocity with help of high speed camera Olympus i-Speed 2 and then find the dependences of this velocity on input parameters. For data analysis two pieces of software were used - i-Speed Control Software and MINITAB. 111 participants took part in this experiment. The results are presented in this paper - especially dependence of mean velocity on time and difference in velocity between genders.

Investigation of the Finite Element Software Packages at KSC

NASA Technical Reports Server (NTRS)

Lu, Chu-Ho

1991-01-01

The useful and powerful features of NASTRAN and three real world problems for the testing of the capabilities of different NASTRAN versions are discussed. The test problems involve direct transient analysis, nonlinear analysis, and static analysis. The experiences in using graphics software packages are also discussed. It was found that MSC/XL can be more useful if it can be improved to generate picture files of the analysis results and to extend its capabilities to support finite element codes other than MSC/NASTRAN. It was found that the current version of SDRC/I-DEAS (version VI) may have bugs in the module 'Data Loader'.

A novel method for automated tracking and quantification of adult zebrafish behaviour during anxiety.

PubMed

Nema, Shubham; Hasan, Whidul; Bhargava, Anamika; Bhargava, Yogesh

2016-09-15

Behavioural neuroscience relies on software driven methods for behavioural assessment, but the field lacks cost-effective, robust, open source software for behavioural analysis. Here we propose a novel method which we called as ZebraTrack. It includes cost-effective imaging setup for distraction-free behavioural acquisition, automated tracking using open-source ImageJ software and workflow for extraction of behavioural endpoints. Our ImageJ algorithm is capable of providing control to users at key steps while maintaining automation in tracking without the need for the installation of external plugins. We have validated this method by testing novelty induced anxiety behaviour in adult zebrafish. Our results, in agreement with established findings, showed that during state-anxiety, zebrafish showed reduced distance travelled, increased thigmotaxis and freezing events. Furthermore, we proposed a method to represent both spatial and temporal distribution of choice-based behaviour which is currently not possible to represent using simple videograms. ZebraTrack method is simple and economical, yet robust enough to give results comparable with those obtained from costly proprietary software like Ethovision XT. We have developed and validated a novel cost-effective method for behavioural analysis of adult zebrafish using open-source ImageJ software. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2015-11-01

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

Assessing symmetry using the mirror stand device with manual and software-assisted methods in postoperative zygomatic fracture patients

NASA Astrophysics Data System (ADS)

Syarif, A. N.; Bangun, K.

2017-08-01

Zygomatic fractures are among the most common fractures to the facial skeleton. However, because no standard and reliable method of evaluation is available to assess postoperative patients, we often rely on photographs and subjective assessments. A portable mirror stand device (MiRS), which is a new method for the standardization of photography, was developed in our institution. Used with image analysis software, this device provides a new method for evaluating outcomes after the open reduction and internal fixation of zygomatic fractures. The portable mirror stand device was set up in our outpatient clinic at the Cleft Craniofacial Center at Cipto Mangunkusumo Hospital. Photographs of 11 postoperative patients were taken using the device, and they were analyzed both manually and using image analysis software (ImageJ 1.46) for symmetry. The two methods were then compared to assess the correlation and agreement of the results. The measurements taken using the manual method and the software-assisted method did not differ significantly, which indicated the good agreement between the two methods. The results of the symmetry achieved atour center were similar to other centers in the Asian region (ΔZy = 3.4±1.5 mm, ΔBc = 2.6±1.6 mm, ΔCh = 2.3±2.4 mm) compared with (ΔZy = 3.2±1.7 mm, ΔBc = 2.6±1.6 mm, ΔCh = 2.3±2.5 mm). The treatment of zygomatic fracture a tour center achieved good results. The portable mirror stand device assisted the image analysis software (ImageJ 1.46), which could be beneficial in assessing symmetry in postoperative zygomatic fracture patients.

Spotlight-8 Image Analysis Software

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2006-01-01

Spotlight is a cross-platform GUI-based software package designed to perform image analysis on sequences of images generated by combustion and fluid physics experiments run in a microgravity environment. Spotlight can perform analysis on a single image in an interactive mode or perform analysis on a sequence of images in an automated fashion. Image processing operations can be employed to enhance the image before various statistics and measurement operations are performed. An arbitrarily large number of objects can be analyzed simultaneously with independent areas of interest. Spotlight saves results in a text file that can be imported into other programs for graphing or further analysis. Spotlight can be run on Microsoft Windows, Linux, and Apple OS X platforms.

Proceedings of the 14th Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1989-01-01

Several software related topics are presented. Topics covered include studies and experiment at the Software Engineering Laboratory at the Goddard Space Flight Center, predicting project success from the Software Project Management Process, software environments, testing in a reuse environment, domain directed reuse, and classification tree analysis using the Amadeus measurement and empirical analysis.

OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.

PubMed

Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi

2014-01-01

The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.

User-driven integrated software lives: ``Paleomag'' paleomagnetics analysis on the Macintosh

NASA Astrophysics Data System (ADS)

Jones, Craig H.

2002-12-01

"PaleoMag," a paleomagnetics analysis package originally developed for the Macintosh operating system in 1988, allows examination of demagnetization of individual samples and analysis of directional data from collections of samples. Prior to recent reinvigorated development of the software for both Macintosh and Windows, it was widely used despite not running properly on machines and operating systems sold after 1995. This somewhat surprising situation demonstrates that there is a continued need for integrated analysis software within the earth sciences, in addition to well-developed scripting and batch-mode software. One distinct advantage of software like PaleoMag is in the ability to combine quality control with analysis within a unique graphical environment. Because such demands are frequent within the earth sciences, means of nurturing the development of similar software should be found.

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.

Design analysis and computer-aided performance evaluation of shuttle orbiter electrical power system. Volume 1: Summary

NASA Technical Reports Server (NTRS)

1974-01-01

Studies were conducted to develop appropriate space shuttle electrical power distribution and control (EPDC) subsystem simulation models and to apply the computer simulations to systems analysis of the EPDC. A previously developed software program (SYSTID) was adapted for this purpose. The following objectives were attained: (1) significant enhancement of the SYSTID time domain simulation software, (2) generation of functionally useful shuttle EPDC element models, and (3) illustrative simulation results in the analysis of EPDC performance, under the conditions of fault, current pulse injection due to lightning, and circuit protection sizing and reaction times.

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

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

Not Available

2012-02-01

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

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

PubMed Central

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

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

Requirements for a multifunctional code architecture

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

Tiihonen, O.; Juslin, K.

1997-07-01

The present paper studies a set of requirements for a multifunctional simulation software architecture in the light of experiences gained in developing and using the APROS simulation environment. The huge steps taken in the development of computer hardware and software during the last ten years are changing the status of the traditional nuclear safety analysis software. The affordable computing power on the safety analysts table by far exceeds the possibilities offered to him/her ten years ago. At the same time the features of everyday office software tend to set standards to the way the input data and calculational results aremore » managed.« less

A model-based approach for automated in vitro cell tracking and chemotaxis analyses.

PubMed

Debeir, Olivier; Camby, Isabelle; Kiss, Robert; Van Ham, Philippe; Decaestecker, Christine

2004-07-01

Chemotaxis may be studied in two main ways: 1) counting cells passing through an insert (e.g., using Boyden chambers), and 2) directly observing cell cultures (e.g., using Dunn chambers), both in response to stationary concentration gradients. This article promotes the use of Dunn chambers and in vitro cell-tracking, achieved by video microscopy coupled with automatic image analysis software, in order to extract quantitative and qualitative measurements characterizing the response of cells to a diffusible chemical agent. Previously, we set up a videomicroscopy system coupled with image analysis software that was able to compute cell trajectories from in vitro cell cultures. In the present study, we are introducing a new software increasing the application field of this system to chemotaxis studies. This software is based on an adapted version of the active contour methodology, enabling each cell to be efficiently tracked for hours and resulting in detailed descriptions of individual cell trajectories. The major advantages of this method come from an improved robustness with respect to variability in cell morphologies between different cell lines and dynamical changes in cell shape during cell migration. Moreover, the software includes a very small number of parameters which do not require overly sensitive tuning. Finally, the running time of the software is very short, allowing improved possibilities in acquisition frequency and, consequently, improved descriptions of complex cell trajectories, i.e. trajectories including cell division and cell crossing. We validated this software on several artificial and real cell culture experiments in Dunn chambers also including comparisons with manual (human-controlled) analyses. We developed new software and data analysis tools for automated cell tracking which enable cell chemotaxis to be efficiently analyzed. Copyright 2004 Wiley-Liss, Inc.

Quantification of myocardial fibrosis by digital image analysis and interactive stereology

PubMed Central

2014-01-01

Background Cardiac fibrosis disrupts the normal myocardial structure and has a direct impact on heart function and survival. Despite already available digital methods, the pathologist’s visual score is still widely considered as ground truth and used as a primary method in histomorphometric evaluations. The aim of this study was to compare the accuracy of digital image analysis tools and the pathologist’s visual scoring for evaluating fibrosis in human myocardial biopsies, based on reference data obtained by point counting performed on the same images. Methods Endomyocardial biopsy material from 38 patients diagnosed with inflammatory dilated cardiomyopathy was used. The extent of total cardiac fibrosis was assessed by image analysis on Masson’s trichrome-stained tissue specimens using automated Colocalization and Genie software, by Stereology grid count and manually by Pathologist’s visual score. Results A total of 116 slides were analyzed. The mean results obtained by the Colocalization software (13.72 ± 12.24%) were closest to the reference value of stereology (RVS), while the Genie software and Pathologist score gave a slight underestimation. RVS values correlated strongly with values obtained using the Colocalization and Genie (r > 0.9, p < 0.001) software as well as the pathologist visual score. Differences in fibrosis quantification by Colocalization and RVS were statistically insignificant. However, significant bias was found in the results obtained by using Genie versus RVS and pathologist score versus RVS with mean difference values of: -1.61% and 2.24%. Bland-Altman plots showed a bidirectional bias dependent on the magnitude of the measurement: Colocalization software overestimated the area fraction of fibrosis in the lower end, and underestimated in the higher end of the RVS values. Meanwhile, Genie software as well as the pathologist score showed more uniform results throughout the values, with a slight underestimation in the mid-range for both. Conclusion Both applied digital image analysis methods revealed almost perfect correlation with the criterion standard obtained by stereology grid count and, in terms of accuracy, outperformed the pathologist’s visual score. Genie algorithm proved to be the method of choice with the only drawback of a slight underestimation bias, which is considered acceptable for both clinical and research evaluations. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9857909611227193 PMID:24912374

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

PubMed Central

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

2013-01-01

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

Simulation for Prediction of Entry Article Demise (SPEAD): An Analysis Tool for Spacecraft Safety Analysis and Ascent/Reentry Risk Assessment

NASA Technical Reports Server (NTRS)

Ling, Lisa

2014-01-01

For the purpose of performing safety analysis and risk assessment for a potential off-nominal atmospheric reentry resulting in vehicle breakup, a synthesis of trajectory propagation coupled with thermal analysis and the evaluation of node failure is required to predict the sequence of events, the timeline, and the progressive demise of spacecraft components. To provide this capability, the Simulation for Prediction of Entry Article Demise (SPEAD) analysis tool was developed. The software and methodology have been validated against actual flights, telemetry data, and validated software, and safety/risk analyses were performed for various programs using SPEAD. This report discusses the capabilities, modeling, validation, and application of the SPEAD analysis tool.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

PubMed Central

2011-01-01

Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. Methods In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8GHz 4GB RAM server with 768x576 pixel size, 1.28Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server – 3.5 seconds, at remote analysis – 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. Conclusions The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system. PMID:21489188

Analysis of Learning Behavior in a Flipped Programing Classroom Adopting Problem-Solving Strategies

ERIC Educational Resources Information Center

Chiang, Tosti Hsu-Cheng

2017-01-01

Programing is difficult for beginners because they need to learn the new language of computers. Developing software, especially complex software, is bound to result in problems, frustration, and the need to think in new ways. Identifying the learning behavior behind programing by way of empirical studies can help beginners learn more easily. In…

Semantic Metrics for Analysis of Software

NASA Technical Reports Server (NTRS)

Etzkorn, Letha H.; Cox, Glenn W.; Farrington, Phil; Utley, Dawn R.; Ghalston, Sampson; Stein, Cara

2005-01-01

A recently conceived suite of object-oriented software metrics focus is on semantic aspects of software, in contradistinction to traditional software metrics, which focus on syntactic aspects of software. Semantic metrics represent a more human-oriented view of software than do syntactic metrics. The semantic metrics of a given computer program are calculated by use of the output of a knowledge-based analysis of the program, and are substantially more representative of software quality and more readily comprehensible from a human perspective than are the syntactic metrics.

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

An easy-to -use user interface was implemented in a highly automated regression analysis tool. The user interface was developed from the start to run on computers that use the Windows, Macintosh, Linux, or UNIX operating system. Many user interface features were specifically designed such that a novice or inexperienced user can apply the regression analysis tool with confidence. Therefore, the user interface s design minimizes interactive input from the user. In addition, reasonable default combinations are assigned to those analysis settings that influence the outcome of the regression analysis. These default combinations will lead to a successful regression analysis result for most experimental data sets. The user interface comes in two versions. The text user interface version is used for the ongoing development of the regression analysis tool. The official release of the regression analysis tool, on the other hand, has a graphical user interface that is more efficient to use. This graphical user interface displays all input file names, output file names, and analysis settings for a specific software application mode on a single screen which makes it easier to generate reliable analysis results and to perform input parameter studies. An object-oriented approach was used for the development of the graphical user interface. This choice keeps future software maintenance costs to a reasonable limit. Examples of both the text user interface and graphical user interface are discussed in order to illustrate the user interface s overall design approach.

VLBI Analysis with the Multi-Technique Software GEOSAT

NASA Technical Reports Server (NTRS)

Kierulf, Halfdan Pascal; Andersen, Per-Helge; Boeckmann, Sarah; Kristiansen, Oddgeir

2010-01-01

GEOSAT is a multi-technique geodetic analysis software developed at Forsvarets Forsknings Institutt (Norwegian defense research establishment). The Norwegian Mapping Authority has now installed the software and has, together with Forsvarets Forsknings Institutt, adapted the software to deliver datum-free normal equation systems in SINEX format. The goal is to be accepted as an IVS Associate Analysis Center and to provide contributions to the IVS EOP combination on a routine basis. GEOSAT is based on an upper diagonal factorized Kalman filter which allows estimation of time variable parameters like the troposphere and clocks as stochastic parameters. The tropospheric delays in various directions are mapped to tropospheric zenith delay using ray-tracing. Meteorological data from ECMWF with a resolution of six hours is used to perform the ray-tracing which depends both on elevation and azimuth. Other models are following the IERS and IVS conventions. The Norwegian Mapping Authority has submitted test SINEX files produced with GEOSAT to IVS. The results have been compared with the existing IVS combined products. In this paper the outcome of these comparisons is presented.

Status and plans for the future of the Vienna VLBI Software

NASA Astrophysics Data System (ADS)

Madzak, Matthias; Böhm, Johannes; Böhm, Sigrid; Girdiuk, Anastasiia; Hellerschmied, Andreas; Hofmeister, Armin; Krasna, Hana; Kwak, Younghee; Landskron, Daniel; Mayer, David; McCallum, Jamie; Plank, Lucia; Schönberger, Caroline; Shabala, Stanislav; Sun, Jing; Teke, Kamil

2016-04-01

The Vienna VLBI Software (VieVS) is a VLBI analysis software developed and maintained at Technische Universität Wien (TU Wien) since 2008 with contributions from groups all over the world. It is used for both academic purposes in university courses as well as for providing VLBI analysis results to the geodetic community. Written in a modular structure in Matlab, VieVS offers easy access to the source code and the possibility to adapt the programs for particular purposes. The new version 2.3, released in December 2015, includes several new parameters to be estimated in the global solution, such as tidal ERP variation coefficients. The graphical user interface was slightly modified for an improved user functionality and, e.g., the possibility of deriving baseline length repeatabilities. The scheduling of satellite observations was refined, the simulator newly includes the effect of source structure which can also be corrected for in the analysis. This poster gives an overview of all VLBI-related activities in Vienna and provides an outlook to future plans concerning the Vienna VLBI Software.

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

FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

PubMed Central

Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

2016-01-01

Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community. PMID:27532626

An experimental evaluation of software redundancy as a strategy for improving reliability

NASA Technical Reports Server (NTRS)

Eckhardt, Dave E., Jr.; Caglayan, Alper K.; Knight, John C.; Lee, Larry D.; Mcallister, David F.; Vouk, Mladen A.; Kelly, John P. J.

1990-01-01

The strategy of using multiple versions of independently developed software as a means to tolerate residual software design faults is suggested by the success of hardware redundancy for tolerating hardware failures. Although, as generally accepted, the independence of hardware failures resulting from physical wearout can lead to substantial increases in reliability for redundant hardware structures, a similar conclusion is not immediate for software. The degree to which design faults are manifested as independent failures determines the effectiveness of redundancy as a method for improving software reliability. Interest in multi-version software centers on whether it provides an adequate measure of increased reliability to warrant its use in critical applications. The effectiveness of multi-version software is studied by comparing estimates of the failure probabilities of these systems with the failure probabilities of single versions. The estimates are obtained under a model of dependent failures and compared with estimates obtained when failures are assumed to be independent. The experimental results are based on twenty versions of an aerospace application developed and certified by sixty programmers from four universities. Descriptions of the application, development and certification processes, and operational evaluation are given together with an analysis of the twenty versions.

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.

PubMed

Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

2013-04-22

For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations.

Structural Performance’s Optimally Analysing and Implementing Based on ANSYS Technology

NASA Astrophysics Data System (ADS)

Han, Na; Wang, Xuquan; Yue, Haifang; Sun, Jiandong; Wu, Yongchun

2017-06-01

Computer-aided Engineering (CAE) is a hotspot both in academic field and in modern engineering practice. Analysis System(ANSYS) simulation software for its excellent performance become outstanding one in CAE family, it is committed to the innovation of engineering simulation to help users to shorten the design process, improve product innovation and performance. Aimed to explore a structural performance’s optimally analyzing model for engineering enterprises, this paper introduced CAE and its development, analyzed the necessity for structural optimal analysis as well as the framework of structural optimal analysis on ANSYS Technology, used ANSYS to implement a reinforced concrete slab structural performance’s optimal analysis, which was display the chart of displacement vector and the chart of stress intensity. Finally, this paper compared ANSYS software simulation results with the measured results,expounded that ANSYS is indispensable engineering calculation tools.

Fully Employing Software Inspections Data

NASA Technical Reports Server (NTRS)

Shull, Forrest; Feldmann, Raimund L.; Seaman, Carolyn; Regardie, Myrna; Godfrey, Sally

2009-01-01

Software inspections provide a proven approach to quality assurance for software products of all kinds, including requirements, design, code, test plans, among others. Common to all inspections is the aim of finding and fixing defects as early as possible, and thereby providing cost savings by minimizing the amount of rework necessary later in the lifecycle. Measurement data, such as the number and type of found defects and the effort spent by the inspection team, provide not only direct feedback about the software product to the project team but are also valuable for process improvement activities. In this paper, we discuss NASA's use of software inspections and the rich set of data that has resulted. In particular, we present results from analysis of inspection data that illustrate the benefits of fully utilizing that data for process improvement at several levels. Examining such data across multiple inspections or projects allows team members to monitor and trigger cross project improvements. Such improvements may focus on the software development processes of the whole organization as well as improvements to the applied inspection process itself.

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

ERIC Educational Resources Information Center

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

2017-01-01

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

Software for analysis of chemical mixtures--composition, occurrence, distribution, and possible toxicity

USGS Publications Warehouse

Scott, Jonathon C.; Skach, Kenneth A.; Toccalino, Patricia L.

2013-01-01

The composition, occurrence, distribution, and possible toxicity of chemical mixtures in the environment are research concerns of the U.S. Geological Survey and others. The presence of specific chemical mixtures may serve as indicators of natural phenomena or human-caused events. Chemical mixtures may also have ecological, industrial, geochemical, or toxicological effects. Chemical-mixture occurrences vary by analyte composition and concentration. Four related computer programs have been developed by the National Water-Quality Assessment Program of the U.S. Geological Survey for research of chemical-mixture compositions, occurrences, distributions, and possible toxicities. The compositions and occurrences are identified for the user-supplied data, and therefore the resultant counts are constrained by the user’s choices for the selection of chemicals, reporting limits for the analytical methods, spatial coverage, and time span for the data supplied. The distribution of chemical mixtures may be spatial, temporal, and (or) related to some other variable, such as chemical usage. Possible toxicities optionally are estimated from user-supplied benchmark data. The software for the analysis of chemical mixtures described in this report is designed to work with chemical-analysis data files retrieved from the U.S. Geological Survey National Water Information System but can also be used with appropriately formatted data from other sources. Installation and usage of the mixture software are documented. This mixture software was designed to function with minimal changes on a variety of computer-operating systems. To obtain the software described herein and other U.S. Geological Survey software, visit http://water.usgs.gov/software/.

Building an experience factory for maintenance

NASA Technical Reports Server (NTRS)

Valett, Jon D.; Condon, Steven E.; Briand, Lionel; Kim, Yong-Mi; Basili, Victor R.

1994-01-01

This paper reports the preliminary results of a study of the software maintenance process in the Flight Dynamics Division (FDD) of the National Aeronautics and Space Administration/Goddard Space Flight Center (NASA/GSFC). This study is being conducted by the Software Engineering Laboratory (SEL), a research organization sponsored by the Software Engineering Branch of the FDD, which investigates the effectiveness of software engineering technologies when applied to the development of applications software. This software maintenance study began in October 1993 and is being conducted using the Quality Improvement Paradigm (QIP), a process improvement strategy based on three iterative steps: understanding, assessing, and packaging. The preliminary results represent the outcome of the understanding phase, during which SEL researchers characterized the maintenance environment, product, and process. Findings indicate that a combination of quantitative and qualitative analysis is effective for studying the software maintenance process, that additional measures should be collected for maintenance (as opposed to new development), and that characteristics such as effort, error rate, and productivity are best considered on a 'release' basis rather than on a project basis. The research thus far has documented some basic differences between new development and software maintenance. It lays the foundation for further application of the QIP to investigate means of improving the maintenance process and product in the FDD.

Understanding software faults and their role in software reliability modeling

NASA Technical Reports Server (NTRS)

Munson, John C.

1994-01-01

This study is a direct result of an on-going project to model the reliability of a large real-time control avionics system. In previous modeling efforts with this system, hardware reliability models were applied in modeling the reliability behavior of this system. In an attempt to enhance the performance of the adapted reliability models, certain software attributes were introduced in these models to control for differences between programs and also sequential executions of the same program. As the basic nature of the software attributes that affect software reliability become better understood in the modeling process, this information begins to have important implications on the software development process. A significant problem arises when raw attribute measures are to be used in statistical models as predictors, for example, of measures of software quality. This is because many of the metrics are highly correlated. Consider the two attributes: lines of code, LOC, and number of program statements, Stmts. In this case, it is quite obvious that a program with a high value of LOC probably will also have a relatively high value of Stmts. In the case of low level languages, such as assembly language programs, there might be a one-to-one relationship between the statement count and the lines of code. When there is a complete absence of linear relationship among the metrics, they are said to be orthogonal or uncorrelated. Usually the lack of orthogonality is not serious enough to affect a statistical analysis. However, for the purposes of some statistical analysis such as multiple regression, the software metrics are so strongly interrelated that the regression results may be ambiguous and possibly even misleading. Typically, it is difficult to estimate the unique effects of individual software metrics in the regression equation. The estimated values of the coefficients are very sensitive to slight changes in the data and to the addition or deletion of variables in the regression equation. Since most of the existing metrics have common elements and are linear combinations of these common elements, it seems reasonable to investigate the structure of the underlying common factors or components that make up the raw metrics. The technique we have chosen to use to explore this structure is a procedure called principal components analysis. Principal components analysis is a decomposition technique that may be used to detect and analyze collinearity in software metrics. When confronted with a large number of metrics measuring a single construct, it may be desirable to represent the set by some smaller number of variables that convey all, or most, of the information in the original set. Principal components are linear transformations of a set of random variables that summarize the information contained in the variables. The transformations are chosen so that the first component accounts for the maximal amount of variation of the measures of any possible linear transform; the second component accounts for the maximal amount of residual variation; and so on. The principal components are constructed so that they represent transformed scores on dimensions that are orthogonal. Through the use of principal components analysis, it is possible to have a set of highly related software attributes mapped into a small number of uncorrelated attribute domains. This definitively solves the problem of multi-collinearity in subsequent regression analysis. There are many software metrics in the literature, but principal component analysis reveals that there are few distinct sources of variation, i.e. dimensions, in this set of metrics. It would appear perfectly reasonable to characterize the measurable attributes of a program with a simple function of a small number of orthogonal metrics each of which represents a distinct software attribute domain.

Analyzing and Predicting Effort Associated with Finding and Fixing Software Faults

NASA Technical Reports Server (NTRS)

Hamill, Maggie; Goseva-Popstojanova, Katerina

2016-01-01

Context: Software developers spend a significant amount of time fixing faults. However, not many papers have addressed the actual effort needed to fix software faults. Objective: The objective of this paper is twofold: (1) analysis of the effort needed to fix software faults and how it was affected by several factors and (2) prediction of the level of fix implementation effort based on the information provided in software change requests. Method: The work is based on data related to 1200 failures, extracted from the change tracking system of a large NASA mission. The analysis includes descriptive and inferential statistics. Predictions are made using three supervised machine learning algorithms and three sampling techniques aimed at addressing the imbalanced data problem. Results: Our results show that (1) 83% of the total fix implementation effort was associated with only 20% of failures. (2) Both safety critical failures and post-release failures required three times more effort to fix compared to non-critical and pre-release counterparts, respectively. (3) Failures with fixes spread across multiple components or across multiple types of software artifacts required more effort. The spread across artifacts was more costly than spread across components. (4) Surprisingly, some types of faults associated with later life-cycle activities did not require significant effort. (5) The level of fix implementation effort was predicted with 73% overall accuracy using the original, imbalanced data. Using oversampling techniques improved the overall accuracy up to 77%. More importantly, oversampling significantly improved the prediction of the high level effort, from 31% to around 85%. Conclusions: This paper shows the importance of tying software failures to changes made to fix all associated faults, in one or more software components and/or in one or more software artifacts, and the benefit of studying how the spread of faults and other factors affect the fix implementation effort.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

PubMed Central

2014-01-01

Motivation Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. Results The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. Conclusion The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user’s needs. Availability The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com. PMID:25068035

Man-machine Integration Design and Analysis System (MIDAS) Task Loading Model (TLM) experimental and software detailed design report

NASA Technical Reports Server (NTRS)

Staveland, Lowell

1994-01-01

This is the experimental and software detailed design report for the prototype task loading model (TLM) developed as part of the man-machine integration design and analysis system (MIDAS), as implemented and tested in phase 6 of the Army-NASA Aircrew/Aircraft Integration (A3I) Program. The A3I program is an exploratory development effort to advance the capabilities and use of computational representations of human performance and behavior in the design, synthesis, and analysis of manned systems. The MIDAS TLM computationally models the demands designs impose on operators to aide engineers in the conceptual design of aircraft crewstations. This report describes TLM and the results of a series of experiments which were run this phase to test its capabilities as a predictive task demand modeling tool. Specifically, it includes discussions of: the inputs and outputs of TLM, the theories underlying it, the results of the test experiments, the use of the TLM as both stand alone tool and part of a complete human operator simulation, and a brief introduction to the TLM software design.

The LHCb software and computing upgrade for Run 3: opportunities and challenges

NASA Astrophysics Data System (ADS)

Bozzi, C.; Roiser, S.; LHCb Collaboration

2017-10-01

The LHCb detector will be upgraded for the LHC Run 3 and will be readout at 30 MHz, corresponding to the full inelastic collision rate, with major implications on the full software trigger and offline computing. If the current computing model and software framework are kept, the data storage capacity and computing power required to process data at this rate, and to generate and reconstruct equivalent samples of simulated events, will exceed the current capacity by at least one order of magnitude. A redesign of the software framework, including scheduling, the event model, the detector description and the conditions database, is needed to fully exploit the computing power of multi-, many-core architectures, and coprocessors. Data processing and the analysis model will also change towards an early streaming of different data types, in order to limit storage resources, with further implications for the data analysis workflows. Fast simulation options will allow to obtain a reasonable parameterization of the detector response in considerably less computing time. Finally, the upgrade of LHCb will be a good opportunity to review and implement changes in the domains of software design, test and review, and analysis workflow and preservation. In this contribution, activities and recent results in all the above areas are presented.

Process Correlation Analysis Model for Process Improvement Identification

PubMed Central

Park, Sooyong

2014-01-01

Software process improvement aims at improving the development process of software systems. It is initiated by process assessment identifying strengths and weaknesses and based on the findings, improvement plans are developed. In general, a process reference model (e.g., CMMI) is used throughout the process of software process improvement as the base. CMMI defines a set of process areas involved in software development and what to be carried out in process areas in terms of goals and practices. Process areas and their elements (goals and practices) are often correlated due to the iterative nature of software development process. However, in the current practice, correlations of process elements are often overlooked in the development of an improvement plan, which diminishes the efficiency of the plan. This is mainly attributed to significant efforts and the lack of required expertise. In this paper, we present a process correlation analysis model that helps identify correlations of process elements from the results of process assessment. This model is defined based on CMMI and empirical data of improvement practices. We evaluate the model using industrial data. PMID:24977170

Process correlation analysis model for process improvement identification.

PubMed

Choi, Su-jin; Kim, Dae-Kyoo; Park, Sooyong

2014-01-01

Software process improvement aims at improving the development process of software systems. It is initiated by process assessment identifying strengths and weaknesses and based on the findings, improvement plans are developed. In general, a process reference model (e.g., CMMI) is used throughout the process of software process improvement as the base. CMMI defines a set of process areas involved in software development and what to be carried out in process areas in terms of goals and practices. Process areas and their elements (goals and practices) are often correlated due to the iterative nature of software development process. However, in the current practice, correlations of process elements are often overlooked in the development of an improvement plan, which diminishes the efficiency of the plan. This is mainly attributed to significant efforts and the lack of required expertise. In this paper, we present a process correlation analysis model that helps identify correlations of process elements from the results of process assessment. This model is defined based on CMMI and empirical data of improvement practices. We evaluate the model using industrial data.

An online database for plant image analysis software tools.

PubMed

Lobet, Guillaume; Draye, Xavier; Périlleux, Claire

2013-10-09

Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment. These solutions are instrumental in supporting various research pipelines, ranging from the localisation of cellular compounds to the quantification of tree canopies. However, due to the variety of existing tools and the lack of central repository, it is challenging for researchers to identify the software that is best suited for their research. We present an online, manually curated, database referencing more than 90 plant image analysis software solutions. The website, plant-image-analysis.org, presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions. The plant-image-analysis.org database provides an overview of existing plant image analysis software. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.

A Framework for Testing Scientific Software: A Case Study of Testing Amsterdam Discrete Dipole Approximation Software

NASA Astrophysics Data System (ADS)

Shao, Hongbing

Software testing with scientific software systems often suffers from test oracle problem, i.e., lack of test oracles. Amsterdam discrete dipole approximation code (ADDA) is a scientific software system that can be used to simulate light scattering of scatterers of various types. Testing of ADDA suffers from "test oracle problem". In this thesis work, I established a testing framework to test scientific software systems and evaluated this framework using ADDA as a case study. To test ADDA, I first used CMMIE code as the pseudo oracle to test ADDA in simulating light scattering of a homogeneous sphere scatterer. Comparable results were obtained between ADDA and CMMIE code. This validated ADDA for use with homogeneous sphere scatterers. Then I used experimental result obtained for light scattering of a homogeneous sphere to validate use of ADDA with sphere scatterers. ADDA produced light scattering simulation comparable to the experimentally measured result. This further validated the use of ADDA for simulating light scattering of sphere scatterers. Then I used metamorphic testing to generate test cases covering scatterers of various geometries, orientations, homogeneity or non-homogeneity. ADDA was tested under each of these test cases and all tests passed. The use of statistical analysis together with metamorphic testing is discussed as a future direction. In short, using ADDA as a case study, I established a testing framework, including use of pseudo oracles, experimental results and the metamorphic testing techniques to test scientific software systems that suffer from test oracle problems. Each of these techniques is necessary and contributes to the testing of the software under test.

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.

Are Earth System model software engineering practices fit for purpose? A case study.

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.; Johns, T. C.

2009-04-01

We present some analysis and conclusions from a case study of the culture and practices of scientists at the Met Office and Hadley Centre working on the development of software for climate and Earth System models using the MetUM infrastructure. The study examined how scientists think about software correctness, prioritize their requirements in making changes, and develop a shared understanding of the resulting models. We conclude that highly customized techniques driven strongly by scientific research goals have evolved for verification and validation of such models. In a formal software engineering context these represents costly, but invaluable, software integration tests with considerable benefits. The software engineering practices seen also exhibit recognisable features of both agile and open source software development projects - self-organisation of teams consistent with a meritocracy rather than top-down organisation, extensive use of informal communication channels, and software developers who are generally also users and science domain experts. We draw some general conclusions on whether these practices work well, and what new software engineering challenges may lie ahead as Earth System models become ever more complex and petascale computing becomes the norm.

Development of a calibrated software reliability model for flight and supporting ground software for avionic systems

NASA Technical Reports Server (NTRS)

Lawrence, Stella

1991-01-01

The object of this project was to develop and calibrate quantitative models for predicting the quality of software. Reliable flight and supporting ground software is a highly important factor in the successful operation of the space shuttle program. The models used in the present study consisted of SMERFS (Statistical Modeling and Estimation of Reliability Functions for Software). There are ten models in SMERFS. For a first run, the results obtained in modeling the cumulative number of failures versus execution time showed fairly good results for our data. Plots of cumulative software failures versus calendar weeks were made and the model results were compared with the historical data on the same graph. If the model agrees with actual historical behavior for a set of data then there is confidence in future predictions for this data. Considering the quality of the data, the models have given some significant results, even at this early stage. With better care in data collection, data analysis, recording of the fixing of failures and CPU execution times, the models should prove extremely helpful in making predictions regarding the future pattern of failures, including an estimate of the number of errors remaining in the software and the additional testing time required for the software quality to reach acceptable levels. It appears that there is no one 'best' model for all cases. It is for this reason that the aim of this project was to test several models. One of the recommendations resulting from this study is that great care must be taken in the collection of data. When using a model, the data should satisfy the model assumptions.

Software Engineering Improvement Activities/Plan

NASA Technical Reports Server (NTRS)

2003-01-01

bd Systems personnel accomplished the technical responsibilities for this reporting period, as planned. A close working relationship was maintained with personnel of the MSFC Avionics Department Software Group (ED14). Work accomplishments included development, evaluation, and enhancement of a software cost model, performing literature search and evaluation of software tools available for code analysis and requirements analysis, and participating in other relevant software engineering activities. Monthly reports were submitted. This support was provided to the Flight Software Group/ED 1 4 in accomplishing the software engineering improvement engineering activities of the Marshall Space Flight Center (MSFC) Software Engineering Improvement Plan.

Study of application of space telescope science operations software for SIRTF use

NASA Technical Reports Server (NTRS)

Dignam, F.; Stetson, E.; Allendoerfer, W.

1985-01-01

The design and development of the Space Telescope Science Operations Ground System (ST SOGS) was evaluated to compile a history of lessons learned that would benefit NASA's Space Infrared Telescope Facility (SIRTF). Forty-nine specific recommendations resulted and were categorized as follows: (1) requirements: a discussion of the content, timeliness and proper allocation of the system and segment requirements and the resulting impact on SOGS development; (2) science instruments: a consideration of the impact of the Science Instrument design and data streams on SOGS software; and (3) contract phasing: an analysis of the impact of beginning the various ST program segments at different times. Approximately half of the software design and source code might be useable for SIRTF. Transportability of this software requires, at minimum, a compatible DEC VAX-based architecture and VMS operating system, system support software similar to that developed for SOGS, and continued evolution of the SIRTF operations concept and requirements such that they remain compatible with ST SOGS operation.

Aeroelastic Analysis Of Joined Wing Of High Altitude Long Endurance (HALE) Aircraft Based On The Sensor-Craft Configuration

NASA Astrophysics Data System (ADS)

Marisarla, Soujanya; Ghia, Urmila; "Karman" Ghia, Kirti

2002-11-01

Towards a comprehensive aeroelastic analysis of a joined wing, fluid dynamics and structural analyses are initially performed separately. Steady flow calculations are currently performed using 3-D compressible Navier-Stokes equations. Flow analysis of M6-Onera wing served to validate the software for the fluid dynamics analysis. The complex flow field of the joined wing is analyzed and the prevailing fluid dynamic forces are computed using COBALT software. Currently, these forces are being transferred as fluid loads on the structure. For the structural analysis, several test cases were run considering the wing as a cantilever beam; these served as validation cases. A nonlinear structural analysis of the wing is being performed using ANSYS software to predict the deflections and stresses on the joined wing. Issues related to modeling, and selecting appropriate mesh for the structure were addressed by first performing a linear analysis. The frequencies and mode shapes of the deformed wing are obtained from modal analysis. Both static and dynamic analyses are carried out, and the results obtained are carefully analyzed. Loose coupling between the fluid and structural analyses is currently being examined.

Automation for System Safety Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Fleming, Land; Throop, David; Thronesbery, Carroll; Flores, Joshua; Bennett, Ted; Wennberg, Paul

2009-01-01

This presentation describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

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

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Development of a New VLBI Data Analysis Software

NASA Technical Reports Server (NTRS)

Bolotin, Sergei; Gipson, John M.; MacMillan, Daniel S.

2010-01-01

We present an overview of a new VLBI analysis software under development at NASA GSFC. The new software will replace CALC/SOLVE and many related utility programs. It will have the capabilities of the current system as well as incorporate new models and data analysis techniques. In this paper we give a conceptual overview of the new software. We formulate the main goals of the software. The software should be flexible and modular to implement models and estimation techniques that currently exist or will appear in future. On the other hand it should be reliable and possess production quality for processing standard VLBI sessions. Also, it needs to be capable of processing observations from a fully deployed network of VLBI2010 stations in a reasonable time. We describe the software development process and outline the software architecture.

Development of Automated Image Analysis Software for Suspended Marine Particle Classification

DTIC Science & Technology

2002-09-30

Development of Automated Image Analysis Software for Suspended Marine Particle Classification Scott Samson Center for Ocean Technology...and global water column. 1 OBJECTIVES The project’s objective is to develop automated image analysis software to reduce the effort and time

Multidisciplinary Concurrent Design Optimization via the Internet

NASA Technical Reports Server (NTRS)

Woodard, Stanley E.; Kelkar, Atul G.; Koganti, Gopichand

2001-01-01

A methodology is presented which uses commercial design and analysis software and the Internet to perform concurrent multidisciplinary optimization. The methodology provides a means to develop multidisciplinary designs without requiring that all software be accessible from the same local network. The procedures are amenable to design and development teams whose members, expertise and respective software are not geographically located together. This methodology facilitates multidisciplinary teams working concurrently on a design problem of common interest. Partition of design software to different machines allows each constituent software to be used on the machine that provides the most economy and efficiency. The methodology is demonstrated on the concurrent design of a spacecraft structure and attitude control system. Results are compared to those derived from performing the design with an autonomous FORTRAN program.

Development of a Software Safety Process and a Case Study of Its Use

NASA Technical Reports Server (NTRS)

Knight, J. C.

1996-01-01

Research in the year covered by this reporting period has been primarily directed toward: continued development of mock-ups of computer screens for operator of a digital reactor control system; development of a reactor simulation to permit testing of various elements of the control system; formal specification of user interfaces; fault-tree analysis including software; evaluation of formal verification techniques; and continued development of a software documentation system. Technical results relating to this grant and the remainder of the principal investigator's research program are contained in various reports and papers.

pyLIMA : The first open source microlensing modeling software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne; Street, Rachel; Bozza, Valerio

2018-01-01

Microlensing is highly sensitive to planets beyond the snowline and distributed along the line of sight towards the Galactic Bulge. The WFIRST-AFTA mission should detect about 3000 of these planets and significantly improves our knowledge of planet formation and statistics, complementing results found by transit and radial velocity methods. However, the modeling of microlensing event is challenging on different aspects leading to a highly time consuming analysis. After a quick summarize of these different challenges, I will present pyLIMA, the first open source microlensing modeling software. The aimed goal of this software are to be flexible, powerful and user friendly. This presentation will focus on various case and early results.

Computational aeroelastic analysis of aircraft wings including geometry nonlinearity

NASA Astrophysics Data System (ADS)

Tian, Binyu

The objective of the present study is to show the ability of solving fluid structural interaction problems more realistically by including the geometric nonlinearity of the structure so that the aeroelastic analysis can be extended into the onset of flutter, or in the post flutter regime. A nonlinear Finite Element Analysis software is developed based on second Piola-Kirchhoff stress and Green-Lagrange strain. The second Piola-Kirchhoff stress and Green-Lagrange strain is a pair of energetically conjugated tensors that can accommodate arbitrary large structural deformations and deflection, to study the flutter phenomenon. Since both of these tensors are objective tensors, i.e., the rigid-body motion has no contribution to their components, the movement of the body, including maneuvers and deformation, can be included. The nonlinear Finite Element Analysis software developed in this study is verified with ANSYS, NASTRAN, ABAQUS, and IDEAS for the linear static, nonlinear static, linear dynamic and nonlinear dynamic structural solutions. To solve the flow problems by Euler/Navier equations, the current nonlinear structural software is then embedded into ENSAERO, which is an aeroelastic analysis software package developed at NASA Ames Research Center. The coupling of the two software, both nonlinear in their own field, is achieved by domain decomposition method first proposed by Guruswamy. A procedure has been set for the aeroelastic analysis process. The aeroelastic analysis results have been obtained for fight wing in the transonic regime for various cases. The influence dynamic pressure on flutter has been checked for a range of Mach number. Even though the current analysis matches the general aeroelastic characteristic, the numerical value not match very well with previous studies and needs farther investigations. The flutter aeroelastic analysis results have also been plotted at several time points. The influences of the deforming wing geometry can be well seen in those plots. The movement of shock changes the aerodynamic load distribution on the wing. The effect of viscous on aeroelastic analysis is also discussed. Also compared are the flutter solutions with, or without the structural nonlinearity. As can be seen, linear structural solution goes to infinite, which can not be true in reality. The nonlinear solution is more realistic and can be used to understand the fluid and structure interaction behavior, to control, or prevent disastrous events. (Abstract shortened by UMI.)

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

PubMed

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

2008-12-01

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

VideoHacking: Automated Tracking and Quantification of Locomotor Behavior with Open Source Software and Off-the-Shelf Video Equipment.

PubMed

Conklin, Emily E; Lee, Kathyann L; Schlabach, Sadie A; Woods, Ian G

2015-01-01

Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs.

Computer-assisted qualitative data analysis software.

PubMed

Cope, Diane G

2014-05-01

Advances in technology have provided new approaches for data collection methods and analysis for researchers. Data collection is no longer limited to paper-and-pencil format, and numerous methods are now available through Internet and electronic resources. With these techniques, researchers are not burdened with entering data manually and data analysis is facilitated by software programs. Quantitative research is supported by the use of computer software and provides ease in the management of large data sets and rapid analysis of numeric statistical methods. New technologies are emerging to support qualitative research with the availability of computer-assisted qualitative data analysis software (CAQDAS).CAQDAS will be presented with a discussion of advantages, limitations, controversial issues, and recommendations for this type of software use.

Emissivity of Rocket Plume Particulates

DTIC Science & Technology

1992-09-01

V. EXPERIMENTAL RESULTS ........ ............... 29 VI. CONCLUSIONS AND RECOMMENDATIONS .... ........ 32 APPENDIX A. CATS -E SOFTWARE...interfaced through the CATS E Thermal Analysis software, which is MS-DOS based, and can be run on any 28b or higher CPU. This system allows real-time...body source to establish the parameters required by the CATS program for proper microscope/scanner interface. A complete description of microscope

IDA Cost Research Symposium Held 25 May 1995.

DTIC Science & Technology

1995-08-01

Excel Spreadsheet Publications: MCR Report TR-9507/01 Category: II.B Keywords: Government, Estimating, Missiles, Analysis, Production, Data...originally developed by Martin Marietta as part of SASET software estimating model. To be implemented as part of SoftEST Software Estimating Tool...following documents to report the results of Its work. Reports Reports are the most authoritative and most carefully considered products IDA

Benefits of Oxygen Saturation Targeting Trials: Oximeter Calibration Software Revision and Infant Saturations.

PubMed

Whyte, Robin K; Nelson, Harvey; Roberts, Robin S; Schmidt, Barbara

2017-03-01

It has been reported in the 3 Benefits of Oxygen Saturation Targeting (BOOST-II) trials that changes in oximeter calibration software resulted in clearer separation between the oxygen saturations in the two trial target groups. A revised analysis of the published BOOST-II data does not support this conclusion. Copyright © 2016 Elsevier Inc. All rights reserved.

The information protection level assessment system implementation

NASA Astrophysics Data System (ADS)

Trapeznikov, E. V.

2018-04-01

Currently, the threat of various attacks increases significantly as automated systems become more widespread. On the basis of the conducted analysis the information protection level assessment system establishing objective was identified. The paper presents the information protection level assessment software implementation in the information system by applying the programming language C #. In conclusions the software features are identified and experimental results are represented.

Simulation Tools Prevent Signal Interference on Spacecraft

NASA Technical Reports Server (NTRS)

2014-01-01

NASA engineers use simulation software to detect and prevent interference between different radio frequency (RF) systems on a rocket and satellite before launch. To speed up the process, Kennedy Space Center awarded SBIR funding to Champaign, Illinois-based Delcross Technologies LLC, which added a drag-and-drop feature to its commercial simulation software, resulting in less time spent preparing for the analysis.

ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite

PubMed Central

2010-01-01

Background Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light") versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a "handle" that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks. Results Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks. Conclusion The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm PMID:20109223

CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477

Characterization of Morphology using MAMA Software

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

Gravelle, Julie

The MAMA (Morphological Analysis for Material Attribution) software was developed at the Los Alamos National Laboratory funded through the National Technical Nuclear Forensics Center in the Department of Homeland Security. The software allows images to be analysed and quantified. The largest project I worked on was to quantify images of plutonium oxides and ammonium diuranates prepared by the group with the software and provide analyses on the particles of each sample. Images were quantified through MAMA, with a color analysis, a lexicon description and powder x-ray diffraction. Through this we were able to visually see a difference between some ofmore » the syntheses. An additional project was to revise the manual for MAMA to help streamline training and provide useful tips to users to more quickly become acclimated to using the software. The third project investigated expanding the scope of MAMA and finding a statistically relevant baseline for the particulates through the analysis of maps in the software and using known measurements to compare the error associated with the software. During this internship, I worked on several different projects dealing with the MAMA software. The revision of the usermanual for the MAMA software was the first project I was able to work and collaborate on. I first learned how to use the software by getting instruction from a skilled user at the laboratory, Dan Schwartz, and by using the existing user manual and examples. After becoming accustomed to the program, I started to go over the manual to correct and change items that were not as useful or descriptive as they could have been. I also added in tips that I learned as I explored the software. The updated manual was also worked on by several others who have been developing the program. The goal of these revisions was to ensure the most concise and simple directions to the software were available to future users. By incorporating tricks and shortcuts that I discovered and picked up from watching other users into the user guide, I believe that anyone who utilizes the software will be able to quickly understand the best way to analyze their image and use the tools the program offers to achieve useful results.« less

Modular Analytical Multicomponent Analysis in Gas Sensor Aarrays

PubMed Central

Chaiyboun, Ali; Traute, Rüdiger; Kiesewetter, Olaf; Ahlers, Simon; Müller, Gerhard; Doll, Theodor

2006-01-01

A multi-sensor system is a chemical sensor system which quantitatively and qualitatively records gases with a combination of cross-sensitive gas sensor arrays and pattern recognition software. This paper addresses the issue of data analysis for identification of gases in a gas sensor array. We introduce a software tool for gas sensor array configuration and simulation. It concerns thereby about a modular software package for the acquisition of data of different sensors. A signal evaluation algorithm referred to as matrix method was used specifically for the software tool. This matrix method computes the gas concentrations from the signals of a sensor array. The software tool was used for the simulation of an array of five sensors to determine gas concentration of CH4, NH3, H2, CO and C2H5OH. The results of the present simulated sensor array indicate that the software tool is capable of the following: (a) identify a gas independently of its concentration; (b) estimate the concentration of the gas, even if the system was not previously exposed to this concentration; (c) tell when a gas concentration exceeds a certain value. A gas sensor data base was build for the configuration of the software. With the data base one can create, generate and manage scenarios and source files for the simulation. With the gas sensor data base and the simulation software an on-line Web-based version was developed, with which the user can configure and simulate sensor arrays on-line.

Sneak Analysis Application Guidelines

DTIC Science & Technology

1982-06-01

Hardware Program Change Cost Trend, Airborne Environment ....... ....................... 111 3-11 Relative Software Program Change Costs...113 3-50 Derived Software Program Change Cost by Phase,* Airborne Environment ..... ............... 114 3-51 Derived Software Program Change...Cost by Phase, Ground/Water Environment ... ............. .... 114 3-52 Total Software Program Change Costs ................ 115 3-53 Sneak Analysis

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

PubMed

Markiewicz, Tomasz

2011-03-30

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8 GHz 4 GB RAM server with 768x576 pixel size, 1.28 Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server - 3.5 seconds, at remote analysis - 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system.

Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.

PubMed

Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O

2013-06-01

Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Comprehensive analysis of NMR data using advanced line shape fitting.

PubMed

Niklasson, Markus; Otten, Renee; Ahlner, Alexandra; Andresen, Cecilia; Schlagnitweit, Judith; Petzold, Katja; Lundström, Patrik

2017-10-01

NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application. The software is a completely redesigned version of PINT ( https://pint-nmr.github.io/PINT/ ). It features a graphical user interface and includes functionality for peak picking, editing of peak lists and line shape fitting. In addition, the obtained peak intensities can be used directly to extract, for instance, relaxation rates, heteronuclear NOE values and exchange parameters. In contrast to most available software the entire process from spectral visualization to preparation of publication-ready figures is done solely using PINT and often within minutes, thereby, increasing productivity for users of all experience levels. Unique to the software are also the outstanding tools for evaluating the quality of the fitting results and extensive, but easy-to-use, customization of the fitting protocol and graphical output. In this communication, we describe the features of the new version of PINT and benchmark its performance.

CONAN: copy number variation analysis software for genome-wide association studies

PubMed Central

2010-01-01

Background Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) promise to shed additional light on the genetic basis of monogenic as well as complex diseases and phenotypes. Indeed, the number of detected associations between CNVs and certain phenotypes are constantly increasing. However, while several software packages support the determination of CNVs from SNP chip data, the downstream statistical inference of CNV-phenotype associations is still subject to complicated and inefficient in-house solutions, thus strongly limiting the performance of GWAS based on CNVs. Results CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes. Moreover, CONAN assists the evaluation process by visualizing detected associations via Manhattan plots in order to enable a rapid identification of genome-wide significant CNV regions. Various file formats including the information on CNVs in population samples are supported as input data. Conclusions CONAN facilitates the performance of GWAS based on CNVs and the visual analysis of calculated results. CONAN provides a rapid, valid and straightforward software solution to identify genetic variation underlying the 'missing' heritability for complex traits that remains unexplained by recent GWAS. The freely available software can be downloaded at http://genepi-conan.i-med.ac.at. PMID:20546565

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

NASA Technical Reports Server (NTRS)

Stefanski, Philip L.

2015-01-01

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

Using CAD/CAM to improve productivity - The IPAD approach

NASA Technical Reports Server (NTRS)

Fulton, R. E.

1981-01-01

Progress in designing and implementing CAD/CAM systems as a result of the NASA Integrated Programs for Aerospace-Vehicle Design is discussed. Essential software packages have been identified as executive, data management, general user, and geometry and graphics software. Data communication, as a means to integrate data over a network of computers of different vendors, provides data management with the capability of meeting design and manufacturing requirements of the vendors. Geometry software is dependent on developmental success with solid geometry software, which is necessary for continual measurements of, for example, a block of metal while it is being machined. Applications in the aerospace industry, such as for design, analysis, tooling, testing, quality control, etc., are outlined.

Analysis on the inbound tourist source market in Fujian Province

NASA Astrophysics Data System (ADS)

YU, Tong

2017-06-01

The paper analyzes the development and structure of inbound tourism in Fujian Province by Excel software and conducts the cluster analysis on the inbound tourism market by SPSS 23.0 software based on the inbound tourism data of Fujian Province from 2006 to 2015. The results show: the rapid development of inbound tourism in Fujian Province and the diversified inbound tourist source countries indicate the stability of inbound tourism market; the inbound tourist source market in Fujian Province can be divided into four categories according to the cluster analysis, and tourists from the United States, Japan, Malaysia, and Singapore are the key of inbound tourism in Fujian Province.

The impact of software quality characteristics on healthcare outcome: a literature review.

PubMed

Aghazadeh, Sakineh; Pirnejad, Habibollah; Moradkhani, Alireza; Aliev, Alvosat

2014-01-01

The aim of this study was to discover the effect of software quality characteristics on healthcare quality and efficiency indicators. Through a systematic literature review, we selected and analyzed 37 original research papers to investigate the impact of the software indicators (coming from the standard ISO 9126 quality characteristics and sub-characteristics) on some of healthcare important outcome indicators and finally ranked these software indicators. The results showed that the software characteristics usability, reliability and efficiency were mostly favored in the studies, indicating their importance. On the other hand, user satisfaction, quality of patient care, clinical workflow efficiency, providers' communication and information exchange, patient satisfaction and care costs were among the healthcare outcome indicators frequently evaluated in relation to the mentioned software characteristics. Regression Logistic Method was the most common assessment methodology, and Confirmatory Factor Analysis and Structural Equation Modeling were performed to test the structural model's fit. The software characteristics were considered to impact the healthcare outcome indicators through other intermediate factors (variables).

Dexterity: A MATLAB-based analysis software suite for processing and visualizing data from tasks that measure arm or forelimb function.

PubMed

Butensky, Samuel D; Sloan, Andrew P; Meyers, Eric; Carmel, Jason B

2017-07-15

Hand function is critical for independence, and neurological injury often impairs dexterity. To measure hand function in people or forelimb function in animals, sensors are employed to quantify manipulation. These sensors make assessment easier and more quantitative and allow automation of these tasks. While automated tasks improve objectivity and throughput, they also produce large amounts of data that can be burdensome to analyze. We created software called Dexterity that simplifies data analysis of automated reaching tasks. Dexterity is MATLAB software that enables quick analysis of data from forelimb tasks. Through a graphical user interface, files are loaded and data are identified and analyzed. These data can be annotated or graphed directly. Analysis is saved, and the graph and corresponding data can be exported. For additional analysis, Dexterity provides access to custom scripts created by other users. To determine the utility of Dexterity, we performed a study to evaluate the effects of task difficulty on the degree of impairment after injury. Dexterity analyzed two months of data and allowed new users to annotate the experiment, visualize results, and save and export data easily. Previous analysis of tasks was performed with custom data analysis, requiring expertise with analysis software. Dexterity made the tools required to analyze, visualize and annotate data easy to use by investigators without data science experience. Dexterity increases accessibility to automated tasks that measure dexterity by making analysis of large data intuitive, robust, and efficient. Copyright © 2017 Elsevier B.V. All rights reserved.

Computational Analysis of Human Blood Flow

NASA Astrophysics Data System (ADS)

Panta, Yogendra; Marie, Hazel; Harvey, Mark

2009-11-01

Fluid flow modeling with commercially available computational fluid dynamics (CFD) software is widely used to visualize and predict physical phenomena related to various biological systems. In this presentation, a typical human aorta model was analyzed assuming the blood flow as laminar with complaint cardiac muscle wall boundaries. FLUENT, a commercially available finite volume software, coupled with Solidworks, a modeling software, was employed for the preprocessing, simulation and postprocessing of all the models.The analysis mainly consists of a fluid-dynamics analysis including a calculation of the velocity field and pressure distribution in the blood and a mechanical analysis of the deformation of the tissue and artery in terms of wall shear stress. A number of other models e.g. T branches, angle shaped were previously analyzed and compared their results for consistency for similar boundary conditions. The velocities, pressures and wall shear stress distributions achieved in all models were as expected given the similar boundary conditions. The three dimensional time dependent analysis of blood flow accounting the effect of body forces with a complaint boundary was also performed.

Theoretical and software considerations for nonlinear dynamic analysis

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1983-01-01

In the finite element method for structural analysis, it is generally necessary to discretize the structural model into a very large number of elements to accurately evaluate displacements, strains, and stresses. As the complexity of the model increases, the number of degrees of freedom can easily exceed the capacity of present-day software system. Improvements of structural analysis software including more efficient use of existing hardware and improved structural modeling techniques are discussed. One modeling technique that is used successfully in static linear and nonlinear analysis is multilevel substructuring. This research extends the use of multilevel substructure modeling to include dynamic analysis and defines the requirements for a general purpose software system capable of efficient nonlinear dynamic analysis. The multilevel substructuring technique is presented, the analytical formulations and computational procedures for dynamic analysis and nonlinear mechanics are reviewed, and an approach to the design and implementation of a general purpose structural software system is presented.

Failure analysis and modeling of a multicomputer system. M.S. Thesis

NASA Technical Reports Server (NTRS)

Subramani, Sujatha Srinivasan

1990-01-01

This thesis describes the results of an extensive measurement-based analysis of real error data collected from a 7-machine DEC VaxCluster multicomputer system. In addition to evaluating basic system error and failure characteristics, we develop reward models to analyze the impact of failures and errors on the system. The results show that, although 98 percent of errors in the shared resources recover, they result in 48 percent of all system failures. The analysis of rewards shows that the expected reward rate for the VaxCluster decreases to 0.5 in 100 days for a 3 out of 7 model, which is well over a 100 times that for a 7-out-of-7 model. A comparison of the reward rates for a range of k-out-of-n models indicates that the maximum increase in reward rate (0.25) occurs in going from the 6-out-of-7 model to the 5-out-of-7 model. The analysis also shows that software errors have the lowest reward (0.2 vs. 0.91 for network errors). The large loss in reward rate for software errors is due to the fact that a large proportion (94 percent) of software errors lead to failure. In comparison, the high reward rate for network errors is due to fast recovery from a majority of these errors (median recovery duration is 0 seconds).

Towards a Methodology for Identifying Program Constraints During Requirements Analysis

NASA Technical Reports Server (NTRS)

Romo, Lilly; Gates, Ann Q.; Della-Piana, Connie Kubo

1997-01-01

Requirements analysis is the activity that involves determining the needs of the customer, identifying the services that the software system should provide and understanding the constraints on the solution. The result of this activity is a natural language document, typically referred to as the requirements definition document. Some of the problems that exist in defining requirements in large scale software projects includes synthesizing knowledge from various domain experts and communicating this information across multiple levels of personnel. One approach that addresses part of this problem is called context monitoring and involves identifying the properties of and relationships between objects that the system will manipulate. This paper examines several software development methodologies, discusses the support that each provide for eliciting such information from experts and specifying the information, and suggests refinements to these methodologies.

Modal Analysis for Grid Operation

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

MANGO software is to provide a solution for improving small signal stability of power systems through adjusting operator-controllable variables using PMU measurement. System oscillation problems are one of the major threats to the grid stability and reliability in California and the Western Interconnection. These problems result in power fluctuations, lower grid operation efficiency, and may even lead to large-scale grid breakup and outages. This MANGO software aims to solve this problem by automatically generating recommended operation procedures termed Modal Analysis for Grid Operation (MANGO) to improve damping of inter-area oscillation modes. The MANGO procedure includes three steps: recognizing small signalmore » stability problems, implementing operating point adjustment using modal sensitivity, and evaluating the effectiveness of the adjustment. The MANGO software package is designed to help implement the MANGO procedure.« less

[Quantitative analysis of landscape patterns at the juncture of Shaanxi, Shanxi and Inner Mongolia, based on remote sensing data--taking Yulin sheet TM image as an example].

PubMed

Li, Tuansheng

2004-03-01

Based on the TM image of Yulin sheet and with the help of ERDAS, ARC/INFO and ARC/VIEW software, the landscape of Yulin sheet was classified. Using the spatial pattern analysis software FRAGSTATS of the vector version, a set of landscape indices were calculated at three scale levels of patches, classes and landscape. The results showed that landscape pattern indices could be successfully used in characterizing the spatial pattern of the studied area. However, this study should be further extended to the landscape of the same area in other period to analyze its dynamic change. FRAGSTATS was a good software, but should be improved by adding some indices such as PD2 developed by us.

Analyzing qualitative data with computer software.

PubMed Central

Weitzman, E A

1999-01-01

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

User's Manual and Final Report for Hot-SMAC GUI Development

NASA Technical Reports Server (NTRS)

Yarrington, Phil

2001-01-01

A new software package called Higher Order Theory-Structural/Micro Analysis Code (HOT-SMAC) has been developed as an effective alternative to the finite element approach for Functionally Graded Material (FGM) modeling. HOT-SMAC is a self-contained package including pre- and post-processing through an intuitive graphical user interface, along with the well-established Higher Order Theory for Functionally Graded Materials (HOTFGM) thermomechanical analysis engine. This document represents a Getting Started/User's Manual for HOT-SMAC and a final report for its development. First, the features of the software are presented in a simple step-by-step example where a HOT-SMAC model representing a functionally graded material is created, mechanical and thermal boundary conditions are applied, the model is analyzed and results are reviewed. In a second step-by-step example, a HOT-SMAC model of an actively cooled metallic channel with ceramic thermal barrier coating is built and analyzed. HOT-SMAC results from this model are compared to recently published results (NASA/TM-2001-210702) for two grid densities. Finally, a prototype integration of HOTSMAC with the commercially available HyperSizer(R) structural analysis and sizing software is presented. In this integration, local strain results from HyperSizer's structural analysis are fed to a detailed HOT-SMAC model of the flange-to-facesheet bond region of a stiffened panel. HOT-SMAC is then used to determine the peak shear and peel (normal) stresses between the facesheet and bonded flange of the panel and determine the "free edge" effects.

An Analysis of Mission Critical Computer Software in Naval Aviation

DTIC Science & Technology

1991-03-01

No. Task No. Work Unit Accesion Number 11. TITLE (Include Security Classification) AN ANALYSIS OF MISSION CRITICAL COMPUTER SOFTWARE IN NAVAL AVIATION...software development schedules were sustained without a milestone change being made. Also, software that was released to the fleet had no major...fleet contain any major defects? This research has revealed that only about half of the original software development schedules were sustained without a

InterProScan 5: genome-scale protein function classification

PubMed Central

Jones, Philip; Binns, David; Chang, Hsin-Yu; Fraser, Matthew; Li, Weizhong; McAnulla, Craig; McWilliam, Hamish; Maslen, John; Mitchell, Alex; Nuka, Gift; Pesseat, Sebastien; Quinn, Antony F.; Sangrador-Vegas, Amaia; Scheremetjew, Maxim; Yong, Siew-Yit; Lopez, Rodrigo; Hunter, Sarah

2014-01-01

Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code. Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/. Contact: http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk PMID:24451626

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

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

Comparison of Aircraft Icing Growth Assessment Software

NASA Technical Reports Server (NTRS)

Wright, William; Potapczuk, Mark G.; Levinson, Laurie H.

2011-01-01

A research project is underway to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. An extensive comparison of the results in a quantifiable manner against the database of ice shapes that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has been performed, including additional data taken to extend the database in the Super-cooled Large Drop (SLD) regime. The project shows the differences in ice shape between LEWICE 3.2.2, GlennICE, and experimental data. The project addresses the validation of the software against a recent set of ice-shape data in the SLD regime. This validation effort mirrors a similar effort undertaken for previous validations of LEWICE. Those reports quantified the ice accretion prediction capabilities of the LEWICE software. Several ice geometry features were proposed for comparing ice shapes in a quantitative manner. The resulting analysis showed that LEWICE compared well to the available experimental data.

How Can Single-Case Data Be Analyzed? Software Resources, Tutorial, and Reflections on Analysis.

PubMed

Manolov, Rumen; Moeyaert, Mariola

2017-03-01

The present article aims to present a series of software developments in the quantitative analysis of data obtained via single-case experimental designs (SCEDs), as well as the tutorial describing these developments. The tutorial focuses on software implementations based on freely available platforms such as R and aims to bring statistical advances closer to applied researchers and help them become autonomous agents in the data analysis stage of a study. The range of analyses dealt with in the tutorial is illustrated on a typical single-case dataset, relying heavily on graphical data representations. We illustrate how visual and quantitative analyses can be used jointly, giving complementary information and helping the researcher decide whether there is an intervention effect, how large it is, and whether it is practically significant. To help applied researchers in the use of the analyses, we have organized the data in the different ways required by the different analytical procedures and made these data available online. We also provide Internet links to all free software available, as well as all the main references to the analytical techniques. Finally, we suggest that appropriate and informative data analysis is likely to be a step forward in documenting and communicating results and also for increasing the scientific credibility of SCEDs.

MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

PubMed Central

Gaunt, Tom R; Rodriguez, Santiago; Zapata, Carlos; Day, Ian NM

2006-01-01

Background Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form. Results We have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection. Conclusion MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers. Availability Available from and PMID:16643648

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, W. A.; Lepicovsky, J.

1992-01-01

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

LV software support for supersonic flow analysis

NASA Technical Reports Server (NTRS)

Bell, William A.

1992-01-01

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

Accuracy of a remote quantitative image analysis in the whole slide images.

PubMed

Słodkowska, Janina; Markiewicz, Tomasz; Grala, Bartłomiej; Kozłowski, Wojciech; Papierz, Wielisław; Pleskacz, Katarzyna; Murawski, Piotr

2011-03-30

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and oligodendrogliomas could be successfully used as an alternative method to the manual reading as well as to the digital images quantitation with CAMI software. According to our observation a need of a remote supervision/consultation and training for the effective use of remote quantitative analysis of WSI is necessary.

Spacelab user implementation assessment study. (Software requirements analysis). Volume 2: Technical report

NASA Technical Reports Server (NTRS)

1976-01-01

The engineering analyses and evaluation studies conducted for the Software Requirements Analysis are discussed. Included are the development of the study data base, synthesis of implementation approaches for software required by both mandatory onboard computer services and command/control functions, and identification and implementation of software for ground processing activities.

CSAM Metrology Software Tool

NASA Technical Reports Server (NTRS)

Vu, Duc; Sandor, Michael; Agarwal, Shri

2005-01-01

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

Excel2Genie: A Microsoft Excel application to improve the flexibility of the Genie-2000 Spectroscopic software.

PubMed

Forgács, Attila; Balkay, László; Trón, Lajos; Raics, Péter

2014-12-01

Excel2Genie, a simple and user-friendly Microsoft Excel interface, has been developed to the Genie-2000 Spectroscopic Software of Canberra Industries. This Excel application can directly control Canberra Multichannel Analyzer (MCA), process the acquired data and visualize them. Combination of Genie-2000 with Excel2Genie results in remarkably increased flexibility and a possibility to carry out repetitive data acquisitions even with changing parameters and more sophisticated analysis. The developed software package comprises three worksheets: display parameters and results of data acquisition, data analysis and mathematical operations carried out on the measured gamma spectra. At the same time it also allows control of these processes. Excel2Genie is freely available to assist gamma spectrum measurements and data evaluation by the interested Canberra users. With access to the Visual Basic Application (VBA) source code of this application users are enabled to modify the developed interface according to their intentions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis of machining accuracy during free form surface milling simulation for different milling strategies

NASA Astrophysics Data System (ADS)

Matras, A.; Kowalczyk, R.

2014-11-01

The analysis results of machining accuracy after the free form surface milling simulations (based on machining EN AW- 7075 alloys) for different machining strategies (Level Z, Radial, Square, Circular) are presented in the work. Particular milling simulations were performed using CAD/CAM Esprit software. The accuracy of obtained allowance is defined as a difference between the theoretical surface of work piece element (the surface designed in CAD software) and the machined surface after a milling simulation. The difference between two surfaces describes a value of roughness, which is as the result of tool shape mapping on the machined surface. Accuracy of the left allowance notifies in direct way a surface quality after the finish machining. Described methodology of usage CAD/CAM software can to let improve a time design of machining process for a free form surface milling by a 5-axis CNC milling machine with omitting to perform the item on a milling machine in order to measure the machining accuracy for the selected strategies and cutting data.

3D visualization software to analyze topological outcomes of topoisomerase reactions

PubMed Central

Darcy, I. K.; Scharein, R. G.; Stasiak, A.

2008-01-01

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases. PMID:18440983

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-06-15

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

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

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

Validation of a free software for unsupervised assessment of abdominal fat in MRI.

PubMed

Maddalo, Michele; Zorza, Ivan; Zubani, Stefano; Nocivelli, Giorgio; Calandra, Giulio; Soldini, Pierantonio; Mascaro, Lorella; Maroldi, Roberto

2017-05-01

To demonstrate the accuracy of an unsupervised (fully automated) software for fat segmentation in magnetic resonance imaging. The proposed software is a freeware solution developed in ImageJ that enables the quantification of metabolically different adipose tissues in large cohort studies. The lumbar part of the abdomen (19cm in craniocaudal direction, centered in L3) of eleven healthy volunteers (age range: 21-46years, BMI range: 21.7-31.6kg/m 2 ) was examined in a breath hold on expiration with a GE T1 Dixon sequence. Single-slice and volumetric data were considered for each subject. The results of the visceral and subcutaneous adipose tissue assessments obtained by the unsupervised software were compared to supervised segmentations of reference. The associated statistical analysis included Pearson correlations, Bland-Altman plots and volumetric differences (VD % ). Values calculated by the unsupervised software significantly correlated with corresponding supervised segmentations of reference for both subcutaneous adipose tissue - SAT (R=0.9996, p<0.001) and visceral adipose tissue - VAT (R=0.995, p<0.001). Bland-Altman plots showed the absence of systematic errors and a limited spread of the differences. In the single-slice analysis, VD % were (1.6±2.9)% for SAT and (4.9±6.9)% for VAT. In the volumetric analysis, VD % were (1.3±0.9)% for SAT and (2.9±2.7)% for VAT. The developed software is capable of segmenting the metabolically different adipose tissues with a high degree of accuracy. This free add-on software for ImageJ can easily have a widespread and enable large-scale population studies regarding the adipose tissue and its related diseases. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

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

PubMed

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

2012-06-01

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

Quantification of myocardial fibrosis by digital image analysis and interactive stereology.

PubMed

Daunoravicius, Dainius; Besusparis, Justinas; Zurauskas, Edvardas; Laurinaviciene, Aida; Bironaite, Daiva; Pankuweit, Sabine; Plancoulaine, Benoit; Herlin, Paulette; Bogomolovas, Julius; Grabauskiene, Virginija; Laurinavicius, Arvydas

2014-06-09

Cardiac fibrosis disrupts the normal myocardial structure and has a direct impact on heart function and survival. Despite already available digital methods, the pathologist's visual score is still widely considered as ground truth and used as a primary method in histomorphometric evaluations. The aim of this study was to compare the accuracy of digital image analysis tools and the pathologist's visual scoring for evaluating fibrosis in human myocardial biopsies, based on reference data obtained by point counting performed on the same images. Endomyocardial biopsy material from 38 patients diagnosed with inflammatory dilated cardiomyopathy was used. The extent of total cardiac fibrosis was assessed by image analysis on Masson's trichrome-stained tissue specimens using automated Colocalization and Genie software, by Stereology grid count and manually by Pathologist's visual score. A total of 116 slides were analyzed. The mean results obtained by the Colocalization software (13.72 ± 12.24%) were closest to the reference value of stereology (RVS), while the Genie software and Pathologist score gave a slight underestimation. RVS values correlated strongly with values obtained using the Colocalization and Genie (r>0.9, p<0.001) software as well as the pathologist visual score. Differences in fibrosis quantification by Colocalization and RVS were statistically insignificant. However, significant bias was found in the results obtained by using Genie versus RVS and pathologist score versus RVS with mean difference values of: -1.61% and 2.24%. Bland-Altman plots showed a bidirectional bias dependent on the magnitude of the measurement: Colocalization software overestimated the area fraction of fibrosis in the lower end, and underestimated in the higher end of the RVS values. Meanwhile, Genie software as well as the pathologist score showed more uniform results throughout the values, with a slight underestimation in the mid-range for both. Both applied digital image analysis methods revealed almost perfect correlation with the criterion standard obtained by stereology grid count and, in terms of accuracy, outperformed the pathologist's visual score. Genie algorithm proved to be the method of choice with the only drawback of a slight underestimation bias, which is considered acceptable for both clinical and research evaluations. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9857909611227193.

The discounting model selector: Statistical software for delay discounting applications.

PubMed

Gilroy, Shawn P; Franck, Christopher T; Hantula, Donald A

2017-05-01

Original, open-source computer software was developed and validated against established delay discounting methods in the literature. The software executed approximate Bayesian model selection methods from user-supplied temporal discounting data and computed the effective delay 50 (ED50) from the best performing model. Software was custom-designed to enable behavior analysts to conveniently apply recent statistical methods to temporal discounting data with the aid of a graphical user interface (GUI). The results of independent validation of the approximate Bayesian model selection methods indicated that the program provided results identical to that of the original source paper and its methods. Monte Carlo simulation (n = 50,000) confirmed that true model was selected most often in each setting. Simulation code and data for this study were posted to an online repository for use by other researchers. The model selection approach was applied to three existing delay discounting data sets from the literature in addition to the data from the source paper. Comparisons of model selected ED50 were consistent with traditional indices of discounting. Conceptual issues related to the development and use of computer software by behavior analysts and the opportunities afforded by free and open-sourced software are discussed and a review of possible expansions of this software are provided. © 2017 Society for the Experimental Analysis of Behavior.

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.

Artificial Intelligence in Mitral Valve Analysis

PubMed Central

Jeganathan, Jelliffe; Knio, Ziyad; Amador, Yannis; Hai, Ting; Khamooshian, Arash; Matyal, Robina; Khabbaz, Kamal R; Mahmood, Feroze

2017-01-01

Background: Echocardiographic analysis of mitral valve (MV) has become essential for diagnosis and management of patients with MV disease. Currently, the various software used for MV analysis require manual input and are prone to interobserver variability in the measurements. Aim: The aim of this study is to determine the interobserver variability in an automated software that uses artificial intelligence for MV analysis. Settings and Design: Retrospective analysis of intraoperative three-dimensional transesophageal echocardiography data acquired from four patients with normal MV undergoing coronary artery bypass graft surgery in a tertiary hospital. Materials and Methods: Echocardiographic data were analyzed using the eSie Valve Software (Siemens Healthcare, Mountain View, CA, USA). Three examiners analyzed three end-systolic (ES) frames from each of the four patients. A total of 36 ES frames were analyzed and included in the study. Statistical Analysis: A multiple mixed-effects ANOVA model was constructed to determine if the examiner, the patient, and the loop had a significant effect on the average value of each parameter. A Bonferroni correction was used to correct for multiple comparisons, and P = 0.0083 was considered to be significant. Results: Examiners did not have an effect on any of the six parameters tested. Patient and loop had an effect on the average parameter value for each of the six parameters as expected (P < 0.0083 for both). Conclusion: We were able to conclude that using automated analysis, it is possible to obtain results with good reproducibility, which only requires minimal user intervention. PMID:28393769

Fully automated corneal endothelial morphometry of images captured by clinical specular microscopy

NASA Astrophysics Data System (ADS)

Bucht, Curry; Söderberg, Per; Manneberg, Göran

2009-02-01

The corneal endothelium serves as the posterior barrier of the cornea. Factors such as clarity and refractive properties of the cornea are in direct relationship to the quality of the endothelium. The endothelial cell density is considered the most important morphological factor. Morphometry of the corneal endothelium is presently done by semi-automated analysis of pictures captured by a Clinical Specular Microscope (CSM). Because of the occasional need of operator involvement, this process can be tedious, having a negative impact on sampling size. This study was dedicated to the development of fully automated analysis of images of the corneal endothelium, captured by CSM, using Fourier analysis. Software was developed in the mathematical programming language Matlab. Pictures of the corneal endothelium, captured by CSM, were read into the analysis software. The software automatically performed digital enhancement of the images. The digitally enhanced images of the corneal endothelium were transformed, using the fast Fourier transform (FFT). Tools were developed and applied for identification and analysis of relevant characteristics of the Fourier transformed images. The data obtained from each Fourier transformed image was used to calculate the mean cell density of its corresponding corneal endothelium. The calculation was based on well known diffraction theory. Results in form of estimated cell density of the corneal endothelium were obtained, using fully automated analysis software on images captured by CSM. The cell density obtained by the fully automated analysis was compared to the cell density obtained from classical, semi-automated analysis and a relatively large correlation was found.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

PubMed

Sturgill, David; Malone, John H; Sun, Xia; Smith, Harold E; Rabinow, Leonard; Samson, Marie-Laure; Oliver, Brian

2013-11-09

The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools.

MathBrowser: Web-Enabled Mathematical Software with Application to the Chemistry Curriculum, v 1.0

NASA Astrophysics Data System (ADS)

Goldsmith, Jack G.

1997-10-01

MathSoft: Cambridge, MA, 1996; free via ftp from www.mathsoft.com. The movement to provide computer-based applications in chemistry has come to focus on three main areas: software aimed at specific applications (drawing, simulation, data analysis, etc.), multimedia applications designed to assist in the presentation of conceptual information, and packages to be used in conjunction with a particular textbook at a specific point in the chemistry curriculum. The result is a situation where no single software package devoted to problem solving can be used across a large segment of the curriculum. Adoption of World Wide Web (WWW) technology by a manufacturer of mathematical software, however, has produced software that provides an attractive means of providing a problem-solving resource to students in courses from freshman through senior level.

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

Flores, Alejandra Parra; Bravo, Oscar Martinez; Ibargueen, Humberto Salazar

The purpose of this work is to show the results of the analysis of a library of synthetic data corresponding to Very Inclined Showers (i.e. those with a zenith angle between 60 and 80 degrees and energies from 50 EeV to 80 EeV). Simulations were performed using the Aires software and then analyzed to narrow down the arrival angles that allow us an efficient shower reconstruction using the Offline software.

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer.

PubMed

Vogel, Sven C; Biwer, Chris M; Rogers, David H; Ahrens, James P; Hackenberg, Robert E; Onken, Drew; Zhang, Jianzhong

2018-06-01

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U-Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr 3 . A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download.

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer

PubMed Central

Biwer, Chris M.; Rogers, David H.; Ahrens, James P.; Hackenberg, Robert E.; Onken, Drew; Zhang, Jianzhong

2018-01-01

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U–Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr3. A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download. PMID:29896062

GammaLib and ctools. A software framework for the analysis of astronomical gamma-ray data

NASA Astrophysics Data System (ADS)

Knödlseder, J.; Mayer, M.; Deil, C.; Cayrou, J.-B.; Owen, E.; Kelley-Hoskins, N.; Lu, C.-C.; Buehler, R.; Forest, F.; Louge, T.; Siejkowski, H.; Kosack, K.; Gerard, L.; Schulz, A.; Martin, P.; Sanchez, D.; Ohm, S.; Hassan, T.; Brau-Nogué, S.

2016-08-01

The field of gamma-ray astronomy has seen important progress during the last decade, yet to date no common software framework has been developed for the scientific analysis of gamma-ray telescope data. We propose to fill this gap by means of the GammaLib software, a generic library that we have developed to support the analysis of gamma-ray event data. GammaLib was written in C++ and all functionality is available in Python through an extension module. Based on this framework we have developed the ctools software package, a suite of software tools that enables flexible workflows to be built for the analysis of Imaging Air Cherenkov Telescope event data. The ctools are inspired by science analysis software available for existing high-energy astronomy instruments, and they follow the modular ftools model developed by the High Energy Astrophysics Science Archive Research Center. The ctools were written in Python and C++, and can be either used from the command line via shell scripts or directly from Python. In this paper we present the GammaLib and ctools software versions 1.0 that were released at the end of 2015. GammaLib and ctools are ready for the science analysis of Imaging Air Cherenkov Telescope event data, and also support the analysis of Fermi-LAT data and the exploitation of the COMPTEL legacy data archive. We propose using ctools as the science tools software for the Cherenkov Telescope Array Observatory.

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.

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

PubMed

Chawade, Aakash; Sandin, Marianne; Teleman, Johan; Malmström, Johan; Levander, Fredrik

2015-02-06

High-throughput multiplexed protein quantification using mass spectrometry is steadily increasing in popularity, with the two major techniques being data-dependent acquisition (DDA) and targeted acquisition using selected reaction monitoring (SRM). However, both techniques involve extensive data processing, which can be performed by a multitude of different software solutions. Analysis of quantitative LC-MS/MS data is mainly performed in three major steps: processing of raw data, normalization, and statistical analysis. To evaluate the impact of data processing steps, we developed two new benchmark data sets, one each for DDA and SRM, with samples consisting of a long-range dilution series of synthetic peptides spiked in a total cell protein digest. The generated data were processed by eight different software workflows and three postprocessing steps. The results show that the choice of the raw data processing software and the postprocessing steps play an important role in the final outcome. Also, the linear dynamic range of the DDA data could be extended by an order of magnitude through feature alignment and a charge state merging algorithm proposed here. Furthermore, the benchmark data sets are made publicly available for further benchmarking and software developments.

Multicriteria analysis of ontologically represented information

NASA Astrophysics Data System (ADS)

Wasielewska, K.; Ganzha, M.; Paprzycki, M.; Bǎdicǎ, C.; Ivanovic, M.; Lirkov, I.

2014-11-01

Our current work concerns the development of a decision support system for the software selection problem. The main idea is to utilize expert knowledge to help the user in selecting the best software / method / computational resource to solve a computational problem. Obviously, this involves multicriterial decision making and the key open question is: which method to choose. The context of the work is provided by the Agents in Grid (AiG) project, where the software selection (and thus multicriterial analysis) is to be realized when all information concerning the problem, the hardware and the software is ontologically represented. Initially, we have considered the Analytical Hierarchy Process (AHP), which is well suited for the hierarchical data structures (e.g., such that have been formulated in terms of ontologies). However, due to its well-known shortcomings, we have decided to extend our search for the multicriterial analysis method best suited for the problem in question. In this paper we report results of our search, which involved: (i) TOPSIS (Technique for Order Preference by Similarity to Ideal Solution), (ii) PROMETHEE, and (iii) GRIP (Generalized Regression with Intensities of Preference). We also briefly argue why other methods have not been considered as valuable candidates.

SpotMetrics: An Open-Source Image-Analysis Software Plugin for Automatic Chromatophore Detection and Measurement

PubMed Central

Hadjisolomou, Stavros P.; El-Haddad, George

2017-01-01

Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented chromatophore organs and reflecting cells. Therefore, a lot can be learned about the cephalopod coloration system by video recording and analyzing the activation of individual chromatophores in time. The fact that adult cephalopods have small chromatophores, up to several hundred thousand in number, makes measurement and analysis over several seconds a difficult task. However, current advancements in videography enable high-resolution and high framerate recording, which can be used to record chromatophore activity in more detail and accuracy in both space and time domains. In turn, the additional pixel information and extra frames per video from such recordings result in large video files of several gigabytes, even when the recording spans only few minutes. We created a software plugin, “SpotMetrics,” that can automatically analyze high resolution, high framerate video of chromatophore organ activation in time. This image analysis software can track hundreds of individual chromatophores over several hundred frames to provide measurements of size and color. This software may also be used to measure differences in chromatophore activation during different behaviors which will contribute to our understanding of the cephalopod sensorimotor integration system. In addition, this software can potentially be utilized to detect numbers of round objects and size changes in time, such as eye pupil size or number of bacteria in a sample. Thus, we are making this software plugin freely available as open-source because we believe it will be of benefit to other colleagues both in the cephalopod biology field and also within other disciplines. PMID:28298896

Utility of coupling nonlinear optimization methods with numerical modeling software

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

Murphy, M.J.

1996-08-05

Results of using GLO (Global Local Optimizer), a general purpose nonlinear optimization software package for investigating multi-parameter problems in science and engineering is discussed. The package consists of the modular optimization control system (GLO), a graphical user interface (GLO-GUI), a pre-processor (GLO-PUT), a post-processor (GLO-GET), and nonlinear optimization software modules, GLOBAL & LOCAL. GLO is designed for controlling and easy coupling to any scientific software application. GLO runs the optimization module and scientific software application in an iterative loop. At each iteration, the optimization module defines new values for the set of parameters being optimized. GLO-PUT inserts the new parametermore » values into the input file of the scientific application. GLO runs the application with the new parameter values. GLO-GET determines the value of the objective function by extracting the results of the analysis and comparing to the desired result. GLO continues to run the scientific application over and over until it finds the ``best`` set of parameters by minimizing (or maximizing) the objective function. An example problem showing the optimization of material model is presented (Taylor cylinder impact test).« less

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

PubMed

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

2017-01-01

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

Processing methods for differential analysis of LC/MS profile data

PubMed Central

Katajamaa, Mikko; Orešič, Matej

2005-01-01

Background Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data. Results We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures. Conclusion The software is freely available under the GNU General Public License and it can be obtained from the project web page at: . PMID:16026613

Development of a software safety process and a case study of its use

NASA Technical Reports Server (NTRS)

Knight, John C.

1993-01-01

The goal of this research is to continue the development of a comprehensive approach to software safety and to evaluate the approach with a case study. The case study is a major part of the project, and it involves the analysis of a specific safety-critical system from the medical equipment domain. The particular application being used was selected because of the availability of a suitable candidate system. We consider the results to be generally applicable and in no way particularly limited by the domain. The research is concentrating on issues raised by the specification and verification phases of the software lifecycle since they are central to our previously-developed rigorous definitions of software safety. The theoretical research is based on our framework of definitions for software safety. In the area of specification, the main topics being investigated are the development of techniques for building system fault trees that correctly incorporate software issues and the development of rigorous techniques for the preparation of software safety specifications. The research results are documented. Another area of theoretical investigation is the development of verification methods tailored to the characteristics of safety requirements. Verification of the correct implementation of the safety specification is central to the goal of establishing safe software. The empirical component of this research is focusing on a case study in order to provide detailed characterizations of the issues as they appear in practice, and to provide a testbed for the evaluation of various existing and new theoretical results, tools, and techniques. The Magnetic Stereotaxis System is summarized.

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

PubMed Central

2014-01-01

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

Elements of strategic capability for software outsourcing enterprises based on the resource

NASA Astrophysics Data System (ADS)

Shi, Wengeng

2011-10-01

Software outsourcing enterprises as an emerging high-tech enterprises, the rise of the speed and the number was very amazing. In addition to Chinese software outsourcing for giving preferential policies, the software outsourcing business has its ability to upgrade, and in general the software companies have not had the related characteristics. View from the resource base of the theory, the analysis software outsourcing companies have the ability and resources of rare and valuable and non-mimic, we try to give an initial framework for theoretical analysis based on this.

Intra- and interrater reliability of the Chicago Classification of achalasia subtypes in pediatric high-resolution esophageal manometry (HRM) recordings.

PubMed

Singendonk, M M J; Rosen, R; Oors, J; Rommel, N; van Wijk, M P; Benninga, M A; Nurko, S; Omari, T I

2017-11-01

Subtyping achalasia by high-resolution manometry (HRM) is clinically relevant as response to therapy and prognosis have shown to vary accordingly. The aim of this study was to assess inter- and intrarater reliability of diagnosing achalasia and achalasia subtyping in children using the Chicago Classification (CC) V3.0. Six observers analyzed 40 pediatric HRM recordings (22 achalasia and 18 non-achalasia) twice by using dedicated analysis software (ManoView 3.0, Given Imaging, Los Angeles, CA, USA). Integrated relaxation pressure (IRP4s), distal contractile integral (DCI), intrabolus pressurization pattern (IBP), and distal latency (DL) were extracted and analyzed hierarchically. Cohen's κ (2 raters) and Fleiss' κ (>2 raters) and the intraclass correlation coefficient (ICC) were used for categorical and ordinal data, respectively. Based on the results of dedicated analysis software only, intra- and interrater reliability was excellent and moderate (κ=0.89 and κ=0.52, respectively) for differentiating achalasia from non-achalasia. For subtyping achalasia, reliability decreased to substantial and fair (κ=0.72 and κ=0.28, respectively). When observers were allowed to change the software-driven diagnosis according to their own interpretation of the manometric patterns, intra- and interrater reliability increased for diagnosing achalasia (κ=0.98 and κ=0.92, respectively) and for subtyping achalasia (κ=0.79 and κ=0.58, respectively). Intra- and interrater agreement for diagnosing achalasia when using HRM and the CC was very good to excellent when results of automated analysis software were interpreted by experienced observers. More variability was seen when relying solely on the software-driven diagnosis and for subtyping achalasia. Therefore, diagnosing and subtyping achalasia should be performed in pediatric motility centers with significant expertise. © 2017 John Wiley & Sons Ltd.

DEIVA: a web application for interactive visual analysis of differential gene expression profiles.

PubMed

Harshbarger, Jayson; Kratz, Anton; Carninci, Piero

2017-01-07

Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features between different biological states. The result of a DGE test is typically further analyzed using statistical software, spreadsheets or custom ad hoc algorithms. We identified a need for a web-based system to share DGE statistical test results, and locate and identify genes in DGE statistical test results with a very low barrier of entry. We have developed DEIVA, a free and open source, browser-based single page application (SPA) with a strong emphasis on being user friendly that enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. By design, DEIVA scales with very large numbers of users and datasets. Compared to existing software, DEIVA offers a unique combination of design decisions that enable inspection and analysis of DGE statistical test results with an emphasis on ease of use.

Bone histomorphometry using free and commonly available software.

PubMed

Egan, Kevin P; Brennan, Tracy A; Pignolo, Robert J

2012-12-01

Histomorphometric analysis is a widely used technique to assess changes in tissue structure and function. Commercially available programs that measure histomorphometric parameters can be cost-prohibitive. In this study, we compared an inexpensive method of histomorphometry to a current proprietary software program. Image J and Adobe Photoshop(®) were used to measure static and kinetic bone histomorphometric parameters. Photomicrographs of Goldner's trichrome-stained femurs were used to generate black-and-white image masks, representing bone and non-bone tissue, respectively, in Adobe Photoshop(®) . The masks were used to quantify histomorphometric parameters (bone volume, tissue volume, osteoid volume, mineralizing surface and interlabel width) in Image J. The resultant values obtained using Image J and the proprietary software were compared and differences found to be statistically non-significant. The wide-ranging use of histomorphometric analysis for assessing the basic morphology of tissue components makes it important to have affordable and accurate measurement options available for a diverse range of applications. Here we have developed and validated an approach to histomorphometry using commonly and freely available software that is comparable to a much more costly, commercially available software program. © 2012 Blackwell Publishing Limited.

The Comparison of VLBI Data Analysis Using Software Globl and Globk

NASA Astrophysics Data System (ADS)

Guangli, W.; Xiaoya, W.; Jinling, L.; Wenyao, Z.

The comparison of different geodetic data analysis software is one of the quite of- ten mentioned topics. In this paper we try to find out the difference between software GLOBL and GLOBK when use them to process the same set of VLBI data. GLOBL is a software developed by VLBI team, geodesy branch, GSFC/NASA to process geode- tic VLBI data using algorithm of arc-parameter-elimination, while GLOBK using al- gorithm of kalman filtering is mainly used in GPS data analysis, and it is also used in VLBI data analysis. Our work focus on whether there are significant difference when use the two softwares to analyze the same VLBI data set and investigate the reasons caused the difference.

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.

SAO mission support software and data standards, version 1.0

NASA Technical Reports Server (NTRS)

Hsieh, P.

1993-01-01

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

Long-term Preservation of Data Analysis Capabilities

NASA Astrophysics Data System (ADS)

Gabriel, C.; Arviset, C.; Ibarra, A.; Pollock, A.

2015-09-01

While the long-term preservation of scientific data obtained by large astrophysics missions is ensured through science archives, the issue of data analysis software preservation has hardly been addressed. Efforts by large data centres have contributed so far to maintain some instrument or mission-specific data reduction packages on top of high-level general purpose data analysis software. However, it is always difficult to keep software alive without support and maintenance once the active phase of a mission is over. This is especially difficult in the budgetary model followed by space agencies. We discuss the importance of extending the lifetime of dedicated data analysis packages and review diverse strategies under development at ESA using new paradigms such as Virtual Machines, Cloud Computing, and Software as a Service for making possible full availability of data analysis and calibration software for decades at minimal cost.

Age estimation using exfoliative cytology and radiovisiography: A comparative study

PubMed Central

Nallamala, Shilpa; Guttikonda, Venkateswara Rao; Manchikatla, Praveen Kumar; Taneeru, Sravya

2017-01-01

Introduction: Age estimation is one of the essential factors in establishing the identity of an individual. Among various methods, exfoliative cytology (EC) is a unique, noninvasive technique, involving simple, and pain-free collection of intact cells from the oral cavity for microscopic examination. Objective: The study was undertaken with an aim to estimate the age of an individual from the average cell size of their buccal smears calculated using image analysis morphometric software and the pulp–tooth area ratio in mandibular canine of the same individual using radiovisiography (RVG). Materials and Methods: Buccal smears were collected from 100 apparently healthy individuals. After fixation in 95% alcohol, the smears were stained using Papanicolaou stain. The average cell size was measured using image analysis software (Image-Pro Insight 8.0). The RVG images of mandibular canines were obtained, pulp and tooth areas were traced using AutoCAD 2010 software, and area ratio was calculated. The estimated age was then calculated using regression analysis. Results: The paired t-test between chronological age and estimated age by cell size and pulp–tooth area ratio was statistically nonsignificant (P > 0.05). Conclusion: In the present study, age estimated by pulp–tooth area ratio and EC yielded good results. PMID:29657491

Helios: History and Anatomy of a Successful In-House Enterprise High-Throughput Screening and Profiling Data Analysis System.

PubMed

Gubler, Hanspeter; Clare, Nicholas; Galafassi, Laurent; Geissler, Uwe; Girod, Michel; Herr, Guy

2018-06-01

We describe the main characteristics of the Novartis Helios data analysis software system (Novartis, Basel, Switzerland) for plate-based screening and profiling assays, which was designed and built about 11 years ago. It has been in productive use for more than 10 years and is one of the important standard software applications running for a large user community at all Novartis Institutes for BioMedical Research sites globally. A high degree of automation is reached by embedding the data analysis capabilities into a software ecosystem that deals with the management of samples, plates, and result data files, including automated data loading. The application provides a series of analytical procedures, ranging from very simple to advanced, which can easily be assembled by users in very flexible ways. This also includes the automatic derivation of a large set of quality control (QC) characteristics at every step. Any of the raw, intermediate, and final results and QC-relevant quantities can be easily explored through linked visualizations. Links to global assay metadata management, data warehouses, and an electronic lab notebook system are in place. Automated transfer of relevant data to data warehouses and electronic lab notebook systems are also implemented.

A field-to-desktop toolchain for X-ray CT densitometry enables tree ring analysis

PubMed Central

De Mil, Tom; Vannoppen, Astrid; Beeckman, Hans; Van Acker, Joris; Van den Bulcke, Jan

2016-01-01

Background and Aims Disentangling tree growth requires more than ring width data only. Densitometry is considered a valuable proxy, yet laborious wood sample preparation and lack of dedicated software limit the widespread use of density profiling for tree ring analysis. An X-ray computed tomography-based toolchain of tree increment cores is presented, which results in profile data sets suitable for visual exploration as well as density-based pattern matching. Methods Two temperate (Quercus petraea, Fagus sylvatica) and one tropical species (Terminalia superba) were used for density profiling using an X-ray computed tomography facility with custom-made sample holders and dedicated processing software. Key Results Density-based pattern matching is developed and able to detect anomalies in ring series that can be corrected via interactive software. Conclusions A digital workflow allows generation of structure-corrected profiles of large sets of cores in a short time span that provide sufficient intra-annual density information for tree ring analysis. Furthermore, visual exploration of such data sets is of high value. The dated profiles can be used for high-resolution chronologies and also offer opportunities for fast screening of lesser studied tropical tree species. PMID:27107414

CFD research and systems in Kawasaki Heavy Industries and its future prospects

NASA Astrophysics Data System (ADS)

Hiraoka, Koichi

1990-09-01

KHI Computational Fluid Dynamics (CFD) system is composed of VP100 computer and 2-D and 3-D Euler and/or Navier-Stokes (NS) analysis softwares. For KHI, this system has become a very powerful aerodynamic tool together with the Kawasaki 1 m Transonic Wind Tunnel. The 2-D Euler/NS software, developed in-house, is fully automated, requires no special skill, and was successfully applied to the design of YXX high lift devices and SST supersonic inlet, etc. The 3-D Euler/NS software, developed under joint research with NAL, has an interactively operated Multi-Block type grid generator and can effectively generate grids around complex airplane shapes. Due to the main memory size limitation, 3-D analysis of relatively simple shape, such as SST wing-body, was computed in-house on VP100, otherwise, such as detailed 3-D analyses of ASUKA and HOPE, were computed on NAL VP400, which is 10 times more powerful than VP100, under KHI-NAL joint research. These analysis results have very good correlation with experimental results. However, the present CFD system is less productive than wind tunnel and has applicability limitations.

VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability.

PubMed

Rathi, Prakash Chandra; Mulnaes, Daniel; Gohlke, Holger

2015-07-15

Constraint network analysis (CNA) is a graph theory-based rigidity analysis approach for linking a biomolecule's structure, flexibility, (thermo)stability and function. Results from CNA are highly information-rich and require intuitive, synchronized and interactive visualization for a comprehensive analysis. We developed VisualCNA, an easy-to-use PyMOL plug-in that allows setup of CNA runs and analysis of CNA results linking plots with molecular graphics representations. From a practical viewpoint, the most striking feature of VisualCNA is that it facilitates interactive protein engineering aimed at improving thermostability. VisualCNA and its dependencies (CNA and FIRST software) are available free of charge under GPL and academic licenses, respectively. VisualCNA and CNA are available at http://cpclab.uni-duesseldorf.de/software; FIRST is available at http://flexweb.asu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Software Dependability and Safety Evaluations ESA's Initiative

NASA Astrophysics Data System (ADS)

Hernek, M.

ESA has allocated funds for an initiative to evaluate Dependability and Safety methods of Software. The objectives of this initiative are; · More extensive validation of Safety and Dependability techniques for Software · Provide valuable results to improve the quality of the Software thus promoting the application of Dependability and Safety methods and techniques. ESA space systems are being developed according to defined PA requirement specifications. These requirements may be implemented through various design concepts, e.g. redundancy, diversity etc. varying from project to project. Analysis methods (FMECA. FTA, HA, etc) are frequently used during requirements analysis and design activities to assure the correct implementation of system PA requirements. The criticality level of failures, functions and systems is determined and by doing that the critical sub-systems are identified, on which dependability and safety techniques are to be applied during development. Proper performance of the software development requires the development of a technical specification for the products at the beginning of the life cycle. Such technical specification comprises both functional and non-functional requirements. These non-functional requirements address characteristics of the product such as quality, dependability, safety and maintainability. Software in space systems is more and more used in critical functions. Also the trend towards more frequent use of COTS and reusable components pose new difficulties in terms of assuring reliable and safe systems. Because of this, its dependability and safety must be carefully analysed. ESA identified and documented techniques, methods and procedures to ensure that software dependability and safety requirements are specified and taken into account during the design and development of a software system and to verify/validate that the implemented software systems comply with these requirements [R1].

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis.

PubMed

Zheng, Qi; Wang, Xiu-Jie

2008-07-01

Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related analysis functions, new tools are still needed to meet the requirements for data generated by newly developed technologies or for advanced analysis purpose. Here, we present a Gene Ontology Enrichment Analysis Software Toolkit (GOEAST), an easy-to-use web-based toolkit that identifies statistically overrepresented GO terms within given gene sets. Compared with available GO analysis tools, GOEAST has the following improved features: (i) GOEAST displays enriched GO terms in graphical format according to their relationships in the hierarchical tree of each GO category (biological process, molecular function and cellular component), therefore, provides better understanding of the correlations among enriched GO terms; (ii) GOEAST supports analysis for data from various sources (probe or probe set IDs of Affymetrix, Illumina, Agilent or customized microarrays, as well as different gene identifiers) and multiple species (about 60 prokaryote and eukaryote species); (iii) One unique feature of GOEAST is to allow cross comparison of the GO enrichment status of multiple experiments to identify functional correlations among them. GOEAST also provides rigorous statistical tests to enhance the reliability of analysis results. GOEAST is freely accessible at http://omicslab.genetics.ac.cn/GOEAST/

A general concept for consistent documentation of computational analyses

PubMed Central

Müller, Fabian; Nordström, Karl; Lengauer, Thomas; Schulz, Marcel H.

2015-01-01

The ever-growing amount of data in the field of life sciences demands standardized ways of high-throughput computational analysis. This standardization requires a thorough documentation of each step in the computational analysis to enable researchers to understand and reproduce the results. However, due to the heterogeneity in software setups and the high rate of change during tool development, reproducibility is hard to achieve. One reason is that there is no common agreement in the research community on how to document computational studies. In many cases, simple flat files or other unstructured text documents are provided by researchers as documentation, which are often missing software dependencies, versions and sufficient documentation to understand the workflow and parameter settings. As a solution we suggest a simple and modest approach for documenting and verifying computational analysis pipelines. We propose a two-part scheme that defines a computational analysis using a Process and an Analysis metadata document, which jointly describe all necessary details to reproduce the results. In this design we separate the metadata specifying the process from the metadata describing an actual analysis run, thereby reducing the effort of manual documentation to an absolute minimum. Our approach is independent of a specific software environment, results in human readable XML documents that can easily be shared with other researchers and allows an automated validation to ensure consistency of the metadata. Because our approach has been designed with little to no assumptions concerning the workflow of an analysis, we expect it to be applicable in a wide range of computational research fields. Database URL: http://deep.mpi-inf.mpg.de/DAC/cmds/pub/pyvalid.zip PMID:26055099

Integration of GIS and Bim for Indoor Geovisual Analytics

NASA Astrophysics Data System (ADS)

Wu, B.; Zhang, S.

2016-06-01

This paper presents an endeavour of integration of GIS (Geographical Information System) and BIM (Building Information Modelling) for indoor geovisual analytics. The merits of two types of technologies, GIS and BIM are firstly analysed in the context of indoor environment. GIS has well-developed capabilities of spatial analysis such as network analysis, while BIM has the advantages for indoor 3D modelling and dynamic simulation. This paper firstly investigates the important aspects for integrating GIS and BIM. Different data standards and formats such as the IFC (Industry Foundation Classes) and GML (Geography Markup Language) are discussed. Their merits and limitations in data transformation between GIS and BIM are analysed in terms of semantic and geometric information. An optimized approach for data exchange between GIS and BIM datasets is then proposed. After that, a strategy of using BIM for 3D indoor modelling, GIS for spatial analysis, and BIM again for visualization and dynamic simulation of the analysis results is presented. Based on the developments, this paper selects a typical problem, optimized indoor emergency evacuation, to demonstrate the integration of GIS and BIM for indoor geovisual analytics. The block Z of the Hong Kong Polytechnic University is selected as a test site. Detailed indoor and outdoor 3D models of the block Z are created using a BIM software Revit. The 3D models are transferred to a GIS software ArcGIS to carry out spatial analysis. Optimized evacuation plans considering dynamic constraints are generated based on network analysis in ArcGIS assuming there is a fire accident inside the building. The analysis results are then transferred back to BIM software for visualization and dynamic simulation. The developed methods and results are of significance to facilitate future development of GIS and BIM integrated solutions in various applications.

Software to model AXAF-I image quality

NASA Technical Reports Server (NTRS)

Ahmad, Anees; Feng, Chen

1995-01-01

A modular user-friendly computer program for the modeling of grazing-incidence type x-ray optical systems has been developed. This comprehensive computer software GRAZTRACE covers the manipulation of input data, ray tracing with reflectivity and surface deformation effects, convolution with x-ray source shape, and x-ray scattering. The program also includes the capabilities for image analysis, detector scan modeling, and graphical presentation of the results. A number of utilities have been developed to interface the predicted Advanced X-ray Astrophysics Facility-Imaging (AXAF-I) mirror structural and thermal distortions with the ray-trace. This software is written in FORTRAN 77 and runs on a SUN/SPARC station. An interactive command mode version and a batch mode version of the software have been developed.

Effect of system workload on operating system reliability - A study on IBM 3081

NASA Technical Reports Server (NTRS)

Iyer, R. K.; Rossetti, D. J.

1985-01-01

This paper presents an analysis of operating system failures on an IBM 3081 running VM/SP. Three broad categories of software failures are found: error handling, program control or logic, and hardware related; it is found that more than 25 percent of software failures occur in the hardware/software interface. Measurements show that results on software reliability cannot be considered representative unless the system workload is taken into account. The overall CPU execution rate, although measured to be close to 100 percent most of the time, is not found to correlate strongly with the occurrence of failures. Possible reasons for the observed workload failure dependency, based on detailed investigations of the failure data, are discussed.

Early experiences building a software quality prediction model

NASA Technical Reports Server (NTRS)

Agresti, W. W.; Evanco, W. M.; Smith, M. C.

1990-01-01

Early experiences building a software quality prediction model are discussed. The overall research objective is to establish a capability to project a software system's quality from an analysis of its design. The technical approach is to build multivariate models for estimating reliability and maintainability. Data from 21 Ada subsystems were analyzed to test hypotheses about various design structures leading to failure-prone or unmaintainable systems. Current design variables highlight the interconnectivity and visibility of compilation units. Other model variables provide for the effects of reusability and software changes. Reported results are preliminary because additional project data is being obtained and new hypotheses are being developed and tested. Current multivariate regression models are encouraging, explaining 60 to 80 percent of the variation in error density of the subsystems.

Using Decision Structures for Policy Analysis in Software Product-line Evolution - A Case Study

NASA Astrophysics Data System (ADS)

Sarang, Nita; Sanglikar, Mukund A.

Project management decisions are the primary basis for project success (or failure). Mostly, such decisions are based on an intuitive understanding of the underlying software engineering and management process and have a likelihood of being misjudged. Our problem domain is product-line evolution. We model the dynamics of the process by incorporating feedback loops appropriate to two decision structures: staffing policy, and the forces of growth associated with long-term software evolution. The model is executable and supports project managers to assess the long-term effects of possible actions. Our work also corroborates results from earlier studies of E-type systems, in particular the FEAST project and the rules for software evolution, planning and management.

Integrated fiducial sample mount and software for correlated microscopy

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

Timothy R McJunkin; Jill R. Scott; Tammy L. Trowbridge

2014-02-01

A novel design sample mount with integrated fiducials and software for assisting operators in easily and efficiently locating points of interest established in previous analytical sessions is described. The sample holder and software were evaluated with experiments to demonstrate the utility and ease of finding the same points of interest in two different microscopy instruments. Also, numerical analysis of expected errors in determining the same position with errors unbiased by a human operator was performed. Based on the results, issues related to acquiring reproducibility and best practices for using the sample mount and software were identified. Overall, the sample mountmore » methodology allows data to be efficiently and easily collected on different instruments for the same sample location.« less

[Job stressors in software developers--a comparison with other occupations].

PubMed

Kadokura, M

1997-09-01

The aim of this study is to investigate the difference in job stressors among software developers, the sales staff and the clerical staff (n = 2,079) in two companies (A Co. and B Co.) using a self-administered questionnaire that included a job stressor scale and the 30-item General Health Questionnaire (GHQ). We developed the job stressor scale based on the interviews with out-patients who engaged in software development and previous studies about job stressors. Factor analysis with a seven-factor solution showed that seven subscales were abstracted from the job stressor scale, namely, quantitative load of work, dissatisfaction with work, demanding work, uneasiness about work, human relations, ambiguity of work and shortage of private time. Each subscale was significantly (r = .313-.442, p < 0.0001) correlated with the GHQ score and proved to be a reliable instrument, as indicated by a Cronbach's alpha of greater than 0.73. Stepwise multiple regression analysis revealed that quantitative load of work and shortage of private time subscale scores were significantly high in software developers in A Co. Software developers in A Co. tended to score higher (P < .10) than the others in demanding work and ambiguity of work subscale. All subscale scores were significantly low in the clerical staff in B Co. There was no significant difference between the sales staff and software developers in B Co. Results of the interviews with out-patients showed that demanding work, hard deadline, ambiguity of work and precarious work would cause trouble in software developers. The implications of these findings with respect to occupational issues related to software developers are discussed.

Spacecraft Trajectory Analysis and Mission Planning Simulation (STAMPS) Software

NASA Technical Reports Server (NTRS)

Puckett, Nancy; Pettinger, Kris; Hallstrom,John; Brownfield, Dana; Blinn, Eric; Williams, Frank; Wiuff, Kelli; McCarty, Steve; Ramirez, Daniel; Lamotte, Nicole;

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

PubMed

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

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

Advances in the REDCAT software package

PubMed Central

2013-01-01

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

On-Orbit Software Analysis

NASA Technical Reports Server (NTRS)

Moran, Susanne I.

2004-01-01

The On-Orbit Software Analysis Research Infusion Project was done by Intrinsyx Technologies Corporation (Intrinsyx) at the National Aeronautics and Space Administration (NASA) Ames Research Center (ARC). The Project was a joint collaborative effort between NASA Codes IC and SL, Kestrel Technology (Kestrel), and Intrinsyx. The primary objectives of the Project were: Discovery and verification of software program properties and dependencies, Detection and isolation of software defects across different versions of software, and Compilation of historical data and technical expertise for future applications

Automated sequence analysis and editing software for HIV drug resistance testing.

PubMed

Struck, Daniel; Wallis, Carole L; Denisov, Gennady; Lambert, Christine; Servais, Jean-Yves; Viana, Raquel V; Letsoalo, Esrom; Bronze, Michelle; Aitken, Sue C; Schuurman, Rob; Stevens, Wendy; Schmit, Jean Claude; Rinke de Wit, Tobias; Perez Bercoff, Danielle

2012-05-01

Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. To develop an automated sequence analysis and editing software to support high throughput automated sequencing. The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention. Copyright © 2012 Elsevier B.V. All rights reserved.

An overview of the mathematical and statistical analysis component of RICIS

NASA Technical Reports Server (NTRS)

Hallum, Cecil R.

1987-01-01

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

Benchmarking the ATLAS software through the Kit Validation engine

NASA Astrophysics Data System (ADS)

De Salvo, Alessandro; Brasolin, Franco

2010-04-01

The measurement of the experiment software performance is a very important metric in order to choose the most effective resources to be used and to discover the bottlenecks of the code implementation. In this work we present the benchmark techniques used to measure the ATLAS software performance through the ATLAS offline testing engine Kit Validation and the online portal Global Kit Validation. The performance measurements, the data collection, the online analysis and display of the results will be presented. The results of the measurement on different platforms and architectures will be shown, giving a full report on the CPU power and memory consumption of the Monte Carlo generation, simulation, digitization and reconstruction of the most CPU-intensive channels. The impact of the multi-core computing on the ATLAS software performance will also be presented, comparing the behavior of different architectures when increasing the number of concurrent processes. The benchmark techniques described in this paper have been used in the HEPiX group since the beginning of 2008 to help defining the performance metrics for the High Energy Physics applications, based on the real experiment software.

Software reliability studies

NASA Technical Reports Server (NTRS)

Wilson, Larry W.

1989-01-01

The longterm goal of this research is to identify or create a model for use in analyzing the reliability of flight control software. The immediate tasks addressed are the creation of data useful to the study of software reliability and production of results pertinent to software reliability through the analysis of existing reliability models and data. The completed data creation portion of this research consists of a Generic Checkout System (GCS) design document created in cooperation with NASA and Research Triangle Institute (RTI) experimenters. This will lead to design and code reviews with the resulting product being one of the versions used in the Terminal Descent Experiment being conducted by the Systems Validations Methods Branch (SVMB) of NASA/Langley. An appended paper details an investigation of the Jelinski-Moranda and Geometric models for software reliability. The models were given data from a process that they have correctly simulated and asked to make predictions about the reliability of that process. It was found that either model will usually fail to make good predictions. These problems were attributed to randomness in the data and replication of data was recommended.

An Integral Study of Galactic Black Hole States

NASA Technical Reports Server (NTRS)

2005-01-01

XTE 51550-564 was clearly detected with INTEGRAL out to 600 keV with the SPI, and is one of only two sources detected with IBISPICSIT. Software difficulties in analyzing the data prevented us from progressing with the analysis past the most elementary stages (see last year's report). The support from the INTEGRAL help desk has been very disappointing. People affiliated with INTEGRAL published a paper on the results of our data before we could master the reduction and analysis software. We are not the only group that got stuck with the analysis without adequate support from the INTEGRAL help desk. This was a rather disappointing experience as we lost many months of valuable time and efforts.

How Safe Is Control Software

NASA Technical Reports Server (NTRS)

Dunn, William R.; Corliss, Lloyd D.

1991-01-01

Paper examines issue of software safety. Presents four case histories of software-safety analysis. Concludes that, to be safe, software, for all practical purposes, must be free of errors. Backup systems still needed to prevent catastrophic software failures.

Space Station communications and tracking systems modeling and RF link simulation

NASA Technical Reports Server (NTRS)

Tsang, Chit-Sang; Chie, Chak M.; Lindsey, William C.

1986-01-01

In this final report, the effort spent on Space Station Communications and Tracking System Modeling and RF Link Simulation is described in detail. The effort is mainly divided into three parts: frequency division multiple access (FDMA) system simulation modeling and software implementation; a study on design and evaluation of a functional computerized RF link simulation/analysis system for Space Station; and a study on design and evaluation of simulation system architecture. This report documents the results of these studies. In addition, a separate User's Manual on Space Communications Simulation System (SCSS) (Version 1) documents the software developed for the Space Station FDMA communications system simulation. The final report, SCSS user's manual, and the software located in the NASA JSC system analysis division's VAX 750 computer together serve as the deliverables from LinCom for this project effort.

Software system safety

NASA Technical Reports Server (NTRS)

Uber, James G.

1988-01-01

Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

Analysis of Wood Structure Connections Using Cylindrical Steel and Carbon Fiber Dowel Pins

NASA Astrophysics Data System (ADS)

Vodiannikov, Mikhail A.; Kashevarova, Galina G., Dr.

2017-06-01

In this paper, the results of the statistical analysis of corrosion processes and moisture saturation of glued laminated timber structures and their joints in corrosive environment are shown. This paper includes calculation results for dowel connections of wood structures using steel and carbon fiber reinforced plastic cylindrical dowel pins in accordance with applicable regulatory documents by means of finite element analysis in ANSYS software, as well as experimental findings. Dependence diagrams are shown; comparative analysis of the results obtained is conducted.

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

NASA Technical Reports Server (NTRS)

Tamayo, Tak Chai

1987-01-01

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

Analysis of a hardware and software fault tolerant processor for critical applications

NASA Technical Reports Server (NTRS)

Dugan, Joanne B.

1993-01-01

Computer systems for critical applications must be designed to tolerate software faults as well as hardware faults. A unified approach to tolerating hardware and software faults is characterized by classifying faults in terms of duration (transient or permanent) rather than source (hardware or software). Errors arising from transient faults can be handled through masking or voting, but errors arising from permanent faults require system reconfiguration to bypass the failed component. Most errors which are caused by software faults can be considered transient, in that they are input-dependent. Software faults are triggered by a particular set of inputs. Quantitative dependability analysis of systems which exhibit a unified approach to fault tolerance can be performed by a hierarchical combination of fault tree and Markov models. A methodology for analyzing hardware and software fault tolerant systems is applied to the analysis of a hypothetical system, loosely based on the Fault Tolerant Parallel Processor. The models consider both transient and permanent faults, hardware and software faults, independent and related software faults, automatic recovery, and reconfiguration.

Improving the performance of minimizers and winnowing schemes

PubMed Central

Marçais, Guillaume; Pellow, David; Bork, Daniel; Orenstein, Yaron; Shamir, Ron; Kingsford, Carl

2017-01-01

Abstract Motivation: The minimizers scheme is a method for selecting k-mers from sequences. It is used in many bioinformatics software tools to bin comparable sequences or to sample a sequence in a deterministic fashion at approximately regular intervals, in order to reduce memory consumption and processing time. Although very useful, the minimizers selection procedure has undesirable behaviors (e.g. too many k-mers are selected when processing certain sequences). Some of these problems were already known to the authors of the minimizers technique, and the natural lexicographic ordering of k-mers used by minimizers was recognized as their origin. Many software tools using minimizers employ ad hoc variations of the lexicographic order to alleviate those issues. Results: We provide an in-depth analysis of the effect of k-mer ordering on the performance of the minimizers technique. By using small universal hitting sets (a recently defined concept), we show how to significantly improve the performance of minimizers and avoid some of its worse behaviors. Based on these results, we encourage bioinformatics software developers to use an ordering based on a universal hitting set or, if not possible, a randomized ordering, rather than the lexicographic order. This analysis also settles negatively a conjecture (by Schleimer et al.) on the expected density of minimizers in a random sequence. Availability and Implementation: The software used for this analysis is available on GitHub: https://github.com/gmarcais/minimizers.git. Contact: gmarcais@cs.cmu.edu or carlk@cs.cmu.edu PMID:28881970

Echo™ User Manual

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

Harvey, Dustin Yewell

Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reportingmore » and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.« less

Optical analysis of electro-optical systems by MTF calculus

NASA Astrophysics Data System (ADS)

Barbarini, Elisa Signoreto; Dos Santos, Daniel, Jr.; Stefani, Mário Antonio; Yasuoka, Fátima Maria Mitsue; Castro Neto, Jarbas C.; Rodrigues, Evandro Luís Linhari

2011-08-01

One of the widely used methods for performance analysis of an optical system is the determination of the Modulation Transfer Function (MTF). The MTF represents a quantitative and direct measure of image quality, and, besides being an objective test, it can be used on concatenated optical system. This paper presents the application of software called SMTF (software modulation transfer function), built in C++ and Open CV platforms for MTF calculation on electro-optical system. Through this technique, it is possible to develop specific method to measure the real time performance of a digital fundus camera, an infrared sensor and an ophthalmological surgery microscope. Each optical instrument mentioned has a particular device to measure the MTF response, which is being developed. Then the MTF information assists the analysis of the optical system alignment, and also defines its resolution limit by the MTF graphic. The result obtained from the implemented software is compared with the theoretical MTF curve from the analyzed systems.

Evaluating Sustainability Models for Interoperability through Brokering Software

NASA Astrophysics Data System (ADS)

Pearlman, Jay; Benedict, Karl; Best, Mairi; Fyfe, Sue; Jacobs, Cliff; Michener, William; Nativi, Stefano; Powers, Lindsay; Turner, Andrew

2016-04-01

Sustainability of software and research support systems is an element of innovation that is not often discussed. Yet, sustainment is essential if we expect research communities to make the time investment to learn and adopt new technologies. As the Research Data Alliance (RDA) is developing new approaches to interoperability, the question of uptake and sustainability is important. Brokering software sustainability is one of the areas that is being addressed in RDA. The Business Models Team of the Research Data Alliance Brokering Governance Working Group examined several support models proposed to promote the long-term sustainability of brokering middleware. The business model analysis includes examination of funding source, implementation frameworks and challenges, and policy and legal considerations. Results of this comprehensive analysis highlight advantages and disadvantages of the various models with respect to the specific requirements for brokering services. We offer recommendations based on the outcomes of this analysis that suggest that hybrid funding models present the most likely avenue to long term sustainability.

Zbrowse: An interactive GWAS results browser

USDA-ARS?s Scientific Manuscript database

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual s...

Status of the MIND simulation and analysis

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

Cervera Villanueva, A.; Martin-Albo, J.; Laing, A.

2010-03-30

A realistic simulation of the Neutrino Factory detectors is required in order to fully understand the sensitivity of such a facility to the remaining parameters and degeneracies of the neutrino mixing matrix. Here described is the status of a modular software framework being developed to accommodate such a study. The results of initial studies of the reconstruction software and expected efficiency curves in the context of the golden channel are given.

Simulation of a Canard in Fluid Flow Driven by a Piezoelectric Beam with a Software Control Loop

DTIC Science & Technology

2014-04-01

The canard is actuated by a piezoelectric beam that bends as voltage is applied. The voltage is controlled by a software subroutine that measures...Dynamic system Modeling Co-simulation Simulation Abaqus Finite element analysis (FEA) Finite element method (FEM) Computational...is unlimited. i CONTENTS Page Introduction 1 Model Description 1 Fluid Model 2 Structural Model 3 Control Subroutine 4 Results 4

Simulation Modeling of Software Development Processes

NASA Technical Reports Server (NTRS)

Calavaro, G. F.; Basili, V. R.; Iazeolla, G.

1996-01-01

A simulation modeling approach is proposed for the prediction of software process productivity indices, such as cost and time-to-market, and the sensitivity analysis of such indices to changes in the organization parameters and user requirements. The approach uses a timed Petri Net and Object Oriented top-down model specification. Results demonstrate the model representativeness, and its usefulness in verifying process conformance to expectations, and in performing continuous process improvement and optimization.

Numerical Analyses of Subsoil-structure Interaction in Original Non-commercial Software based on FEM

NASA Astrophysics Data System (ADS)

Cajka, R.; Vaskova, J.; Vasek, J.

2018-04-01

For decades attention has been paid to interaction of foundation structures and subsoil and development of interaction models. Given that analytical solutions of subsoil-structure interaction could be deduced only for some simple shapes of load, analytical solutions are increasingly being replaced by numerical solutions (eg. FEM – Finite element method). Numerical analyses provides greater possibilities for taking into account the real factors involved in the subsoil-structure interaction and was also used in this article. This makes it possible to design the foundation structures more efficiently and still reliably and securely. Currently there are several software that, can deal with the interaction of foundations and subsoil. It has been demonstrated that non-commercial software called MKPINTER (created by Cajka) provides appropriately results close to actual measured values. In MKPINTER software stress-strain analysis of elastic half-space by means of Gauss numerical integration and Jacobean of transformation is done. Input data for numerical analysis were observed by experimental loading test of concrete slab. The loading was performed using unique experimental equipment which was constructed in the area Faculty of Civil Engineering, VŠB-TU Ostrava. The purpose of this paper is to compare resulting deformation of the slab with values observed during experimental loading test.

Content analysis of cancer blog posts.

PubMed

Kim, Sujin

2009-10-01

The efficacy of user-defined subject tagging and software-generated subject tagging for describing and organizing cancer blog contents was explored. The Technorati search engine was used to search the blogosphere for cancer blog postings generated during a two-month period. Postings were mined for relevant subject concepts, and blogger-defined tags and Text Analysis Portal for Research (TAPoR) software-defined tags were generated for each message. Descriptive data were collected, and the blogger-defined tags were compared with software-generated tags. Three standard vocabularies (Opinion Templates, Basic Resource, and Medical Subject Headings [MeSH] Resource) were used to assign subject terms to the blogs, with results compared for efficacy in information retrieval. Descriptive data showed that most of the studied cancer blogs (80%) contained fewer than 500 words each. The numbers of blogger-defined tags per posting (M = 4.49 per posting) were significantly smaller than the TAPoR keywords (M = 23.55 per posting). Both blogger-defined subject tags and software-generated subject tags were often overly broad or overly narrow in focus, producing less than effective search results for those seeking to extract information from cancer blogs. Additional exploration into methods for systematically organizing cancer blog postings is necessary if blogs are to become stable and efficacious information resources for cancer patients, friends, families, or providers.

Light extraction efficiency analysis of GaN-based light-emitting diodes with nanopatterned sapphire substrates.

PubMed

Pan, Jui-Wen; Tsai, Pei-Jung; Chang, Kao-Der; Chang, Yung-Yuan

2013-03-01

In this paper, we propose a method to analyze the light extraction efficiency (LEE) enhancement of a nanopatterned sapphire substrates (NPSS) light-emitting diode (LED) by comparing wave optics software with ray optics software. Finite-difference time-domain (FDTD) simulations represent the wave optics software and Light Tools (LTs) simulations represent the ray optics software. First, we find the trends of and an optimal solution for the LEE enhancement when the 2D-FDTD simulations are used to save on simulation time and computational memory. The rigorous coupled-wave analysis method is utilized to explain the trend we get from the 2D-FDTD algorithm. The optimal solution is then applied in 3D-FDTD and LTs simulations. The results are similar and the difference in LEE enhancement between the two simulations does not exceed 8.5% in the small LED chip area. More than 10(4) times computational memory is saved during the LTs simulation in comparison to the 3D-FDTD simulation. Moreover, LEE enhancement from the side of the LED can be obtained in the LTs simulation. An actual-size NPSS LED is simulated using the LTs. The results show a more than 307% improvement in the total LEE enhancement of the NPSS LED with the optimal solution compared to the conventional LED.

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

State-of-the-Art Resources (SOAR) for Software Vulnerability Detection, Test, and Evaluation

DTIC Science & Technology

2014-07-01

preclude in-depth analysis, and widespread use of a Software -as-a- Service ( SaaS ) model that limits data availability and application to DoD systems...provide mobile application analysis using a Software - as-a- Service ( SaaS ) model. In this case, any software to be analyzed must be sent to the...tools are only available through a SaaS model. The widespread use of a Software -as-a- Service ( SaaS ) model as a sole evaluation model limits data

A Method for Populating the Knowledge Base of AFIT’s Domain-Oriented Application Composition System

DTIC Science & Technology

1993-12-01

Analysis ( FODA ). The approach identifies prominent features (similarities) and distinctive features (differences) of software systems within an... analysis approaches we have summarized, the re- searchers described FODA in sufficient detail to use on large domain analysis projects (ones with...Software Technology Center, July 1991. 18. Kang, Kyo C. and others. Feature-Oriented Domain Analysis ( FODA ) Feasibility Study. Technical Report, Software

Selection of software for mechanical engineering undergraduates

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

Cheah, C. T.; Yin, C. S.; Halim, T.

A major problem with the undergraduate mechanical course is the limited exposure of students to software packages coupled with the long learning curve on the existing software packages. This work proposes the use of appropriate software packages for the entire mechanical engineering curriculum to ensure students get sufficient exposure real life design problems. A variety of software packages are highlighted as being suitable for undergraduate work in mechanical engineering, e.g. simultaneous non-linear equations; uncertainty analysis; 3-D modeling software with the FEA; analysis tools for the solution of problems in thermodynamics, fluid mechanics, mechanical system design, and solid mechanics.

A Case Study of Measuring Process Risk for Early Insights into Software Safety

NASA Technical Reports Server (NTRS)

Layman, Lucas; Basili, Victor; Zelkowitz, Marvin V.; Fisher, Karen L.

2011-01-01

In this case study, we examine software safety risk in three flight hardware systems in NASA's Constellation spaceflight program. We applied our Technical and Process Risk Measurement (TPRM) methodology to the Constellation hazard analysis process to quantify the technical and process risks involving software safety in the early design phase of these projects. We analyzed 154 hazard reports and collected metrics to measure the prevalence of software in hazards and the specificity of descriptions of software causes of hazardous conditions. We found that 49-70% of 154 hazardous conditions could be caused by software or software was involved in the prevention of the hazardous condition. We also found that 12-17% of the 2013 hazard causes involved software, and that 23-29% of all causes had a software control. The application of the TPRM methodology identified process risks in the application of the hazard analysis process itself that may lead to software safety risk.

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

PubMed

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

2013-01-01

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

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

PubMed

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

1997-12-01

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

SU-E-T-472: A Multi-Dimensional Measurements Comparison to Analyze a 3D Patient Specific QA Tool

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

Ashmeg, S; Jackson, J; Zhang, Y

Purpose: To quantitatively evaluate a 3D patient specific QA tool using 2D film and 3D Presage dosimetry. Methods: A brain IMRT case was delivered to Delta4, EBT2 film and Presage plastic dosimeter. The film was inserted in the solid water slabs at 7.5cm depth for measurement. The Presage dosimeter was inserted into a head phantom for 3D dose measurement. Delta4's Anatomy software was used to calculate the corresponding dose to the film in solid water slabs and to Presage in the head phantom. The results from Anatomy were compared to both calculated results from Eclipse and measured dose from filmmore » and Presage to evaluate its accuracy. Using RIT software, we compared the “Anatomy” dose to the EBT2 film measurement and the film measurement to ECLIPSE calculation. For 3D analysis, DICOM file of “Anatomy” was extracted and imported to CERR software, which was used to compare the Presage dose to both “Anatomy” calculation and ECLIPSE calculation. Gamma criteria of 3% - 3mm and 5% - 5mm was used for comparison. Results: Gamma passing rates of film vs “Anatomy”, “Anatomy” vs ECLIPSE and film vs ECLIPSE were 82.8%, 70.9% and 87.6% respectively when 3% - 3mm criteria is used. When the criteria is changed to 5% - 5mm, the passing rates became 87.8%, 76.3% and 90.8% respectively. For 3D analysis, Anatomy vs ECLIPSE showed gamma passing rate of 86.4% and 93.3% for 3% - 3mm and 5% - 5mm respectively. The rate is 77.0% for Presage vs ECLIPSE analysis. The Anatomy vs ECLIPSE were absolute dose comparison. However, film and Presage analysis were relative comparison Conclusion: The results show higher passing rate in 3D than 2D in “Anatomy” software. This could be due to the higher degrees of freedom in 3D than in 2D for gamma analysis.« less

FunRich proteomics software analysis, let the fun begin!

PubMed

Benito-Martin, Alberto; Peinado, Héctor

2015-08-01

Protein MS analysis is the preferred method for unbiased protein identification. It is normally applied to a large number of both small-scale and high-throughput studies. However, user-friendly computational tools for protein analysis are still needed. In this issue, Mathivanan and colleagues (Proteomics 2015, 15, 2597-2601) report the development of FunRich software, an open-access software that facilitates the analysis of proteomics data, providing tools for functional enrichment and interaction network analysis of genes and proteins. FunRich is a reinterpretation of proteomic software, a standalone tool combining ease of use with customizable databases, free access, and graphical representations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Development of a new software for analyzing 3-D fracture network

NASA Astrophysics Data System (ADS)

Um, Jeong-Gi; Noh, Young-Hwan; Choi, Yosoon

2014-05-01

A new software is presented to analyze fracture network in 3-D. Recently, we completed the software package based on information given in EGU2013. The software consists of several modules that play roles in management of borehole data, stochastic modelling of fracture network, construction of analysis domain, visualization of fracture geometry in 3-D, calculation of equivalent pipes and production of cross-section diagrams. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. A case study was performed to analyze 3-D fracture network system at the Upper Devonian Grosmont Formation in Alberta, Canada. The results have suggested that the developed software is effective in modelling and visualizing 3-D fracture network system, and can provide useful information to tackle the geomechanical problems related to strength, deformability and hydraulic behaviours of the fractured rock masses. This presentation describes the concept and details of the development and implementation of the software.

LevRad software as a tool to learn how to proceed with an evaluation of barriers.

PubMed

Ferreira, C C; Souza, S O

2011-05-30

We developed the software LevRad with the objective of teaching how to proceed in an analysis of barriers shielding against x-rays to minimize the contact of the professional or the student with x-rays and also to prevent wearing out of the x-ray equipment. Some tests of the software were made, and preliminary results indicate that LevRad is efficient as a complementary tool for the development of professionals related to diagnostic radiology. In the case of education, an advantage is gained when the beginner uses the software before his or her first contact with x-ray equipment in locu. The software introduces a basic knowledge about evaluation of barriers, prevents wearing out of the x—ray tube, reinforces teaching of evaluation of barriers, and reduces the collective effective dose by avoiding unnecessary exposures when possible.

CognitionMaster: an object-based image analysis framework

PubMed Central

2013-01-01

Background Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired. Results In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose “analysis pipelines“ that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept. Conclusions We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis. PMID:23445542

SU-G-BRB-02: An Open-Source Software Analysis Library for Linear Accelerator Quality Assurance

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

Kerns, J; Yaldo, D

Purpose: Routine linac quality assurance (QA) tests have become complex enough to require automation of most test analyses. A new data analysis software library was built that allows physicists to automate routine linear accelerator quality assurance tests. The package is open source, code tested, and benchmarked. Methods: Images and data were generated on a TrueBeam linac for the following routine QA tests: VMAT, starshot, CBCT, machine logs, Winston Lutz, and picket fence. The analysis library was built using the general programming language Python. Each test was analyzed with the library algorithms and compared to manual measurements taken at the timemore » of acquisition. Results: VMAT QA results agreed within 0.1% between the library and manual measurements. Machine logs (dynalogs & trajectory logs) were successfully parsed; mechanical axis positions were verified for accuracy and MLC fluence agreed well with EPID measurements. CBCT QA measurements were within 10 HU and 0.2mm where applicable. Winston Lutz isocenter size measurements were within 0.2mm of TrueBeam’s Machine Performance Check. Starshot analysis was within 0.2mm of the Winston Lutz results for the same conditions. Picket fence images with and without a known error showed that the library was capable of detecting MLC offsets within 0.02mm. Conclusion: A new routine QA software library has been benchmarked and is available for use by the community. The library is open-source and extensible for use in larger systems.« less

Earth Science Informatics Community Requirements for Improving Sustainable Science Software Practices: User Perspectives and Implications for Organizational Action

NASA Astrophysics Data System (ADS)

Downs, R. R.; Lenhardt, W. C.; Robinson, E.

2014-12-01

Science software is integral to the scientific process and must be developed and managed in a sustainable manner to ensure future access to scientific data and related resources. Organizations that are part of the scientific enterprise, as well as members of the scientific community who work within these entities, can contribute to the sustainability of science software and to practices that improve scientific community capabilities for science software sustainability. As science becomes increasingly digital and therefore, dependent on software, improving community practices for sustainable science software will contribute to the sustainability of science. Members of the Earth science informatics community, including scientific data producers and distributers, end-user scientists, system and application developers, and data center managers, use science software regularly and face the challenges and the opportunities that science software presents for the sustainability of science. To gain insight on practices needed for the sustainability of science software from the science software experiences of the Earth science informatics community, an interdisciplinary group of 300 community members were asked to engage in simultaneous roundtable discussions and report on their answers to questions about the requirements for improving scientific software sustainability. This paper will present an analysis of the issues reported and the conclusions offered by the participants. These results provide perspectives for science software sustainability practices and have implications for actions that organizations and their leadership can initiate to improve the sustainability of science software.

Noninvasive Test Detects Cardiovascular Disease

NASA Technical Reports Server (NTRS)

2007-01-01

At NASA's Jet Propulsion Laboratory (JPL), NASA-developed Video Imaging Communication and Retrieval (VICAR) software laid the groundwork for analyzing images of all kinds. A project seeking to use imaging technology for health care diagnosis began when the imaging team considered using the VICAR software to analyze X-ray images of soft tissue. With marginal success using X-rays, the team applied the same methodology to ultrasound imagery, which was already digitally formatted. The new approach proved successful for assessing amounts of plaque build-up and arterial wall thickness, direct predictors of heart disease, and the result was a noninvasive diagnostic system with the ability to accurately predict heart health. Medical Technologies International Inc. (MTI) further developed and then submitted the technology to a vigorous review process at the FDA, which cleared the software for public use. The software, patented under the name Prowin, is being used in MTI's patented ArterioVision, a carotid intima-media thickness (CIMT) test that uses ultrasound image-capturing and analysis software to noninvasively identify the risk for the major cause of heart attack and strokes: atherosclerosis. ArterioVision provides a direct measurement of atherosclerosis by safely and painlessly measuring the thickness of the first two layers of the carotid artery wall using an ultrasound procedure and advanced image-analysis software. The technology is now in use in all 50 states and in many countries throughout the world.

Second Generation Product Line Engineering Takes Hold in the DoD

DTIC Science & Technology

2014-01-01

Feature- Oriented Domain Analysis ( FODA ) Feasibility Study” (CMU/SEI-90- TR-021, ADA235785). Pittsburgh, PA: Software Engineering Institute...software product line engineering and software architecture documentation and analysis . Clements is co-author of three practitioner-oriented books about

Increasing the trustworthiness of research results: the role of computers in qualitative text analysis

Treesearch

Lynne M. Westphal

2000-01-01

By using computer packages designed for qualitative data analysis a researcher can increase trustworthiness (i.e., validity and reliability) of conclusions drawn from qualitative research results. This paper examines trustworthiness issues and therole of computer software (QSR's NUD*IST) in the context of a current research project investigating the social...

The Holistic Targeting (HOT) Methodology as the Means to Improve Information Operations (IO) Target Development and Prioritization

DTIC Science & Technology

2008-09-01

software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi-automated means to...the use of compendium software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi...OBJECTIVES USING COMPENDIUM SOFTWARE .....63 E. HOT TARGET PRIORITIZATION AND DEVELOPMENT USING PALANTIR SOFTWARE .................................69 1

Software Defined Network Monitoring Scheme Using Spectral Graph Theory and Phantom Nodes

DTIC Science & Technology

2014-09-01

networks is the emergence of software - defined networking ( SDN ) [1]. SDN has existed for the...Chapter III for network monitoring. A. SOFTWARE DEFINED NETWORKS SDNs provide a new and innovative method to simplify network hardware by logically...and R. Giladi, “Performance analysis of software - defined networking ( SDN ),” in Proc. of IEEE 21st International Symposium on Modeling, Analysis

Maximum entropy analysis of polarized fluorescence decay of (E)GFP in aqueous solution

NASA Astrophysics Data System (ADS)

Novikov, Eugene G.; Skakun, Victor V.; Borst, Jan Willem; Visser, Antonie J. W. G.

2018-01-01

The maximum entropy method (MEM) was used for the analysis of polarized fluorescence decays of enhanced green fluorescent protein (EGFP) in buffered water/glycerol mixtures, obtained with time-correlated single-photon counting (Visser et al 2016 Methods Appl. Fluoresc. 4 035002). To this end, we used a general-purpose software module of MEM that was earlier developed to analyze (complex) laser photolysis kinetics of ligand rebinding reactions in oxygen binding proteins. We demonstrate that the MEM software provides reliable results and is easy to use for the analysis of both total fluorescence decay and fluorescence anisotropy decay of aqueous solutions of EGFP. The rotational correlation times of EGFP in water/glycerol mixtures, obtained by MEM as maxima of the correlation-time distributions, are identical to the single correlation times determined by global analysis of parallel and perpendicular polarized decay components. The MEM software is also able to determine homo-FRET in another dimeric GFP, for which the transfer correlation time is an order of magnitude shorter than the rotational correlation time. One important advantage utilizing MEM analysis is that no initial guesses of parameters are required, since MEM is able to select the least correlated solution from the feasible set of solutions.

STIS Target Acquisitions During SMOV

NASA Astrophysics Data System (ADS)

Katsanis, Rocio M.; Downes, Ron; Hartig, George; Kraemer, Steve

1997-07-01

We summarize the first results on the analysis of in-flight STIS target acquisition (ACQ and ACQ/PEAK). These results show that the STIS target acquisition (ACQ) is working very accurately for point sources (within 0.5 pixels = 0.025 arcseconds), about 4 times better than specified in the Instrument Handbook. As a result of the accuracy of the ACQ algorithm, we are no longer recommending to perform ACQ/PEAKs for the 0.2 arcsecond wide slits. For diffuse acquisitions the accuracy varies with target size. Although analysis of ACQ/PEAK data is hampered by a flight software problem, we anticipate that peakups will be accurate to roughly ±5% of the slit width (instead of the ±15% pr eviously advertised). We are implementing several enhancements to the flight software that will take effect by mid- August to improve the quality of the acquisitions.

Integrating automated structured analysis and design with Ada programming support environments

NASA Technical Reports Server (NTRS)

Hecht, Alan; Simmons, Andy

1986-01-01

Ada Programming Support Environments (APSE) include many powerful tools that address the implementation of Ada code. These tools do not address the entire software development process. Structured analysis is a methodology that addresses the creation of complete and accurate system specifications. Structured design takes a specification and derives a plan to decompose the system subcomponents, and provides heuristics to optimize the software design to minimize errors and maintenance. It can also produce the creation of useable modules. Studies have shown that most software errors result from poor system specifications, and that these errors also become more expensive to fix as the development process continues. Structured analysis and design help to uncover error in the early stages of development. The APSE tools help to insure that the code produced is correct, and aid in finding obscure coding errors. However, they do not have the capability to detect errors in specifications or to detect poor designs. An automated system for structured analysis and design TEAMWORK, which can be integrated with an APSE to support software systems development from specification through implementation is described. These tools completement each other to help developers improve quality and productivity, as well as to reduce development and maintenance costs. Complete system documentation and reusable code also resultss from the use of these tools. Integrating an APSE with automated tools for structured analysis and design provide capabilities and advantages beyond those realized with any of these systems used by themselves.

SPICE Module for the Satellite Orbit Analysis Program (SOAP)

NASA Technical Reports Server (NTRS)

Coggi, John; Carnright, Robert; Hildebrand, Claude

2008-01-01

A SPICE module for the Satellite Orbit Analysis Program (SOAP) precisely represents complex motion and maneuvers in an interactive, 3D animated environment with support for user-defined quantitative outputs. (SPICE stands for Spacecraft, Planet, Instrument, Camera-matrix, and Events). This module enables the SOAP software to exploit NASA mission ephemeris represented in the JPL Ancillary Information Facility (NAIF) SPICE formats. Ephemeris types supported include position, velocity, and orientation for spacecraft and planetary bodies including the Sun, planets, natural satellites, comets, and asteroids. Entire missions can now be imported into SOAP for 3D visualization, playback, and analysis. The SOAP analysis and display features can now leverage detailed mission files to offer the analyst both a numerically correct and aesthetically pleasing combination of results that can be varied to study many hypothetical scenarios. The software provides a modeling and simulation environment that can encompass a broad variety of problems using orbital prediction. For example, ground coverage analysis, communications analysis, power and thermal analysis, and 3D visualization that provide the user with insight into complex geometric relations are included. The SOAP SPICE module allows distributed science and engineering teams to share common mission models of known pedigree, which greatly reduces duplication of effort and the potential for error. The use of the software spans all phases of the space system lifecycle, from the study of future concepts to operations and anomaly analysis. It allows SOAP software to correctly position and orient all of the principal bodies of the Solar System within a single simulation session along with multiple spacecraft trajectories and the orientation of mission payloads. In addition to the 3D visualization, the user can define numeric variables and x-y plots to quantitatively assess metrics of interest.

The Implication of Using NVivo Software in Qualitative Data Analysis: Evidence-Based Reflections.

PubMed

Zamawe, F C

2015-03-01

For a long time, electronic data analysis has been associated with quantitative methods. However, Computer Assisted Qualitative Data Analysis Software (CAQDAS) are increasingly being developed. Although the CAQDAS has been there for decades, very few qualitative health researchers report using it. This may be due to the difficulties that one has to go through to master the software and the misconceptions that are associated with using CAQDAS. While the issue of mastering CAQDAS has received ample attention, little has been done to address the misconceptions associated with CAQDAS. In this paper, the author reflects on his experience of interacting with one of the popular CAQDAS (NVivo) in order to provide evidence-based implications of using the software. The key message is that unlike statistical software, the main function of CAQDAS is not to analyse data but rather to aid the analysis process, which the researcher must always remain in control of. In other words, researchers must equally know that no software can analyse qualitative data. CAQDAS are basically data management packages, which support the researcher during analysis.

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

NASA Technical Reports Server (NTRS)

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

Analytical and Methodological Issues in the Use of Qualitative Data Analysis Software: A Description of Three Studies.

ERIC Educational Resources Information Center

Margerum-Leys, Jon; Kupperman, Jeff; Boyle-Heimann, Kristen

This paper presents perspectives on the use of data analysis software in the process of qualitative research. These perspectives were gained in the conduct of three qualitative research studies that differed in theoretical frames, areas of interests, and scope. Their common use of a particular data analysis software package allows the exploration…

ElectroMagnetoEncephalography Software: Overview and Integration with Other EEG/MEG Toolboxes

PubMed Central

Peyk, Peter; De Cesarei, Andrea; Junghöfer, Markus

2011-01-01

EMEGS (electromagnetic encephalography software) is a MATLAB toolbox designed to provide novice as well as expert users in the field of neuroscience with a variety of functions to perform analysis of EEG and MEG data. The software consists of a set of graphical interfaces devoted to preprocessing, analysis, and visualization of electromagnetic data. Moreover, it can be extended using a plug-in interface. Here, an overview of the capabilities of the toolbox is provided, together with a simple tutorial for both a standard ERP analysis and a time-frequency analysis. Latest features and future directions of the software development are presented in the final section. PMID:21577273

ElectroMagnetoEncephalography software: overview and integration with other EEG/MEG toolboxes.

PubMed

Peyk, Peter; De Cesarei, Andrea; Junghöfer, Markus

2011-01-01

EMEGS (electromagnetic encephalography software) is a MATLAB toolbox designed to provide novice as well as expert users in the field of neuroscience with a variety of functions to perform analysis of EEG and MEG data. The software consists of a set of graphical interfaces devoted to preprocessing, analysis, and visualization of electromagnetic data. Moreover, it can be extended using a plug-in interface. Here, an overview of the capabilities of the toolbox is provided, together with a simple tutorial for both a standard ERP analysis and a time-frequency analysis. Latest features and future directions of the software development are presented in the final section.

Archiving Software Systems: Approaches to Preserve Computational Capabilities

NASA Astrophysics Data System (ADS)

King, T. A.

2014-12-01

A great deal of effort is made to preserve scientific data. Not only because data is knowledge, but it is often costly to acquire and is sometimes collected under unique circumstances. Another part of the science enterprise is the development of software to process and analyze the data. Developed software is also a large investment and worthy of preservation. However, the long term preservation of software presents some challenges. Software often requires a specific technology stack to operate. This can include software, operating systems and hardware dependencies. One past approach to preserve computational capabilities is to maintain ancient hardware long past its typical viability. On an archive horizon of 100 years, this is not feasible. Another approach to preserve computational capabilities is to archive source code. While this can preserve details of the implementation and algorithms, it may not be possible to reproduce the technology stack needed to compile and run the resulting applications. This future forward dilemma has a solution. Technology used to create clouds and process big data can also be used to archive and preserve computational capabilities. We explore how basic hardware, virtual machines, containers and appropriate metadata can be used to preserve computational capabilities and to archive functional software systems. In conjunction with data archives, this provides scientist with both the data and capability to reproduce the processing and analysis used to generate past scientific results.

Report: Scientific Software.

ERIC Educational Resources Information Center

Borman, Stuart A.

1985-01-01

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

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

Ahmed, A.; Chadwick, T.; Makhlouf, M.

This paper deals with the effects of various solidification variables such as cooling rate, temperature gradient, solidification rate, etc. on the microstructure and shrinkage defects in aluminum alloy (A356) castings. The effects are first predicted using commercial solidification modeling softwares and then verified experimentally. For this work, the authors are considering a rectangular bar cast in a sand mold. Simulation is performed using SIMULOR, a finite volume based casting simulation program. Microstructural variables such as dendritic arm spacing (DAS) and defects (percentage porosity) are calculated from the temperature fields, cooling rate, solidification time, etc. predicted by the computer softwares. Themore » same variables are then calculated experimentally in the foundry. The test piece is cast in a resin (Sodium Silicate) bonded sand mold and the DAS and porosity variables are calculated using Scanning Electron Microscopy and Image Analysis. The predictions from the software are compared with the experimental results. The results are presented and critically analyzed to determine the quality of the predicted results. The usefulness of the commercial solidification modeling softwares as a tool for the foundry are also discussed.« less

Software and mathematical support of Kazakhstani star tracker

NASA Astrophysics Data System (ADS)

Akhmedov, D.; Yelubayev, S.; Ten, V.; Bopeyev, T.; Alipbayev, K.; Sukhenko, A.

2016-10-01

Currently the specialists of Kazakhstan have been developing the star tracker that is further planned to use on Kazakhstani satellites of various purposes. At the first stage it has been developed the experimental model of star tracker that has following characteristics: field of view 20°, update frequency 2 Hz, exclusion angle 40°, accuracy of attitude determination of optical axis/around optical axis 15/50 arcsec. Software and mathematical support are the most high technology parts of star tracker. The results of software and mathematical support development of experimental model of Kazakhstani star tracker are represented in this article. In particular, there are described the main mathematical models and algorithms that have been used as a basis for program units of preliminary image processing of starry sky, stars identification and star tracker attitude determination. The results of software and mathematical support testing with the help of program simulation complex using various configurations of defects including image sensor noises, point spread function modeling, optical system distortion up to 2% are presented. Analysis of testing results has shown that accuracy of attitude determination of star tracker is within the permissible range

Energy loss analysis of an integrated space power distribution system

NASA Technical Reports Server (NTRS)

Kankam, M. D.; Ribeiro, P. F.

1992-01-01

The results of studies related to conceptual topologies of an integrated utility-like space power system are described. The system topologies are comparatively analyzed by considering their transmission energy losses as functions of mainly distribution voltage level and load composition. The analysis is expedited by use of a Distribution System Analysis and Simulation (DSAS) software. This recently developed computer program by the Electric Power Research Institute (EPRI) uses improved load models to solve the power flow within the system. However, present shortcomings of the software with regard to space applications, and incompletely defined characteristics of a space power system make the results applicable to only the fundamental trends of energy losses of the topologies studied. Accountability, such as included, for the effects of the various parameters on the system performance can constitute part of a planning tool for a space power distribution system.

MTF measurements on real time for performance analysis of electro-optical systems

NASA Astrophysics Data System (ADS)

Stuchi, Jose Augusto; Signoreto Barbarini, Elisa; Vieira, Flavio Pascoal; dos Santos, Daniel, Jr.; Stefani, Mário Antonio; Yasuoka, Fatima Maria Mitsue; Castro Neto, Jarbas C.; Linhari Rodrigues, Evandro Luis

2012-06-01

The need of methods and tools that assist in determining the performance of optical systems is actually increasing. One of the most used methods to perform analysis of optical systems is to measure the Modulation Transfer Function (MTF). The MTF represents a direct and quantitative verification of the image quality. This paper presents the implementation of the software, in order to calculate the MTF of electro-optical systems. The software was used for calculating the MTF of Digital Fundus Camera, Thermal Imager and Ophthalmologic Surgery Microscope. The MTF information aids the analysis of alignment and measurement of optical quality, and also defines the limit resolution of optical systems. The results obtained with the Fundus Camera and Thermal Imager was compared with the theoretical values. For the Microscope, the results were compared with MTF measured of Microscope Zeiss model, which is the quality standard of ophthalmological microscope.

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

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

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

Identifying Contingency Requirements using Obstacle Analysis on an Unpiloted Aerial Vehicle

NASA Technical Reports Server (NTRS)

Lutz, Robyn R.; Nelson, Stacy; Patterson-Hine, Ann; Frost, Chad R.; Tal, Doron

2005-01-01

This paper describes experience using Obstacle Analysis to identify contingency requirements on an unpiloted aerial vehicle. A contingency is an operational anomaly, and may or may not involve component failure. The challenges to this effort were: ( I ) rapid evolution of the system while operational, (2) incremental autonomy as capabilities were transferred from ground control to software control and (3) the eventual safety-criticality of such systems as they begin to fly over populated areas. The results reported here are preliminary but show that Obstacle Analysis helped (1) identify new contingencies that appeared as autonomy increased; (2) identify new alternatives for handling both previously known and new contingencies; and (3) investigate the continued validity of existing software requirements for contingency handling. Since many mobile, intelligent systems are built using a development process that poses the same challenges, the results appear to have applicability to other similar systems.

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

Multivariate matching pursuit in optimal Gabor dictionaries: theory and software with interface for EEG/MEG via Svarog

PubMed Central

2013-01-01

Background Matching pursuit algorithm (MP), especially with recent multivariate extensions, offers unique advantages in analysis of EEG and MEG. Methods We propose a novel construction of an optimal Gabor dictionary, based upon the metrics introduced in this paper. We implement this construction in a freely available software for MP decomposition of multivariate time series, with a user friendly interface via the Svarog package (Signal Viewer, Analyzer and Recorder On GPL, http://braintech.pl/svarog), and provide a hands-on introduction to its application to EEG. Finally, we describe numerical and mathematical optimizations used in this implementation. Results Optimal Gabor dictionaries, based on the metric introduced in this paper, for the first time allowed for a priori assessment of maximum one-step error of the MP algorithm. Variants of multivariate MP, implemented in the accompanying software, are organized according to the mathematical properties of the algorithms, relevant in the light of EEG/MEG analysis. Some of these variants have been successfully applied to both multichannel and multitrial EEG and MEG in previous studies, improving preprocessing for EEG/MEG inverse solutions and parameterization of evoked potentials in single trials; we mention also ongoing work and possible novel applications. Conclusions Mathematical results presented in this paper improve our understanding of the basics of the MP algorithm. Simple introduction of its properties and advantages, together with the accompanying stable and user-friendly Open Source software package, pave the way for a widespread and reproducible analysis of multivariate EEG and MEG time series and novel applications, while retaining a high degree of compatibility with the traditional, visual analysis of EEG. PMID:24059247

Hybrid Energy System Design of Micro Hydro-PV-biogas Based Micro-grid

NASA Astrophysics Data System (ADS)

Nishrina; Abdullah, A. G.; Risdiyanto, A.; Nandiyanto, ABD

2017-03-01

Hybrid renewable energy system is an arrangement of one or more sources of renewable energy and also conventional energy. This paper describes a simulation results of hybrid renewable power system based on the available potential in an educational institution in Indonesia. HOMER software was used to simulate and analyse both in terms of optimization and economic terms. This software was developed through 3 main principles; simulation, optimization, and sensitivity analysis. Generally, the presented results show that the software can demonstrate a feasible hybrid power system as well to be realized. The entire demand in case study area can be supplied by the system configuration and can be met by ¾ of electricity production. So, there are ¼ of generated energy became an excess electricity.

Progress on automated data analysis algorithms for ultrasonic inspection of composites

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Learning Photogrammetry with Interactive Software Tool PhoX

NASA Astrophysics Data System (ADS)

Luhmann, T.

2016-06-01

Photogrammetry is a complex topic in high-level university teaching, especially in the fields of geodesy, geoinformatics and metrology where high quality results are demanded. In addition, more and more black-box solutions for 3D image processing and point cloud generation are available that generate nice results easily, e.g. by structure-from-motion approaches. Within this context, the classical approach of teaching photogrammetry (e.g. focusing on aerial stereophotogrammetry) has to be reformed in order to educate students and professionals with new topics and provide them with more information behind the scene. Since around 20 years photogrammetry courses at the Jade University of Applied Sciences in Oldenburg, Germany, include the use of digital photogrammetry software that provide individual exercises, deep analysis of calculation results and a wide range of visualization tools for almost all standard tasks in photogrammetry. During the last years the software package PhoX has been developed that is part of a new didactic concept in photogrammetry and related subjects. It also serves as analysis tool in recent research projects. PhoX consists of a project-oriented data structure for images, image data, measured points and features and 3D objects. It allows for almost all basic photogrammetric measurement tools, image processing, calculation methods, graphical analysis functions, simulations and much more. Students use the program in order to conduct predefined exercises where they have the opportunity to analyse results in a high level of detail. This includes the analysis of statistical quality parameters but also the meaning of transformation parameters, rotation matrices, calibration and orientation data. As one specific advantage, PhoX allows for the interactive modification of single parameters and the direct view of the resulting effect in image or object space.

Analysis and visualization of intracardiac electrograms in diagnosis and research: Concept and application of KaPAVIE.

PubMed

Oesterlein, Tobias Georg; Schmid, Jochen; Bauer, Silvio; Jadidi, Amir; Schmitt, Claus; Dössel, Olaf; Luik, Armin

2016-04-01

Progress in biomedical engineering has improved the hardware available for diagnosis and treatment of cardiac arrhythmias. But although huge amounts of intracardiac electrograms (EGMs) can be acquired during electrophysiological examinations, there is still a lack of software aiding diagnosis. The development of novel algorithms for the automated analysis of EGMs has proven difficult, due to the highly interdisciplinary nature of this task and hampered data access in clinical systems. Thus we developed a software platform, which allows rapid implementation of new algorithms, verification of their functionality and suitable visualization for discussion in the clinical environment. A software for visualization was developed in Qt5 and C++ utilizing the class library of VTK. The algorithms for signal analysis were implemented in MATLAB. Clinical data for analysis was exported from electroanatomical mapping systems. The visualization software KaPAVIE (Karlsruhe Platform for Analysis and Visualization of Intracardiac Electrograms) was implemented and tested on several clinical datasets. Both common and novel algorithms were implemented which address important clinical questions in diagnosis of different arrhythmias. It proved useful in discussions with clinicians due to its interactive and user-friendly design. Time after export from the clinical mapping system to visualization is below 5min. KaPAVIE(2) is a powerful platform for the development of novel algorithms in the clinical environment. Simultaneous and interactive visualization of measured EGM data and the results of analysis will aid diagnosis and help understanding the underlying mechanisms of complex arrhythmias like atrial fibrillation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Framework for Risk Analysis in Multimedia Environmental Systems: Modeling Individual Steps of a Risk Assessment Process

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

Shah, Anuj; Castleton, Karl J.; Hoopes, Bonnie L.

2004-06-01

The study of the release and effects of chemicals in the environment and their associated risks to humans is central to public and private decision making. FRAMES 1.X, Framework for Risk Analysis in Multimedia Environmental Systems, is a systems modeling software platform, developed by PNNL, Pacific Northwest National Laboratory, that helps scientists study the release and effects of chemicals on a source to outcome basis, create environmental models for similar risk assessment and management problems. The unique aspect of FRAMES is to dynamically introduce software modules representing individual components of a risk assessment (e.g., source release of contaminants, fate andmore » transport in various environmental media, exposure, etc.) within a software framework, manipulate their attributes and run simulations to obtain results. This paper outlines the fundamental constituents of FRAMES 2.X, an enhanced version of FRAMES 1.X, that greatly improve the ability of the module developers to “plug” their self-developed software modules into the system. The basic design, the underlying principles and a discussion of the guidelines for module developers are presented.« less

Optomechanical design software for segmented mirrors

NASA Astrophysics Data System (ADS)

Marrero, Juan

2016-08-01

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

Micrometeoroid and Orbital Debris (MMOD) Shield Ballistic Limit Analysis Program

NASA Technical Reports Server (NTRS)

Ryan, Shannon

2013-01-01

This software implements penetration limit equations for common micrometeoroid and orbital debris (MMOD) shield configurations, windows, and thermal protection systems. Allowable MMOD risk is formulated in terms of the probability of penetration (PNP) of the spacecraft pressure hull. For calculating the risk, spacecraft geometry models, mission profiles, debris environment models, and penetration limit equations for installed shielding configurations are required. Risk assessment software such as NASA's BUMPERII is used to calculate mission PNP; however, they are unsuitable for use in shield design and preliminary analysis studies. The software defines a single equation for the design and performance evaluation of common MMOD shielding configurations, windows, and thermal protection systems, along with a description of their validity range and guidelines for their application. Recommendations are based on preliminary reviews of fundamental assumptions, and accuracy in predicting experimental impact test results. The software is programmed in Visual Basic for Applications for installation as a simple add-in for Microsoft Excel. The user is directed to a graphical user interface (GUI) that requires user inputs and provides solutions directly in Microsoft Excel workbooks.

Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations

PubMed Central

García-Dorado, Aurora; Wang, Jinliang; López-Cortegano, Eugenio

2016-01-01

The inbreeding depression of fitness traits can be a major threat to the survival of populations experiencing inbreeding. However, its accurate prediction requires taking into account the genetic purging induced by inbreeding, which can be achieved using a “purged inbreeding coefficient”. We have developed a method to compute purged inbreeding at the individual level in pedigreed populations with overlapping generations. Furthermore, we derive the inbreeding depression slope for individual logarithmic fitness, which is larger than that for the logarithm of the population fitness average. In addition, we provide a new software, PURGd, based on these theoretical results that allows analyzing pedigree data to detect purging, and to estimate the purging coefficient, which is the parameter necessary to predict the joint consequences of inbreeding and purging. The software also calculates the purged inbreeding coefficient for each individual, as well as standard and ancestral inbreeding. Analysis of simulation data show that this software produces reasonably accurate estimates for the inbreeding depression rate and for the purging coefficient that are useful for predictive purposes. PMID:27605515

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.

Consolidated View on Space Software Engineering Problems - An Empirical Study

NASA Astrophysics Data System (ADS)

Silva, N.; Vieira, M.; Ricci, D.; Cotroneo, D.

2015-09-01

Independent software verification and validation (ISVV) has been a key process for engineering quality assessment for decades, and is considered in several international standards. The “European Space Agency (ESA) ISVV Guide” is used for the European Space market to drive the ISVV tasks and plans, and to select applicable tasks and techniques. Software artefacts have room for improvement due to the amount if issues found during ISVV tasks. This article presents the analysis of the results of a large set of ISVV issues originated from three different ESA missions-amounting to more than 1000 issues. The study presents the main types, triggers and impacts related to the ISVV issues found and sets the path for a global software engineering improvement based on the most common deficiencies identified for space projects.

Cost-Sensitive Radial Basis Function Neural Network Classifier for Software Defect Prediction

PubMed Central

Venkatesan, R.

2016-01-01

Effective prediction of software modules, those that are prone to defects, will enable software developers to achieve efficient allocation of resources and to concentrate on quality assurance activities. The process of software development life cycle basically includes design, analysis, implementation, testing, and release phases. Generally, software testing is a critical task in the software development process wherein it is to save time and budget by detecting defects at the earliest and deliver a product without defects to the customers. This testing phase should be carefully operated in an effective manner to release a defect-free (bug-free) software product to the customers. In order to improve the software testing process, fault prediction methods identify the software parts that are more noted to be defect-prone. This paper proposes a prediction approach based on conventional radial basis function neural network (RBFNN) and the novel adaptive dimensional biogeography based optimization (ADBBO) model. The developed ADBBO based RBFNN model is tested with five publicly available datasets from the NASA data program repository. The computed results prove the effectiveness of the proposed ADBBO-RBFNN classifier approach with respect to the considered metrics in comparison with that of the early predictors available in the literature for the same datasets. PMID:27738649

Cost-Sensitive Radial Basis Function Neural Network Classifier for Software Defect Prediction.

PubMed

Kumudha, P; Venkatesan, R

Effective prediction of software modules, those that are prone to defects, will enable software developers to achieve efficient allocation of resources and to concentrate on quality assurance activities. The process of software development life cycle basically includes design, analysis, implementation, testing, and release phases. Generally, software testing is a critical task in the software development process wherein it is to save time and budget by detecting defects at the earliest and deliver a product without defects to the customers. This testing phase should be carefully operated in an effective manner to release a defect-free (bug-free) software product to the customers. In order to improve the software testing process, fault prediction methods identify the software parts that are more noted to be defect-prone. This paper proposes a prediction approach based on conventional radial basis function neural network (RBFNN) and the novel adaptive dimensional biogeography based optimization (ADBBO) model. The developed ADBBO based RBFNN model is tested with five publicly available datasets from the NASA data program repository. The computed results prove the effectiveness of the proposed ADBBO-RBFNN classifier approach with respect to the considered metrics in comparison with that of the early predictors available in the literature for the same datasets.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

Software selection based on analysis and forecasting methods, practised in 1C

NASA Astrophysics Data System (ADS)

Vazhdaev, A. N.; Chernysheva, T. Y.; Lisacheva, E. I.

2015-09-01

The research focuses on the problem of a “1C: Enterprise 8” platform inboard mechanisms for data analysis and forecasting. It is important to evaluate and select proper software to develop effective strategies for customer relationship management in terms of sales, as well as implementation and further maintenance of software. Research data allows creating new forecast models to schedule further software distribution.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

The effect of proposed software products' features on the satisfaction and dissatisfaction of potential customers

NASA Astrophysics Data System (ADS)

Hussain, Azham; Mkpojiogu, Emmanuel O. C.; Yusof, Muhammad Mat

2016-08-01

This paper reports the effect of proposed software products features on the satisfaction and dissatisfaction of potential customers of proposed software products. Kano model's functional and dysfunctional technique was used along with Berger et al.'s customer satisfaction coefficients. The result shows that only two features performed the most in influencing the satisfaction and dissatisfaction of would-be customers of the proposed software product. Attractive and one-dimensional features had the highest impact on the satisfaction and dissatisfaction of customers. This result will benefit requirements analysts, developers, designers, projects and sales managers in preparing for proposed products. Additional analysis showed that the Kano model's satisfaction and dissatisfaction scores were highly related to the Park et al.'s average satisfaction coefficient (r=96%), implying that these variables can be used interchangeably or in place of one another to elicit customer satisfaction. Furthermore, average satisfaction coefficients and satisfaction and dissatisfaction indexes were all positively and linearly correlated.

Performance of student software development teams: the influence of personality and identifying as team members

NASA Astrophysics Data System (ADS)

Monaghan, Conal; Bizumic, Boris; Reynolds, Katherine; Smithson, Michael; Johns-Boast, Lynette; van Rooy, Dirk

2015-01-01

One prominent approach in the exploration of the variations in project team performance has been to study two components of the aggregate personalities of the team members: conscientiousness and agreeableness. A second line of research, known as self-categorisation theory, argues that identifying as team members and the team's performance norms should substantially influence the team's performance. This paper explores the influence of both these perspectives in university software engineering project teams. Eighty students worked to complete a piece of software in small project teams during 2007 or 2008. To reduce limitations in statistical analysis, Monte Carlo simulation techniques were employed to extrapolate from the results of the original sample to a larger simulated sample (2043 cases, within 319 teams). The results emphasise the importance of taking into account personality (particularly conscientiousness), and both team identification and the team's norm of performance, in order to cultivate higher levels of performance in student software engineering project teams.

Software ion scan functions in analysis of glycomic and lipidomic MS/MS datasets.

PubMed

Haramija, Marko

2018-03-01

Hardware ion scan functions unique to tandem mass spectrometry (MS/MS) mode of data acquisition, such as precursor ion scan (PIS) and neutral loss scan (NLS), are important for selective extraction of key structural data from complex MS/MS spectra. However, their software counterparts, software ion scan (SIS) functions, are still not regularly available. Software ion scan functions can be easily coded for additional functionalities, such as software multiple precursor ion scan, software no ion scan, and software variable ion scan functions. These are often necessary, since they allow more efficient analysis of complex MS/MS datasets, often encountered in glycomics and lipidomics. Software ion scan functions can be easily coded by using modern script languages and can be independent of instrument manufacturer. Here we demonstrate the utility of SIS functions on a medium-size glycomic MS/MS dataset. Knowledge of sample properties, as well as of diagnostic and conditional diagnostic ions crucial for data analysis, was needed. Based on the tables constructed with the output data from the SIS functions performed, a detailed analysis of a complex MS/MS glycomic dataset could be carried out in a quick, accurate, and efficient manner. Glycomic research is progressing slowly, and with respect to the MS experiments, one of the key obstacles for moving forward is the lack of appropriate bioinformatic tools necessary for fast analysis of glycomic MS/MS datasets. Adding novel SIS functionalities to the glycomic MS/MS toolbox has a potential to significantly speed up the glycomic data analysis process. Similar tools are useful for analysis of lipidomic MS/MS datasets as well, as will be discussed briefly. Copyright © 2017 John Wiley & Sons, Ltd.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

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

2011-01-01

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

The analysis of the accuracy of spatial models using photogrammetric software: Agisoft Photoscan and Pix4D

NASA Astrophysics Data System (ADS)

Barbasiewicz, Adrianna; Widerski, Tadeusz; Daliga, Karol

2018-01-01

This article was created as a result of research conducted within the master thesis. The purpose of the measurements was to analyze the accuracy of the positioning of points by computer programs. Selected software was a specialized computer software dedicated to photogrammetric work. For comparative purposes it was decided to use tools with similar functionality. As the basic parameters that affect the results selected the resolution of the photos on which the key points were searched. In order to determine the location of the determined points, it was decided to follow the photogrammetric resection rule. In order to automate the measurement, the measurement session planning was omitted. The coordinates of the points collected by the tachymetric measure were used as a reference system. The resulting deviations and linear displacements oscillate in millimeters. The visual aspects of the cloud points have also been briefly analyzed.

Development of Cell Analysis Software for Cultivated Corneal Endothelial Cells.

PubMed

Okumura, Naoki; Ishida, Naoya; Kakutani, Kazuya; Hongo, Akane; Hiwa, Satoru; Hiroyasu, Tomoyuki; Koizumi, Noriko

2017-11-01

To develop analysis software for cultured human corneal endothelial cells (HCECs). Software was designed to recognize cell borders and to provide parameters such as cell density, coefficient of variation, and polygonality of cultured HCECs based on phase contrast images. Cultured HCECs with high or low cell density were incubated with Ca-free and Mg-free phosphate-buffered saline for 10 minutes to reveal the cell borders and were then analyzed with software (n = 50). Phase contrast images showed that cell borders were not distinctly outlined, but these borders became more distinctly outlined after phosphate-buffered saline treatment and were recognized by cell analysis software. The cell density value provided by software was similar to that obtained using manual cell counting by an experienced researcher. Morphometric parameters, such as the coefficient of variation and polygonality, were also produced by software, and these values were significantly correlated with cell density (Pearson correlation coefficients -0.62 and 0.63, respectively). The software described here provides morphometric information from phase contrast images, and it enables subjective and noninvasive quality assessment for tissue engineering therapy of the corneal endothelium.

Design and Analysis of Tooth Impact Test Rig for Spur Gear

NASA Astrophysics Data System (ADS)

Ghazali, Wafiuddin Bin Md; Aziz, Ismail Ali Bin Abdul; Daing Idris, Daing Mohamad Nafiz Bin; Ismail, Nurazima Binti; Sofian, Azizul Helmi Bin

2016-02-01

This paper is about the design and analysis of a prototype of tooth impact test rig for spur gear. The test rig was fabricated and analysis was conducted to study its’ limitation and capabilities. The design of the rig is analysed to ensure that there will be no problem occurring during the test and reliable data can be obtained. From the result of the analysis, the maximum amount of load that can be applied, the factor of safety of the machine, the stresses on the test rig parts were determined. This is important in the design consideration of the test rig. The materials used for the fabrication of the test rig were also discussed and analysed. MSC Nastran Patran software was used to analyse the model, which was designed by using SolidWorks 2014 software. Based from the results, there were limitations found from the initial design and the test rig design needs to be improved in order for the test rig to operate properly.

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

PubMed

Välikangas, Tommi; Suomi, Tomi; Elo, Laura L

2017-05-31

Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them.In this study, we evaluated the performance of five popular quantitative label-free proteomics software workflows using four different spike-in data sets. Our extensive testing included the number of proteins quantified and the number of missing values produced by each workflow, the accuracy of detecting differential expression and logarithmic fold change and the effect of different imputation and filtering methods on the differential expression results. We found that the Progenesis software performed consistently well in the differential expression analysis and produced few missing values. The missing values produced by the other software decreased their performance, but this difference could be mitigated using proper data filtering or imputation methods. Among the imputation methods, we found that the local least squares (lls) regression imputation consistently increased the performance of the software in the differential expression analysis, and a combination of both data filtering and local least squares imputation increased performance the most in the tested data sets. © The Author 2017. Published by Oxford University Press.

Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

PubMed

Gorgolewski, Krzysztof; Burns, Christopher D; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O; Waskom, Michael L; Ghosh, Satrajit S

2011-01-01

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python

PubMed Central

Gorgolewski, Krzysztof; Burns, Christopher D.; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O.; Waskom, Michael L.; Ghosh, Satrajit S.

2011-01-01

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research. PMID:21897815

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

PubMed

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

2014-09-29

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

Composable Framework Support for Software-FMEA Through Model Execution

NASA Astrophysics Data System (ADS)

Kocsis, Imre; Patricia, Andras; Brancati, Francesco; Rossi, Francesco

2016-08-01

Performing Failure Modes and Effect Analysis (FMEA) during software architecture design is becoming a basic requirement in an increasing number of domains; however, due to the lack of standardized early design phase model execution, classic SW-FMEA approaches carry significant risks and are human effort-intensive even in processes that use Model-Driven Engineering.Recently, modelling languages with standardized executable semantics have emerged. Building on earlier results, this paper describes framework support for generating executable error propagation models from such models during software architecture design. The approach carries the promise of increased precision, decreased risk and more automated execution for SW-FMEA during dependability- critical system development.

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

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Hoadley, Sherwood T.

1998-01-01

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

The Design and Analysis of the Hydraulic-pressure Seal of the Engine Box

NASA Astrophysics Data System (ADS)

Chen, Zhenya; Shen, Xingquan; Xin, Zhijie; Guo, Tingting; Liao, Kewei

2017-12-01

According to the sealing requirements of engine casing, using NX software to establish three-dimensional solid model of the engine box. Designing two seals suppress schemes basing on analyzing the characteristics of the case structure, one of seal is using two pins on one side to localize, the other is using cylinder to top tight and fasten, Clarifying the reasons for the using the former scheme have a lower cost. At the same time analysesing of the forces and deformation of the former scheme using finite element analysis software and the NX software, results proved that the pressure scheme can meet the actual needs of the program. It illustrated the composition of the basic principles of manual pressure and hydraulic system, verifed the feasibility of the seal program using experiment, providing reference for the experimental program of hydrostatic pressure in the future.

Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

PubMed

Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

2014-02-01

Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications.

The Kepler Science Data Processing Pipeline Source Code Road Map

NASA Technical Reports Server (NTRS)

Wohler, Bill; Jenkins, Jon M.; Twicken, Joseph D.; Bryson, Stephen T.; Clarke, Bruce Donald; Middour, Christopher K.; Quintana, Elisa Victoria; Sanderfer, Jesse Thomas; Uddin, Akm Kamal; Sabale, Anima;

Circumnutation Tracker: novel software for investigation of circumnutation

PubMed Central

2014-01-01

Background An endogenous, helical plant organ movement named circumnutation is ubiquitous in the plant kingdom. Plant shoots, stems, tendrils, leaves, and roots commonly circumnutate but their appearance is still poorly described. To support such investigations, novel software Circumnutation Tracker (CT) for spatial-temporal analysis of circumnutation has been developed. Results CT works on time-lapse video and collected circumnutation parameters: period, length, rate, shape, angle, and clockwise- and counterclockwise directions. The CT combines a filtering algorithm with a graph-based method to describe the parameters of circumnutation. The parameters of circumnutation of Helianthus annuus hypocotyls and the relationship between cotyledon arrangement and circumnutation geometry are presented here to demonstrate the CT options. Conclusions We have established that CT facilitates and accelerates analysis of circumnutation. In combination with the physiological, molecular, and genetic methods, this software may be a powerful tool also for investigations of gravitropism, biological clock, and membrane transport, i.e. processes involved in the mechanism of circumnutation.

Tokamak-independent software analysis suite for multi-spectral line-polarization MSE diagnostics

DOE PAGES

Scott, S. D.; Mumgaard, R. T.

2016-07-20

A tokamak-independent analysis suite has been developed to process data from Motional Stark Effect (mse) diagnostics. The software supports multi-spectral line-polarization mse diagnostics which simultaneously measure emission at the mse σ and π lines as well as at two "background" wavelengths that are displaced from the mse spectrum by a few nanometers. This analysis accurately estimates the amplitude of partially polarized background light at the σ and π wavelengths even in situations where the background light changes rapidly in time and space, a distinct improvement over traditional "time-interpolation" background estimation. The signal amplitude at many frequencies is computed using amore » numerical-beat algorithm which allows the retardance of the mse photo-elastic modulators (pem's) to be monitored during routine operation. It also allows the use of summed intensities at multiple frequencies in the calculation of polarization direction, which increases the effective signal strength and reduces sensitivity to pem retardance drift. The software allows the polarization angles to be corrected for calibration drift using a system that illuminates the mse diagnostic with polarized light at four known polarization angles within ten seconds of a plasma discharge. As a result, the software suite is modular, parallelized, and portable to other facilities.« less

Tokamak-independent software analysis suite for multi-spectral line-polarization MSE diagnostics

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

Scott, S. D.; Mumgaard, R. T.

A tokamak-independent analysis suite has been developed to process data from Motional Stark Effect (mse) diagnostics. The software supports multi-spectral line-polarization mse diagnostics which simultaneously measure emission at the mse σ and π lines as well as at two "background" wavelengths that are displaced from the mse spectrum by a few nanometers. This analysis accurately estimates the amplitude of partially polarized background light at the σ and π wavelengths even in situations where the background light changes rapidly in time and space, a distinct improvement over traditional "time-interpolation" background estimation. The signal amplitude at many frequencies is computed using amore » numerical-beat algorithm which allows the retardance of the mse photo-elastic modulators (pem's) to be monitored during routine operation. It also allows the use of summed intensities at multiple frequencies in the calculation of polarization direction, which increases the effective signal strength and reduces sensitivity to pem retardance drift. The software allows the polarization angles to be corrected for calibration drift using a system that illuminates the mse diagnostic with polarized light at four known polarization angles within ten seconds of a plasma discharge. As a result, the software suite is modular, parallelized, and portable to other facilities.« less